check_function_exists(sysconf HAVE_SYSCONF)
check_function_exists(sched_setaffinity HAVE_SCHED_SETAFFINITY)
check_function_exists(sched_getaffinity HAVE_SCHED_GETAFFINITY)
+check_function_exists(rsqrt HAVE_RSQRT)
+check_function_exists(rsqrtf HAVE_RSQRTF)
+check_function_exists(sqrtf HAVE_SQRTF)
include(CheckLibraryExists)
check_library_exists(m sqrt "" HAVE_LIBM)
gmx_test_inline(INLINE_KEYWORD)
include(gmxTestRestrict)
-gmx_test_inline(RESTRICT_KEYWORD)
+gmx_test_restrict(RESTRICT_KEYWORD)
include(gmxTestPipes)
gmx_test_pipes(HAVE_PIPES)
MESSAGE(STATUS "Checking for inline keyword")
- FOREACH(KEYWORD "inline" "__inline__" "__inline")
+ FOREACH(KEYWORD "__inline__" "__inline" "inline")
IF(NOT TEST_${VARIABLE})
TRY_COMPILE(TEST_${VARIABLE} "${CMAKE_BINARY_DIR}"
"${CMAKE_SOURCE_DIR}/cmake/TestInline.c"
COMPILE_DEFINITIONS "-DTESTINLINEDEF=${KEYWORD}" )
- SET(CHK_INLINE_KEYWORD ${KEYWORD})
- ENDIF(NOT TEST_${VARIABLE})
+ SET(LAST_INLINE_KEYWORD ${KEYWORD})
+ ENDIF(NOT TEST_${VARIABLE})
ENDFOREACH(KEYWORD)
-
+
IF(TEST_${VARIABLE})
- SET(${VARIABLE} ${KEYWORD})
- MESSAGE(STATUS "Checking for inline keyword - ${CHK_INLINE_KEYWORD}")
+ SET(${VARIABLE} ${LAST_INLINE_KEYWORD} CACHE INTERNAL "Inline keyword" FORCE)
+ MESSAGE(STATUS "Checking for inline keyword - ${LAST_INLINE_KEYWORD}")
ELSE(TEST_${VARIABLE})
- SET(${VARIABLE} " ")
+ SET(${VARIABLE} " " CACHE INTERNAL "Inline keyword" FORCE)
MESSAGE(STATUS "Checking for inline keyword - not found")
ENDIF(TEST_${VARIABLE})
TRY_COMPILE(TEST_${VARIABLE} "${CMAKE_BINARY_DIR}"
"${CMAKE_SOURCE_DIR}/cmake/TestRestrict.c"
COMPILE_DEFINITIONS "-DTESTRESTRICTDEF=${KEYWORD}" )
- SET(CHK_RESTRICT_KEYWORD ${KEYWORD})
+ SET(LAST_RESTRICT_KEYWORD ${KEYWORD})
ENDIF(NOT TEST_${VARIABLE})
ENDFOREACH(KEYWORD)
-
+
IF(TEST_${VARIABLE})
- SET(${VARIABLE} ${KEYWORD})
- MESSAGE(STATUS "Checking for restrict keyword - ${CHK_RESTRICT_KEYWORD}")
+ SET(${VARIABLE} ${LAST_RESTRICT_KEYWORD} CACHE INTERNAL "Restrict keyword" FORCE)
+ MESSAGE(STATUS "Checking for restrict keyword - ${LAST_RESTRICT_KEYWORD}")
ELSE(TEST_${VARIABLE})
- SET(${VARIABLE} " ")
+ SET(${VARIABLE} " " CACHE INTERNAL "Restrict keyword" FORCE)
MESSAGE(STATUS "Checking for restrict keyword - not found")
ENDIF(TEST_${VARIABLE})
void init_interaction_const_tables(FILE *fp,
interaction_const_t *ic,
- int verlet_kernel_type);
+ int cutoff_scheme,
+ int verlet_kernel_type,
+ real rtab);
/* Initializes the tables in the interaction constant data structure.
+ * Setting verlet_kernel_type to -1 always initializes tables for
+ * use with group kernels.
*/
void init_interaction_const(FILE *fp,
interaction_const_t **interaction_const,
- const t_forcerec *fr);
+ const t_forcerec *fr,
+ real rtab);
/* Initializes the interaction constant data structure. Currently it
* uses forcerec as input.
*/
real *dvdlambda,
gmx_grppairener_t *grppener,
gmx_bool bFillGrid,
- gmx_bool bDoLongRange,
- gmx_bool bDoForces,
- rvec *f);
+ gmx_bool bDoLongRangeNS);
/* Call the neighborsearcher */
extern void do_force_lowlevel(FILE *fplog,
t_grpopts *opts,
rvec x[],
history_t *hist,
- rvec f[],
+ rvec f_shortrange[],
+ rvec f_longrange[],
gmx_enerdata_t *enerd,
t_fcdata *fcd,
gmx_mtop_t *mtop,
extern const char *separate_dhdl_file_names[esepdhdlfileNR+1];
extern const char *dhdl_derivatives_names[edhdlderivativesNR+1];
extern const char *esol_names[esolNR+1];
-extern const char *enlist_names[enlistNR+1];
extern const char *edispc_names[edispcNR+1];
extern const char *ecm_names[ecmNR+1];
extern const char *eann_names[eannNR+1];
extern const char *eAdresstype_names[eAdressNR+1];
extern const char *eAdressICtype_names[eAdressICNR+1];
extern const char *eAdressSITEtype_names[eAdressSITENR+1];
+extern const char *gmx_nblist_geometry_names[GMX_NBLIST_GEOMETRY_NR+1];
+extern const char *gmx_nbkernel_elec_names[GMX_NBKERNEL_ELEC_NR+1];
+extern const char *gmx_nbkernel_vdw_names[GMX_NBKERNEL_VDW_NR+1];
#define UNDEFINED "UNDEFINED"
#define ENUM_NAME(e,max,names) ((((e)<0)||((e)>=(max)))?UNDEFINED:(names)[e])
#ifdef __cplusplus
extern "C" {
#endif
+#if 0
+} /* fixes auto-indentation problems */
+#endif
+
+
+
+void
+gmx_nonbonded_setup(FILE * fplog,
+ t_forcerec * fr,
+ gmx_bool bGenericKernelOnly);
+
+
+
+
+
+void
+gmx_nonbonded_set_kernel_pointers(FILE * fplog,
+ t_nblist * nl);
+
-void gmx_setup_kernels(FILE *fplog,t_forcerec *fr,gmx_bool bGenericKernelOnly);
-void gmx_setup_adress_kernels(FILE *fplog,gmx_bool bGenericKernelOnly);
-#define GMX_DONB_LR (1<<0)
-#define GMX_DONB_FORCES (1<<1)
-#define GMX_DONB_FOREIGNLAMBDA (1<<2)
+#define GMX_NONBONDED_DO_LR (1<<0)
+#define GMX_NONBONDED_DO_FORCE (1<<1)
+#define GMX_NONBONDED_DO_FOREIGNLAMBDA (1<<2)
+#define GMX_NONBONDED_DO_POTENTIAL (1<<3)
+#define GMX_NONBONDED_DO_SR (1<<4)
void
do_nonbonded(t_commrec *cr,t_forcerec *fr,
- rvec x[],rvec f[],t_mdatoms *md,t_blocka *excl,
- real egnb[],real egcoul[],real egb[],rvec box_size,
+ rvec x[],rvec f_shortrange[],rvec f_longrange[],t_mdatoms *md,t_blocka *excl,
+ gmx_grppairener_t *grppener,rvec box_size,
t_nrnb *nrnb,real *lambda,real dvdlambda[],
int nls,int eNL,int flags);
-/* Calculate VdW/charge pair interactions (usually 1-4 interactions).
+/* Calculate VdW/charge listed pair interactions (usually 1-4 interactions).
* global_atom_index is only passed for printing error messages.
*/
real
-do_listed_vdw_q(int ftype,int nbonds,
- const t_iatom iatoms[],const t_iparams iparams[],
- const rvec x[],rvec f[],rvec fshift[],
- const t_pbc *pbc,const t_graph *g,
- real *lambda,real *dvdlambda,
- const t_mdatoms *md,
- const t_forcerec *fr,gmx_grppairener_t *grppener,
- int *global_atom_index);
+do_nonbonded_listed(int ftype,int nbonds,const t_iatom iatoms[],const t_iparams iparams[],
+ const rvec x[],rvec f[],rvec fshift[],const t_pbc *pbc,const t_graph *g,
+ real *lambda, real *dvdl,const t_mdatoms *md,const t_forcerec *fr,
+ gmx_grppairener_t *grppener,int *global_atom_index);
#ifdef __cplusplus
}
real *lambda,real *dvdlambda,
gmx_grppairener_t *grppener,
gmx_bool bFillGrid,
- gmx_bool bDoLongRange,
- gmx_bool bDoForces,rvec *f);
+ gmx_bool bDoLongRangeNS);
/* Debugging routines from wnblist.c */
#ifdef __cplusplus
extern "C" {
#endif
+#if 0
+}
+#endif
#define CONTINUE '\\'
#define COMMENTSIGN ';'
char *gmx_strdup(const char *src);
char *gmx_strndup(const char *src, int n);
+
+/* Magic hash initialization number from Dan J. Bernstein. */
+extern const unsigned int
+gmx_string_hash_init;
+
+/* Return a hash of the string according to Dan J. Bernsteins algorithm.
+ * This routine only uses characters for which isalnum(c) is true,
+ * and all characters are converted to upper case.
+ * On the first invocation for a new string, use the constant
+ * gmx_string_hash_init for the second argument. If you want to create a hash
+ * corresponding to several concatenated strings, provide the returned hash
+ * value as hash_init for the second string, etc.
+ */
+unsigned int
+gmx_string_hash_func(const char *s, unsigned int hash_init);
/** Pattern matcing with wildcards. */
int gmx_wcmatch(const char *pattern, const char *src);
/* Implementation of the well-known Perl function split */
gmx_large_int_t str_to_large_int_t(const char *str, char **endptr);
-
+
#ifdef GMX_NATIVE_WINDOWS
#define snprintf _snprintf
#endif
#ifdef __cplusplus
extern "C" {
#endif
+#if 0
+}
+#endif
-
-void table_spline3_fill_ewald_lr(real *tabf,real *tabv,
- int ntab,int tableformat,
- real dr,real beta);
-/* Fill table tabf of size ntab with spacing dr with the ewald long-range
- * (mesh) force and with tableformatF and tabv!=NULL, fill tabv energy.
- * With tableformatFDV0 the size of the tabf array should be ntab*4, tabv=NULL.
+void table_spline3_fill_ewald_lr(real *table_F,
+ real *table_V,
+ real *table_FDV0,
+ int ntab,
+ real dx,
+ real beta);
+/* Fill tables of ntab points with spacing dr with the ewald long-range
+ * (mesh) force.
+ * There are three separate tables with format FDV0, F, and V.
* This function interpolates the Ewald mesh potential contribution
* with coefficient beta using a quadratic spline.
* The force can then be interpolated linearly.
#ifdef __cplusplus
extern "C" {
#endif
+#if 0
+} /* fixes auto-indentation problems */
+#endif
/* note: these enums should correspond to the names in gmxlib/names.c */
erscNO, erscALL, erscCOM, erscNR
};
-enum {
+enum {
ecutsGROUP, ecutsVERLET, ecutsNR
};
/* Coulomb / VdW interaction modifiers.
* grompp replaces eintmodPOTSHIFT_VERLET by eintmodPOTSHIFT or eintmodNONE.
+ * Exactcutoff is only used by Reaction-field-zero, and is not user-selectable.
*/
-enum {
- eintmodPOTSHIFT_VERLET, eintmodPOTSHIFT, eintmodNONE, eintmodNR
+enum eintmod {
+ eintmodPOTSHIFT_VERLET, eintmodPOTSHIFT, eintmodNONE, eintmodPOTSWITCH, eintmodEXACTCUTOFF, eintmodNR
};
/*
eAdressSITEcom,eAdressSITEcog, eAdressSITEatom, eAdressSITEatomatom, eAdressSITENR
};
+
+/* The interactions contained in a (possibly merged) table
+ * for computing electrostatic, VDW repulsion and/or VDW dispersion
+ * contributions.
+ */
+enum gmx_table_interaction
+{
+ GMX_TABLE_INTERACTION_ELEC,
+ GMX_TABLE_INTERACTION_VDWREP_VDWDISP,
+ GMX_TABLE_INTERACTION_VDWEXPREP_VDWDISP,
+ GMX_TABLE_INTERACTION_VDWDISP,
+ GMX_TABLE_INTERACTION_ELEC_VDWREP_VDWDISP,
+ GMX_TABLE_INTERACTION_ELEC_VDWEXPREP_VDWDISP,
+ GMX_TABLE_INTERACTION_ELEC_VDWDISP,
+ GMX_TABLE_INTERACTION_NR
+};
+
+/* Different formats for table data. Cubic spline tables are typically stored
+ * with the four Y,F,G,H intermediate values (check tables.c for format), which
+ * makes it easy to load with a single 4-way SIMD instruction too.
+ * Linear tables only need one value per table point, or two if both V and F
+ * are calculated. However, with SIMD instructions this makes the loads unaligned,
+ * and in that case we store the data as F, D=F(i+1)-F(i), V, and then a blank value,
+ * which again makes it possible to load as a single instruction.
+ */
+enum gmx_table_format
+{
+ GMX_TABLE_FORMAT_CUBICSPLINE_YFGH,
+ GMX_TABLE_FORMAT_LINEAR_VF,
+ GMX_TABLE_FORMAT_LINEAR_V,
+ GMX_TABLE_FORMAT_LINEAR_F,
+ GMX_TABLE_FORMAT_LINEAR_FDV0,
+ GMX_TABLE_FORMAT_NR
+};
+
+/* Neighborlist geometry type.
+ * Kernels will compute interactions between two particles,
+ * 3-center water, 4-center water or coarse-grained beads.
+ */
+enum gmx_nblist_kernel_geometry
+{
+ GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE,
+ GMX_NBLIST_GEOMETRY_WATER3_PARTICLE,
+ GMX_NBLIST_GEOMETRY_WATER3_WATER3,
+ GMX_NBLIST_GEOMETRY_WATER4_PARTICLE,
+ GMX_NBLIST_GEOMETRY_WATER4_WATER4,
+ GMX_NBLIST_GEOMETRY_CG_CG,
+ GMX_NBLIST_GEOMETRY_NR
+};
+
+/* Types of electrostatics calculations available inside nonbonded kernels.
+ * Note that these do NOT necessarily correspond to the user selections in the MDP file;
+ * many interactions for instance map to tabulated kernels.
+ */
+enum gmx_nbkernel_elec
+{
+ GMX_NBKERNEL_ELEC_NONE,
+ GMX_NBKERNEL_ELEC_COULOMB,
+ GMX_NBKERNEL_ELEC_REACTIONFIELD,
+ GMX_NBKERNEL_ELEC_CUBICSPLINETABLE,
+ GMX_NBKERNEL_ELEC_GENERALIZEDBORN,
+ GMX_NBKERNEL_ELEC_EWALD,
+ GMX_NBKERNEL_ELEC_NR
+};
+
+/* Types of vdw calculations available inside nonbonded kernels.
+ * Note that these do NOT necessarily correspond to the user selections in the MDP file;
+ * many interactions for instance map to tabulated kernels.
+ */
+enum gmx_nbkernel_vdw
+{
+ GMX_NBKERNEL_VDW_NONE,
+ GMX_NBKERNEL_VDW_LENNARDJONES,
+ GMX_NBKERNEL_VDW_BUCKINGHAM,
+ GMX_NBKERNEL_VDW_CUBICSPLINETABLE,
+ GMX_NBKERNEL_VDW_NR
+};
+
+
+
#ifdef __cplusplus
}
#endif
#define GMX_FORCE_DYNAMICBOX (1<<1)
/* Do neighbor searching */
#define GMX_FORCE_NS (1<<2)
-/* Calculate long-range energies/forces */
-#define GMX_FORCE_DOLR (1<<3)
+/* Update long-range neighborlists */
+#define GMX_FORCE_LRNS (1<<3)
/* Calculate bonded energies/forces */
#define GMX_FORCE_BONDED (1<<4)
/* Store long-range forces in a separate array */
#define GMX_FORCE_ENERGY (1<<9)
/* Calculate dHdl */
#define GMX_FORCE_DHDL (1<<10)
+/* Calculate long-range energies/forces */
+#define GMX_FORCE_DO_LR (1<<11)
+
/* Normally one want all energy terms and forces */
#define GMX_FORCE_ALLFORCES (GMX_FORCE_BONDED | GMX_FORCE_NONBONDED | GMX_FORCE_FORCES)
#ifdef __cplusplus
extern "C" {
#endif
+#if 0
+} /* fixes auto-indentation problems */
+#endif
/* Abstract type for PME that is defined only in the routine that use them. */
typedef struct gmx_pme *gmx_pme_t;
-typedef struct {
- real r; /* range of the table */
- int n; /* n+1 is the number of points */
- real scale; /* distance between two points */
- real scale_exp; /* distance for exponential Buckingham table */
- real *tab; /* the actual tables, per point there are 4 numbers for
- * Coulomb, dispersion and repulsion (in total 12 numbers)
- */
+
+
+/* Structure describing the data in a single table */
+typedef struct
+{
+ enum gmx_table_interaction interaction; /* Types of interactions stored in this table */
+ enum gmx_table_format format; /* Interpolation type and data format */
+
+ real r; /* range of the table */
+ int n; /* n+1 is the number of table points */
+ real scale; /* distance (nm) between two table points */
+ real scale_exp; /* distance for exponential part of VdW table, not always used */
+ real * data; /* the actual table data */
+
+ /* Some information about the table layout. This can also be derived from the interpolation
+ * type and the table interactions, but it is convenient to have here for sanity checks, and it makes it
+ * much easier to access the tables in the nonbonded kernels when we can set the data from variables.
+ * It is always true that stride = formatsize*ninteractions
+ */
+ int formatsize; /* Number of fp variables for each table point (1 for F, 2 for VF, 4 for YFGH, etc.) */
+ int ninteractions; /* Number of interactions in table, 1 for coul-only, 3 for coul+rep+disp. */
+ int stride; /* Distance to next table point (number of fp variables per table point in total) */
} t_forcetable;
-typedef struct {
- t_forcetable tab;
- /* We duplicate tables for cache optimization purposes */
- real *coultab; /* Coul only */
- real *vdwtab; /* Vdw only */
- /* The actual neighbor lists, short and long range, see enum above
- * for definition of neighborlist indices.
- */
- t_nblist nlist_sr[eNL_NR];
- t_nblist nlist_lr[eNL_NR];
+typedef struct
+{
+ t_forcetable table_elec;
+ t_forcetable table_vdw;
+ t_forcetable table_elec_vdw;
+
+ /* The actual neighbor lists, short and long range, see enum above
+ * for definition of neighborlist indices.
+ */
+ t_nblist nlist_sr[eNL_NR];
+ t_nblist nlist_lr[eNL_NR];
} t_nblists;
/* macros for the cginfo data in forcerec */
gmx_hw_info_t *hwinfo;
gmx_bool use_cpu_acceleration;
+ /* Interaction for calculated in kernels. In many cases this is similar to
+ * the electrostatics settings in the inputrecord, but the difference is that
+ * these variables always specify the actual interaction in the kernel - if
+ * we are tabulating reaction-field the inputrec will say reaction-field, but
+ * the kernel interaction will say cubic-spline-table. To be safe we also
+ * have a kernel-specific setting for the modifiers - if the interaction is
+ * tabulated we already included the inputrec modification there, so the kernel
+ * modification setting will say 'none' in that case.
+ */
+ int nbkernel_elec_interaction;
+ int nbkernel_vdw_interaction;
+ int nbkernel_elec_modifier;
+ int nbkernel_vdw_modifier;
+
/* Use special N*N kernels? */
gmx_bool bAllvsAll;
/* Private work data */
* Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
*/
real rlist,rlistlong;
-
+
/* Dielectric constant resp. multiplication factor for charges */
real zsquare,temp;
real epsilon_r,epsilon_rf,epsfac;
/* Dispersion correction stuff */
int eDispCorr;
+
/* The shift of the shift or user potentials */
real enershiftsix;
real enershifttwelve;
t_forcetable tab14; /* for 1-4 interactions only */
/* PPPM & Shifting stuff */
- gmx_bool coul_pot_shift;
+ int coulomb_modifier;
real rcoulomb_switch,rcoulomb;
real *phi;
/* VdW stuff */
- gmx_bool vdw_pot_shift;
+ int vdw_modifier;
double reppow;
real rvdw_switch,rvdw;
real bham_b_max;
int *gid2nblists;
t_nblists *nblists;
- int cutoff_scheme; /* old- or Verlet-style cutoff */
+ int cutoff_scheme; /* group- or Verlet-style cutoff */
gmx_bool bNonbonded; /* true if nonbonded calculations are *not* turned off */
nonbonded_verlet_t *nbv;
int *excl_load;
} t_forcerec;
+/* Important: Starting with Gromacs-4.6, the values of c6 and c12 in the nbfp array have
+ * been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere
+ * in the code, but beware if you are using these macros externally.
+ */
#define C6(nbfp,ntp,ai,aj) (nbfp)[2*((ntp)*(ai)+(aj))]
#define C12(nbfp,ntp,ai,aj) (nbfp)[2*((ntp)*(ai)+(aj))+1]
#define BHAMC(nbfp,ntp,ai,aj) (nbfp)[3*((ntp)*(ai)+(aj))]
typedef struct {
int n; /* n+1 is the number of points */
real scale; /* distance between two points */
- real *tab; /* the actual tables, per point there are 4 numbers */
+ real *data; /* the actual table data, per point there are 4 numbers */
} bondedtable_t;
#ifdef __cplusplus
int simulation_part; /* Used in checkpointing to separate chunks */
gmx_large_int_t init_step; /* start at a stepcount >0 (used w. tpbconv) */
int nstcalcenergy; /* frequency of energy calc. and T/P coupl. upd. */
- int cutoff_scheme; /* cut-off scheme: group or verlet */
+ int cutoff_scheme; /* group or verlet cutoffs */
int ns_type; /* which ns method should we use? */
int nstlist; /* number of steps before pairlist is generated */
int ndelta; /* number of cells per rlong */
rvec posres_comB; /* The B-state COM of the posres atoms */
int andersen_seed; /* Random seed for Andersen thermostat (obsolete) */
real verletbuf_drift; /* Max. drift (kJ/mol/ps/atom) for list buffer */
- real rlist; /* short range pairlist cut-off (nm) */
- real rlistlong; /* long range pairlist cut-off (nm) */
+ real rlist; /* short range pairlist cut-off (nm) */
+ real rlistlong; /* long range pairlist cut-off (nm) */
+ int nstcalclr; /* Frequency of evaluating direct space long-range interactions */
real rtpi; /* Radius for test particle insertion */
int coulombtype; /* Type of electrostatics treatment */
int coulomb_modifier; /* Modify the Coulomb interaction */
extern "C" {
#endif
-enum { tableformatNONE, tableformatF, tableformatFDV0 };
-
typedef struct {
/* VdW */
real rvdw;
/* Cut-off */
real rlist;
-
+ real rlistlong;
+
/* PME/Ewald */
real ewaldcoeff;
real sh_ewald; /* For shifting the Ewald potential */
/* Force/energy interpolation tables, linear in force, quadratic in V */
real tabq_scale;
int tabq_size;
- int tabq_format;
/* Coulomb force table, size of array is tabq_size (when used) */
real *tabq_coul_F;
/* Coulomb energy table, size of array is tabq_size (when used) */
extern "C" {
#endif
-/* Neighborlist type */
-enum {
- enlistATOM_ATOM,
- enlistSPC_ATOM, enlistSPC_SPC,
- enlistTIP4P_ATOM, enlistTIP4P_TIP4P,
- enlistCG_CG,
- enlistNR
-};
typedef unsigned long t_excl;
typedef struct
{
- int enlist; /* The type of nblist, enum, see above */
- int il_code; /* Innerloop index from nrnb.h, used */
- /* for flop accounting. */
- int icoul; /* Coulomb loop type index for kernels */
- int ivdw; /* VdW loop type index for kernels */
- int free_energy; /* Free energy setting for this list */
+ int igeometry; /* The type of list (atom, water, etc.) */
+ int ielec; /* Coulomb loop type index for kernels */
+ int ielecmod; /* Coulomb modifier (e.g. switch/shift) */
+ int ivdw; /* VdW loop type index for kernels */
+ int ivdwmod; /* VdW modifier (e.g. switch/shift) */
+ int free_energy; /* Free energy setting for this list */
- int nri,maxnri; /* Current/max number of i particles */
- int nrj,maxnrj; /* Current/max number of j particles */
- int maxlen; /* maxnr of j atoms for a single i atom */
- int * iinr; /* The i-elements */
- int * iinr_end; /* The end atom, only with enlistCG */
- int * gid; /* Index in energy arrays */
- int * shift; /* Shift vector index */
- int * jindex; /* Index in jjnr */
- int * jjnr; /* The j-atom list */
- int * jjnr_end; /* The end atom, only with enltypeCG */
- t_excl * excl; /* Exclusions, only with enltypeCG */
- int count; /* counter to multithread the innerloops */
- void * mtx; /* mutex to lock the counter */
+ int nri,maxnri; /* Current/max number of i particles */
+ int nrj,maxnrj; /* Current/max number of j particles */
+ int maxlen; /* maxnr of j atoms for a single i atom */
+ int * iinr; /* The i-elements */
+ int * iinr_end; /* The end atom, only with enlistCG */
+ int * gid; /* Index in energy arrays */
+ int * shift; /* Shift vector index */
+ int * jindex; /* Index in jjnr */
+ int * jjnr; /* The j-atom list */
+ int * jjnr_end; /* The end atom, only with enltypeCG */
+ t_excl * excl; /* Exclusions, only with enltypeCG */
+
+ /* We use separate pointers for kernels that compute both potential
+ * and force (vf suffix), only potential (v) or only force (f)
+ */
+ void * kernelptr_vf;
+ void * kernelptr_v;
+ void * kernelptr_f;
} t_nblist;
#ifdef __cplusplus
extern "C" {
#endif
+#if 0
+} /* fixes auto-indentation problems */
+#endif
-/* The nonbonded kernels are documented in gmxlib/nonbonded_kernels,
- * but here's a lazy version of the numbering. The first position
- * is the Coulomb interaction (0 for none), second is Van der Waals
- * (again, 0 means no interaction), and the third is the water optimization
- * (0 meaning no water optimization = standard atom-atom loop)
- *
- * value
- * pos 1 2 3 4
- * 1st Coul Normal,1/r Reaction-field Table Generalized born
- * 2nd Vdw Lennard-Jones Buckingham Table n/a
- * 3rd Water. opt SPC-other atom SPC-SPC TIP4p-other at. TIP4p-TIP4p
- */
#define eNR_NBKERNEL_NONE -1
enum
{
- eNR_NBKERNEL010, eNR_NBKERNEL020, eNR_NBKERNEL030,
- eNR_NBKERNEL100, eNR_NBKERNEL101, eNR_NBKERNEL102, eNR_NBKERNEL103, eNR_NBKERNEL104,
- eNR_NBKERNEL110, eNR_NBKERNEL111, eNR_NBKERNEL112, eNR_NBKERNEL113, eNR_NBKERNEL114,
- eNR_NBKERNEL120, eNR_NBKERNEL121, eNR_NBKERNEL122, eNR_NBKERNEL123, eNR_NBKERNEL124,
- eNR_NBKERNEL130, eNR_NBKERNEL131, eNR_NBKERNEL132, eNR_NBKERNEL133, eNR_NBKERNEL134,
- eNR_NBKERNEL200, eNR_NBKERNEL201, eNR_NBKERNEL202, eNR_NBKERNEL203, eNR_NBKERNEL204,
- eNR_NBKERNEL210, eNR_NBKERNEL211, eNR_NBKERNEL212, eNR_NBKERNEL213, eNR_NBKERNEL214,
- eNR_NBKERNEL220, eNR_NBKERNEL221, eNR_NBKERNEL222, eNR_NBKERNEL223, eNR_NBKERNEL224,
- eNR_NBKERNEL230, eNR_NBKERNEL231, eNR_NBKERNEL232, eNR_NBKERNEL233, eNR_NBKERNEL234,
- eNR_NBKERNEL300, eNR_NBKERNEL301, eNR_NBKERNEL302, eNR_NBKERNEL303, eNR_NBKERNEL304,
- eNR_NBKERNEL310, eNR_NBKERNEL311, eNR_NBKERNEL312, eNR_NBKERNEL313, eNR_NBKERNEL314,
- eNR_NBKERNEL320, eNR_NBKERNEL321, eNR_NBKERNEL322, eNR_NBKERNEL323, eNR_NBKERNEL324,
- eNR_NBKERNEL330, eNR_NBKERNEL331, eNR_NBKERNEL332, eNR_NBKERNEL333, eNR_NBKERNEL334,
- eNR_NBKERNEL400, eNR_NBKERNEL410, eNR_NBKERNEL430,
- eNR_NBKERNEL010NF, eNR_NBKERNEL020NF, eNR_NBKERNEL030NF,
- eNR_NBKERNEL100NF, eNR_NBKERNEL101NF, eNR_NBKERNEL102NF, eNR_NBKERNEL103NF, eNR_NBKERNEL104NF,
- eNR_NBKERNEL110NF, eNR_NBKERNEL111NF, eNR_NBKERNEL112NF, eNR_NBKERNEL113NF, eNR_NBKERNEL114NF,
- eNR_NBKERNEL120NF, eNR_NBKERNEL121NF, eNR_NBKERNEL122NF, eNR_NBKERNEL123NF, eNR_NBKERNEL124NF,
- eNR_NBKERNEL130NF, eNR_NBKERNEL131NF, eNR_NBKERNEL132NF, eNR_NBKERNEL133NF, eNR_NBKERNEL134NF,
- eNR_NBKERNEL200NF, eNR_NBKERNEL201NF, eNR_NBKERNEL202NF, eNR_NBKERNEL203NF, eNR_NBKERNEL204NF,
- eNR_NBKERNEL210NF, eNR_NBKERNEL211NF, eNR_NBKERNEL212NF, eNR_NBKERNEL213NF, eNR_NBKERNEL214NF,
- eNR_NBKERNEL220NF, eNR_NBKERNEL221NF, eNR_NBKERNEL222NF, eNR_NBKERNEL223NF, eNR_NBKERNEL224NF,
- eNR_NBKERNEL230NF, eNR_NBKERNEL231NF, eNR_NBKERNEL232NF, eNR_NBKERNEL233NF, eNR_NBKERNEL234NF,
- eNR_NBKERNEL300NF, eNR_NBKERNEL301NF, eNR_NBKERNEL302NF, eNR_NBKERNEL303NF, eNR_NBKERNEL304NF,
- eNR_NBKERNEL310NF, eNR_NBKERNEL311NF, eNR_NBKERNEL312NF, eNR_NBKERNEL313NF, eNR_NBKERNEL314NF,
- eNR_NBKERNEL320NF, eNR_NBKERNEL321NF, eNR_NBKERNEL322NF, eNR_NBKERNEL323NF, eNR_NBKERNEL324NF,
- eNR_NBKERNEL330NF, eNR_NBKERNEL331NF, eNR_NBKERNEL332NF, eNR_NBKERNEL333NF, eNR_NBKERNEL334NF,
- eNR_NBKERNEL400NF, eNR_NBKERNEL410NF, eNR_NBKERNEL430NF,
- eNR_NBKERNEL_NR,
- eNR_NBKERNEL_FREE_ENERGY = eNR_NBKERNEL_NR,
+ eNR_NBKERNEL_VDW_VF,
+ eNR_NBKERNEL_VDW_F,
+ eNR_NBKERNEL_ELEC_VF,
+ eNR_NBKERNEL_ELEC_F,
+ eNR_NBKERNEL_ELEC_W3_VF,
+ eNR_NBKERNEL_ELEC_W3_F,
+ eNR_NBKERNEL_ELEC_W3W3_VF,
+ eNR_NBKERNEL_ELEC_W3W3_F,
+ eNR_NBKERNEL_ELEC_W4_VF,
+ eNR_NBKERNEL_ELEC_W4_F,
+ eNR_NBKERNEL_ELEC_W4W4_VF,
+ eNR_NBKERNEL_ELEC_W4W4_F,
+ eNR_NBKERNEL_ELEC_VDW_VF,
+ eNR_NBKERNEL_ELEC_VDW_F,
+ eNR_NBKERNEL_ELEC_VDW_W3_VF,
+ eNR_NBKERNEL_ELEC_VDW_W3_F,
+ eNR_NBKERNEL_ELEC_VDW_W3W3_VF,
+ eNR_NBKERNEL_ELEC_VDW_W3W3_F,
+ eNR_NBKERNEL_ELEC_VDW_W4_VF,
+ eNR_NBKERNEL_ELEC_VDW_W4_F,
+ eNR_NBKERNEL_ELEC_VDW_W4W4_VF,
+ eNR_NBKERNEL_ELEC_VDW_W4W4_F,
+
+ eNR_NBKERNEL_NR, /* Total number of interaction-specific kernel entries */
+
+ eNR_NBKERNEL_GENERIC = eNR_NBKERNEL_NR, /* Reuse number; KERNEL_NR is not an entry itself */
+ eNR_NBKERNEL_FREE_ENERGY, /* Add other generic kernels _before_ the free energy one */
+
eNR_NBKERNEL_ALLVSALL,
eNR_NBKERNEL_ALLVSALLGB,
- eNR_NBKERNEL_OUTER,
+
eNR_NBNXN_DIST2,
eNR_NBNXN_LJ_RF, eNR_NBNXN_LJ_RF_E,
eNR_NBNXN_LJ_TAB, eNR_NBNXN_LJ_TAB_E,
eNR_VSITE2, eNR_VSITE3, eNR_VSITE3FD,
eNR_VSITE3FAD, eNR_VSITE3OUT, eNR_VSITE4FD,
eNR_VSITE4FDN, eNR_VSITEN, eNR_GB,
- eNR_CMAP,
+ eNR_CMAP,
eNRNB
};
-typedef struct {
- double n[eNRNB];
-} t_nrnb;
+typedef struct
+{
+ double n[eNRNB];
+}
+t_nrnb;
typedef struct gmx_wallcycle *gmx_wallcycle_t;
#endif
+#ifndef gmx_inline
+/* config.h tests for inline definitions and should work on a much wider range
+ * of compilers, but does not work with installed headers. These compiler checks
+ * still enable a real inline keyword for the most common compilers.
+ */
+
/* Try to define suitable inline keyword for gmx_inline.
* Set it to empty if we cannot find one (and dont complain to the user)
*/
#endif
#else
+/* C++ */
# define gmx_inline inline
#endif
+#endif /* ifndef gmx_inline */
+
+
+/* Restrict keywords. Note that this has to be done for C++ too, unless
+ * it was set from the more general checks if we had config.h (gmx internal)
+ */
+#ifndef gmx_restrict
-/* Restrict keywords. Note that this has to be done for C++ too. */
#ifdef __GNUC__
/* GCC */
# define gmx_restrict __restrict__
# define gmx_restrict
#endif
+#endif
/* Standard sizes for char* string buffers */
#define STRLEN 4096
#define INVSQRT_DONE
#endif /* powerpc_invsqrt */
-
#ifndef INVSQRT_DONE
-#define gmx_invsqrt(x) (1.0f/sqrt(x))
+# ifdef GMX_DOUBLE
+# ifdef HAVE_RSQRT
+# define gmx_invsqrt(x) rsqrt(x)
+# else
+# define gmx_invsqrt(x) (1.0/sqrt(x))
+# endif
+# else /* single */
+# ifdef HAVE_RSQRTF
+# define gmx_invsqrt(x) rsqrtf(x)
+# elif defined HAVE_RSQRT
+# define gmx_invsqrt(x) rsqrt(x)
+# elif defined HAVE_SQRTF
+# define gmx_invsqrt(x) (1.0/sqrtf(x))
+# else
+# define gmx_invsqrt(x) (1.0/sqrt(x))
+# endif
+# endif
#endif
-
-
-
static real sqr(real x)
{
return (x*x);
* float/double case here instead to avoid gmx_sqrt() being accidentally used. */
#ifdef GMX_DOUBLE
return dnorm(a);
-#else
+#elif defined HAVE_SQRTF
return sqrtf(iprod(a, a));
+#else
+ return sqrt(iprod(a, a));
#endif
}
<li><a HREF="#xmdrun"><b>shell molecular dynamics</b></a>(emtol,niter,fcstep)
<li><a HREF="#tpi"><b>test particle insertion</b></a>(rtpi)
<li><A HREF="#out"><b>output control</b></A> (nstxout, nstvout, nstfout, nstlog, nstcalcenergy, nstenergy, nstxtcout, xtc-precision, xtc-grps, energygrps)
-<li><A HREF="#nl"><b>neighbor searching</b></A> (cutoff-scheme, nstlist, ns-type, pbc, periodic-molecules, verlet-buffer-drift, rlist, rlistlong)
+<li><A HREF="#nl"><b>neighbor searching</b></A> (cutoff-scheme, nstlist, nstcalclr, ns-type, pbc, periodic-molecules, verlet-buffer-drift, rlist, rlistlong)
<li><A HREF="#el"><b>electrostatics</b></A> (coulombtype, coulomb-modifier, rcoulomb-switch, rcoulomb, epsilon-r, epsilon-rf)
<li><A HREF="#vdw"><b>VdW</b></A> (vdwtype, vdw-modifier, rvdw-switch, rvdw, DispCorr)
<li><A HREF="#table"><b>tables</b></A> (table-extension, energygrp-table)
</dd>
</dl></dd>
+<dt><b>nstcalclr: (-1) [steps]</b></dt>
+<dd><dl compact>
+Controls the period between calculations of long-range forces. Useful
+only with <b>cutoff-scheme</b>=<b>group</b>.
+<dt><b>1</b></dt>
+<dd>Calculate the long-range forces every single step. This is useful
+to have separate neighbor lists with buffers for electrostatics and Van
+der Waals interactions, and in particular it makes it possible to have
+the Van der Waals cutoff longer than electrostatics (useful e.g. with
+PME). However, there is no point in having identical long-range
+cutoffs for both interaction forms and update them every step - then
+it will be slightly faster to put everything in the short-range
+list.</dd>
+<dt><b>>1</b></dt>
+<dd>Calculate the long-range forces every <b>nstcalclr</b> steps and
+use a multiple-time-step integrator to combine forces. This can now be
+done more frequently than <b>nstlist</b> since the lists are stored,
+and it might be a good idea e.g. for Van der Waals interactions that
+vary slower than electrostatics.</dd>
+<dt><b>-1</b></dt>
+<dd>Calculate long-range forces on steps where neighbor searching is
+performed. While this is the default value, you might want to consider
+updating the long-range forces more frequently.</dd>
+Note that twin-range force evaluation might be enabled automatically
+by PP-PME load balancing. This is done in order to maintain the chosen
+Van der Waals interaction radius even if the load balancing is
+changing the electrostatics cutoff. If the <tt>.mdp</tt> file already
+specifies twin-range interactions (e.g. to evaluate Lennard-Jones
+interactions with a longer cutoff than the PME electrostatics every
+2-3 steps), the load balancing will have also a small effect on
+Lennard-Jones, since the short-range cutoff (inside which forces are
+evaluated every step) is changed.</dl>
+</dd>
+
+
+
<dt><b>ns-type:</b></dt>
<dd><dl compact>
<dt><b>grid</b></dt>
/* Define to 1 if you have the sigaction() function. */
#cmakedefine HAVE_SIGACTION
+/* Define to 1 if you have the rsqrt() function. */
+#cmakedefine HAVE_RSQRT
+
+/* Define to 1 if you have the rsqrtf() function. */
+#cmakedefine HAVE_RSQRTF
+
+/* Define to 1 if you have the sqrtf() function. */
+#cmakedefine HAVE_SQRTF
+
/* Define to 1 if you have the <string.h> header file. */
#cmakedefine HAVE_STRING_H
#cmakedefine gid_t int
/* Define to __inline__ or __inline if that is what the C compiler
- calls it, or to nothing if inline is not supported under any name. */
+ calls it, or to nothing if inline is not supported under any name.
+ Please do NOT remove the gmx_inline keyword from here. The classical
+ C++ inline keyword is merely a recommendation to the compiler, and
+ many compilers support stronger alternatives (e.g. __forceinline)
+ that we might want to use. */
+#define gmx_inline ${INLINE_KEYWORD}
#ifndef __cplusplus
#define inline ${INLINE_KEYWORD}
#endif
/* Define to __restrict__ or __restrict if that is what the C compiler
- calls it, or to nothing if restrict is not supported under any name. */
-#define restrict ${RESTRICT_KEYWORD}
+ calls it, unless we are on C99 when it is simply called restrict.
+ Since restrict is a reserved key word in C99 we are not allowed to
+ redefine the word itself, so call this gmx_restrict to avoid having
+ to identify the language standard level. If it is not supported, it
+ is still defined to an empty string here. */
+#define gmx_restrict ${RESTRICT_KEYWORD}
#ifndef CPLUSPLUS
#ifdef __cplusplus
k = (1.0 - lambda)*kA + lambda*kB;
tabscale = table->scale;
- VFtab = table->tab;
+ VFtab = table->data;
rt = r*tabscale;
n0 = rt;
}
else
{
- v = do_listed_vdw_q(ftype,nbn,iatoms+nb0,
- idef->iparams,
- (const rvec*)x,f,fshift,
- pbc,g,lambda,dvdl,
- md,fr,grpp,global_atom_index);
+ v = do_nonbonded_listed(ftype,nbn,iatoms+nb0,idef->iparams,(const rvec*)x,f,fshift,
+ pbc,g,lambda,dvdl,md,fr,grpp,global_atom_index);
+
+ enerd->dvdl_nonlin[efptCOUL] += dvdl[efptCOUL];
+ enerd->dvdl_nonlin[efptVDW] += dvdl[efptVDW];
if (bPrintSepPot)
{
}
else
{
- v = do_listed_vdw_q(ftype,nbonds,iatoms,
- idef->iparams,
- (const rvec*)x,f,fr->fshift,
- pbc,g,lambda,dvdl,
- md,fr,&enerd->grpp,global_atom_index);
+ v = do_nonbonded_listed(ftype,nbonds,iatoms,
+ idef->iparams,
+ (const rvec*)x,f,fr->fshift,
+ pbc,g,lambda,dvdl,
+ md,fr,&enerd->grpp,global_atom_index);
}
if (ind != -1)
{
};
const char *eintmod_names[eintmodNR+1] = {
- "Potential-shift-Verlet","Potential-shift","None", NULL
+ "Potential-shift-Verlet","Potential-shift","None","Potential-switch","Exact-cutoff", NULL
};
const char *egrp_nm[egNR+1] = {
"No", "SPC", "TIP4p", NULL
};
-const char *enlist_names[enlistNR+1] = {
- "Atom-Atom", "SPC-Atom", "SPC-SPC", "TIP4p-Atom", "TIP4p-TIP4p", "CG-CG", NULL
-};
-
const char *edispc_names[edispcNR+1] = {
"No", "EnerPres", "Ener", "AllEnerPres", "AllEner", NULL
};
"com","cog", "atom", "atomperatom", NULL
};
+const char *gmx_nblist_geometry_names[GMX_NBLIST_GEOMETRY_NR+1] = {
+ "Particle-Particle", "Water3-Particle", "Water3-Water3", "Water4-Particle", "Water4-Water4", "CG-CG", NULL
+};
+
+const char *gmx_nbkernel_elec_names[GMX_NBKERNEL_ELEC_NR+1] =
+{
+ "None", "Coulomb", "Reaction-Field", "Cubic-Spline-Table", "Generalized-Born", "Ewald", NULL
+};
+
+const char *gmx_nbkernel_vdw_names[GMX_NBKERNEL_VDW_NR+1] =
+{
+ "None", "Lennard-Jones", "Buckingham", "Cubic-Spline-Table", NULL
+};
+
+
+
# Sources that should always be built
-file(GLOB NONBONDED_SOURCES *.c nb_kernel_c/*.c nb_kernel_adress_c/*.c)
-
-# Conditionally included ones
-if(GMX_FORTRAN)
- if (GMX_DOUBLE)
- file(GLOB NB_KERNEL_FORTRAN_SOURCES nb_kernel_f77_double/*.[cf])
- else(GMX_DOUBLE)
- file(GLOB NB_KERNEL_FORTRAN_SOURCES nb_kernel_f77_single/*.[cf])
- endif(GMX_DOUBLE)
-endif(GMX_FORTRAN)
-
-if(GMX_POWER6)
- file(GLOB NB_KERNEL_FORTRAN_SOURCES nb_kernel_power6/*.[cF])
-endif(GMX_POWER6)
-
-if(GMX_BLUEGENE)
- file(GLOB NB_KERNEL_BLUEGENE_SOURCES nb_kernel_bluegene/*.c)
-endif(GMX_BLUEGENE)
-
-list(APPEND NONBONDED_SOURCES ${NB_KERNEL_FORTRAN_SOURCES} ${NB_KERNEL_BLUEGENE_SOURCES})
+file(GLOB NONBONDED_SOURCES *.c nb_kernel_c/*.c)
# These sources will be used in the parent directory's CMakeLists.txt
set(NONBONDED_SOURCES ${NONBONDED_SOURCES} PARENT_SCOPE)
#include "vec.h"
#include "typedefs.h"
+#include "nonbonded.h"
+#include "nb_kernel.h"
+#include "nrnb.h"
void
-gmx_nb_free_energy_kernel(int icoul,
- int ivdw,
- int nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * x,
- real * f,
- real * chargeA,
- real * chargeB,
- real facel,
- real krf,
- real crf,
- real ewc,
- real * Vc,
- int * typeA,
- int * typeB,
- int ntype,
- real * nbfp,
- real * Vv,
- real tabscale,
- real * VFtab,
- real lambda_coul,
- real lambda_vdw,
- real * dvdl,
- real alpha_coul,
- real alpha_vdw,
- int lam_power,
- real sc_r_power,
- real sigma6_def,
- real sigma6_min,
- gmx_bool bDoForces,
- int * outeriter,
- int * inneriter)
+gmx_nb_free_energy_kernel(t_nblist * nlist,
+ rvec * xx,
+ rvec * ff,
+ t_forcerec * fr,
+ t_mdatoms * mdatoms,
+ nb_kernel_data_t * kernel_data,
+ t_nrnb * nrnb)
{
#define STATE_A 0
int n0,n1C,n1V,nnn;
real Y,F,G,H,Fp,Geps,Heps2,epsC,eps2C,epsV,eps2V,VV,FF;
double isp=0.564189583547756;
+ int icoul,ivdw;
+ int nri;
+ int * iinr;
+ int * jindex;
+ int * jjnr;
+ int * shift;
+ int * gid;
+ int * typeA;
+ int * typeB;
+ int ntype;
+ real * shiftvec;
real dvdl_part;
+ real * fshift;
+ real tabscale;
+ real * VFtab;
+ real * x;
+ real * f;
+ real facel,krf,crf;
+ real * chargeA;
+ real * chargeB;
+ real sigma6_min,sigma6_def,lam_power,sc_power,sc_r_power;
+ real alpha_coul,alpha_vdw,lambda_coul,lambda_vdw,ewc;
+ real * nbfp;
+ real * dvdl;
+ real * Vv;
+ real * Vc;
+ gmx_bool bDoForces;
+ real rcoulomb,rvdw,factor_coul,factor_vdw,sh_invrc6;
+ gmx_bool bExactElecCutoff,bExactVdwCutoff;
+ real rcutoff,rcutoff2,rswitch,d,d2,swV3,swV4,swV5,swF2,swF3,swF4,sw,dsw,rinvcorr;
+
+ x = xx[0];
+ f = ff[0];
+
+ fshift = fr->fshift[0];
+ Vc = kernel_data->energygrp_elec;
+ Vv = kernel_data->energygrp_vdw;
+ tabscale = kernel_data->table_elec_vdw->scale;
+ VFtab = kernel_data->table_elec_vdw->data;
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ icoul = nlist->ielec;
+ ivdw = nlist->ivdw;
+ shift = nlist->shift;
+ gid = nlist->gid;
+
+ shiftvec = fr->shift_vec[0];
+ chargeA = mdatoms->chargeA;
+ chargeB = mdatoms->chargeB;
+ facel = fr->epsfac;
+ krf = fr->k_rf;
+ crf = fr->c_rf;
+ ewc = fr->ewaldcoeff;
+ Vc = kernel_data->energygrp_elec;
+ typeA = mdatoms->typeA;
+ typeB = mdatoms->typeB;
+ ntype = fr->ntype;
+ nbfp = fr->nbfp;
+ Vv = kernel_data->energygrp_vdw;
+ tabscale = kernel_data->table_elec_vdw->scale;
+ VFtab = kernel_data->table_elec_vdw->data;
+ lambda_coul = kernel_data->lambda[efptCOUL];
+ lambda_vdw = kernel_data->lambda[efptVDW];
+ dvdl = kernel_data->dvdl;
+ alpha_coul = fr->sc_alphacoul;
+ alpha_vdw = fr->sc_alphavdw;
+ lam_power = fr->sc_power;
+ sc_r_power = fr->sc_r_power;
+ sigma6_def = fr->sc_sigma6_def;
+ sigma6_min = fr->sc_sigma6_min;
+ bDoForces = kernel_data->flags & GMX_NONBONDED_DO_FORCE;
+
+ rcoulomb = fr->rcoulomb;
+ rvdw = fr->rvdw;
+ sh_invrc6 = fr->ic->sh_invrc6;
+
+ if(fr->coulomb_modifier==eintmodPOTSWITCH || fr->vdw_modifier==eintmodPOTSWITCH)
+ {
+ rcutoff = (fr->coulomb_modifier==eintmodPOTSWITCH) ? fr->rcoulomb : fr->rvdw;
+ rcutoff2 = rcutoff*rcutoff;
+ rswitch = (fr->coulomb_modifier==eintmodPOTSWITCH) ? fr->rcoulomb_switch : fr->rvdw_switch;
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+ }
+ else
+ {
+ /* Stupid compilers dont realize these variables will not be used */
+ rswitch = 0.0;
+ swV3 = 0.0;
+ swV4 = 0.0;
+ swV5 = 0.0;
+ swF2 = 0.0;
+ swF3 = 0.0;
+ swF4 = 0.0;
+ }
+
+ bExactElecCutoff = (fr->coulomb_modifier!=eintmodNONE) || fr->eeltype == eelRF_ZERO;
+ bExactVdwCutoff = (fr->vdw_modifier!=eintmodNONE);
/* fix compiler warnings */
nj1 = 0;
/* Ewald (not PME) table is special (icoul==enbcoulFEWALD) */
- do_coultab = (icoul==enbcoulTAB);
- do_vdwtab = (ivdw==enbcoulTAB);
+ do_coultab = (icoul==GMX_NBKERNEL_ELEC_CUBICSPLINETABLE);
+ do_vdwtab = (ivdw==GMX_NBKERNEL_VDW_CUBICSPLINETABLE);
do_tab = do_coultab || do_vdwtab;
for(n=0; (n<nri); n++)
{
- is3 = 3*shift[n];
+ is3 = 3*shift[n];
shX = shiftvec[is3];
shY = shiftvec[is3+1];
shZ = shiftvec[is3+2];
- nj0 = jindex[n];
+ nj0 = jindex[n];
nj1 = jindex[n+1];
ii = iinr[n];
ii3 = 3*ii;
qq[STATE_A] = iqA*chargeA[jnr];
qq[STATE_B] = iqB*chargeB[jnr];
- for (i=0;i<NSTATES;i++)
+ for (i=0;i<NSTATES;i++)
{
c6[i] = nbfp[tj[i]];
c12[i] = nbfp[tj[i]+1];
if((c6[i] > 0) && (c12[i] > 0))
{
- sigma6[i] = c12[i]/c6[i];
- sigma2[i] = pow(c12[i]/c6[i],1.0/3.0);
+ /* c12 is stored scaled with 12.0 and c6 is scaled with 6.0 - correct for this */
+ sigma6[i] = 0.5*c12[i]/c6[i];
+ sigma2[i] = pow(sigma6[i],1.0/3.0);
/* should be able to get rid of this ^^^ internal pow call eventually. Will require agreement on
what data to store externally. Can't be fixed without larger scale changes, so not 4.6 */
if (sigma6[i] < sigma6_min) { /* for disappearing coul and vdw with soft core at the same time */
rinvV = pow(rpinvV,1.0/sc_r_power);
rV = 1.0/rinvV;
+ factor_coul = (rC<=rcoulomb) ? 1.0 : 0.0;
+ factor_vdw = (rV<=rvdw) ? 1.0 : 0.0;
+
if (do_tab)
{
rtC = rC*tabscale;
n1V = tab_elemsize*n0;
}
- if(icoul==enbcoulOOR || icoul==enbcoulFEWALD)
+ if(qq[i] != 0)
{
- /* simple cutoff */
- Vcoul[i] = qq[i]*rinvC;
- FscalC[i] = Vcoul[i]*rpinvC;
- }
- else if(icoul==enbcoulRF)
- {
- /* reaction-field */
- krsq = krf*rC*rC;
- Vcoul[i] = qq[i]*(rinvC+krsq-crf);
- FscalC[i] = qq[i]*(rinvC-2.0*krsq)*rpinvC;
- }
- else if (icoul==enbcoulTAB)
- {
- /* non-Ewald tabulated coulomb */
- nnn = n1C;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = epsC*VFtab[nnn+2];
- Heps2 = eps2C*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+epsC*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vcoul[i] = qq[i]*VV;
- FscalC[i] = -qq[i]*tabscale*FF*rC*rpinvC;
+ switch(icoul)
+ {
+ case GMX_NBKERNEL_ELEC_COULOMB:
+ case GMX_NBKERNEL_ELEC_EWALD:
+ /* simple cutoff (yes, ewald is done all on direct space for free energy) */
+ Vcoul[i] = qq[i]*rinvC;
+ FscalC[i] = Vcoul[i]*rpinvC;
+ break;
+
+ case GMX_NBKERNEL_ELEC_REACTIONFIELD:
+ /* reaction-field */
+ Vcoul[i] = qq[i]*(rinvC+krf*rC*rC-crf);
+ FscalC[i] = qq[i]*(rinvC*rpinvC-2.0*krf);
+ break;
+
+ case GMX_NBKERNEL_ELEC_CUBICSPLINETABLE:
+ /* non-Ewald tabulated coulomb */
+ nnn = n1C;
+ Y = VFtab[nnn];
+ F = VFtab[nnn+1];
+ Geps = epsC*VFtab[nnn+2];
+ Heps2 = eps2C*VFtab[nnn+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+epsC*Fp;
+ FF = Fp+Geps+2.0*Heps2;
+ Vcoul[i] = qq[i]*VV;
+ FscalC[i] = -qq[i]*tabscale*FF*rC*rpinvC;
+ break;
+
+ default:
+ FscalC[i] = 0.0;
+ Vcoul[i] = 0.0;
+ break;
+ }
+
+ if(fr->coulomb_modifier==eintmodPOTSWITCH)
+ {
+ d = rC-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ Vcoul[i] *= sw;
+ FscalC[i] = FscalC[i]*sw + Vcoul[i]*dsw;
+ }
+
+ if(bExactElecCutoff)
+ {
+ FscalC[i] = (rC<rcoulomb) ? FscalC[i] : 0.0;
+ Vcoul[i] = (rC<rcoulomb) ? Vcoul[i] : 0.0;
+ }
}
- if(ivdw==enbvdwLJ)
+ if((c6[i] != 0) || (c12[i] != 0))
{
- /* cutoff LJ */
- if (sc_r_power == 6.0)
+ switch(ivdw)
{
- rinv6 = rpinvV;
+ case GMX_NBKERNEL_VDW_LENNARDJONES:
+ /* cutoff LJ */
+ if (sc_r_power == 6.0)
+ {
+ rinv6 = rpinvV;
+ }
+ else
+ {
+ rinv6 = pow(rinvV,6.0);
+ }
+ Vvdw6 = c6[i]*rinv6;
+ Vvdw12 = c12[i]*rinv6*rinv6;
+ if(fr->vdw_modifier==eintmodPOTSHIFT)
+ {
+ Vvdw[i] = ( (Vvdw12-c12[i]*sh_invrc6*sh_invrc6)*(1.0/12.0)
+ -(Vvdw6-c6[i]*sh_invrc6)*(1.0/6.0));
+ }
+ else
+ {
+ Vvdw[i] = Vvdw12*(1.0/12.0)-Vvdw6*(1.0/6.0);
+ }
+ FscalV[i] = (Vvdw12-Vvdw6)*rpinvV;
+ break;
+
+ case GMX_NBKERNEL_VDW_BUCKINGHAM:
+ gmx_fatal(FARGS,"Buckingham free energy not supported.");
+ break;
+
+ case GMX_NBKERNEL_VDW_CUBICSPLINETABLE:
+ /* Table LJ */
+ nnn = n1V+4;
+ /* dispersion */
+ Y = VFtab[nnn];
+ F = VFtab[nnn+1];
+ Geps = epsV*VFtab[nnn+2];
+ Heps2 = eps2V*VFtab[nnn+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+epsV*Fp;
+ FF = Fp+Geps+2.0*Heps2;
+ Vvdw[i] += c6[i]*VV;
+ FscalV[i] -= c6[i]*tabscale*FF*rV*rpinvV;
+
+ /* repulsion */
+ Y = VFtab[nnn+4];
+ F = VFtab[nnn+5];
+ Geps = epsV*VFtab[nnn+6];
+ Heps2 = eps2V*VFtab[nnn+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+epsV*Fp;
+ FF = Fp+Geps+2.0*Heps2;
+ Vvdw[i] += c12[i]*VV;
+ FscalV[i] -= c12[i]*tabscale*FF*rV*rpinvV;
+ break;
+
+ default:
+ Vvdw[i] = 0.0;
+ FscalV[i] = 0.0;
+ break;
}
- else
+
+ if(fr->vdw_modifier==eintmodPOTSWITCH)
{
- rinv6 = pow(rinvV,6.0);
+ d = rV-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ Vvdw[i] *= sw;
+ FscalV[i] = FscalV[i]*sw + Vvdw[i]*dsw;
+
+ FscalV[i] = (rV<rvdw) ? FscalV[i] : 0.0;
+ Vvdw[i] = (rV<rvdw) ? Vvdw[i] : 0.0;
}
- Vvdw6 = c6[i]*rinv6;
- Vvdw12 = c12[i]*rinv6*rinv6;
- Vvdw[i] = Vvdw12-Vvdw6;
- FscalV[i] = (12.0*Vvdw12-6.0*Vvdw6)*rpinvV;
}
- else if(ivdw==enbvdwTAB)
- {
- /* Table LJ */
- nnn = n1V+4;
-
- /* dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = epsV*VFtab[nnn+2];
- Heps2 = eps2V*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+epsV*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw[i] += c6[i]*VV;
- FscalV[i] -= c6[i]*tabscale*FF*rV*rpinvV;
-
- /* repulsion */
- Y = VFtab[nnn+4];
- F = VFtab[nnn+5];
- Geps = epsV*VFtab[nnn+6];
- Heps2 = eps2V*VFtab[nnn+7];
- Fp = F+Geps+Heps2;
- VV = Y+epsV*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw[i] += c12[i]*VV;
- FscalV[i] -= c12[i]*tabscale*FF*rV*rpinvV;
- }
- /* Buckingham vdw free energy not supported for now */
}
}
Fscal = 0;
- if (icoul==enbcoulFEWALD) {
+ if (icoul==GMX_NBKERNEL_ELEC_EWALD)
+ {
/* because we compute the softcore normally,
- we have to remove the ewald short range portion. Done outside of
- the states loop because this part doesn't depend on the scaled R */
+ we have to remove the ewald short range portion. Done outside of
+ the states loop because this part doesn't depend on the scaled R */
- if (r != 0)
+ if (r != 0)
{
VV = gmx_erf(ewc*r)*rinv;
FF = rinv*rinv*(VV - 2.0*ewc*isp*exp(-ewc*ewc*rsq));
}
- else
+ else
{
VV = ewc*2.0/sqrt(M_PI);
FF = 0;
dvdl[efptCOUL] += dvdl_coul;
dvdl[efptVDW] += dvdl_vdw;
- *outeriter = nri;
- *inneriter = nj1;
+
+ /* Estimate flops, average for free energy stuff:
+ * 12 flops per outer iteration
+ * 150 flops per inner iteration
+ */
+ inc_nrnb(nrnb,eNR_NBKERNEL_FREE_ENERGY,nlist->nri*12 + nlist->jindex[n]*150);
+}
+
+real
+nb_free_energy_evaluate_single(real r2,real sc_r_power,real alpha_coul,real alpha_vdw,
+ real tabscale,real *vftab,
+ real qqA, real c6A, real c12A, real qqB, real c6B, real c12B,
+ real LFC[2], real LFV[2],real DLF[2],
+ real lfac_coul[2], real lfac_vdw[2],real dlfac_coul[2], real dlfac_vdw[2],
+ real sigma6_def, real sigma6_min,real sigma2_def, real sigma2_min,
+ real *velectot, real *vvdwtot, real *dvdl)
+{
+ real r,rp,rpm2,rtab,eps,eps2,Y,F,Geps,Heps2,Fp,VV,FF,fscal;
+ real qq[2],c6[2],c12[2],sigma6[2],sigma2[2],sigma_pow[2],sigma_powm2[2];
+ real alpha_coul_eff,alpha_vdw_eff,dvdl_coul,dvdl_vdw;
+ real rpinv,r_coul,r_vdw,velecsum,vvdwsum;
+ real fscal_vdw[2],fscal_elec[2];
+ real velec[2],vvdw[2];
+ int i,ntab;
+
+ qq[0] = qqA;
+ qq[1] = qqB;
+ c6[0] = c6A;
+ c6[1] = c6B;
+ c12[0] = c12A;
+ c12[1] = c12B;
+
+ if (sc_r_power == 6.0)
+ {
+ rpm2 = r2*r2; /* r4 */
+ rp = rpm2*r2; /* r6 */
+ }
+ else if (sc_r_power == 48.0)
+ {
+ rp = r2*r2*r2; /* r6 */
+ rp = rp*rp; /* r12 */
+ rp = rp*rp; /* r24 */
+ rp = rp*rp; /* r48 */
+ rpm2 = rp/r2; /* r46 */
+ }
+ else
+ {
+ rp = pow(r2,0.5*sc_r_power); /* not currently supported as input, but can handle it */
+ rpm2 = rp/r2;
+ }
+
+ /* Loop over state A(0) and B(1) */
+ for (i=0;i<2;i++)
+ {
+ if((c6[i] > 0) && (c12[i] > 0))
+ {
+ sigma6[i] = c12[i]/c6[i];
+ sigma2[i] = pow(c12[i]/c6[i],1.0/3.0);
+ /* should be able to get rid of this ^^^ internal pow call eventually. Will require agreement on
+ what data to store externally. Can't be fixed without larger scale changes, so not 4.6 */
+ if (sigma6[i] < sigma6_min) { /* for disappearing coul and vdw with soft core at the same time */
+ sigma6[i] = sigma6_min;
+ sigma2[i] = sigma2_min;
+ }
+ }
+ else
+ {
+ sigma6[i] = sigma6_def;
+ sigma2[i] = sigma2_def;
+ }
+ if (sc_r_power == 6.0)
+ {
+ sigma_pow[i] = sigma6[i];
+ sigma_powm2[i] = sigma6[i]/sigma2[i];
+ }
+ else if (sc_r_power == 48.0)
+ {
+ sigma_pow[i] = sigma6[i]*sigma6[i]; /* sigma^12 */
+ sigma_pow[i] = sigma_pow[i]*sigma_pow[i]; /* sigma^24 */
+ sigma_pow[i] = sigma_pow[i]*sigma_pow[i]; /* sigma^48 */
+ sigma_powm2[i] = sigma_pow[i]/sigma2[i];
+ }
+ else
+ { /* not really supported as input, but in here for testing the general case*/
+ sigma_pow[i] = pow(sigma2[i],sc_r_power/2);
+ sigma_powm2[i] = sigma_pow[i]/(sigma2[i]);
+ }
+ }
+
+ /* only use softcore if one of the states has a zero endstate - softcore is for avoiding infinities!*/
+ if ((c12[0] > 0) && (c12[1] > 0)) {
+ alpha_vdw_eff = 0;
+ alpha_coul_eff = 0;
+ } else {
+ alpha_vdw_eff = alpha_vdw;
+ alpha_coul_eff = alpha_coul;
+ }
+
+ /* Loop over A and B states again */
+ for (i=0;i<2;i++)
+ {
+ fscal_elec[i] = 0;
+ fscal_vdw[i] = 0;
+ velec[i] = 0;
+ vvdw[i] = 0;
+
+ /* Only spend time on A or B state if it is non-zero */
+ if( (qq[i] != 0) || (c6[i] != 0) || (c12[i] != 0) )
+ {
+ /* Coulomb */
+ rpinv = 1.0/(alpha_coul_eff*lfac_coul[i]*sigma_pow[i]+rp);
+ r_coul = pow(rpinv,-1.0/sc_r_power);
+
+ /* Electrostatics table lookup data */
+ rtab = r_coul*tabscale;
+ ntab = rtab;
+ eps = rtab-ntab;
+ eps2 = eps*eps;
+ ntab = 12*ntab;
+ /* Electrostatics */
+ Y = vftab[ntab];
+ F = vftab[ntab+1];
+ Geps = eps*vftab[ntab+2];
+ Heps2 = eps2*vftab[ntab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+eps*Fp;
+ FF = Fp+Geps+2.0*Heps2;
+ velec[i] = qq[i]*VV;
+ fscal_elec[i] = -qq[i]*FF*r_coul*rpinv*tabscale;
+
+ /* Vdw */
+ rpinv = 1.0/(alpha_vdw_eff*lfac_vdw[i]*sigma_pow[i]+rp);
+ r_vdw = pow(rpinv,-1.0/sc_r_power);
+ /* Vdw table lookup data */
+ rtab = r_vdw*tabscale;
+ ntab = rtab;
+ eps = rtab-ntab;
+ eps2 = eps*eps;
+ ntab = 12*ntab;
+ /* Dispersion */
+ Y = vftab[ntab+4];
+ F = vftab[ntab+5];
+ Geps = eps*vftab[ntab+6];
+ Heps2 = eps2*vftab[ntab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+eps*Fp;
+ FF = Fp+Geps+2.0*Heps2;
+ vvdw[i] = c6[i]*VV;
+ fscal_vdw[i] = -c6[i]*FF;
+
+ /* Repulsion */
+ Y = vftab[ntab+8];
+ F = vftab[ntab+9];
+ Geps = eps*vftab[ntab+10];
+ Heps2 = eps2*vftab[ntab+11];
+ Fp = F+Geps+Heps2;
+ VV = Y+eps*Fp;
+ FF = Fp+Geps+2.0*Heps2;
+ vvdw[i] += c12[i]*VV;
+ fscal_vdw[i] -= c12[i]*FF;
+ fscal_vdw[i] *= r_vdw*rpinv*tabscale;
+ }
+ }
+ /* Now we have velec[i], vvdw[i], and fscal[i] for both states */
+ /* Assemble A and B states */
+ velecsum = 0;
+ vvdwsum = 0;
+ dvdl_coul = 0;
+ dvdl_vdw = 0;
+ fscal = 0;
+ for (i=0;i<2;i++)
+ {
+ velecsum += LFC[i]*velec[i];
+ vvdwsum += LFV[i]*vvdw[i];
+
+ fscal += (LFC[i]*fscal_elec[i]+LFV[i]*fscal_vdw[i])*rpm2;
+
+ dvdl_coul += velec[i]*DLF[i] + LFC[i]*alpha_coul_eff*dlfac_coul[i]*fscal_elec[i]*sigma_pow[i];
+ dvdl_vdw += vvdw[i]*DLF[i] + LFV[i]*alpha_vdw_eff*dlfac_vdw[i]*fscal_vdw[i]*sigma_pow[i];
+ }
+
+ dvdl[efptCOUL] += dvdl_coul;
+ dvdl[efptVDW] += dvdl_vdw;
+
+ *velectot = velecsum;
+ *vvdwtot = vvdwsum;
+
+ return fscal;
}
+
#ifndef _nb_free_energy_h_
#define _nb_free_energy_h_
+#include "nb_kernel.h"
#include <typedefs.h>
void
-gmx_nb_free_energy_kernel(int icoul,
- int ivdw,
- int nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * x,
- real * f,
- real * chargeA,
- real * chargeB,
- real facel,
- real krf,
- real crf,
- real ewc,
- real * Vc,
- int * typeA,
- int * typeB,
- int ntype,
- real * nbfp,
- real * Vvdw,
- real tabscale,
- real * VFtab,
- real lambda_coul,
- real lambda_vdw,
- real * dvdl,
- real alpha_coul,
- real alpha_vdw,
- int lam_power,
- real sc_r_power,
- real sigma6_def,
- real sigma6_min,
- gmx_bool bDoForces,
- int * outeriter,
- int * inneriter);
+gmx_nb_free_energy_kernel(t_nblist * nlist,
+ rvec * x,
+ rvec * f,
+ t_forcerec * fr,
+ t_mdatoms * mdatoms,
+ nb_kernel_data_t * kernel_data,
+ t_nrnb * nrnb);
+
+real
+nb_free_energy_evaluate_single(real r2,real sc_r_power,real alpha_coul,
+ real alpha_vdw,real tabscale,real *vftab,
+ real qqA, real c6A, real c12A, real qqB,
+ real c6B, real c12B,real LFC[2], real LFV[2],real DLF[2],
+ real lfac_coul[2], real lfac_vdw[2],real dlfac_coul[2],
+ real dlfac_vdw[2],real sigma6_def, real sigma6_min,
+ real sigma2_def, real sigma2_min,
+ real *velectot, real *vvdwtot, real *dvdl);
#endif
#include "vec.h"
#include "typedefs.h"
#include "nb_generic.h"
+#include "nrnb.h"
+
+#include "nonbonded.h"
+#include "nb_kernel.h"
+
void
-gmx_nb_generic_kernel(t_nblist * nlist,
- t_forcerec * fr,
- t_mdatoms * mdatoms,
- real * x,
- real * f,
- real * fshift,
- real * Vc,
- real * Vvdw,
- real tabscale,
- real * VFtab,
- int * outeriter,
- int * inneriter)
+gmx_nb_generic_kernel(t_nblist * nlist,
+ rvec * xx,
+ rvec * ff,
+ t_forcerec * fr,
+ t_mdatoms * mdatoms,
+ nb_kernel_data_t * kernel_data,
+ t_nrnb * nrnb)
{
- int nri,ntype,table_nelements,icoul,ivdw;
+ int nri,ntype,table_nelements,ielec,ivdw;
real facel,gbtabscale;
int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid,nnn,n0;
real shX,shY,shZ;
- real fscal,tx,ty,tz;
+ real fscal,felec,fvdw,velec,vvdw,tx,ty,tz;
real rinvsq;
real iq;
- real qq,vcoul,krsq,vctot;
+ real qq,vctot;
int nti,nvdwparam;
int tj;
- real rt,r,eps,eps2,Y,F,Geps,Heps2,VV,FF,Fp,fijD,fijR;
+ real rt,r,eps,eps2,Y,F,Geps,Heps2,VV,FF,Fp,fijD,fijR;
real rinvsix;
- real Vvdwtot;
- real Vvdw_rep,Vvdw_disp;
+ real vvdwtot;
+ real vvdw_rep,vvdw_disp;
real ix,iy,iz,fix,fiy,fiz;
real jx,jy,jz;
real dx,dy,dz,rsq,rinv;
real c6,c12,cexp1,cexp2,br;
- real * charge;
- real * shiftvec;
- real * vdwparam;
- int * shift;
- int * type;
-
- icoul = nlist->icoul;
- ivdw = nlist->ivdw;
-
- /* avoid compiler warnings for cases that cannot happen */
- nnn = 0;
- vcoul = 0.0;
- eps = 0.0;
- eps2 = 0.0;
-
- /* 3 VdW parameters for buckingham, otherwise 2 */
- nvdwparam = (nlist->ivdw==2) ? 3 : 2;
- table_nelements = (icoul==3) ? 4 : 0;
- table_nelements += (ivdw==3) ? 8 : 0;
-
+ real * charge;
+ real * shiftvec;
+ real * vdwparam;
+ int * shift;
+ int * type;
+ real * fshift;
+ real * velecgrp;
+ real * vvdwgrp;
+ real tabscale;
+ real * VFtab;
+ real * x;
+ real * f;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real * ewtab;
+ real rcoulomb2,rvdw,rvdw2,sh_invrc6;
+ real rcutoff,rcutoff2;
+ real rswitch_elec,rswitch_vdw,d,d2,sw,dsw,rinvcorr;
+ real elec_swV3,elec_swV4,elec_swV5,elec_swF2,elec_swF3,elec_swF4;
+ real vdw_swV3,vdw_swV4,vdw_swV5,vdw_swF2,vdw_swF3,vdw_swF4;
+ gmx_bool bExactElecCutoff,bExactVdwCutoff,bExactCutoff;
+
+ x = xx[0];
+ f = ff[0];
+ ielec = nlist->ielec;
+ ivdw = nlist->ivdw;
+
+ fshift = fr->fshift[0];
+ velecgrp = kernel_data->energygrp_elec;
+ vvdwgrp = kernel_data->energygrp_vdw;
+ tabscale = kernel_data->table_elec_vdw->scale;
+ VFtab = kernel_data->table_elec_vdw->data;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ rcoulomb2 = fr->rcoulomb*fr->rcoulomb;
+ rvdw = fr->rvdw;
+ rvdw2 = rvdw*rvdw;
+ sh_invrc6 = fr->ic->sh_invrc6;
+
+ if(fr->coulomb_modifier==eintmodPOTSWITCH)
+ {
+ d = fr->rcoulomb-fr->rcoulomb_switch;
+ elec_swV3 = -10.0/(d*d*d);
+ elec_swV4 = 15.0/(d*d*d*d);
+ elec_swV5 = -6.0/(d*d*d*d*d);
+ elec_swF2 = -30.0/(d*d*d);
+ elec_swF3 = 60.0/(d*d*d*d);
+ elec_swF4 = -30.0/(d*d*d*d*d);
+ }
+ else
+ {
+ /* Avoid warnings from stupid compilers (looking at you, Clang!) */
+ elec_swV3 = elec_swV4 = elec_swV5 = elec_swF2 = elec_swF3 = elec_swF4 = 0.0;
+ }
+ if(fr->vdw_modifier==eintmodPOTSWITCH)
+ {
+ d = fr->rvdw-fr->rvdw_switch;
+ vdw_swV3 = -10.0/(d*d*d);
+ vdw_swV4 = 15.0/(d*d*d*d);
+ vdw_swV5 = -6.0/(d*d*d*d*d);
+ vdw_swF2 = -30.0/(d*d*d);
+ vdw_swF3 = 60.0/(d*d*d*d);
+ vdw_swF4 = -30.0/(d*d*d*d*d);
+ }
+ else
+ {
+ /* Avoid warnings from stupid compilers (looking at you, Clang!) */
+ vdw_swV3 = vdw_swV4 = vdw_swV5 = vdw_swF2 = vdw_swF3 = vdw_swF4 = 0.0;
+ }
+
+ bExactElecCutoff = (fr->coulomb_modifier!=eintmodNONE) || fr->eeltype == eelRF_ZERO;
+ bExactVdwCutoff = (fr->vdw_modifier!=eintmodNONE);
+ bExactCutoff = bExactElecCutoff || bExactVdwCutoff;
+
+ if(bExactCutoff)
+ {
+ rcutoff = ( fr->rcoulomb > fr->rvdw ) ? fr->rcoulomb : fr->rvdw;
+ rcutoff2 = rcutoff*rcutoff;
+ }
+ else
+ {
+ /* Fix warnings for stupid compilers */
+ rcutoff = rcutoff2 = 1e30;
+ }
+
+ /* avoid compiler warnings for cases that cannot happen */
+ nnn = 0;
+ eps = 0.0;
+ eps2 = 0.0;
+
+ /* 3 VdW parameters for buckingham, otherwise 2 */
+ nvdwparam = (ivdw==GMX_NBKERNEL_VDW_BUCKINGHAM) ? 3 : 2;
+ table_nelements = 12;
+
charge = mdatoms->chargeA;
- type = mdatoms->typeA;
- facel = fr->epsfac;
- shiftvec = fr->shift_vec[0];
- vdwparam = fr->nbfp;
- ntype = fr->ntype;
-
- for(n=0; (n<nlist->nri); n++)
+ type = mdatoms->typeA;
+ facel = fr->epsfac;
+ shiftvec = fr->shift_vec[0];
+ vdwparam = fr->nbfp;
+ ntype = fr->ntype;
+
+ for(n=0; (n<nlist->nri); n++)
{
- is3 = 3*nlist->shift[n];
+ is3 = 3*nlist->shift[n];
shX = shiftvec[is3];
shY = shiftvec[is3+1];
shZ = shiftvec[is3+2];
iq = facel*charge[ii];
nti = nvdwparam*ntype*type[ii];
vctot = 0;
- Vvdwtot = 0;
- fix = 0;
- fiy = 0;
+ vvdwtot = 0;
+ fix = 0;
+ fiy = 0;
fiz = 0;
for(k=nj0; (k<nj1); k++)
rsq = dx*dx+dy*dy+dz*dz;
rinv = gmx_invsqrt(rsq);
rinvsq = rinv*rinv;
- fscal = 0;
-
- if(icoul==3 || ivdw==3)
- {
- r = rsq*rinv;
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = table_nelements*n0;
- }
-
- /* Coulomb interaction. icoul==0 means no interaction */
- if(icoul>0)
- {
- qq = iq*charge[jnr];
-
- switch(icoul)
- {
- case 1:
- /* Vanilla cutoff coulomb */
- vcoul = qq*rinv;
- fscal = vcoul*rinvsq;
- break;
-
- case 2:
- /* Reaction-field */
- krsq = fr->k_rf*rsq;
- vcoul = qq*(rinv+krsq-fr->c_rf);
- fscal = qq*(rinv-2.0*krsq)*rinvsq;
- break;
-
- case 3:
- /* Tabulated coulomb */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- nnn += 4;
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fscal = -qq*FF*tabscale*rinv;
- break;
-
- case 4:
- /* GB */
- gmx_fatal(FARGS,"Death & horror! GB generic interaction not implemented.\n");
- break;
-
- default:
- gmx_fatal(FARGS,"Death & horror! No generic coulomb interaction for icoul=%d.\n",icoul);
- break;
- }
- vctot = vctot+vcoul;
- } /* End of coulomb interactions */
-
-
- /* VdW interaction. ivdw==0 means no interaction */
- if(ivdw>0)
- {
- tj = nti+nvdwparam*type[jnr];
-
- switch(ivdw)
- {
- case 1:
- /* Vanilla Lennard-Jones cutoff */
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw_disp = c6*rinvsix;
- Vvdw_rep = c12*rinvsix*rinvsix;
- fscal += (12.0*Vvdw_rep-6.0*Vvdw_disp)*rinvsq;
- Vvdwtot = Vvdwtot+Vvdw_rep-Vvdw_disp;
- break;
-
- case 2:
- /* Buckingham */
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
-
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw_disp = c6*rinvsix;
- br = cexp2*rsq*rinv;
- Vvdw_rep = cexp1*exp(-br);
- fscal += (br*Vvdw_rep-6.0*Vvdw_disp)*rinvsq;
- Vvdwtot = Vvdwtot+Vvdw_rep-Vvdw_disp;
- break;
-
- case 3:
- /* Tabulated VdW */
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw_disp = c6*VV;
- fijD = c6*FF;
- nnn += 4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw_rep = c12*VV;
- fijR = c12*FF;
- fscal += -(fijD+fijR)*tabscale*rinv;
- Vvdwtot = Vvdwtot + Vvdw_disp + Vvdw_rep;
- break;
-
- default:
- gmx_fatal(FARGS,"Death & horror! No generic VdW interaction for ivdw=%d.\n",ivdw);
- break;
- }
- } /* end VdW interactions */
-
-
- tx = fscal*dx;
- ty = fscal*dy;
- tz = fscal*dz;
- fix = fix + tx;
- fiy = fiy + ty;
- fiz = fiz + tz;
+ felec = 0;
+ fvdw = 0;
+ velec = 0;
+ vvdw = 0;
+
+ if(bExactCutoff && rsq>rcutoff2)
+ {
+ continue;
+ }
+
+ if(ielec==GMX_NBKERNEL_ELEC_CUBICSPLINETABLE || ivdw==GMX_NBKERNEL_VDW_CUBICSPLINETABLE)
+ {
+ r = rsq*rinv;
+ rt = r*tabscale;
+ n0 = rt;
+ eps = rt-n0;
+ eps2 = eps*eps;
+ nnn = table_nelements*n0;
+ }
+
+ /* Coulomb interaction. ielec==0 means no interaction */
+ if(ielec!=GMX_NBKERNEL_ELEC_NONE)
+ {
+ qq = iq*charge[jnr];
+
+ switch(ielec)
+ {
+ case GMX_NBKERNEL_ELEC_NONE:
+ break;
+
+ case GMX_NBKERNEL_ELEC_COULOMB:
+ /* Vanilla cutoff coulomb */
+ velec = qq*rinv;
+ felec = velec*rinvsq;
+ break;
+
+ case GMX_NBKERNEL_ELEC_REACTIONFIELD:
+ /* Reaction-field */
+ velec = qq*(rinv+fr->k_rf*rsq-fr->c_rf);
+ felec = qq*(rinv*rinvsq-2.0*fr->k_rf);
+ break;
+
+ case GMX_NBKERNEL_ELEC_CUBICSPLINETABLE:
+ /* Tabulated coulomb */
+ Y = VFtab[nnn];
+ F = VFtab[nnn+1];
+ Geps = eps*VFtab[nnn+2];
+ Heps2 = eps2*VFtab[nnn+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+eps*Fp;
+ FF = Fp+Geps+2.0*Heps2;
+ velec = qq*VV;
+ felec = -qq*FF*tabscale*rinv;
+ break;
+
+ case GMX_NBKERNEL_ELEC_GENERALIZEDBORN:
+ /* GB */
+ gmx_fatal(FARGS,"Death & horror! GB generic interaction not implemented.\n");
+ break;
+
+ case GMX_NBKERNEL_ELEC_EWALD:
+ ewrt = rsq*rinv*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ rinvcorr = (fr->coulomb_modifier==eintmodPOTSHIFT) ? rinv-fr->ic->sh_ewald : rinv;
+ velec = qq*(rinvcorr-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq*rinv*(rinvsq-felec);
+ break;
+
+ default:
+ gmx_fatal(FARGS,"Death & horror! No generic coulomb interaction for ielec=%d.\n",ielec);
+ break;
+ }
+ if(fr->coulomb_modifier==eintmodPOTSWITCH)
+ {
+ d = rsq*rinv-fr->rcoulomb_switch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(elec_swV3+d*(elec_swV4+d*elec_swV5));
+ dsw = d2*(elec_swF2+d*(elec_swF3+d*elec_swF4));
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+ }
+ if(bExactElecCutoff)
+ {
+ felec = (rsq<=rcoulomb2) ? felec : 0.0;
+ velec = (rsq<=rcoulomb2) ? velec : 0.0;
+ }
+ vctot += velec;
+ } /* End of coulomb interactions */
+
+
+ /* VdW interaction. ivdw==0 means no interaction */
+ if(ivdw!=GMX_NBKERNEL_VDW_NONE)
+ {
+ tj = nti+nvdwparam*type[jnr];
+
+ switch(ivdw)
+ {
+ case GMX_NBKERNEL_VDW_NONE:
+ break;
+
+ case GMX_NBKERNEL_VDW_LENNARDJONES:
+ /* Vanilla Lennard-Jones cutoff */
+ c6 = vdwparam[tj];
+ c12 = vdwparam[tj+1];
+ rinvsix = rinvsq*rinvsq*rinvsq;
+ vvdw_disp = c6*rinvsix;
+ vvdw_rep = c12*rinvsix*rinvsix;
+ fvdw = (vvdw_rep-vvdw_disp)*rinvsq;
+ if(fr->vdw_modifier==eintmodPOTSHIFT)
+ {
+ vvdw = (vvdw_rep-c12*sh_invrc6*sh_invrc6)*(1.0/12.0)-(vvdw_disp-c6*sh_invrc6)*(1.0/6.0);
+ }
+ else
+ {
+ vvdw = vvdw_rep/12.0-vvdw_disp/6.0;
+ }
+ break;
+
+ case GMX_NBKERNEL_VDW_BUCKINGHAM:
+ /* Buckingham */
+ c6 = vdwparam[tj];
+ cexp1 = vdwparam[tj+1];
+ cexp2 = vdwparam[tj+2];
+
+ rinvsix = rinvsq*rinvsq*rinvsq;
+ vvdw_disp = c6*rinvsix;
+ br = cexp2*rsq*rinv;
+ vvdw_rep = cexp1*exp(-br);
+ fvdw = (br*vvdw_rep-vvdw_disp)*rinvsq;
+ if(fr->vdw_modifier==eintmodPOTSHIFT)
+ {
+ vvdw = (vvdw_rep-cexp1*exp(-cexp2*rvdw))-(vvdw_disp-c6*sh_invrc6)/6.0;
+ }
+ else
+ {
+ vvdw = vvdw_rep-vvdw_disp/6.0;
+ }
+ break;
+
+ case GMX_NBKERNEL_VDW_CUBICSPLINETABLE:
+ /* Tabulated VdW */
+ c6 = vdwparam[tj];
+ c12 = vdwparam[tj+1];
+ Y = VFtab[nnn+4];
+ F = VFtab[nnn+5];
+ Geps = eps*VFtab[nnn+6];
+ Heps2 = eps2*VFtab[nnn+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+eps*Fp;
+ FF = Fp+Geps+2.0*Heps2;
+ vvdw_disp = c6*VV;
+ fijD = c6*FF;
+ Y = VFtab[nnn+8];
+ F = VFtab[nnn+9];
+ Geps = eps*VFtab[nnn+10];
+ Heps2 = eps2*VFtab[nnn+11];
+ Fp = F+Geps+Heps2;
+ VV = Y+eps*Fp;
+ FF = Fp+Geps+2.0*Heps2;
+ vvdw_rep = c12*VV;
+ fijR = c12*FF;
+ fvdw = -(fijD+fijR)*tabscale*rinv;
+ vvdw = vvdw_disp + vvdw_rep;
+ break;
+
+ default:
+ gmx_fatal(FARGS,"Death & horror! No generic VdW interaction for ivdw=%d.\n",ivdw);
+ break;
+ }
+ if(fr->vdw_modifier==eintmodPOTSWITCH)
+ {
+ d = rsq*rinv-fr->rvdw_switch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(vdw_swV3+d*(vdw_swV4+d*vdw_swV5));
+ dsw = d2*(vdw_swF2+d*(vdw_swF3+d*vdw_swF4));
+ vvdw *= sw;
+ fvdw = fvdw*sw + vvdw*dsw;
+ }
+ if(bExactVdwCutoff)
+ {
+ fvdw = (rsq<=rvdw2) ? fvdw : 0.0;
+ vvdw = (rsq<=rvdw2) ? vvdw : 0.0;
+ }
+ vvdwtot += vvdw;
+ } /* end VdW interactions */
+
+ fscal = felec+fvdw;
+
+ tx = fscal*dx;
+ ty = fscal*dy;
+ tz = fscal*dz;
+ fix = fix + tx;
+ fiy = fiy + ty;
+ fiz = fiz + tz;
f[j3+0] = f[j3+0] - tx;
f[j3+1] = f[j3+1] - ty;
f[j3+2] = f[j3+2] - tz;
}
-
+
f[ii3+0] = f[ii3+0] + fix;
f[ii3+1] = f[ii3+1] + fiy;
f[ii3+2] = f[ii3+2] + fiz;
fshift[is3] = fshift[is3]+fix;
fshift[is3+1] = fshift[is3+1]+fiy;
fshift[is3+2] = fshift[is3+2]+fiz;
- ggid = nlist->gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
+ ggid = nlist->gid[n];
+ velecgrp[ggid] += vctot;
+ vvdwgrp[ggid] += vvdwtot;
}
-
- *outeriter = nlist->nri;
- *inneriter = nlist->jindex[n];
+ /* Estimate flops, average for generic kernel:
+ * 12 flops per outer iteration
+ * 50 flops per inner iteration
+ */
+ inc_nrnb(nrnb,eNR_NBKERNEL_GENERIC,nlist->nri*12 + nlist->jindex[n]*50);
}
-
#ifndef _nb_generic_h_
#define _nb_generic_h_
+#include "nb_kernel.h"
#include "types/simple.h"
#include "typedefs.h"
void
-gmx_nb_generic_kernel(t_nblist * nlist,
- t_forcerec * fr,
- t_mdatoms * mdatoms,
- real * x,
- real * f,
- real * fshift,
- real * Vc,
- real * Vvdw,
- real tabscale,
- real * VFtab,
- int * outeriter,
- int * inneriter);
+gmx_nb_generic_kernel(t_nblist * nlist,
+ rvec * x,
+ rvec * f,
+ t_forcerec * fr,
+ t_mdatoms * mdatoms,
+ nb_kernel_data_t * kernel_data,
+ t_nrnb * nrnb);
+
#endif
#define ALMOST_ONE 1-(1e-30)
void
gmx_nb_generic_adress_kernel(t_nblist * nlist,
- t_forcerec * fr,
- t_mdatoms * mdatoms,
- real * x,
- real * f,
- real * fshift,
- real * Vc,
- real * Vvdw,
- real tabscale,
- real * VFtab,
- int * outeriter,
- int * inneriter,
- gmx_bool bCG)
+ t_forcerec * fr,
+ t_mdatoms * mdatoms,
+ real * x,
+ real * f,
+ real * fshift,
+ real * Vc,
+ real * Vvdw,
+ real tabscale,
+ real * VFtab,
+ int * outeriter,
+ int * inneriter,
+ gmx_bool bCG)
{
- int nri,ntype,table_nelements,icoul,ivdw;
+ int nri,ntype,table_nelements,ielec,ivdw;
real facel,gbtabscale;
int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid,nnn,n0;
real shX,shY,shZ;
force_cap = fr->adress_ex_forcecap;
- icoul = nlist->icoul;
+ ielec = nlist->ielec;
ivdw = nlist->ivdw;
/* avoid compiler warnings for cases that cannot happen */
/* 3 VdW parameters for buckingham, otherwise 2 */
nvdwparam = (nlist->ivdw==2) ? 3 : 2;
- table_nelements = (icoul==3) ? 4 : 0;
+ table_nelements = (ielec==3) ? 4 : 0;
table_nelements += (ivdw==3) ? 8 : 0;
charge = mdatoms->chargeA;
rinvsq = rinv*rinv;
- fscal = 0;
+ fscal = 0;
- if(icoul==3 || ivdw==3)
- {
- r = rsq*rinv;
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = table_nelements*n0;
- }
-
- /* Coulomb interaction. icoul==0 means no interaction */
- if(icoul>0)
- {
- qq = iq*charge[jnr];
-
- switch(icoul)
- {
- case 1:
- /* Vanilla cutoff coulomb */
- vcoul = qq*rinv;
- fscal = vcoul*rinvsq;
- break;
-
- case 2:
- /* Reaction-field */
- krsq = fr->k_rf*rsq;
- vcoul = qq*(rinv+krsq-fr->c_rf);
- fscal = qq*(rinv-2.0*krsq)*rinvsq;
- break;
-
- case 3:
- /* Tabulated coulomb */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- nnn += 4;
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fscal = -qq*FF*tabscale*rinv;
- break;
-
- case 4:
- /* GB */
- gmx_fatal(FARGS,"Death & horror! GB generic interaction not implemented.\n");
- break;
+ if(ielec==3 || ivdw==3)
+ {
+ r = rsq*rinv;
+ rt = r*tabscale;
+ n0 = rt;
+ eps = rt-n0;
+ eps2 = eps*eps;
+ nnn = table_nelements*n0;
+ }
- default:
- gmx_fatal(FARGS,"Death & horror! No generic coulomb interaction for icoul=%d.\n",icoul);
- break;
- }
- vctot = vctot+vcoul;
- } /* End of coulomb interactions */
+ /* Coulomb interaction. ielec==0 means no interaction */
+ if(ielec>0)
+ {
+ qq = iq*charge[jnr];
+ switch(ielec)
+ {
+ case 1:
+ /* Vanilla cutoff coulomb */
+ vcoul = qq*rinv;
+ fscal = vcoul*rinvsq;
+ break;
+
+ case 2:
+ /* Reaction-field */
+ krsq = fr->k_rf*rsq;
+ vcoul = qq*(rinv+krsq-fr->c_rf);
+ fscal = qq*(rinv-2.0*krsq)*rinvsq;
+ break;
+
+ case 3:
+ /* Tabulated coulomb */
+ Y = VFtab[nnn];
+ F = VFtab[nnn+1];
+ Geps = eps*VFtab[nnn+2];
+ Heps2 = eps2*VFtab[nnn+3];
+ nnn += 4;
+ Fp = F+Geps+Heps2;
+ VV = Y+eps*Fp;
+ FF = Fp+Geps+2.0*Heps2;
+ vcoul = qq*VV;
+ fscal = -qq*FF*tabscale*rinv;
+ break;
+
+ case 4:
+ /* GB */
+ gmx_fatal(FARGS,"Death & horror! GB generic interaction not implemented.\n");
+ break;
+
+ default:
+ gmx_fatal(FARGS,"Death & horror! No generic coulomb interaction for ielec=%d.\n",ielec);
+ break;
+ }
+ vctot = vctot+vcoul;
+ } /* End of coulomb interactions */
- /* VdW interaction. ivdw==0 means no interaction */
- if(ivdw>0)
- {
- tj = nti+nvdwparam*type[jnr];
+ /* VdW interaction. ivdw==0 means no interaction */
+ if(ivdw>0)
+ {
+ tj = nti+nvdwparam*type[jnr];
- switch(ivdw)
- {
+ switch(ivdw)
+ {
case 1:
/* Vanilla Lennard-Jones cutoff */
c6 = vdwparam[tj];
#include "vec.h"
#include "typedefs.h"
#include "nb_generic_cg.h"
+#include "nonbonded.h"
+#include "nb_kernel.h"
+#include "nrnb.h"
void
- gmx_nb_generic_cg_kernel(t_nblist * nlist,
- t_forcerec * fr,
- t_mdatoms * mdatoms,
- real * x,
- real * f,
- real * fshift,
- real * Vc,
- real * Vvdw,
- real tabscale,
- real * VFtab,
- int * outeriter,
- int * inneriter)
+gmx_nb_generic_cg_kernel(t_nblist * nlist,
+ rvec * xx,
+ rvec * ff,
+ t_forcerec * fr,
+ t_mdatoms * mdatoms,
+ nb_kernel_data_t * kernel_data,
+ t_nrnb * nrnb)
{
- int nri,ntype,table_nelements,icoul,ivdw;
+ int nri,ntype,table_nelements,ielec,ivdw;
real facel,gbtabscale;
int n,is3,i3,k,nj0,nj1,j3,ggid,nnn,n0;
int ai0,ai1,ai,aj0,aj1,aj;
int * shift;
int * type;
t_excl * excl;
-
- icoul = nlist->icoul;
+ real * fshift;
+ real * Vc;
+ real * Vvdw;
+ real tabscale;
+ real * VFtab;
+ real * x;
+ real * f;
+
+ x = xx[0];
+ f = ff[0];
+ ielec = nlist->ielec;
ivdw = nlist->ivdw;
-
+
+ fshift = fr->fshift[0];
+ Vc = kernel_data->energygrp_elec;
+ Vvdw = kernel_data->energygrp_vdw;
+ tabscale = kernel_data->table_elec_vdw->scale;
+ VFtab = kernel_data->table_elec_vdw->data;
+
/* avoid compiler warnings for cases that cannot happen */
nnn = 0;
vcoul = 0.0;
/* 3 VdW parameters for buckingham, otherwise 2 */
nvdwparam = (nlist->ivdw==2) ? 3 : 2;
- table_nelements = (icoul==3) ? 4 : 0;
+ table_nelements = (ielec==3) ? 4 : 0;
table_nelements += (ivdw==3) ? 8 : 0;
charge = mdatoms->chargeA;
rinvsq = rinv*rinv;
fscal = 0;
- if (icoul==3 || ivdw==3)
+ if (ielec==3 || ivdw==3)
{
r = rsq*rinv;
rt = r*tabscale;
nnn = table_nelements*n0;
}
- /* Coulomb interaction. icoul==0 means no interaction */
- if (icoul > 0)
+ /* Coulomb interaction. ielec==0 means no interaction */
+ if (ielec > 0)
{
qq = iq*charge[aj];
- switch(icoul)
+ switch(ielec)
{
case 1:
/* Vanilla cutoff coulomb */
break;
default:
- gmx_fatal(FARGS,"Death & horror! No generic coulomb interaction for icoul=%d.\n",icoul);
+ gmx_fatal(FARGS,"Death & horror! No generic coulomb interaction for ielec=%d.\n",ielec);
break;
}
vctot = vctot+vcoul;
Vc[ggid] += vctot;
Vvdw[ggid] += Vvdwtot;
}
-
- *outeriter = nlist->nri;
- *inneriter = nlist->jindex[n];
+ /* Estimate flops, average for generic cg kernel:
+ * 12 flops per outer iteration
+ * 100 flops per inner iteration
+ */
+ inc_nrnb(nrnb,eNR_NBKERNEL_FREE_ENERGY,nlist->nri*12 + nlist->jindex[n]*100);
}
#include "types/simple.h"
#include "typedefs.h"
+#include "nb_kernel.h"
+#include "nrnb.h"
void
-gmx_nb_generic_cg_kernel(t_nblist * nlist,
- t_forcerec * fr,
- t_mdatoms * mdatoms,
- real * x,
- real * f,
- real * fshift,
- real * Vc,
- real * Vvdw,
- real tabscale,
- real * VFtab,
- int * outeriter,
- int * inneriter);
+gmx_nb_generic_cg_kernel(t_nblist * nlist,
+ rvec * x,
+ rvec * f,
+ t_forcerec * fr,
+ t_mdatoms * mdatoms,
+ nb_kernel_data_t * kernel_data,
+ t_nrnb * nrnb);
#endif
--- /dev/null
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+ *
+ * This file is part of GROMACS.
+ * Copyright (c) 2012-
+ *
+ * Written by the Gromacs development team under coordination of
+ * David van der Spoel, Berk Hess, and Erik Lindahl.
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org
+ *
+ * And Hey:
+ * Gnomes, ROck Monsters And Chili Sauce
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+#include <stdio.h>
+#include <string.h>
+
+#include "nb_kernel.h"
+#include "smalloc.h"
+#include "string2.h"
+
+
+/* Static data structures to find kernels */
+static nb_kernel_info_t * kernel_list = NULL;
+static unsigned int kernel_list_size = 0;
+static int * kernel_list_hash = NULL;
+static unsigned int kernel_list_hash_size = 0;
+
+static unsigned int
+nb_kernel_hash_func(const char * arch,
+ const char * elec,
+ const char * elec_mod,
+ const char * vdw,
+ const char * vdw_mod,
+ const char * geom,
+ const char * other,
+ const char * vf)
+{
+ unsigned int hash;
+
+ hash = gmx_string_hash_func(arch,gmx_string_hash_init);
+ hash = gmx_string_hash_func(elec,hash);
+ hash = gmx_string_hash_func(elec_mod,hash);
+ hash = gmx_string_hash_func(vdw,hash);
+ hash = gmx_string_hash_func(vdw_mod,hash);
+ hash = gmx_string_hash_func(geom,hash);
+ hash = gmx_string_hash_func(other,hash);
+ hash = gmx_string_hash_func(vf,hash);
+
+ return hash;
+}
+
+void
+nb_kernel_list_add_kernels(nb_kernel_info_t * new_kernel_list,
+ int new_kernel_list_size)
+{
+ srenew(kernel_list,kernel_list_size+new_kernel_list_size);
+ memcpy(kernel_list+kernel_list_size,new_kernel_list,new_kernel_list_size*sizeof(nb_kernel_info_t));
+ kernel_list_size += new_kernel_list_size;
+}
+
+
+int
+nb_kernel_list_hash_init(void)
+{
+ unsigned int i;
+ unsigned int index;
+
+ kernel_list_hash_size = kernel_list_size*5;
+ snew(kernel_list_hash,kernel_list_hash_size);
+
+ for(i=0;i<kernel_list_hash_size;i++)
+ {
+ kernel_list_hash[i] = -1;
+ }
+ for(i=0;i<kernel_list_size;i++)
+ {
+ index=nb_kernel_hash_func(kernel_list[i].architecture,
+ kernel_list[i].electrostatics,
+ kernel_list[i].electrostatics_modifier,
+ kernel_list[i].vdw,
+ kernel_list[i].vdw_modifier,
+ kernel_list[i].geometry,
+ kernel_list[i].other,
+ kernel_list[i].vf) % kernel_list_hash_size;
+
+ /* Check for collisions and advance if necessary */
+ while( kernel_list_hash[index] != -1 )
+ {
+ index = (index+1) % kernel_list_hash_size;
+ }
+
+ kernel_list_hash[index] = i;
+ }
+ return 0;
+}
+
+void
+nb_kernel_list_hash_destroy()
+{
+ sfree(kernel_list_hash);
+ kernel_list_hash = NULL;
+ kernel_list_hash_size = 0;
+}
+
+
+nb_kernel_t *
+nb_kernel_list_findkernel(FILE * log,
+ const char * arch,
+ const char * electrostatics,
+ const char * electrostatics_modifier,
+ const char * vdw,
+ const char * vdw_modifier,
+ const char * geometry,
+ const char * other,
+ const char * vf)
+{
+ int i;
+ unsigned int index;
+ nb_kernel_info_t * kernelinfo_ptr;
+
+ if(kernel_list_hash_size==0)
+ {
+ return NULL;
+ }
+
+ index=nb_kernel_hash_func(arch,
+ electrostatics,
+ electrostatics_modifier,
+ vdw,
+ vdw_modifier,
+ geometry,
+ other,
+ vf) % kernel_list_hash_size;
+
+ kernelinfo_ptr = NULL;
+ while( (i=kernel_list_hash[index]) != -1)
+ {
+ if(!gmx_strcasecmp_min(kernel_list[i].architecture,arch) &&
+ !gmx_strcasecmp_min(kernel_list[i].electrostatics,electrostatics) &&
+ !gmx_strcasecmp_min(kernel_list[i].electrostatics_modifier,electrostatics_modifier) &&
+ !gmx_strcasecmp_min(kernel_list[i].vdw,vdw) &&
+ !gmx_strcasecmp_min(kernel_list[i].vdw_modifier,vdw_modifier) &&
+ !gmx_strcasecmp_min(kernel_list[i].geometry,geometry) &&
+ !gmx_strcasecmp_min(kernel_list[i].other,other) &&
+ !gmx_strcasecmp_min(kernel_list[i].vf,vf))
+ {
+ kernelinfo_ptr = kernel_list+i;
+ break;
+ }
+ index = (index+1) % kernel_list_hash_size;
+ }
+
+ if(log && kernelinfo_ptr!=NULL)
+ {
+ fprintf(log,
+ "NB kernel %s() with architecture '%s' used for neighborlist with\n"
+ " Elec: '%s', Modifier: '%s'\n"
+ " Vdw: '%s', Modifier: '%s'\n"
+ " Geom: '%s', Other: '%s', Calc: '%s'\n\n",
+ kernelinfo_ptr->kernelname,arch,electrostatics,electrostatics_modifier,
+ vdw,vdw_modifier,geometry,other,vf);
+ }
+
+ /* If we did not find any kernel the pointer will still be NULL */
+ return (kernelinfo_ptr !=NULL) ? kernelinfo_ptr->kernelptr : NULL;
+}
--- /dev/null
+/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
+ *
+ * This file is part of GROMACS.
+ * Copyright (c) 2012-
+ *
+ * Written by the Gromacs development team under coordination of
+ * David van der Spoel, Berk Hess, and Erik Lindahl.
+ *
+ * This library is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org
+ *
+ * And Hey:
+ * Gnomes, ROck Monsters And Chili Sauce
+ */
+#ifndef _nb_kernel_h_
+#define _nb_kernel_h_
+
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+#if 0
+} /* fixes auto-indentation problems */
+#endif
+
+
+#include "types/simple.h"
+#include "typedefs.h"
+
+/* Structure to collect kernel data not available in forcerec or mdatoms structures.
+ * This is only used inside the nonbonded module.
+ */
+typedef struct
+{
+ int flags;
+ t_blocka * exclusions;
+ real * lambda;
+ real * dvdl;
+
+ /* pointers to tables */
+ t_forcetable * table_elec;
+ t_forcetable * table_vdw;
+ t_forcetable * table_elec_vdw;
+
+ /* potentials */
+ real * energygrp_elec;
+ real * energygrp_vdw;
+ real * energygrp_polarization;
+}
+nb_kernel_data_t;
+
+
+typedef void
+nb_kernel_t(t_nblist * nlist,
+ rvec * x,
+ rvec * f,
+ t_forcerec * fr,
+ t_mdatoms * mdatoms,
+ nb_kernel_data_t * kernel_data,
+ t_nrnb * nrnb);
+
+
+/* Structure with a kernel pointer and settings. This cannot be abstract
+ * since we define the kernel list statically for each architecture in a header,
+ * and use it to set up the kernel hash functions to find kernels.
+ *
+ * The electrostatics/vdw names should be obvious and correspond to the
+ * forms of the interactions calculated in this function, and the interaction
+ * modifiers describe switch/shift and similar alterations. Geometry refers
+ * to whether this kernel calculates interactions between single particles or
+ * waters (groups of 3/4 atoms) for better performance. Finally, the VF string
+ * selects whether the kernel calculates only potential, only force, or both
+ *
+ * The allowed values for kernel interactions are described by the
+ * enumerated types gmx_nbkernel_elec and gmx_nbkernel_vdw (see types/enums.h).
+ * Note that these are deliberately NOT identical to the interactions the
+ * user can set, since some user-specified interactions will be tabulated, and
+ * Lennard-Jones and Buckingham use different kernels while their setting in
+ * the input is decided by nonbonded parameter formats rather than mdp options.
+ *
+ * The interaction modifiers are described by the eintmod enum type, while
+ * the kernel geometry is decided from the neighborlist geometry, which is
+ * described by the enum gmx_nblist_kernel_geometry (again, see types/enums.h).
+ * The
+ *
+ * Note that any particular implementation of kernels might not support all of
+ * these strings. In fact, some might not be supported by any architecture yet.
+ * The whole point of using strings and hashes is that we do not have to define a
+ * unique set of strings in a single place. Thus, as long as you implement a
+ * corresponding kernel, you could in theory provide any string you want.
+ */
+typedef struct nb_kernel_info
+{
+ nb_kernel_t * kernelptr;
+ const char * kernelname;
+ const char * architecture; /* e.g. "C", "SSE", "BlueGene", etc. */
+
+ const char * electrostatics;
+ const char * electrostatics_modifier;
+ const char * vdw;
+ const char * vdw_modifier;
+ const char * geometry;
+ const char * other; /* Any extra info you want/need to select a kernel */
+ const char * vf; /* "PotentialAndForce", "Potential", or "Force" */
+}
+nb_kernel_info_t;
+
+
+void
+nb_kernel_list_add_kernels(nb_kernel_info_t * new_kernelinfo,
+ int new_size);
+
+int
+nb_kernel_list_hash_init(void);
+
+/* Return a function pointer to the nonbonded kernel pointer with
+ * settings according to the text strings provided. GROMACS does not guarantee
+ * the existence of accelerated kernels for any combination, so the return value
+ * can be NULL.
+ * In that case, you can try a different/lower-level acceleration, and
+ * eventually you need to prepare to fall back to generic kernels or change
+ * your settings and try again.
+ *
+ * The names of the text strings are obviously meant to reflect settings in
+ * GROMACS, but inside this routine they are merely used as a set of text
+ * strings not defined here. The routine will simply compare the arguments with
+ * the contents of the corresponding strings in the nb_kernel_list_t structure.
+ *
+ * This function does not check whether the kernel in question can run on the
+ * present architecture since that would require a slow cpuid call for every
+ * single invocation.
+ */
+nb_kernel_t *
+nb_kernel_list_findkernel(FILE * log,
+ const char * architecture,
+ const char * electrostatics,
+ const char * electrostatics_modifier,
+ const char * vdw,
+ const char * vdw_modifier,
+ const char * geometry,
+ const char * other,
+ const char * vf);
+
+
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _nb_kernel_h_ */
#include "types/nrnb.h"
#include "nb_kernel_c_adress.h"
-#include "../nb_kerneltype.h"
+#include "../nb_kernel.h"
/* Include standard kernel headers in local directory */
#include <stdio.h>
-#include "../nb_kerneltype.h"
+#include "../nb_kernel.h"
void
nb_kernel_setup_adress(FILE *fplog,nb_adress_kernel_t **list);
-#include "../nb_kerneltype.h"
+#include "../nb_kernel.h"
#include "nb_kernel_bluegene.h"
#include <types/simple.h>
-#include "../nb_kerneltype.h"
+#include "../nb_kernel.h"
void
nb_kernel_setup_bluegene(FILE *log,nb_kernel_t **list);
--- /dev/null
+#!/usr/bin/python
+
+import sys
+import os
+sys.path.append ( "../preprocessor" )
+from gmxpreprocess import gmxpreprocess
+
+# "The happiest programs are programs that write other programs."
+#
+#
+# This script controls the generation of Gromacs nonbonded kernels.
+#
+# We no longer generate kernels on-the-fly, so this file is not run
+# during a Gromacs compile - only when we need to update the kernels (=rarely).
+#
+# To maximize performance, each combination of interactions in Gromacs
+# has a separate nonbonded kernel without conditionals in the code.
+# To avoid writing hundreds of different routines for each architecture,
+# we instead use a custom preprocessor so we can encode the conditionals
+# and expand for-loops (e.g, for water-water interactions)
+# from a general kernel template. While that file will contain quite a
+# few preprocessor directives, it is still an order of magnitude easier
+# to maintain than ~200 different kernels (not to mention it avoids bugs).
+#
+# To actually generate the kernels, this program iteratively calls the
+# preprocessor with different define settings corresponding to all
+# combinations of coulomb/van-der-Waals/geometry options.
+#
+# A main goal in the design was to make this new generator _general_. For
+# this reason we have used a lot of different fields to identify a particular
+# kernel and interaction. Basically, each kernel will have a name like
+#
+# nbkernel_ElecXX_VdwYY_GeomZZ_VF_QQ()
+#
+# Where XX/YY/ZZ/VF are strings to identify what the kernel computes.
+#
+# Elec/Vdw describe the type of interaction for electrostatics and van der Waals.
+# The geometry settings correspond e.g. to water-water or water-particle kernels,
+# and finally the VF setting is V,F,or VF depending on whether we calculate
+# only the potential, only the force, or both of them. The final string (QQ)
+# is the architecture/language/optimization of the kernel.
+#
+Arch = 'c'
+
+# Explanation of the 'properties':
+#
+# It is cheap to compute r^2, and the kernels require various other functions of r for
+# different kinds of interaction. Depending on the needs of the kernel and the available
+# processor instructions, this will be done in different ways.
+#
+# 'rinv' means we need 1/r, which is calculated as 1/sqrt(r^2).
+# 'rinvsq' means we need 1/(r*r). This is calculated as rinv*rinv if we already did rinv, otherwise 1/r^2.
+# 'r' is similarly calculated as r^2*rinv when needed
+# 'table' means the interaction is tabulated, in which case we will calculate a table index before the interaction
+# 'shift' means the interaction will be modified by a constant to make it zero at the cutoff.
+# 'cutoff' means the interaction is set to 0.0 outside the cutoff
+#
+
+FileHeader = \
+'/*\n' \
+' * Note: this file was generated by the Gromacs '+Arch+' kernel generator.\n' \
+' *\n' \
+' * This source code is part of\n' \
+' *\n' \
+' * G R O M A C S\n' \
+' *\n' \
+' * Copyright (c) 2001-2012, The GROMACS Development Team\n' \
+' *\n' \
+' * Gromacs is a library for molecular simulation and trajectory analysis,\n' \
+' * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for\n' \
+' * a full list of developers and information, check out http://www.gromacs.org\n' \
+' *\n' \
+' * This program is free software; you can redistribute it and/or modify it under\n' \
+' * the terms of the GNU Lesser General Public License as published by the Free\n' \
+' * Software Foundation; either version 2 of the License, or (at your option) any\n' \
+' * later version.\n' \
+' *\n' \
+' * To help fund GROMACS development, we humbly ask that you cite\n' \
+' * the papers people have written on it - you can find them on the website.\n' \
+' */\n'
+
+###############################################
+# ELECTROSTATICS
+# Interactions and flags for them
+###############################################
+ElectrostaticsList = {
+ 'None' : [],
+ 'Coulomb' : ['rinv','rinvsq'],
+ 'ReactionField' : ['rinv','rinvsq'],
+ 'GeneralizedBorn' : ['rinv','r'],
+ 'CubicSplineTable' : ['rinv','r','table'],
+ 'Ewald' : ['rinv','rinvsq','r'],
+}
+
+
+###############################################
+# VAN DER WAALS
+# Interactions and flags for them
+###############################################
+VdwList = {
+ 'None' : [],
+ 'LennardJones' : ['rinvsq'],
+ 'Buckingham' : ['rinv','rinvsq','r'],
+ 'CubicSplineTable' : ['rinv','r','table'],
+}
+
+
+###############################################
+# MODIFIERS
+# Different ways to adjust/modify interactions to conserve energy
+###############################################
+ModifierList = {
+ 'None' : [],
+ 'ExactCutoff' : ['exactcutoff'], # Zero the interaction outside the cutoff, used for reaction-field-zero
+ 'PotentialShift' : ['shift','exactcutoff'],
+ 'PotentialSwitch' : ['r','switch','exactcutoff']
+}
+
+
+###############################################
+# GEOMETRY COMBINATIONS
+###############################################
+GeometryNameList = [
+ [ 'Particle' , 'Particle' ],
+ [ 'Water3' , 'Particle' ],
+ [ 'Water3' , 'Water3' ],
+ [ 'Water4' , 'Particle' ],
+ [ 'Water4' , 'Water4' ]
+]
+
+
+###############################################
+# POTENTIAL / FORCE
+###############################################
+VFList = [
+ 'PotentialAndForce',
+# 'Potential', # Not used yet
+ 'Force'
+]
+
+
+###############################################
+# GEOMETRY PROPERTIES
+###############################################
+# Dictionaries with lists telling which interactions are present
+# 1,2,3 means particles 1,2,3 (but not 0) have electrostatics!
+GeometryElectrostatics = {
+ 'Particle' : [ 0 ],
+ 'Particle2' : [ 0 , 1 ],
+ 'Particle3' : [ 0 , 1 , 2 ],
+ 'Particle4' : [ 0 , 1 , 2 , 3 ],
+ 'Water3' : [ 0 , 1 , 2 ],
+ 'Water4' : [ 1 , 2 , 3 ]
+}
+
+GeometryVdw = {
+ 'Particle' : [ 0 ],
+ 'Particle2' : [ 0 , 1 ],
+ 'Particle3' : [ 0 , 1 , 2 ],
+ 'Particle4' : [ 0 , 1 , 2 , 3 ],
+ 'Water3' : [ 0 ],
+ 'Water4' : [ 0 ]
+}
+
+
+
+
+# Dictionary to abbreviate all strings (mixed from all the lists)
+Abbreviation = {
+ 'None' : 'None',
+ 'Coulomb' : 'Coul',
+ 'Ewald' : 'Ew',
+ 'ReactionField' : 'RF',
+ 'GeneralizedBorn' : 'GB',
+ 'CubicSplineTable' : 'CSTab',
+ 'LennardJones' : 'LJ',
+ 'Buckingham' : 'Bham',
+ 'PotentialShift' : 'Sh',
+ 'PotentialSwitch' : 'Sw',
+ 'ExactCutoff' : 'Cut',
+ 'PotentialAndForce' : 'VF',
+ 'Potential' : 'V',
+ 'Force' : 'F',
+ 'Water3' : 'W3',
+ 'Water4' : 'W4',
+ 'Particle' : 'P1',
+ 'Particle2' : 'P2',
+ 'Particle3' : 'P3',
+ 'Particle4' : 'P4'
+}
+
+
+###############################################
+# Functions
+###############################################
+
+# Return a string with the kernel name from current settings
+def MakeKernelFileName(KernelElec,KernelElecMod,KernelVdw,KernelVdwMod,KernelGeom):
+ ElecStr = 'Elec' + Abbreviation[KernelElec]
+ if(KernelElecMod!='None'):
+ ElecStr = ElecStr + Abbreviation[KernelElecMod]
+ VdwStr = 'Vdw' + Abbreviation[KernelVdw]
+ if(KernelVdwMod!='None'):
+ VdwStr = VdwStr + Abbreviation[KernelVdwMod]
+ GeomStr = 'Geom' + Abbreviation[KernelGeom[0]] + Abbreviation[KernelGeom[1]]
+ return 'nb_kernel_' + ElecStr + '_' + VdwStr + '_' + GeomStr + '_' + Arch
+
+def MakeKernelName(KernelElec,KernelElecMod,KernelVdw,KernelVdwMod,KernelGeom,KernelVF):
+ ElecStr = 'Elec' + Abbreviation[KernelElec]
+ if(KernelElecMod!='None'):
+ ElecStr = ElecStr + Abbreviation[KernelElecMod]
+ VdwStr = 'Vdw' + Abbreviation[KernelVdw]
+ if(KernelVdwMod!='None'):
+ VdwStr = VdwStr + Abbreviation[KernelVdwMod]
+ GeomStr = 'Geom' + Abbreviation[KernelGeom[0]] + Abbreviation[KernelGeom[1]]
+ VFStr = Abbreviation[KernelVF]
+ return 'nb_kernel_' + ElecStr + '_' + VdwStr + '_' + GeomStr + '_' + VFStr + '_' + Arch
+
+# Return a string with a declaration to use for the kernel;
+# this will be a sequence of string combinations as well as the actual function name
+# Dont worry about field widths - that is just pretty-printing for the header!
+def MakeKernelDecl(KernelName,KernelElec,KernelElecMod,KernelVdw,KernelVdwMod,KernelGeom,KernelOther,KernelVF):
+ KernelStr = '\"'+KernelName+'\"'
+ ArchStr = '\"'+Arch+'\"'
+ ElecStr = '\"'+KernelElec+'\"'
+ ElecModStr = '\"'+KernelElecMod+'\"'
+ VdwStr = '\"'+KernelVdw+'\"'
+ VdwModStr = '\"'+KernelVdwMod+'\"'
+ GeomStr = '\"'+KernelGeom[0]+KernelGeom[1]+'\"'
+ OtherStr = '\"'+KernelOther+'\"'
+ VFStr = '\"'+KernelVF+'\"'
+
+ ThisSpec = ArchStr+', '+ElecStr+', '+ElecModStr+', '+VdwStr+', '+VdwModStr+', '+GeomStr+', '+OtherStr+', '+VFStr
+ ThisDecl = ' { '+KernelName+', '+KernelStr+', '+ThisSpec+' }'
+ return ThisDecl
+
+
+# Returns 1 if this kernel should be created, 0 if we should skip it
+# This routine is not critical - it is not the end of the world if we create more kernels,
+# but since the number is pretty large we save both space and compile-time by reducing it a bit.
+def KeepKernel(KernelElec,KernelElecMod,KernelVdw,KernelVdwMod,KernelGeom,KernelVF):
+
+ # No need for kernels without interactions
+ if(KernelElec=='None' and KernelVdw=='None'):
+ return 0
+
+ # No need for modifiers without interactions
+ if((KernelElec=='None' and KernelElecMod!='None') or (KernelVdw=='None' and KernelVdwMod!='None')):
+ return 0
+
+ # No need for LJ-only water optimization, or water optimization with implicit solvent.
+ if('Water' in KernelGeom[0] and (KernelElec=='None' or 'GeneralizedBorn' in KernelElec)):
+ return 0
+
+ # Non-matching table settings are pointless
+ if( ('Table' in KernelElec) and ('Table' in KernelVdw) and KernelElec!=KernelVdw ):
+ return 0
+
+ # Try to reduce the number of different switch/shift options to get a reasonable number of kernels
+ # For electrostatics, reaction-field can use 'exactcutoff', and ewald can use switch or shift.
+ if(KernelElecMod=='ExactCutoff' and KernelElec!='ReactionField'):
+ return 0
+ if(KernelElecMod in ['PotentialShift','PotentialSwitch'] and KernelElec!='Ewald'):
+ return 0
+ # For Vdw, we support switch and shift for Lennard-Jones/Buckingham
+ if((KernelVdwMod=='ExactCutoff') or
+ (KernelVdwMod in ['PotentialShift','PotentialSwitch'] and KernelVdw not in ['LennardJones','Buckingham'])):
+ return 0
+
+ # Choose either switch or shift and don't mix them...
+ if((KernelElecMod=='PotentialShift' and KernelVdwMod=='PotentialSwitch') or
+ (KernelElecMod=='PotentialSwitch' and KernelVdwMod=='PotentialShift')):
+ return 0
+
+ # Don't use a Vdw kernel with a modifier if the electrostatics one does not have one
+ if(KernelElec!='None' and KernelElecMod=='None' and KernelVdwMod!='None'):
+ return 0
+
+ # Don't use an electrostatics kernel with a modifier if the vdw one does not have one,
+ # unless the electrostatics one is reaction-field with exact cutoff.
+ if(KernelVdw!='None' and KernelVdwMod=='None' and KernelElecMod!='None'):
+ if(KernelElec=='ReactionField' and KernelVdw!='CubicSplineTable'):
+ return 0
+ elif(KernelElec!='ReactionField'):
+ return 0
+
+ return 1
+
+
+
+#
+# The preprocessor will automatically expand the interactions for water and other
+# geometries inside the kernel, but to get this right we need to setup a couple
+# of defines - we do them in a separate routine to keep the main loop clean.
+#
+# While this routine might look a bit complex it is actually quite straightforward,
+# and the best news is that you wont have to modify _anything_ for a new geometry
+# as long as you correctly define its Electrostatics/Vdw geometry in the lists above!
+#
+def SetDefines(KernelElec,KernelElecMod,KernelVdw,KernelVdwMod,KernelGeom,KernelVF,defines):
+ # What is the _name_ for the i/j group geometry?
+ igeometry = KernelGeom[0]
+ jgeometry = KernelGeom[1]
+ # define so we can access it in the source when the preprocessor runs
+ defines['GEOMETRY_I'] = igeometry
+ defines['GEOMETRY_J'] = jgeometry
+
+ # For the i/j groups, extract a python list of which sites have electrostatics
+ # For SPC/TIP3p this will be [1,1,1], while TIP4p (no elec on first site) will be [0,1,1,1]
+ ielec = GeometryElectrostatics[igeometry]
+ jelec = GeometryElectrostatics[jgeometry]
+ # Zero out the corresponding lists in case we dont do Elec
+ if(KernelElec=='None'):
+ ielec = []
+ jelec = []
+
+ # Extract similar interaction lists for Vdw interactions (example for SPC: [1,0,0])
+ iVdw = GeometryVdw[igeometry]
+ jVdw = GeometryVdw[jgeometry]
+
+ # Zero out the corresponding lists in case we dont do Vdw
+ if(KernelVdw=='None'):
+ iVdw = []
+ jVdw = []
+
+ # iany[] and jany[] contains lists of the particles actually used (for interactions) in this kernel
+ iany = list(set(ielec+iVdw)) # convert to+from set to make elements unique
+ jany = list(set(jelec+jVdw))
+
+ defines['PARTICLES_ELEC_I'] = ielec
+ defines['PARTICLES_ELEC_J'] = jelec
+ defines['PARTICLES_VDW_I'] = iVdw
+ defines['PARTICLES_VDW_J'] = jVdw
+ defines['PARTICLES_I'] = iany
+ defines['PARTICLES_J'] = jany
+
+ # elecij,Vdwij are sets with pairs of particles for which the corresponding interaction is done
+ # (and anyij again corresponds to either electrostatics or Vdw)
+ elecij = []
+ Vdwij = []
+ anyij = []
+
+ for i in ielec:
+ for j in jelec:
+ elecij.append([i,j])
+
+ for i in iVdw:
+ for j in jVdw:
+ Vdwij.append([i,j])
+
+ for i in iany:
+ for j in jany:
+ if [i,j] in elecij or [i,j] in Vdwij:
+ anyij.append([i,j])
+
+ defines['PAIRS_IJ'] = anyij
+
+ # Make an 2d list-of-distance-properties-to-calculate for i,j
+ ni = max(iany)+1
+ nj = max(jany)+1
+ # Each element properties[i][j] is an empty list
+ properties = [ [ [] for j in range(0,nj) ] for i in range (0,ni) ]
+ # Add properties to each set
+ for i in range(0,ni):
+ for j in range(0,nj):
+ if [i,j] in elecij:
+ properties[i][j] = properties[i][j] + ['electrostatics'] + ElectrostaticsList[KernelElec] + ModifierList[KernelElecMod]
+ if [i,j] in Vdwij:
+ properties[i][j] = properties[i][j] + ['vdw'] + VdwList[KernelVdw] + ModifierList[KernelVdwMod]
+ # Add rinv if we need r
+ if 'r' in properties[i][j]:
+ properties[i][j] = properties[i][j] + ['rinv']
+ # Add rsq if we need rinv or rinsq
+ if 'rinv' in properties[i][j] or 'rinvsq' in properties[i][j]:
+ properties[i][j] = properties[i][j] + ['rsq']
+
+ defines['INTERACTION_FLAGS'] = properties
+
+
+
+def PrintStatistics(ratio):
+ ratio = 100.0*ratio
+ print '\rGenerating %s nonbonded kernels... %5.1f%%' % (Arch,ratio),
+ sys.stdout.flush()
+
+
+
+defines = {}
+kerneldecl = []
+
+cnt = 0.0
+nelec = len(ElectrostaticsList)
+nVdw = len(VdwList)
+nmod = len(ModifierList)
+ngeom = len(GeometryNameList)
+
+ntot = nelec*nmod*nVdw*nmod*ngeom
+
+numKernels = 0
+
+fpdecl = open('nb_kernel_' + Arch + '.c','w')
+fpdecl.write( FileHeader )
+fpdecl.write( '#ifndef nb_kernel_' + Arch + '_h\n' )
+fpdecl.write( '#define nb_kernel_' + Arch + '_h\n\n' )
+fpdecl.write( '#include "../nb_kernel.h"\n\n' )
+
+for KernelElec in ElectrostaticsList:
+ defines['KERNEL_ELEC'] = KernelElec
+
+ for KernelElecMod in ModifierList:
+ defines['KERNEL_MOD_ELEC'] = KernelElecMod
+
+ for KernelVdw in VdwList:
+ defines['KERNEL_VDW'] = KernelVdw
+
+ for KernelVdwMod in ModifierList:
+ defines['KERNEL_MOD_VDW'] = KernelVdwMod
+
+ for KernelGeom in GeometryNameList:
+
+ cnt += 1
+ KernelFilename = MakeKernelFileName(KernelElec,KernelElecMod,KernelVdw,KernelVdwMod,KernelGeom) + '.c'
+ fpkernel = open(KernelFilename,'w')
+ defines['INCLUDE_HEADER'] = 1 # Include header first time in new file
+ DoHeader = 1
+
+ for KernelVF in VFList:
+
+ KernelName = MakeKernelName(KernelElec,KernelElecMod,KernelVdw,KernelVdwMod,KernelGeom,KernelVF)
+
+ defines['KERNEL_NAME'] = KernelName
+ defines['KERNEL_VF'] = KernelVF
+
+ # Check if this is a valid/sane/usable combination
+ if not KeepKernel(KernelElec,KernelElecMod,KernelVdw,KernelVdwMod,KernelGeom,KernelVF):
+ continue;
+
+ # The overall kernel settings determine what the _kernel_ calculates, but for the water
+ # kernels this does not mean that every pairwise interaction has e.g. Vdw interactions.
+ # This routine sets defines of what to calculate for each pair of particles in those cases.
+ SetDefines(KernelElec,KernelElecMod,KernelVdw,KernelVdwMod,KernelGeom,KernelVF,defines)
+
+ if(DoHeader==1):
+ fpkernel.write( FileHeader )
+
+ gmxpreprocess('nb_kernel_template_' + Arch + '.pre', KernelName+'.tmp' , defines, force=1,contentType='C')
+ numKernels = numKernels + 1
+
+ defines['INCLUDE_HEADER'] = 0 # Header has been included once now
+ DoHeader=0
+
+ # Append temp file contents to the common kernelfile
+ fptmp = open(KernelName+'.tmp','r')
+ fpkernel.writelines(fptmp.readlines())
+ fptmp.close()
+ os.remove(KernelName+'.tmp')
+
+ # Add a declaration for this kernel
+ fpdecl.write('nb_kernel_t ' + KernelName + ';\n');
+
+ # Add declaration to the buffer
+ KernelOther=''
+ kerneldecl.append(MakeKernelDecl(KernelName,KernelElec,KernelElecMod,KernelVdw,KernelVdwMod,KernelGeom,KernelOther,KernelVF))
+
+ filesize = fpkernel.tell()
+ fpkernel.close()
+ if(filesize==0):
+ os.remove(KernelFilename)
+
+ PrintStatistics(cnt/ntot)
+ pass
+ pass
+ pass
+ pass
+pass
+
+# Write out the list of settings and corresponding kernels to the declaration file
+fpdecl.write( '\n\n' )
+fpdecl.write( 'nb_kernel_info_t\n' )
+fpdecl.write( 'kernellist_'+Arch+'[] =\n' )
+fpdecl.write( '{\n' )
+for decl in kerneldecl[0:-1]:
+ fpdecl.write( decl + ',\n' )
+fpdecl.write( kerneldecl[-1] + '\n' )
+fpdecl.write( '};\n\n' )
+fpdecl.write( 'int\n' )
+fpdecl.write( 'kernellist_'+Arch+'_size = sizeof(kernellist_'+Arch+')/sizeof(kernellist_'+Arch+'[0]);\n\n')
+fpdecl.write( '#endif\n')
+fpdecl.close()
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel010.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel010
- * Coulomb interaction: Not calculated
- * VdW interaction: Lennard-Jones
- * water optimization: No
- * Calculate forces: yes
- */
-void nb_kernel010(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- nti = 2*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinvsq = 1.0/rsq11;
-
- /* Load parameters for j atom */
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
- fscal = (12.0*Vvdw12-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Inner loop uses 33 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- fshift[is3] = fshift[is3]+fix1;
- fshift[is3+1] = fshift[is3+1]+fiy1;
- fshift[is3+2] = fshift[is3+2]+fiz1;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 10 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel010nf
- * Coulomb interaction: Not calculated
- * VdW interaction: Lennard-Jones
- * water optimization: No
- * Calculate forces: no
- */
-void nb_kernel010nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real ix1,iy1,iz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- nti = 2*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinvsq = 1.0/rsq11;
-
- /* Load parameters for j atom */
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
-
- /* Inner loop uses 19 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 4 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL010_H_
-#define _NBKERNEL010_H_
-
-/*! \file nb_kernel010.h
- * \brief Nonbonded kernel 010 (LJ)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 010 with forces.
- *
- * <b>Coulomb interaction:</b> No <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel010
- (int * nri, int * iinr,
- int * jindex, int * jjnr,
- int * shift, real * shiftvec,
- real * fshift, int * gid,
- real * pos, real * faction,
- real * charge, real * facel,
- real * krf, real * crf,
- real * Vc, int * type,
- int * ntype, real * vdwparam,
- real * Vvdw, real * tabscale,
- real * VFtab, real * invsqrta,
- real * dvda, real * gbtabscale,
- real * GBtab, int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real * work);
-
-
-/*! \brief Nonbonded kernel 010 without forces.
- *
- * <b>Coulomb interaction:</b> No <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel010nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real * work);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL010_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel020.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel020
- * Coulomb interaction: Not calculated
- * VdW interaction: Buckingham
- * water optimization: No
- * Calculate forces: yes
- */
-void nb_kernel020(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdwexp,br;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- nti = 3*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- tj = nti+3*type[jnr];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
- rinvsq = rinv11*rinv11;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
- fscal = (br*Vvdwexp-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Inner loop uses 61 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- fshift[is3] = fshift[is3]+fix1;
- fshift[is3+1] = fshift[is3+1]+fiy1;
- fshift[is3+2] = fshift[is3+2]+fiz1;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 10 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel020nf
- * Coulomb interaction: Not calculated
- * VdW interaction: Buckingham
- * water optimization: No
- * Calculate forces: no
- */
-void nb_kernel020nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdwexp,br;
- real ix1,iy1,iz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- nti = 3*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- tj = nti+3*type[jnr];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
- rinvsq = rinv11*rinv11;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
-
- /* Inner loop uses 48 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 4 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL020_H_
-#define _NBKERNEL020_H_
-
-/*! \file nb_kernel020.h
- * \brief Nonbonded kernel 020 (Bham)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 020 with forces.
- *
- * <b>Coulomb interaction:</b> No <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel020
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 020 without forces.
- *
- * <b>Coulomb interaction:</b> No <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel020nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL020_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel030.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel030
- * Coulomb interaction: Not calculated
- * VdW interaction: Tabulated
- * water optimization: No
- * Calculate forces: yes
- */
-void nb_kernel030(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- int nti;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijD,fijR;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- nti = 2*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw6 = c6*VV;
- fijD = c6*FF;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw12 = c12*VV;
- fijR = c12*FF;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
- fscal = -((fijD+fijR)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Inner loop uses 54 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- fshift[is3] = fshift[is3]+fix1;
- fshift[is3+1] = fshift[is3+1]+fiy1;
- fshift[is3+2] = fshift[is3+2]+fiz1;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 10 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel030nf
- * Coulomb interaction: Not calculated
- * VdW interaction: Tabulated
- * water optimization: No
- * Calculate forces: no
- */
-void nb_kernel030nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- int nti;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real ix1,iy1,iz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- nti = 2*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw6 = c6*VV;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw12 = c12*VV;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
-
- /* Inner loop uses 33 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 4 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL030_H_
-#define _NBKERNEL030_H_
-
-/*! \file nb_kernel030.h
- * \brief Nonbonded kernel 030 (Tab VdW)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 030 with forces.
- *
- * <b>Coulomb interaction:</b> No <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel030
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 030 without forces.
- *
- * <b>Coulomb interaction:</b> No <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel030nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL030_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel100.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel100
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Not calculated
- * water optimization: No
- * Calculate forces: yes
- */
-void nb_kernel100(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real iq;
- real qq,vcoul,vctot;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
- rinvsq = rinv11*rinv11;
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Inner loop uses 27 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- fshift[is3] = fshift[is3]+fix1;
- fshift[is3+1] = fshift[is3+1]+fiy1;
- fshift[is3+2] = fshift[is3+2]+fiz1;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 11 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel100nf
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Not calculated
- * water optimization: No
- * Calculate forces: no
- */
-void nb_kernel100nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real iq;
- real qq,vcoul,vctot;
- real ix1,iy1,iz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
-
- /* Inner loop uses 16 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 5 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL100_H_
-#define _NBKERNEL100_H_
-
-/*! \file nb_kernel100.h
- * \brief Nonbonded kernel 100 (Coul)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 100 with forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel100
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 100 without forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel100nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL100_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel101.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel101
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Not calculated
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel101(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
- rinvsq = rinv11*rinv11;
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qH*jq;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- rinvsq = rinv31*rinv31;
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 80 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 28 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel101nf
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Not calculated
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: no
- */
-void nb_kernel101nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real jq;
- real qq,vcoul,vctot;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qH*jq;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
-
- /* Inner loop uses 47 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 10 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL101_H_
-#define _NBKERNEL101_H_
-
-/*! \file nb_kernel101.h
- * \brief Nonbonded kernel 101 (Coul, SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 101 with forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel101
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 101 without forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel101nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL101_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel102.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel102
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Not calculated
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: yes
- */
-void nb_kernel102(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real qq,vcoul,vctot;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
- rinvsq = rinv11*rinv11;
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv12*rinv12;
-
- /* Coulomb interaction */
- vcoul = qq*rinv12;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx12;
- ty = fscal*dy12;
- tz = fscal*dz12;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv13*rinv13;
-
- /* Coulomb interaction */
- vcoul = qq*rinv13;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx13;
- ty = fscal*dy13;
- tz = fscal*dz13;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv22*rinv22;
-
- /* Coulomb interaction */
- vcoul = qq*rinv22;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv23*rinv23;
-
- /* Coulomb interaction */
- vcoul = qq*rinv23;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv31*rinv31;
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv32*rinv32;
-
- /* Coulomb interaction */
- vcoul = qq*rinv32;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv33*rinv33;
-
- /* Coulomb interaction */
- vcoul = qq*rinv33;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Inner loop uses 234 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 28 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel102nf
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Not calculated
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: no
- */
-void nb_kernel102nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real qq,vcoul,vctot;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv12;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv13;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv22;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv23;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv32;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv33;
- vctot = vctot+vcoul;
-
- /* Inner loop uses 135 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 10 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL102_H_
-#define _NBKERNEL102_H_
-
-/*! \file nb_kernel102.h
- * \brief Nonbonded kernel 102 (Coul, SPC-SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 102 with forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel102
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 102 without forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel102nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL102_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel103.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel103
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Not calculated
- * water optimization: TIP4P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel103(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- rinvsq = rinv31*rinv31;
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qM*jq;
- rinvsq = rinv41*rinv41;
-
- /* Coulomb interaction */
- vcoul = qq*rinv41;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx41;
- ty = fscal*dy41;
- tz = fscal*dz41;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 80 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 28 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel103nf
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Not calculated
- * water optimization: TIP4P - other atoms
- * Calculate forces: no
- */
-void nb_kernel103nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real jq;
- real qq,vcoul,vctot;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx1,jy1,jz1;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qM*jq;
-
- /* Coulomb interaction */
- vcoul = qq*rinv41;
- vctot = vctot+vcoul;
-
- /* Inner loop uses 47 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 10 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL103_H_
-#define _NBKERNEL103_H_
-
-/*! \file nb_kernel103.h
- * \brief Nonbonded kernel 103 (Coul, TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 103 with forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel103
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 103 without forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel103nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL103_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel104.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel104
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Not calculated
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: yes
- */
-void nb_kernel104(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real qq,vcoul,vctot;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real jx4,jy4,jz4,fjx4,fjy4,fjz4;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv22*rinv22;
-
- /* Coulomb interaction */
- vcoul = qq*rinv22;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv23*rinv23;
-
- /* Coulomb interaction */
- vcoul = qq*rinv23;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv24*rinv24;
-
- /* Coulomb interaction */
- vcoul = qq*rinv24;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx24;
- ty = fscal*dy24;
- tz = fscal*dz24;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx4 = faction[j3+9] - tx;
- fjy4 = faction[j3+10] - ty;
- fjz4 = faction[j3+11] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv32*rinv32;
-
- /* Coulomb interaction */
- vcoul = qq*rinv32;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv33*rinv33;
-
- /* Coulomb interaction */
- vcoul = qq*rinv33;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv34*rinv34;
-
- /* Coulomb interaction */
- vcoul = qq*rinv34;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx34;
- ty = fscal*dy34;
- tz = fscal*dz34;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx4 = fjx4 - tx;
- fjy4 = fjy4 - ty;
- fjz4 = fjz4 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv42*rinv42;
-
- /* Coulomb interaction */
- vcoul = qq*rinv42;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx42;
- ty = fscal*dy42;
- tz = fscal*dz42;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv43*rinv43;
-
- /* Coulomb interaction */
- vcoul = qq*rinv43;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx43;
- ty = fscal*dy43;
- tz = fscal*dz43;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMM;
- rinvsq = rinv44*rinv44;
-
- /* Coulomb interaction */
- vcoul = qq*rinv44;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx44;
- ty = fscal*dy44;
- tz = fscal*dz44;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+9] = fjx4 - tx;
- faction[j3+10] = fjy4 - ty;
- faction[j3+11] = fjz4 - tz;
-
- /* Inner loop uses 234 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 28 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel104nf
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Not calculated
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: no
- */
-void nb_kernel104nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real qq,vcoul,vctot;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real jx4,jy4,jz4;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv22;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv23;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv24;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv32;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv33;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv34;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv42;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv43;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMM;
-
- /* Coulomb interaction */
- vcoul = qq*rinv44;
- vctot = vctot+vcoul;
-
- /* Inner loop uses 135 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 10 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL104_H_
-#define _NBKERNEL104_H_
-
-/*! \file nb_kernel104.h
- * \brief Nonbonded kernel 104 (Coul, TIP4p-TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 104 with forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel104
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 104 without forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel104nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL104_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel110.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel110
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Lennard-Jones
- * water optimization: No
- * Calculate forces: yes
- */
-void nb_kernel110(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- nti = 2*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
- rinvsq = rinv11*rinv11;
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
- fscal = (vcoul+12.0*Vvdw12-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Inner loop uses 38 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- fshift[is3] = fshift[is3]+fix1;
- fshift[is3+1] = fshift[is3+1]+fiy1;
- fshift[is3+2] = fshift[is3+2]+fiz1;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 12 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel110nf
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Lennard-Jones
- * water optimization: No
- * Calculate forces: no
- */
-void nb_kernel110nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real ix1,iy1,iz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- nti = 2*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
- rinvsq = rinv11*rinv11;
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
-
- /* Inner loop uses 24 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 6 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL110_H_
-#define _NBKERNEL110_H_
-
-/*! \file nb_kernel110.h
- * \brief Nonbonded kernel 110 (Coul + LJ)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 110 with forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel110
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 110 without forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel110nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL110_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel111.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel111
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Lennard-Jones
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel111(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
- rinvsq = rinv11*rinv11;
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
- fscal = (vcoul+12.0*Vvdw12-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qH*jq;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- rinvsq = rinv31*rinv31;
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 91 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 29 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel111nf
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Lennard-Jones
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: no
- */
-void nb_kernel111nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
- rinvsq = rinv11*rinv11;
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
-
- /* Load parameters for j atom */
- qq = qH*jq;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
-
- /* Inner loop uses 55 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 11 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL111_H_
-#define _NBKERNEL111_H_
-
-/*! \file nb_kernel111.h
- * \brief Nonbonded kernel 111 (Coul + LJ, SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 111 with forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel111
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 111 without forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel111nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL111_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel112.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel112
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Lennard-Jones
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: yes
- */
-void nb_kernel112(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
- rinvsq = rinv11*rinv11;
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
- fscal = (vcoul+12.0*Vvdw12-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv12*rinv12;
-
- /* Coulomb interaction */
- vcoul = qq*rinv12;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx12;
- ty = fscal*dy12;
- tz = fscal*dz12;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv13*rinv13;
-
- /* Coulomb interaction */
- vcoul = qq*rinv13;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx13;
- ty = fscal*dy13;
- tz = fscal*dz13;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv22*rinv22;
-
- /* Coulomb interaction */
- vcoul = qq*rinv22;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv23*rinv23;
-
- /* Coulomb interaction */
- vcoul = qq*rinv23;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv31*rinv31;
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv32*rinv32;
-
- /* Coulomb interaction */
- vcoul = qq*rinv32;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv33*rinv33;
-
- /* Coulomb interaction */
- vcoul = qq*rinv33;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Inner loop uses 245 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 29 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel112nf
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Lennard-Jones
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: no
- */
-void nb_kernel112nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
- rinvsq = rinv11*rinv11;
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv12;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv13;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv22;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv23;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv32;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv33;
- vctot = vctot+vcoul;
-
- /* Inner loop uses 143 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 11 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL112_H_
-#define _NBKERNEL112_H_
-
-/*! \file nb_kernel112.h
- * \brief Nonbonded kernel 112 (Coul + LJ, SPC-SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 112 with forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel112
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 112 without forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel112nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL112_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel113.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel113
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Lennard-Jones
- * water optimization: TIP4P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel113(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx11,dy11,dz11,rsq11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinvsq = 1.0/rsq11;
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
- fscal = (12.0*Vvdw12-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- rinvsq = rinv31*rinv31;
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qM*jq;
- rinvsq = rinv41*rinv41;
-
- /* Coulomb interaction */
- vcoul = qq*rinv41;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx41;
- ty = fscal*dy41;
- tz = fscal*dz41;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 113 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 38 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel113nf
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Lennard-Jones
- * water optimization: TIP4P - other atoms
- * Calculate forces: no
- */
-void nb_kernel113nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinvsq = 1.0/rsq11;
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qM*jq;
-
- /* Coulomb interaction */
- vcoul = qq*rinv41;
- vctot = vctot+vcoul;
-
- /* Inner loop uses 66 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 14 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL113_H_
-#define _NBKERNEL113_H_
-
-/*! \file nb_kernel113.h
- * \brief Nonbonded kernel 113 (Coul + LJ, TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 113 with forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel113
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 113 without forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel113nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL113_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel114.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel114
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Lennard-Jones
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: yes
- */
-void nb_kernel114(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real jx4,jy4,jz4,fjx4,fjy4,fjz4;
- real dx11,dy11,dz11,rsq11;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinvsq = 1.0/rsq11;
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
- fscal = (12.0*Vvdw12-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv22*rinv22;
-
- /* Coulomb interaction */
- vcoul = qq*rinv22;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv23*rinv23;
-
- /* Coulomb interaction */
- vcoul = qq*rinv23;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv24*rinv24;
-
- /* Coulomb interaction */
- vcoul = qq*rinv24;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx24;
- ty = fscal*dy24;
- tz = fscal*dz24;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx4 = faction[j3+9] - tx;
- fjy4 = faction[j3+10] - ty;
- fjz4 = faction[j3+11] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv32*rinv32;
-
- /* Coulomb interaction */
- vcoul = qq*rinv32;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv33*rinv33;
-
- /* Coulomb interaction */
- vcoul = qq*rinv33;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv34*rinv34;
-
- /* Coulomb interaction */
- vcoul = qq*rinv34;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx34;
- ty = fscal*dy34;
- tz = fscal*dz34;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx4 = fjx4 - tx;
- fjy4 = fjy4 - ty;
- fjz4 = fjz4 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv42*rinv42;
-
- /* Coulomb interaction */
- vcoul = qq*rinv42;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx42;
- ty = fscal*dy42;
- tz = fscal*dz42;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv43*rinv43;
-
- /* Coulomb interaction */
- vcoul = qq*rinv43;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx43;
- ty = fscal*dy43;
- tz = fscal*dz43;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMM;
- rinvsq = rinv44*rinv44;
-
- /* Coulomb interaction */
- vcoul = qq*rinv44;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx44;
- ty = fscal*dy44;
- tz = fscal*dz44;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+9] = fjx4 - tx;
- faction[j3+10] = fjy4 - ty;
- faction[j3+11] = fjz4 - tz;
-
- /* Inner loop uses 267 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 38 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel114nf
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Lennard-Jones
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: no
- */
-void nb_kernel114nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real jx4,jy4,jz4;
- real dx11,dy11,dz11,rsq11;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinvsq = 1.0/rsq11;
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv22;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv23;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv24;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv32;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv33;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv34;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv42;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv43;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMM;
-
- /* Coulomb interaction */
- vcoul = qq*rinv44;
- vctot = vctot+vcoul;
-
- /* Inner loop uses 154 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 14 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL114_H_
-#define _NBKERNEL114_H_
-
-/*! \file nb_kernel114.h
- * \brief Nonbonded kernel 114 (Coul + LJ, TIP4p-TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 114 with forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel114
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 114 without forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel114nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL114_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel120.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel120
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Buckingham
- * water optimization: No
- * Calculate forces: yes
- */
-void nb_kernel120(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdwexp,br;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- nti = 3*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
- tj = nti+3*type[jnr];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
- rinvsq = rinv11*rinv11;
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
- fscal = (vcoul+br*Vvdwexp-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Inner loop uses 64 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- fshift[is3] = fshift[is3]+fix1;
- fshift[is3+1] = fshift[is3+1]+fiy1;
- fshift[is3+2] = fshift[is3+2]+fiz1;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 12 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel120nf
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Buckingham
- * water optimization: No
- * Calculate forces: no
- */
-void nb_kernel120nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdwexp,br;
- real ix1,iy1,iz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- nti = 3*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
- tj = nti+3*type[jnr];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
- rinvsq = rinv11*rinv11;
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
-
- /* Inner loop uses 51 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 6 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL120_H_
-#define _NBKERNEL120_H_
-
-/*! \file nb_kernel120.h
- * \brief Nonbonded kernel 120 (Coul + Bham)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 120 with forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel120
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 120 without forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel120nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL120_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel121.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel121
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Buckingham
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel121(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdwexp,br;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
- nti = 3*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
- tj = nti+3*type[jnr];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
- rinvsq = rinv11*rinv11;
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
- fscal = (vcoul+br*Vvdwexp-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qH*jq;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- rinvsq = rinv31*rinv31;
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 117 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 29 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel121nf
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Buckingham
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: no
- */
-void nb_kernel121nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdwexp,br;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
- nti = 3*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
- tj = nti+3*type[jnr];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
- rinvsq = rinv11*rinv11;
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
-
- /* Load parameters for j atom */
- qq = qH*jq;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
-
- /* Inner loop uses 82 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 11 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL121_H_
-#define _NBKERNEL121_H_
-
-/*! \file nb_kernel121.h
- * \brief Nonbonded kernel 121 (Coul + Bham, SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 121 with forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel121
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 121 without forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel121nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL121_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel122.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel122
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Buckingham
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: yes
- */
-void nb_kernel122(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdwexp,br;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
- tj = 3*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
- rinvsq = rinv11*rinv11;
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
- fscal = (vcoul+br*Vvdwexp-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv12*rinv12;
-
- /* Coulomb interaction */
- vcoul = qq*rinv12;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx12;
- ty = fscal*dy12;
- tz = fscal*dz12;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv13*rinv13;
-
- /* Coulomb interaction */
- vcoul = qq*rinv13;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx13;
- ty = fscal*dy13;
- tz = fscal*dz13;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv22*rinv22;
-
- /* Coulomb interaction */
- vcoul = qq*rinv22;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv23*rinv23;
-
- /* Coulomb interaction */
- vcoul = qq*rinv23;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv31*rinv31;
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv32*rinv32;
-
- /* Coulomb interaction */
- vcoul = qq*rinv32;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv33*rinv33;
-
- /* Coulomb interaction */
- vcoul = qq*rinv33;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Inner loop uses 271 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 29 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel122nf
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Buckingham
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: no
- */
-void nb_kernel122nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdwexp,br;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
- tj = 3*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
- rinvsq = rinv11*rinv11;
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv12;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv13;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv22;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv23;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv32;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv33;
- vctot = vctot+vcoul;
-
- /* Inner loop uses 170 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 11 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL122_H_
-#define _NBKERNEL122_H_
-
-/*! \file nb_kernel122.h
- * \brief Nonbonded kernel 122 (Coul + Bham, SPC-SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 122 with forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel122
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 122 without forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel122nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL122_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel123.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel123
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Buckingham
- * water optimization: TIP4P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel123(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdwexp,br;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
- nti = 3*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- tj = nti+3*type[jnr];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
- rinvsq = rinv11*rinv11;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
- fscal = (br*Vvdwexp-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- rinvsq = rinv31*rinv31;
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qM*jq;
- rinvsq = rinv41*rinv41;
-
- /* Coulomb interaction */
- vcoul = qq*rinv41;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx41;
- ty = fscal*dy41;
- tz = fscal*dz41;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 141 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 38 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel123nf
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Buckingham
- * water optimization: TIP4P - other atoms
- * Calculate forces: no
- */
-void nb_kernel123nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdwexp,br;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
- nti = 3*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- tj = nti+3*type[jnr];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
- rinvsq = rinv11*rinv11;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qM*jq;
-
- /* Coulomb interaction */
- vcoul = qq*rinv41;
- vctot = vctot+vcoul;
-
- /* Inner loop uses 95 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 14 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL123_H_
-#define _NBKERNEL123_H_
-
-/*! \file nb_kernel123.h
- * \brief Nonbonded kernel 123 (Coul + Bham, TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 123 with forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel123
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 123 without forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel123nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL123_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel124.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel124
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Buckingham
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: yes
- */
-void nb_kernel124(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdwexp,br;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real jx4,jy4,jz4,fjx4,fjy4,fjz4;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
- tj = 3*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
- rinvsq = rinv11*rinv11;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
- fscal = (br*Vvdwexp-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv22*rinv22;
-
- /* Coulomb interaction */
- vcoul = qq*rinv22;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv23*rinv23;
-
- /* Coulomb interaction */
- vcoul = qq*rinv23;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv24*rinv24;
-
- /* Coulomb interaction */
- vcoul = qq*rinv24;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx24;
- ty = fscal*dy24;
- tz = fscal*dz24;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx4 = faction[j3+9] - tx;
- fjy4 = faction[j3+10] - ty;
- fjz4 = faction[j3+11] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv32*rinv32;
-
- /* Coulomb interaction */
- vcoul = qq*rinv32;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv33*rinv33;
-
- /* Coulomb interaction */
- vcoul = qq*rinv33;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv34*rinv34;
-
- /* Coulomb interaction */
- vcoul = qq*rinv34;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx34;
- ty = fscal*dy34;
- tz = fscal*dz34;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx4 = fjx4 - tx;
- fjy4 = fjy4 - ty;
- fjz4 = fjz4 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv42*rinv42;
-
- /* Coulomb interaction */
- vcoul = qq*rinv42;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx42;
- ty = fscal*dy42;
- tz = fscal*dz42;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv43*rinv43;
-
- /* Coulomb interaction */
- vcoul = qq*rinv43;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx43;
- ty = fscal*dy43;
- tz = fscal*dz43;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMM;
- rinvsq = rinv44*rinv44;
-
- /* Coulomb interaction */
- vcoul = qq*rinv44;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx44;
- ty = fscal*dy44;
- tz = fscal*dz44;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+9] = fjx4 - tx;
- faction[j3+10] = fjy4 - ty;
- faction[j3+11] = fjz4 - tz;
-
- /* Inner loop uses 295 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 38 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel124nf
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Buckingham
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: no
- */
-void nb_kernel124nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdwexp,br;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real jx4,jy4,jz4;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
- tj = 3*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
- rinvsq = rinv11*rinv11;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv22;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv23;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv24;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv32;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv33;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv34;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv42;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv43;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMM;
-
- /* Coulomb interaction */
- vcoul = qq*rinv44;
- vctot = vctot+vcoul;
-
- /* Inner loop uses 183 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 14 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL124_H_
-#define _NBKERNEL124_H_
-
-/*! \file nb_kernel124.h
- * \brief Nonbonded kernel 124 (Coul + Bham, TIP4p-TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 124 with forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel124
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 124 without forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel124nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL124_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel130.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel130
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Tabulated
- * water optimization: No
- * Calculate forces: yes
- */
-void nb_kernel130(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijD,fijR;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- nti = 2*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
- rinvsq = rinv11*rinv11;
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw6 = c6*VV;
- fijD = c6*FF;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw12 = c12*VV;
- fijR = c12*FF;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
- fscal = (vcoul)*rinvsq-((fijD+fijR)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Inner loop uses 59 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- fshift[is3] = fshift[is3]+fix1;
- fshift[is3+1] = fshift[is3+1]+fiy1;
- fshift[is3+2] = fshift[is3+2]+fiz1;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 12 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel130nf
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Tabulated
- * water optimization: No
- * Calculate forces: no
- */
-void nb_kernel130nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real ix1,iy1,iz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- nti = 2*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw6 = c6*VV;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw12 = c12*VV;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
-
- /* Inner loop uses 36 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 6 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL130_H_
-#define _NBKERNEL130_H_
-
-/*! \file nb_kernel130.h
- * \brief Nonbonded kernel 130 (Coul + Tab VdW)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 130 with forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel130
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 130 without forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel130nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL130_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel131.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel131
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Tabulated
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel131(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijD,fijR;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
- rinvsq = rinv11*rinv11;
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw6 = c6*VV;
- fijD = c6*FF;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw12 = c12*VV;
- fijR = c12*FF;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
- fscal = (vcoul)*rinvsq-((fijD+fijR)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qH*jq;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- rinvsq = rinv31*rinv31;
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 112 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 29 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel131nf
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Tabulated
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: no
- */
-void nb_kernel131nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw6 = c6*VV;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw12 = c12*VV;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
-
- /* Load parameters for j atom */
- qq = qH*jq;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
-
- /* Inner loop uses 67 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 11 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL131_H_
-#define _NBKERNEL131_H_
-
-/*! \file nb_kernel131.h
- * \brief Nonbonded kernel 131 (Coul + Tab VdW, SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 131 with forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel131
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 131 without forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel131nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL131_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel132.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel132
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Tabulated
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: yes
- */
-void nb_kernel132(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijD,fijR;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
- rinvsq = rinv11*rinv11;
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw6 = c6*VV;
- fijD = c6*FF;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw12 = c12*VV;
- fijR = c12*FF;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
- fscal = (vcoul)*rinvsq-((fijD+fijR)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv12*rinv12;
-
- /* Coulomb interaction */
- vcoul = qq*rinv12;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx12;
- ty = fscal*dy12;
- tz = fscal*dz12;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv13*rinv13;
-
- /* Coulomb interaction */
- vcoul = qq*rinv13;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx13;
- ty = fscal*dy13;
- tz = fscal*dz13;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv22*rinv22;
-
- /* Coulomb interaction */
- vcoul = qq*rinv22;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv23*rinv23;
-
- /* Coulomb interaction */
- vcoul = qq*rinv23;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv31*rinv31;
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv32*rinv32;
-
- /* Coulomb interaction */
- vcoul = qq*rinv32;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv33*rinv33;
-
- /* Coulomb interaction */
- vcoul = qq*rinv33;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Inner loop uses 266 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 29 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel132nf
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Tabulated
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: no
- */
-void nb_kernel132nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real qq,vcoul,vctot;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
-
- /* Coulomb interaction */
- vcoul = qq*rinv11;
- vctot = vctot+vcoul;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw6 = c6*VV;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw12 = c12*VV;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv12;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv13;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv22;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv23;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv32;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv33;
- vctot = vctot+vcoul;
-
- /* Inner loop uses 155 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 11 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL132_H_
-#define _NBKERNEL132_H_
-
-/*! \file nb_kernel132.h
- * \brief Nonbonded kernel 132 (Coul + Tab VdW, SPC-SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 132 with forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel132
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 132 without forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel132nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL132_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel133.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel133
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Tabulated
- * water optimization: TIP4P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel133(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijD,fijR;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw6 = c6*VV;
- fijD = c6*FF;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw12 = c12*VV;
- fijR = c12*FF;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
- fscal = -((fijD+fijR)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- rinvsq = rinv31*rinv31;
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qM*jq;
- rinvsq = rinv41*rinv41;
-
- /* Coulomb interaction */
- vcoul = qq*rinv41;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx41;
- ty = fscal*dy41;
- tz = fscal*dz41;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 134 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 38 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel133nf
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Tabulated
- * water optimization: TIP4P - other atoms
- * Calculate forces: no
- */
-void nb_kernel133nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw6 = c6*VV;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw12 = c12*VV;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
-
- /* Coulomb interaction */
- vcoul = qq*rinv21;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
-
- /* Coulomb interaction */
- vcoul = qq*rinv31;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qM*jq;
-
- /* Coulomb interaction */
- vcoul = qq*rinv41;
- vctot = vctot+vcoul;
-
- /* Inner loop uses 80 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 14 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL133_H_
-#define _NBKERNEL133_H_
-
-/*! \file nb_kernel133.h
- * \brief Nonbonded kernel 133 (Coul + Tab VdW, TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 133 with forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel133
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 133 without forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel133nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL133_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel134.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel134
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Tabulated
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: yes
- */
-void nb_kernel134(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijD,fijR;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real jx4,jy4,jz4,fjx4,fjy4,fjz4;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw6 = c6*VV;
- fijD = c6*FF;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw12 = c12*VV;
- fijR = c12*FF;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
- fscal = -((fijD+fijR)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv22*rinv22;
-
- /* Coulomb interaction */
- vcoul = qq*rinv22;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv23*rinv23;
-
- /* Coulomb interaction */
- vcoul = qq*rinv23;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv24*rinv24;
-
- /* Coulomb interaction */
- vcoul = qq*rinv24;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx24;
- ty = fscal*dy24;
- tz = fscal*dz24;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx4 = faction[j3+9] - tx;
- fjy4 = faction[j3+10] - ty;
- fjz4 = faction[j3+11] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv32*rinv32;
-
- /* Coulomb interaction */
- vcoul = qq*rinv32;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv33*rinv33;
-
- /* Coulomb interaction */
- vcoul = qq*rinv33;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv34*rinv34;
-
- /* Coulomb interaction */
- vcoul = qq*rinv34;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx34;
- ty = fscal*dy34;
- tz = fscal*dz34;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx4 = fjx4 - tx;
- fjy4 = fjy4 - ty;
- fjz4 = fjz4 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv42*rinv42;
-
- /* Coulomb interaction */
- vcoul = qq*rinv42;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx42;
- ty = fscal*dy42;
- tz = fscal*dz42;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv43*rinv43;
-
- /* Coulomb interaction */
- vcoul = qq*rinv43;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx43;
- ty = fscal*dy43;
- tz = fscal*dz43;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMM;
- rinvsq = rinv44*rinv44;
-
- /* Coulomb interaction */
- vcoul = qq*rinv44;
- vctot = vctot+vcoul;
- fscal = (vcoul)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx44;
- ty = fscal*dy44;
- tz = fscal*dz44;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+9] = fjx4 - tx;
- faction[j3+10] = fjy4 - ty;
- faction[j3+11] = fjz4 - tz;
-
- /* Inner loop uses 288 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 38 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel134nf
- * Coulomb interaction: Normal Coulomb
- * VdW interaction: Tabulated
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: no
- */
-void nb_kernel134nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real qq,vcoul,vctot;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real jx4,jy4,jz4;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw6 = c6*VV;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw12 = c12*VV;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv22;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv23;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv24;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv32;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv33;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv34;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv42;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb interaction */
- vcoul = qq*rinv43;
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMM;
-
- /* Coulomb interaction */
- vcoul = qq*rinv44;
- vctot = vctot+vcoul;
-
- /* Inner loop uses 168 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 14 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL134_H_
-#define _NBKERNEL134_H_
-
-/*! \file nb_kernel134.h
- * \brief Nonbonded kernel 134 (Coul + Tab VdW, TIP4p-TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 134 with forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel134
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 134 without forces.
- *
- * <b>Coulomb interaction:</b> Standard 1/r <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel134nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL134_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel200.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel200
- * Coulomb interaction: Reaction field
- * VdW interaction: Not calculated
- * water optimization: No
- * Calculate forces: yes
- */
-void nb_kernel200(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real iq;
- real qq,vcoul,vctot;
- real krsq;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
- rinvsq = rinv11*rinv11;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv11-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Inner loop uses 33 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- fshift[is3] = fshift[is3]+fix1;
- fshift[is3+1] = fshift[is3+1]+fiy1;
- fshift[is3+2] = fshift[is3+2]+fiz1;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 11 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel200nf
- * Coulomb interaction: Reaction field
- * VdW interaction: Not calculated
- * water optimization: No
- * Calculate forces: no
- */
-void nb_kernel200nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real iq;
- real qq,vcoul,vctot;
- real krsq;
- real ix1,iy1,iz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Inner loop uses 19 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 5 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL200_H_
-#define _NBKERNEL200_H_
-
-/*! \file nb_kernel200.h
- * \brief Nonbonded kernel 200 (RF Coul)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 200 with forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel200
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 200 without forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel200nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL200_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel201.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel201
- * Coulomb interaction: Reaction field
- * VdW interaction: Not calculated
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel201(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- real krsq;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
- rinvsq = rinv11*rinv11;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv11-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qH*jq;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv21-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- rinvsq = rinv31*rinv31;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv31-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 98 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 28 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel201nf
- * Coulomb interaction: Reaction field
- * VdW interaction: Not calculated
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: no
- */
-void nb_kernel201nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real jq;
- real qq,vcoul,vctot;
- real krsq;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qH*jq;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Inner loop uses 56 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 10 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL201_H_
-#define _NBKERNEL201_H_
-
-/*! \file nb_kernel201.h
- * \brief Nonbonded kernel 201 (RF Coul, SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 201 with forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel201
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 201 without forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel201nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL201_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel202.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel202
- * Coulomb interaction: Reaction field
- * VdW interaction: Not calculated
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: yes
- */
-void nb_kernel202(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real qq,vcoul,vctot;
- real krsq;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
- rinvsq = rinv11*rinv11;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv11-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv12*rinv12;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq12;
- vcoul = qq*(rinv12+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv12-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx12;
- ty = fscal*dy12;
- tz = fscal*dz12;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv13*rinv13;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq13;
- vcoul = qq*(rinv13+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv13-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx13;
- ty = fscal*dy13;
- tz = fscal*dz13;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv21-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv22*rinv22;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq22;
- vcoul = qq*(rinv22+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv22-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv23*rinv23;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq23;
- vcoul = qq*(rinv23+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv23-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv31*rinv31;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv31-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv32*rinv32;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq32;
- vcoul = qq*(rinv32+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv32-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv33*rinv33;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq33;
- vcoul = qq*(rinv33+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv33-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Inner loop uses 288 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 28 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel202nf
- * Coulomb interaction: Reaction field
- * VdW interaction: Not calculated
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: no
- */
-void nb_kernel202nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real qq,vcoul,vctot;
- real krsq;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq12;
- vcoul = qq*(rinv12+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq13;
- vcoul = qq*(rinv13+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq22;
- vcoul = qq*(rinv22+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq23;
- vcoul = qq*(rinv23+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq32;
- vcoul = qq*(rinv32+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq33;
- vcoul = qq*(rinv33+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Inner loop uses 162 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 10 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL202_H_
-#define _NBKERNEL202_H_
-
-/*! \file nb_kernel202.h
- * \brief Nonbonded kernel 202 (RF Coul, SPC-SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 202 with forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel202
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 202 without forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel202nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL202_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel203.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel203
- * Coulomb interaction: Reaction field
- * VdW interaction: Not calculated
- * water optimization: TIP4P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel203(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- real krsq;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv21-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- rinvsq = rinv31*rinv31;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv31-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qM*jq;
- rinvsq = rinv41*rinv41;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq41;
- vcoul = qq*(rinv41+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv41-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx41;
- ty = fscal*dy41;
- tz = fscal*dz41;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 98 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 28 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel203nf
- * Coulomb interaction: Reaction field
- * VdW interaction: Not calculated
- * water optimization: TIP4P - other atoms
- * Calculate forces: no
- */
-void nb_kernel203nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real jq;
- real qq,vcoul,vctot;
- real krsq;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx1,jy1,jz1;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qM*jq;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq41;
- vcoul = qq*(rinv41+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Inner loop uses 56 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 10 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL203_H_
-#define _NBKERNEL203_H_
-
-/*! \file nb_kernel203.h
- * \brief Nonbonded kernel 203 (RF Coul, TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 203 with forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel203
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 203 without forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel203nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL203_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel204.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel204
- * Coulomb interaction: Reaction field
- * VdW interaction: Not calculated
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: yes
- */
-void nb_kernel204(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real qq,vcoul,vctot;
- real krsq;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real jx4,jy4,jz4,fjx4,fjy4,fjz4;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv22*rinv22;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq22;
- vcoul = qq*(rinv22+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv22-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv23*rinv23;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq23;
- vcoul = qq*(rinv23+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv23-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv24*rinv24;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq24;
- vcoul = qq*(rinv24+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv24-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx24;
- ty = fscal*dy24;
- tz = fscal*dz24;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx4 = faction[j3+9] - tx;
- fjy4 = faction[j3+10] - ty;
- fjz4 = faction[j3+11] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv32*rinv32;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq32;
- vcoul = qq*(rinv32+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv32-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv33*rinv33;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq33;
- vcoul = qq*(rinv33+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv33-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv34*rinv34;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq34;
- vcoul = qq*(rinv34+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv34-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx34;
- ty = fscal*dy34;
- tz = fscal*dz34;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx4 = fjx4 - tx;
- fjy4 = fjy4 - ty;
- fjz4 = fjz4 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv42*rinv42;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq42;
- vcoul = qq*(rinv42+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv42-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx42;
- ty = fscal*dy42;
- tz = fscal*dz42;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv43*rinv43;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq43;
- vcoul = qq*(rinv43+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv43-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx43;
- ty = fscal*dy43;
- tz = fscal*dz43;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMM;
- rinvsq = rinv44*rinv44;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq44;
- vcoul = qq*(rinv44+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv44-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx44;
- ty = fscal*dy44;
- tz = fscal*dz44;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+9] = fjx4 - tx;
- faction[j3+10] = fjy4 - ty;
- faction[j3+11] = fjz4 - tz;
-
- /* Inner loop uses 288 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 28 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel204nf
- * Coulomb interaction: Reaction field
- * VdW interaction: Not calculated
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: no
- */
-void nb_kernel204nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real qq,vcoul,vctot;
- real krsq;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real jx4,jy4,jz4;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq22;
- vcoul = qq*(rinv22+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq23;
- vcoul = qq*(rinv23+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq24;
- vcoul = qq*(rinv24+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq32;
- vcoul = qq*(rinv32+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq33;
- vcoul = qq*(rinv33+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq34;
- vcoul = qq*(rinv34+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq42;
- vcoul = qq*(rinv42+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq43;
- vcoul = qq*(rinv43+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMM;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq44;
- vcoul = qq*(rinv44+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Inner loop uses 162 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 10 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL204_H_
-#define _NBKERNEL204_H_
-
-/*! \file nb_kernel204.h
- * \brief Nonbonded kernel 204 (RF Coul, TIP4p-TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 204 with forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel204
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 204 without forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel204nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL204_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel210.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel210
- * Coulomb interaction: Reaction field
- * VdW interaction: Lennard-Jones
- * water optimization: No
- * Calculate forces: yes
- */
-void nb_kernel210(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real krsq;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- nti = 2*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
- rinvsq = rinv11*rinv11;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
- fscal = (qq*(rinv11-2.0*krsq)+12.0*Vvdw12-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Inner loop uses 44 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- fshift[is3] = fshift[is3]+fix1;
- fshift[is3+1] = fshift[is3+1]+fiy1;
- fshift[is3+2] = fshift[is3+2]+fiz1;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 12 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel210nf
- * Coulomb interaction: Reaction field
- * VdW interaction: Lennard-Jones
- * water optimization: No
- * Calculate forces: no
- */
-void nb_kernel210nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real krsq;
- real ix1,iy1,iz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- nti = 2*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
- rinvsq = rinv11*rinv11;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
-
- /* Inner loop uses 27 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 6 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL210_H_
-#define _NBKERNEL210_H_
-
-/*! \file nb_kernel210.h
- * \brief Nonbonded kernel 210 (RF Coul + LJ)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 210 with forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel210
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 210 without forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel210nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL210_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel211.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel211
- * Coulomb interaction: Reaction field
- * VdW interaction: Lennard-Jones
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel211(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real krsq;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
- rinvsq = rinv11*rinv11;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
- fscal = (qq*(rinv11-2.0*krsq)+12.0*Vvdw12-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qH*jq;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv21-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- rinvsq = rinv31*rinv31;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv31-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 109 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 29 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel211nf
- * Coulomb interaction: Reaction field
- * VdW interaction: Lennard-Jones
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: no
- */
-void nb_kernel211nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real krsq;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
- rinvsq = rinv11*rinv11;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
-
- /* Load parameters for j atom */
- qq = qH*jq;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Inner loop uses 64 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 11 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL211_H_
-#define _NBKERNEL211_H_
-
-/*! \file nb_kernel211.h
- * \brief Nonbonded kernel 211 (RF Coul + LJ, SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 211 with forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel211
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 211 without forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel211nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL211_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel212.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel212
- * Coulomb interaction: Reaction field
- * VdW interaction: Lennard-Jones
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: yes
- */
-void nb_kernel212(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real krsq;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
- rinvsq = rinv11*rinv11;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
- fscal = (qq*(rinv11-2.0*krsq)+12.0*Vvdw12-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv12*rinv12;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq12;
- vcoul = qq*(rinv12+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv12-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx12;
- ty = fscal*dy12;
- tz = fscal*dz12;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv13*rinv13;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq13;
- vcoul = qq*(rinv13+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv13-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx13;
- ty = fscal*dy13;
- tz = fscal*dz13;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv21-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv22*rinv22;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq22;
- vcoul = qq*(rinv22+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv22-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv23*rinv23;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq23;
- vcoul = qq*(rinv23+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv23-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv31*rinv31;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv31-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv32*rinv32;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq32;
- vcoul = qq*(rinv32+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv32-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv33*rinv33;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq33;
- vcoul = qq*(rinv33+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv33-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Inner loop uses 299 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 29 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel212nf
- * Coulomb interaction: Reaction field
- * VdW interaction: Lennard-Jones
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: no
- */
-void nb_kernel212nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real krsq;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
- rinvsq = rinv11*rinv11;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq12;
- vcoul = qq*(rinv12+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq13;
- vcoul = qq*(rinv13+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq22;
- vcoul = qq*(rinv22+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq23;
- vcoul = qq*(rinv23+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq32;
- vcoul = qq*(rinv32+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq33;
- vcoul = qq*(rinv33+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Inner loop uses 170 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 11 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL212_H_
-#define _NBKERNEL212_H_
-
-/*! \file nb_kernel212.h
- * \brief Nonbonded kernel 212 (RF Coul + LJ, SPC-SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 212 with forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel212
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 212 without forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel212nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL212_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel213.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel213
- * Coulomb interaction: Reaction field
- * VdW interaction: Lennard-Jones
- * water optimization: TIP4P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel213(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real krsq;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx11,dy11,dz11,rsq11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinvsq = 1.0/rsq11;
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
- fscal = (12.0*Vvdw12-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv21-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- rinvsq = rinv31*rinv31;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv31-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qM*jq;
- rinvsq = rinv41*rinv41;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq41;
- vcoul = qq*(rinv41+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv41-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx41;
- ty = fscal*dy41;
- tz = fscal*dz41;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 131 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 38 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel213nf
- * Coulomb interaction: Reaction field
- * VdW interaction: Lennard-Jones
- * water optimization: TIP4P - other atoms
- * Calculate forces: no
- */
-void nb_kernel213nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real krsq;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinvsq = 1.0/rsq11;
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qM*jq;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq41;
- vcoul = qq*(rinv41+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Inner loop uses 75 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 14 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL213_H_
-#define _NBKERNEL213_H_
-
-/*! \file nb_kernel213.h
- * \brief Nonbonded kernel 213 (RF Coul + LJ, TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 213 with forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel213
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 213 without forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel213nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL213_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel214.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel214
- * Coulomb interaction: Reaction field
- * VdW interaction: Lennard-Jones
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: yes
- */
-void nb_kernel214(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real krsq;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real jx4,jy4,jz4,fjx4,fjy4,fjz4;
- real dx11,dy11,dz11,rsq11;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinvsq = 1.0/rsq11;
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
- fscal = (12.0*Vvdw12-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv22*rinv22;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq22;
- vcoul = qq*(rinv22+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv22-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv23*rinv23;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq23;
- vcoul = qq*(rinv23+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv23-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv24*rinv24;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq24;
- vcoul = qq*(rinv24+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv24-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx24;
- ty = fscal*dy24;
- tz = fscal*dz24;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx4 = faction[j3+9] - tx;
- fjy4 = faction[j3+10] - ty;
- fjz4 = faction[j3+11] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv32*rinv32;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq32;
- vcoul = qq*(rinv32+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv32-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv33*rinv33;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq33;
- vcoul = qq*(rinv33+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv33-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv34*rinv34;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq34;
- vcoul = qq*(rinv34+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv34-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx34;
- ty = fscal*dy34;
- tz = fscal*dz34;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx4 = fjx4 - tx;
- fjy4 = fjy4 - ty;
- fjz4 = fjz4 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv42*rinv42;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq42;
- vcoul = qq*(rinv42+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv42-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx42;
- ty = fscal*dy42;
- tz = fscal*dz42;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv43*rinv43;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq43;
- vcoul = qq*(rinv43+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv43-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx43;
- ty = fscal*dy43;
- tz = fscal*dz43;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMM;
- rinvsq = rinv44*rinv44;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq44;
- vcoul = qq*(rinv44+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv44-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx44;
- ty = fscal*dy44;
- tz = fscal*dz44;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+9] = fjx4 - tx;
- faction[j3+10] = fjy4 - ty;
- faction[j3+11] = fjz4 - tz;
-
- /* Inner loop uses 321 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 38 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel214nf
- * Coulomb interaction: Reaction field
- * VdW interaction: Lennard-Jones
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: no
- */
-void nb_kernel214nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real krsq;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real jx4,jy4,jz4;
- real dx11,dy11,dz11,rsq11;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinvsq = 1.0/rsq11;
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq22;
- vcoul = qq*(rinv22+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq23;
- vcoul = qq*(rinv23+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq24;
- vcoul = qq*(rinv24+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq32;
- vcoul = qq*(rinv32+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq33;
- vcoul = qq*(rinv33+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq34;
- vcoul = qq*(rinv34+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq42;
- vcoul = qq*(rinv42+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq43;
- vcoul = qq*(rinv43+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMM;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq44;
- vcoul = qq*(rinv44+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Inner loop uses 181 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 14 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL214_H_
-#define _NBKERNEL214_H_
-
-/*! \file nb_kernel214.h
- * \brief Nonbonded kernel 214 (RF Coul + LJ, TIP4p-TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 214 with forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel214
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 214 without forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel214nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL214_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel220.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel220
- * Coulomb interaction: Reaction field
- * VdW interaction: Buckingham
- * water optimization: No
- * Calculate forces: yes
- */
-void nb_kernel220(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real krsq;
- real Vvdwexp,br;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- nti = 3*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
- tj = nti+3*type[jnr];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
- rinvsq = rinv11*rinv11;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
- fscal = (qq*(rinv11-2.0*krsq)+br*Vvdwexp-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Inner loop uses 70 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- fshift[is3] = fshift[is3]+fix1;
- fshift[is3+1] = fshift[is3+1]+fiy1;
- fshift[is3+2] = fshift[is3+2]+fiz1;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 12 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel220nf
- * Coulomb interaction: Reaction field
- * VdW interaction: Buckingham
- * water optimization: No
- * Calculate forces: no
- */
-void nb_kernel220nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real krsq;
- real Vvdwexp,br;
- real ix1,iy1,iz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- nti = 3*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
- tj = nti+3*type[jnr];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
- rinvsq = rinv11*rinv11;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
-
- /* Inner loop uses 54 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 6 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL220_H_
-#define _NBKERNEL220_H_
-
-/*! \file nb_kernel220.h
- * \brief Nonbonded kernel 220 (RF Coul + Bham)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 220 with forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel220
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 220 without forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel220nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL220_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel221.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel221
- * Coulomb interaction: Reaction field
- * VdW interaction: Buckingham
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel221(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real krsq;
- real Vvdwexp,br;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
- nti = 3*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
- tj = nti+3*type[jnr];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
- rinvsq = rinv11*rinv11;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
- fscal = (qq*(rinv11-2.0*krsq)+br*Vvdwexp-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qH*jq;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv21-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- rinvsq = rinv31*rinv31;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv31-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 135 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 29 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel221nf
- * Coulomb interaction: Reaction field
- * VdW interaction: Buckingham
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: no
- */
-void nb_kernel221nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real krsq;
- real Vvdwexp,br;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
- nti = 3*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
- tj = nti+3*type[jnr];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
- rinvsq = rinv11*rinv11;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
-
- /* Load parameters for j atom */
- qq = qH*jq;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Inner loop uses 91 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 11 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL221_H_
-#define _NBKERNEL221_H_
-
-/*! \file nb_kernel221.h
- * \brief Nonbonded kernel 221 (RF Coul + Bham, SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 221 with forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel221
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 221 without forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel221nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL221_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel222.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel222
- * Coulomb interaction: Reaction field
- * VdW interaction: Buckingham
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: yes
- */
-void nb_kernel222(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real krsq;
- real Vvdwexp,br;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
- tj = 3*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
- rinvsq = rinv11*rinv11;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
- fscal = (qq*(rinv11-2.0*krsq)+br*Vvdwexp-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv12*rinv12;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq12;
- vcoul = qq*(rinv12+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv12-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx12;
- ty = fscal*dy12;
- tz = fscal*dz12;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv13*rinv13;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq13;
- vcoul = qq*(rinv13+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv13-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx13;
- ty = fscal*dy13;
- tz = fscal*dz13;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv21-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv22*rinv22;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq22;
- vcoul = qq*(rinv22+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv22-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv23*rinv23;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq23;
- vcoul = qq*(rinv23+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv23-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv31*rinv31;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv31-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv32*rinv32;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq32;
- vcoul = qq*(rinv32+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv32-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv33*rinv33;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq33;
- vcoul = qq*(rinv33+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv33-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Inner loop uses 325 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 29 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel222nf
- * Coulomb interaction: Reaction field
- * VdW interaction: Buckingham
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: no
- */
-void nb_kernel222nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real krsq;
- real Vvdwexp,br;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
- tj = 3*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
- rinvsq = rinv11*rinv11;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq12;
- vcoul = qq*(rinv12+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq13;
- vcoul = qq*(rinv13+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq22;
- vcoul = qq*(rinv22+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq23;
- vcoul = qq*(rinv23+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq32;
- vcoul = qq*(rinv32+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq33;
- vcoul = qq*(rinv33+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Inner loop uses 197 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 11 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL222_H_
-#define _NBKERNEL222_H_
-
-/*! \file nb_kernel222.h
- * \brief Nonbonded kernel 222 (RF Coul + Bham, SPC-SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 222 with forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel222
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 222 without forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel222nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL222_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel223.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel223
- * Coulomb interaction: Reaction field
- * VdW interaction: Buckingham
- * water optimization: TIP4P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel223(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real krsq;
- real Vvdwexp,br;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
- nti = 3*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- tj = nti+3*type[jnr];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
- rinvsq = rinv11*rinv11;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
- fscal = (br*Vvdwexp-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv21-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- rinvsq = rinv31*rinv31;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv31-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qM*jq;
- rinvsq = rinv41*rinv41;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq41;
- vcoul = qq*(rinv41+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv41-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx41;
- ty = fscal*dy41;
- tz = fscal*dz41;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 159 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 38 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel223nf
- * Coulomb interaction: Reaction field
- * VdW interaction: Buckingham
- * water optimization: TIP4P - other atoms
- * Calculate forces: no
- */
-void nb_kernel223nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real krsq;
- real Vvdwexp,br;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
- nti = 3*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- tj = nti+3*type[jnr];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
- rinvsq = rinv11*rinv11;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qM*jq;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq41;
- vcoul = qq*(rinv41+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Inner loop uses 104 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 14 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL223_H_
-#define _NBKERNEL223_H_
-
-/*! \file nb_kernel223.h
- * \brief Nonbonded kernel 223 (RF Coul + Bham, TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 223 with forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel223
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 223 without forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel223nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL223_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel224.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel224
- * Coulomb interaction: Reaction field
- * VdW interaction: Buckingham
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: yes
- */
-void nb_kernel224(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real krsq;
- real Vvdwexp,br;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real jx4,jy4,jz4,fjx4,fjy4,fjz4;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
- tj = 3*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
- rinvsq = rinv11*rinv11;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
- fscal = (br*Vvdwexp-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv22*rinv22;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq22;
- vcoul = qq*(rinv22+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv22-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv23*rinv23;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq23;
- vcoul = qq*(rinv23+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv23-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv24*rinv24;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq24;
- vcoul = qq*(rinv24+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv24-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx24;
- ty = fscal*dy24;
- tz = fscal*dz24;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx4 = faction[j3+9] - tx;
- fjy4 = faction[j3+10] - ty;
- fjz4 = faction[j3+11] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv32*rinv32;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq32;
- vcoul = qq*(rinv32+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv32-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv33*rinv33;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq33;
- vcoul = qq*(rinv33+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv33-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv34*rinv34;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq34;
- vcoul = qq*(rinv34+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv34-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx34;
- ty = fscal*dy34;
- tz = fscal*dz34;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx4 = fjx4 - tx;
- fjy4 = fjy4 - ty;
- fjz4 = fjz4 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv42*rinv42;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq42;
- vcoul = qq*(rinv42+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv42-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx42;
- ty = fscal*dy42;
- tz = fscal*dz42;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv43*rinv43;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq43;
- vcoul = qq*(rinv43+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv43-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx43;
- ty = fscal*dy43;
- tz = fscal*dz43;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMM;
- rinvsq = rinv44*rinv44;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq44;
- vcoul = qq*(rinv44+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv44-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx44;
- ty = fscal*dy44;
- tz = fscal*dz44;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+9] = fjx4 - tx;
- faction[j3+10] = fjy4 - ty;
- faction[j3+11] = fjz4 - tz;
-
- /* Inner loop uses 349 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 38 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel224nf
- * Coulomb interaction: Reaction field
- * VdW interaction: Buckingham
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: no
- */
-void nb_kernel224nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real krsq;
- real Vvdwexp,br;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real jx4,jy4,jz4;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
- tj = 3*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
- rinvsq = rinv11*rinv11;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq22;
- vcoul = qq*(rinv22+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq23;
- vcoul = qq*(rinv23+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq24;
- vcoul = qq*(rinv24+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq32;
- vcoul = qq*(rinv32+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq33;
- vcoul = qq*(rinv33+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq34;
- vcoul = qq*(rinv34+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq42;
- vcoul = qq*(rinv42+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq43;
- vcoul = qq*(rinv43+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMM;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq44;
- vcoul = qq*(rinv44+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Inner loop uses 210 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 14 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL224_H_
-#define _NBKERNEL224_H_
-
-/*! \file nb_kernel224.h
- * \brief Nonbonded kernel 224 (RF Coul + Bham, TIP4p-TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 224 with forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel224
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 224 without forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel224nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL224_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel230.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel230
- * Coulomb interaction: Reaction field
- * VdW interaction: Tabulated
- * water optimization: No
- * Calculate forces: yes
- */
-void nb_kernel230(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijD,fijR;
- real krsq;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- nti = 2*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
- rinvsq = rinv11*rinv11;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw6 = c6*VV;
- fijD = c6*FF;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw12 = c12*VV;
- fijR = c12*FF;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
- fscal = (qq*(rinv11-2.0*krsq))*rinvsq-((fijD+fijR)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Inner loop uses 65 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- fshift[is3] = fshift[is3]+fix1;
- fshift[is3+1] = fshift[is3+1]+fiy1;
- fshift[is3+2] = fshift[is3+2]+fiz1;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 12 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel230nf
- * Coulomb interaction: Reaction field
- * VdW interaction: Tabulated
- * water optimization: No
- * Calculate forces: no
- */
-void nb_kernel230nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real krsq;
- real ix1,iy1,iz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- nti = 2*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw6 = c6*VV;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw12 = c12*VV;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
-
- /* Inner loop uses 39 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 6 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL230_H_
-#define _NBKERNEL230_H_
-
-/*! \file nb_kernel230.h
- * \brief Nonbonded kernel 230 (RF Coul + Tab VdW)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 230 with forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel230
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 230 without forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel230nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL230_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel231.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel231
- * Coulomb interaction: Reaction field
- * VdW interaction: Tabulated
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel231(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijD,fijR;
- real krsq;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
- rinvsq = rinv11*rinv11;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw6 = c6*VV;
- fijD = c6*FF;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw12 = c12*VV;
- fijR = c12*FF;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
- fscal = (qq*(rinv11-2.0*krsq))*rinvsq-((fijD+fijR)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qH*jq;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv21-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- rinvsq = rinv31*rinv31;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv31-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 130 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 29 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel231nf
- * Coulomb interaction: Reaction field
- * VdW interaction: Tabulated
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: no
- */
-void nb_kernel231nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real krsq;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw6 = c6*VV;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw12 = c12*VV;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
-
- /* Load parameters for j atom */
- qq = qH*jq;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Inner loop uses 76 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 11 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL231_H_
-#define _NBKERNEL231_H_
-
-/*! \file nb_kernel231.h
- * \brief Nonbonded kernel 231 (RF Coul + Tab VdW, SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 231 with forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel231
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 231 without forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel231nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL231_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel232.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel232
- * Coulomb interaction: Reaction field
- * VdW interaction: Tabulated
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: yes
- */
-void nb_kernel232(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijD,fijR;
- real krsq;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
- rinvsq = rinv11*rinv11;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw6 = c6*VV;
- fijD = c6*FF;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw12 = c12*VV;
- fijR = c12*FF;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
- fscal = (qq*(rinv11-2.0*krsq))*rinvsq-((fijD+fijR)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv12*rinv12;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq12;
- vcoul = qq*(rinv12+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv12-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx12;
- ty = fscal*dy12;
- tz = fscal*dz12;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv13*rinv13;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq13;
- vcoul = qq*(rinv13+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv13-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx13;
- ty = fscal*dy13;
- tz = fscal*dz13;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv21-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv22*rinv22;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq22;
- vcoul = qq*(rinv22+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv22-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv23*rinv23;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq23;
- vcoul = qq*(rinv23+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv23-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
- rinvsq = rinv31*rinv31;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv31-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv32*rinv32;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq32;
- vcoul = qq*(rinv32+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv32-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv33*rinv33;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq33;
- vcoul = qq*(rinv33+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv33-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Inner loop uses 320 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 29 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel232nf
- * Coulomb interaction: Reaction field
- * VdW interaction: Tabulated
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: no
- */
-void nb_kernel232nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real qq,vcoul,vctot;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real krsq;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq11;
- vcoul = qq*(rinv11+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw6 = c6*VV;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw12 = c12*VV;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq12;
- vcoul = qq*(rinv12+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq13;
- vcoul = qq*(rinv13+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq22;
- vcoul = qq*(rinv22+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq23;
- vcoul = qq*(rinv23+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq32;
- vcoul = qq*(rinv32+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq33;
- vcoul = qq*(rinv33+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Inner loop uses 182 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 11 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL232_H_
-#define _NBKERNEL232_H_
-
-/*! \file nb_kernel232.h
- * \brief Nonbonded kernel 232 (RF Coul + Tab VdW, SPC-SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 232 with forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel232
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 232 without forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel232nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL232_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel233.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel233
- * Coulomb interaction: Reaction field
- * VdW interaction: Tabulated
- * water optimization: TIP4P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel233(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijD,fijR;
- real krsq;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw6 = c6*VV;
- fijD = c6*FF;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw12 = c12*VV;
- fijR = c12*FF;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
- fscal = -((fijD+fijR)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
- rinvsq = rinv21*rinv21;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv21-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- rinvsq = rinv31*rinv31;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv31-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qM*jq;
- rinvsq = rinv41*rinv41;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq41;
- vcoul = qq*(rinv41+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv41-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx41;
- ty = fscal*dy41;
- tz = fscal*dz41;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 152 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 38 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel233nf
- * Coulomb interaction: Reaction field
- * VdW interaction: Tabulated
- * water optimization: TIP4P - other atoms
- * Calculate forces: no
- */
-void nb_kernel233nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real krsq;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw6 = c6*VV;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw12 = c12*VV;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq21;
- vcoul = qq*(rinv21+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq31;
- vcoul = qq*(rinv31+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qM*jq;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq41;
- vcoul = qq*(rinv41+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Inner loop uses 89 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 14 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL233_H_
-#define _NBKERNEL233_H_
-
-/*! \file nb_kernel233.h
- * \brief Nonbonded kernel 233 (RF Coul + Tab VdW, TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 233 with forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel233
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 233 without forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel233nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL233_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel234.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel234
- * Coulomb interaction: Reaction field
- * VdW interaction: Tabulated
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: yes
- */
-void nb_kernel234(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijD,fijR;
- real krsq;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real jx4,jy4,jz4,fjx4,fjy4,fjz4;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw6 = c6*VV;
- fijD = c6*FF;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw12 = c12*VV;
- fijR = c12*FF;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
- fscal = -((fijD+fijR)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv22*rinv22;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq22;
- vcoul = qq*(rinv22+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv22-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv23*rinv23;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq23;
- vcoul = qq*(rinv23+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv23-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv24*rinv24;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq24;
- vcoul = qq*(rinv24+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv24-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx24;
- ty = fscal*dy24;
- tz = fscal*dz24;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx4 = faction[j3+9] - tx;
- fjy4 = faction[j3+10] - ty;
- fjz4 = faction[j3+11] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv32*rinv32;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq32;
- vcoul = qq*(rinv32+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv32-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
- rinvsq = rinv33*rinv33;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq33;
- vcoul = qq*(rinv33+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv33-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv34*rinv34;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq34;
- vcoul = qq*(rinv34+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv34-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx34;
- ty = fscal*dy34;
- tz = fscal*dz34;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx4 = fjx4 - tx;
- fjy4 = fjy4 - ty;
- fjz4 = fjz4 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv42*rinv42;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq42;
- vcoul = qq*(rinv42+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv42-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx42;
- ty = fscal*dy42;
- tz = fscal*dz42;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
- rinvsq = rinv43*rinv43;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq43;
- vcoul = qq*(rinv43+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv43-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx43;
- ty = fscal*dy43;
- tz = fscal*dz43;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMM;
- rinvsq = rinv44*rinv44;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq44;
- vcoul = qq*(rinv44+krsq-crf);
- vctot = vctot+vcoul;
- fscal = (qq*(rinv44-2.0*krsq))*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx44;
- ty = fscal*dy44;
- tz = fscal*dz44;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+9] = fjx4 - tx;
- faction[j3+10] = fjy4 - ty;
- faction[j3+11] = fjz4 - tz;
-
- /* Inner loop uses 342 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 38 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel234nf
- * Coulomb interaction: Reaction field
- * VdW interaction: Tabulated
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: no
- */
-void nb_kernel234nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real qq,vcoul,vctot;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real krsq;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real jx4,jy4,jz4;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw6 = c6*VV;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw12 = c12*VV;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq22;
- vcoul = qq*(rinv22+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq23;
- vcoul = qq*(rinv23+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq24;
- vcoul = qq*(rinv24+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq32;
- vcoul = qq*(rinv32+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq33;
- vcoul = qq*(rinv33+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq34;
- vcoul = qq*(rinv34+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq42;
- vcoul = qq*(rinv42+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq43;
- vcoul = qq*(rinv43+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Load parameters for j atom */
- qq = qqMM;
-
- /* Coulomb reaction-field interaction */
- krsq = krf*rsq44;
- vcoul = qq*(rinv44+krsq-crf);
- vctot = vctot+vcoul;
-
- /* Inner loop uses 195 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 14 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL234_H_
-#define _NBKERNEL234_H_
-
-/*! \file nb_kernel234.h
- * \brief Nonbonded kernel 234 (RF Coul + Tab VdW, TIP4p-TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 234 with forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel234
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 234 without forces.
- *
- * <b>Coulomb interaction:</b> Reaction-Field <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel234nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL234_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel300.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel300
- * Coulomb interaction: Tabulated
- * VdW interaction: Not calculated
- * water optimization: No
- * Calculate forces: yes
- */
-void nb_kernel300(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real iq;
- real qq,vcoul,vctot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Inner loop uses 42 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- fshift[is3] = fshift[is3]+fix1;
- fshift[is3+1] = fshift[is3+1]+fiy1;
- fshift[is3+2] = fshift[is3+2]+fiz1;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 11 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel300nf
- * Coulomb interaction: Tabulated
- * VdW interaction: Not calculated
- * water optimization: No
- * Calculate forces: no
- */
-void nb_kernel300nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real iq;
- real qq,vcoul,vctot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real ix1,iy1,iz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Inner loop uses 26 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 5 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL300_H_
-#define _NBKERNEL300_H_
-
-/*! \file nb_kernel300.h
- * \brief Nonbonded kernel 300 (Tab Coul)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 300 with forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel300
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 300 without forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel300nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL300_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel301.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel301
- * Coulomb interaction: Tabulated
- * VdW interaction: Not calculated
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel301(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real jq;
- real qq,vcoul,vctot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qH*jq;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv21;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv31;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 125 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 28 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel301nf
- * Coulomb interaction: Tabulated
- * VdW interaction: Not calculated
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: no
- */
-void nb_kernel301nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real jq;
- real qq,vcoul,vctot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qH*jq;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Inner loop uses 77 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 10 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL301_H_
-#define _NBKERNEL301_H_
-
-/*! \file nb_kernel301.h
- * \brief Nonbonded kernel 301 (Tab Coul, SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 301 with forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel301
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 301 without forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel301nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL301_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel302.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel302
- * Coulomb interaction: Tabulated
- * VdW interaction: Not calculated
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: yes
- */
-void nb_kernel302(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real qq,vcoul,vctot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq12*rinv12;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv12;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx12;
- ty = fscal*dy12;
- tz = fscal*dz12;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq13*rinv13;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv13;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx13;
- ty = fscal*dy13;
- tz = fscal*dz13;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv21;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq22*rinv22;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv22;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq23*rinv23;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv23;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv31;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq32*rinv32;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv32;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq33*rinv33;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv33;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Inner loop uses 369 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 28 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel302nf
- * Coulomb interaction: Tabulated
- * VdW interaction: Not calculated
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: no
- */
-void nb_kernel302nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real qq,vcoul,vctot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq12*rinv12;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq13*rinv13;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq22*rinv22;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq23*rinv23;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq32*rinv32;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq33*rinv33;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Inner loop uses 225 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 10 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL302_H_
-#define _NBKERNEL302_H_
-
-/*! \file nb_kernel302.h
- * \brief Nonbonded kernel 302 (Tab Coul, SPC-SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 302 with forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel302
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 302 without forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel302nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL302_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel303.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel303
- * Coulomb interaction: Tabulated
- * VdW interaction: Not calculated
- * water optimization: TIP4P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel303(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real jq;
- real qq,vcoul,vctot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv21;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv31;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qM*jq;
-
- /* Calculate table index */
- r = rsq41*rinv41;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv41;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx41;
- ty = fscal*dy41;
- tz = fscal*dz41;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 125 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 28 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel303nf
- * Coulomb interaction: Tabulated
- * VdW interaction: Not calculated
- * water optimization: TIP4P - other atoms
- * Calculate forces: no
- */
-void nb_kernel303nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real jq;
- real qq,vcoul,vctot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx1,jy1,jz1;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qM*jq;
-
- /* Calculate table index */
- r = rsq41*rinv41;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Inner loop uses 77 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 10 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL303_H_
-#define _NBKERNEL303_H_
-
-/*! \file nb_kernel303.h
- * \brief Nonbonded kernel 303 (Tab Coul, TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 303 with forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel303
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 303 without forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel303nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL303_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel304.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel304
- * Coulomb interaction: Tabulated
- * VdW interaction: Not calculated
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: yes
- */
-void nb_kernel304(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real qq,vcoul,vctot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real jx4,jy4,jz4,fjx4,fjy4,fjz4;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq22*rinv22;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv22;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq23*rinv23;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv23;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq24*rinv24;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv24;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx24;
- ty = fscal*dy24;
- tz = fscal*dz24;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx4 = faction[j3+9] - tx;
- fjy4 = faction[j3+10] - ty;
- fjz4 = faction[j3+11] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq32*rinv32;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv32;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq33*rinv33;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv33;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq34*rinv34;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv34;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx34;
- ty = fscal*dy34;
- tz = fscal*dz34;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx4 = fjx4 - tx;
- fjy4 = fjy4 - ty;
- fjz4 = fjz4 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq42*rinv42;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv42;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx42;
- ty = fscal*dy42;
- tz = fscal*dz42;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq43*rinv43;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv43;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx43;
- ty = fscal*dy43;
- tz = fscal*dz43;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMM;
-
- /* Calculate table index */
- r = rsq44*rinv44;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv44;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx44;
- ty = fscal*dy44;
- tz = fscal*dz44;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+9] = fjx4 - tx;
- faction[j3+10] = fjy4 - ty;
- faction[j3+11] = fjz4 - tz;
-
- /* Inner loop uses 369 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 28 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel304nf
- * Coulomb interaction: Tabulated
- * VdW interaction: Not calculated
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: no
- */
-void nb_kernel304nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real qq,vcoul,vctot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real jx4,jy4,jz4;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq22*rinv22;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq23*rinv23;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq24*rinv24;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq32*rinv32;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq33*rinv33;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq34*rinv34;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq42*rinv42;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq43*rinv43;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqMM;
-
- /* Calculate table index */
- r = rsq44*rinv44;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Inner loop uses 225 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 10 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL304_H_
-#define _NBKERNEL304_H_
-
-/*! \file nb_kernel304.h
- * \brief Nonbonded kernel 304 (Tab Coul, TIP4p-TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 304 with forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel304
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 304 without forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel304nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL304_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel310.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel310
- * Coulomb interaction: Tabulated
- * VdW interaction: Lennard-Jones
- * water optimization: No
- * Calculate forces: yes
- */
-void nb_kernel310(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- nti = 2*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
- rinvsq = rinv11*rinv11;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
- fscal = (12.0*Vvdw12-6.0*Vvdw6)*rinvsq-((fijC)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Inner loop uses 55 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- fshift[is3] = fshift[is3]+fix1;
- fshift[is3+1] = fshift[is3+1]+fiy1;
- fshift[is3+2] = fshift[is3+2]+fiz1;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 12 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel310nf
- * Coulomb interaction: Tabulated
- * VdW interaction: Lennard-Jones
- * water optimization: No
- * Calculate forces: no
- */
-void nb_kernel310nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real ix1,iy1,iz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- nti = 2*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
- rinvsq = rinv11*rinv11;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
-
- /* Inner loop uses 34 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 6 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL310_H_
-#define _NBKERNEL310_H_
-
-/*! \file nb_kernel310.h
- * \brief Nonbonded kernel 310 (Tab Coul + LJ)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 310 with forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel310
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 310 without forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel310nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL310_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel311.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel311
- * Coulomb interaction: Tabulated
- * VdW interaction: Lennard-Jones
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel311(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
- rinvsq = rinv11*rinv11;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
- fscal = (12.0*Vvdw12-6.0*Vvdw6)*rinvsq-((fijC)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qH*jq;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv21;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv31;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 138 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 29 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel311nf
- * Coulomb interaction: Tabulated
- * VdW interaction: Lennard-Jones
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: no
- */
-void nb_kernel311nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
- rinvsq = rinv11*rinv11;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
-
- /* Load parameters for j atom */
- qq = qH*jq;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Inner loop uses 85 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 11 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL311_H_
-#define _NBKERNEL311_H_
-
-/*! \file nb_kernel311.h
- * \brief Nonbonded kernel 311 (Tab Coul + LJ, SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 311 with forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel311
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 311 without forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel311nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL311_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel312.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel312
- * Coulomb interaction: Tabulated
- * VdW interaction: Lennard-Jones
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: yes
- */
-void nb_kernel312(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
- rinvsq = rinv11*rinv11;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
- fscal = (12.0*Vvdw12-6.0*Vvdw6)*rinvsq-((fijC)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq12*rinv12;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv12;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx12;
- ty = fscal*dy12;
- tz = fscal*dz12;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq13*rinv13;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv13;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx13;
- ty = fscal*dy13;
- tz = fscal*dz13;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv21;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq22*rinv22;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv22;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq23*rinv23;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv23;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv31;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq32*rinv32;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv32;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq33*rinv33;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv33;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Inner loop uses 382 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 29 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel312nf
- * Coulomb interaction: Tabulated
- * VdW interaction: Lennard-Jones
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: no
- */
-void nb_kernel312nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
- rinvsq = rinv11*rinv11;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq12*rinv12;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq13*rinv13;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq22*rinv22;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq23*rinv23;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq32*rinv32;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq33*rinv33;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Inner loop uses 233 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 11 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL312_H_
-#define _NBKERNEL312_H_
-
-/*! \file nb_kernel312.h
- * \brief Nonbonded kernel 312 (Tab Coul + LJ, SPC-SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C"
-{
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 312 with forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel312
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 312 without forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel312nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL312_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel313.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel313
- * Coulomb interaction: Tabulated
- * VdW interaction: Lennard-Jones
- * water optimization: TIP4P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel313(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx11,dy11,dz11,rsq11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinvsq = 1.0/rsq11;
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
- fscal = (12.0*Vvdw12-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv21;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv31;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qM*jq;
-
- /* Calculate table index */
- r = rsq41*rinv41;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv41;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx41;
- ty = fscal*dy41;
- tz = fscal*dz41;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 158 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 38 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel313nf
- * Coulomb interaction: Tabulated
- * VdW interaction: Lennard-Jones
- * water optimization: TIP4P - other atoms
- * Calculate forces: no
- */
-void nb_kernel313nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinvsq = 1.0/rsq11;
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qM*jq;
-
- /* Calculate table index */
- r = rsq41*rinv41;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Inner loop uses 96 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 14 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL313_H_
-#define _NBKERNEL313_H_
-
-/*! \file nb_kernel313.h
- * \brief Nonbonded kernel 313 (Tab Coul + LJ, TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 313 with forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel313
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 313 without forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel313nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL313_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel314.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel314
- * Coulomb interaction: Tabulated
- * VdW interaction: Lennard-Jones
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: yes
- */
-void nb_kernel314(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real jx4,jy4,jz4,fjx4,fjy4,fjz4;
- real dx11,dy11,dz11,rsq11;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinvsq = 1.0/rsq11;
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
- fscal = (12.0*Vvdw12-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq22*rinv22;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv22;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq23*rinv23;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv23;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq24*rinv24;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv24;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx24;
- ty = fscal*dy24;
- tz = fscal*dz24;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx4 = faction[j3+9] - tx;
- fjy4 = faction[j3+10] - ty;
- fjz4 = faction[j3+11] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq32*rinv32;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv32;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq33*rinv33;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv33;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq34*rinv34;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv34;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx34;
- ty = fscal*dy34;
- tz = fscal*dz34;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx4 = fjx4 - tx;
- fjy4 = fjy4 - ty;
- fjz4 = fjz4 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq42*rinv42;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv42;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx42;
- ty = fscal*dy42;
- tz = fscal*dz42;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq43*rinv43;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv43;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx43;
- ty = fscal*dy43;
- tz = fscal*dz43;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMM;
-
- /* Calculate table index */
- r = rsq44*rinv44;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv44;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx44;
- ty = fscal*dy44;
- tz = fscal*dz44;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+9] = fjx4 - tx;
- faction[j3+10] = fjy4 - ty;
- faction[j3+11] = fjz4 - tz;
-
- /* Inner loop uses 402 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 38 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel314nf
- * Coulomb interaction: Tabulated
- * VdW interaction: Lennard-Jones
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: no
- */
-void nb_kernel314nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real jx4,jy4,jz4;
- real dx11,dy11,dz11,rsq11;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinvsq = 1.0/rsq11;
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq22*rinv22;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq23*rinv23;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq24*rinv24;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq32*rinv32;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq33*rinv33;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq34*rinv34;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq42*rinv42;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq43*rinv43;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqMM;
-
- /* Calculate table index */
- r = rsq44*rinv44;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Inner loop uses 244 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 14 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL314_H_
-#define _NBKERNEL314_H_
-
-/*! \file nb_kernel314.h
- * \brief Nonbonded kernel 314 (Tab Coul + LJ, TIP4p-TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 314 with forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel314
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 314 without forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel314nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL314_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel320.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel320
- * Coulomb interaction: Tabulated
- * VdW interaction: Buckingham
- * water optimization: No
- * Calculate forces: yes
- */
-void nb_kernel320(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real Vvdwexp,br;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- nti = 3*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
- tj = nti+3*type[jnr];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
- rinvsq = rinv11*rinv11;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
- fscal = (br*Vvdwexp-6.0*Vvdw6)*rinvsq-((fijC)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Inner loop uses 81 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- fshift[is3] = fshift[is3]+fix1;
- fshift[is3+1] = fshift[is3+1]+fiy1;
- fshift[is3+2] = fshift[is3+2]+fiz1;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 12 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel320nf
- * Coulomb interaction: Tabulated
- * VdW interaction: Buckingham
- * water optimization: No
- * Calculate forces: no
- */
-void nb_kernel320nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real Vvdwexp,br;
- real ix1,iy1,iz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- nti = 3*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
- tj = nti+3*type[jnr];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
- rinvsq = rinv11*rinv11;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
-
- /* Inner loop uses 61 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 6 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL320_H_
-#define _NBKERNEL320_H_
-
-/*! \file nb_kernel320.h
- * \brief Nonbonded kernel 320 (Tab Coul + Bham)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 320 with forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel320
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 320 without forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel320nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL320_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel321.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel321
- * Coulomb interaction: Tabulated
- * VdW interaction: Buckingham
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel321(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real Vvdwexp,br;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
- nti = 3*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
- tj = nti+3*type[jnr];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
- rinvsq = rinv11*rinv11;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
- fscal = (br*Vvdwexp-6.0*Vvdw6)*rinvsq-((fijC)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qH*jq;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv21;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv31;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 164 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 29 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel321nf
- * Coulomb interaction: Tabulated
- * VdW interaction: Buckingham
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: no
- */
-void nb_kernel321nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real Vvdwexp,br;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
- nti = 3*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
- tj = nti+3*type[jnr];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
- rinvsq = rinv11*rinv11;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
-
- /* Load parameters for j atom */
- qq = qH*jq;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Inner loop uses 112 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 11 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL321_H_
-#define _NBKERNEL321_H_
-
-/*! \file nb_kernel321.h
- * \brief Nonbonded kernel 321 (Tab Coul + Bham, SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 321 with forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel321
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 321 without forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel321nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL321_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel322.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel322
- * Coulomb interaction: Tabulated
- * VdW interaction: Buckingham
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: yes
- */
-void nb_kernel322(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real Vvdwexp,br;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
- tj = 3*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
- rinvsq = rinv11*rinv11;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
- fscal = (br*Vvdwexp-6.0*Vvdw6)*rinvsq-((fijC)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq12*rinv12;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv12;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx12;
- ty = fscal*dy12;
- tz = fscal*dz12;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq13*rinv13;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv13;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx13;
- ty = fscal*dy13;
- tz = fscal*dz13;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv21;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq22*rinv22;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv22;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq23*rinv23;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv23;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv31;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq32*rinv32;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv32;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq33*rinv33;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv33;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Inner loop uses 408 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 29 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel322nf
- * Coulomb interaction: Tabulated
- * VdW interaction: Buckingham
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: no
- */
-void nb_kernel322nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real Vvdwexp,br;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
- tj = 3*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
- rinvsq = rinv11*rinv11;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq12*rinv12;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq13*rinv13;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq22*rinv22;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq23*rinv23;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq32*rinv32;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq33*rinv33;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Inner loop uses 260 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 11 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL322_H_
-#define _NBKERNEL322_H_
-
-/*! \file nb_kernel322.h
- * \brief Nonbonded kernel 322 (Tab Coul + Bham, SPC-SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 322 with forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel322
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 322 without forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel322nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL322_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel323.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel323
- * Coulomb interaction: Tabulated
- * VdW interaction: Buckingham
- * water optimization: TIP4P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel323(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real Vvdwexp,br;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
- nti = 3*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- tj = nti+3*type[jnr];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
- rinvsq = rinv11*rinv11;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
- fscal = (br*Vvdwexp-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv21;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv31;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qM*jq;
-
- /* Calculate table index */
- r = rsq41*rinv41;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv41;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx41;
- ty = fscal*dy41;
- tz = fscal*dz41;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 186 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 38 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel323nf
- * Coulomb interaction: Tabulated
- * VdW interaction: Buckingham
- * water optimization: TIP4P - other atoms
- * Calculate forces: no
- */
-void nb_kernel323nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real Vvdwexp,br;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
- nti = 3*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- tj = nti+3*type[jnr];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
- rinvsq = rinv11*rinv11;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qM*jq;
-
- /* Calculate table index */
- r = rsq41*rinv41;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Inner loop uses 125 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 14 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL323_H_
-#define _NBKERNEL323_H_
-
-/*! \file nb_kernel323.h
- * \brief Nonbonded kernel 323 (Tab Coul + Bham, TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 323 with forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel323
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 323 without forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel323nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL323_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel324.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel324
- * Coulomb interaction: Tabulated
- * VdW interaction: Buckingham
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: yes
- */
-void nb_kernel324(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real Vvdwexp,br;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real jx4,jy4,jz4,fjx4,fjy4,fjz4;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
- tj = 3*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
- rinvsq = rinv11*rinv11;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
- fscal = (br*Vvdwexp-6.0*Vvdw6)*rinvsq;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq22*rinv22;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv22;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq23*rinv23;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv23;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq24*rinv24;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv24;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx24;
- ty = fscal*dy24;
- tz = fscal*dz24;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx4 = faction[j3+9] - tx;
- fjy4 = faction[j3+10] - ty;
- fjz4 = faction[j3+11] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq32*rinv32;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv32;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq33*rinv33;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv33;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq34*rinv34;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv34;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx34;
- ty = fscal*dy34;
- tz = fscal*dz34;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx4 = fjx4 - tx;
- fjy4 = fjy4 - ty;
- fjz4 = fjz4 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq42*rinv42;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv42;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx42;
- ty = fscal*dy42;
- tz = fscal*dz42;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq43*rinv43;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv43;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx43;
- ty = fscal*dy43;
- tz = fscal*dz43;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMM;
-
- /* Calculate table index */
- r = rsq44*rinv44;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv44;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx44;
- ty = fscal*dy44;
- tz = fscal*dz44;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+9] = fjx4 - tx;
- faction[j3+10] = fjy4 - ty;
- faction[j3+11] = fjz4 - tz;
-
- /* Inner loop uses 430 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 38 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel324nf
- * Coulomb interaction: Tabulated
- * VdW interaction: Buckingham
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: no
- */
-void nb_kernel324nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real qq,vcoul,vctot;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real Vvdwexp,br;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real jx4,jy4,jz4;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
- tj = 3*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
- rinvsq = rinv11*rinv11;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq22*rinv22;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq23*rinv23;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq24*rinv24;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq32*rinv32;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq33*rinv33;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq34*rinv34;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq42*rinv42;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq43*rinv43;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqMM;
-
- /* Calculate table index */
- r = rsq44*rinv44;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Inner loop uses 273 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 14 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL324_H_
-#define _NBKERNEL324_H_
-
-/*! \file nb_kernel324.h
- * \brief Nonbonded kernel 324 (Tab Coul + Bham, TIP4p-TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 324 with forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel324
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 324 without forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel324nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL324_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel330.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel330
- * Coulomb interaction: Tabulated
- * VdW interaction: Tabulated
- * water optimization: No
- * Calculate forces: yes
- */
-void nb_kernel330(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real fijD,fijR;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- nti = 2*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
-
- /* Tabulated VdW interaction - dispersion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw6 = c6*VV;
- fijD = c6*FF;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw12 = c12*VV;
- fijR = c12*FF;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
- fscal = -((fijC+fijD+fijR)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Inner loop uses 68 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- fshift[is3] = fshift[is3]+fix1;
- fshift[is3+1] = fshift[is3+1]+fiy1;
- fshift[is3+2] = fshift[is3+2]+fiz1;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 12 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel330nf
- * Coulomb interaction: Tabulated
- * VdW interaction: Tabulated
- * water optimization: No
- * Calculate forces: no
- */
-void nb_kernel330nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real ix1,iy1,iz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- nti = 2*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- qq = iq*charge[jnr];
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Tabulated VdW interaction - dispersion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw6 = c6*VV;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw12 = c12*VV;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
-
- /* Inner loop uses 42 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 6 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL330_H_
-#define _NBKERNEL330_H_
-
-/*! \file nb_kernel330.h
- * \brief Nonbonded kernel 330 (Tab Coul + Tab VdW)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 330 with forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel330
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 330 without forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel330nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL330_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel331.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel331
- * Coulomb interaction: Tabulated
- * VdW interaction: Tabulated
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel331(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real fijD,fijR;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
-
- /* Tabulated VdW interaction - dispersion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw6 = c6*VV;
- fijD = c6*FF;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw12 = c12*VV;
- fijR = c12*FF;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
- fscal = -((fijC+fijD+fijR)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qH*jq;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv21;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv31;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 151 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 29 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel331nf
- * Coulomb interaction: Tabulated
- * VdW interaction: Tabulated
- * water optimization: SPC/TIP3P - other atoms
- * Calculate forces: no
- */
-void nb_kernel331nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real qO,qH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = facel*charge[ii];
- qH = facel*charge[ii+1];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qO*jq;
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Tabulated VdW interaction - dispersion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw6 = c6*VV;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw12 = c12*VV;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
-
- /* Load parameters for j atom */
- qq = qH*jq;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Inner loop uses 93 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 11 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL331_H_
-#define _NBKERNEL331_H_
-
-/*! \file nb_kernel331.h
- * \brief Nonbonded kernel 331 (Tab Coul + Tab VdW, SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 331 with forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel331
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 331 without forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> SPC - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel331nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL331_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel332.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel332
- * Coulomb interaction: Tabulated
- * VdW interaction: Tabulated
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: yes
- */
-void nb_kernel332(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real qq,vcoul,vctot;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real fijD,fijR;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
-
- /* Tabulated VdW interaction - dispersion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw6 = c6*VV;
- fijD = c6*FF;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw12 = c12*VV;
- fijR = c12*FF;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
- fscal = -((fijC+fijD+fijR)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq12*rinv12;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv12;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx12;
- ty = fscal*dy12;
- tz = fscal*dz12;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq13*rinv13;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv13;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx13;
- ty = fscal*dy13;
- tz = fscal*dz13;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv21;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq22*rinv22;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv22;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq23*rinv23;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv23;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv31;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq32*rinv32;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv32;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq33*rinv33;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv33;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Inner loop uses 395 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 29 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel332nf
- * Coulomb interaction: Tabulated
- * VdW interaction: Tabulated
- * water optimization: pairs of SPC/TIP3P interactions
- * Calculate forces: no
- */
-void nb_kernel332nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real qq,vcoul,vctot;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx12,dy12,dz12,rsq12,rinv12;
- real dx13,dy13,dz13,rsq13,rinv13;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real qO,qH,qqOO,qqOH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qO = charge[ii];
- qH = charge[ii+1];
- qqOO = facel*qO*qO;
- qqOH = facel*qO*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx12 = ix1 - jx2;
- dy12 = iy1 - jy2;
- dz12 = iz1 - jz2;
- rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
- dx13 = ix1 - jx3;
- dy13 = iy1 - jy3;
- dz13 = iz1 - jz3;
- rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv12 = gmx_invsqrt(rsq12);
- rinv13 = gmx_invsqrt(rsq13);
- rinv21 = gmx_invsqrt(rsq21);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv31 = gmx_invsqrt(rsq31);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
-
- /* Load parameters for j atom */
- qq = qqOO;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Tabulated VdW interaction - dispersion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw6 = c6*VV;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw12 = c12*VV;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq12*rinv12;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq13*rinv13;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq22*rinv22;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq23*rinv23;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqOH;
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq32*rinv32;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq33*rinv33;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Inner loop uses 241 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 11 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL332_H_
-#define _NBKERNEL332_H_
-
-/*! \file nb_kernel332.h
- * \brief Nonbonded kernel 332 (Tab Coul + Tab VdW, SPC-SPC)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 332 with forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel332
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 332 without forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> SPC - SPC <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel332nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL332_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel333.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel333
- * Coulomb interaction: Tabulated
- * VdW interaction: Tabulated
- * water optimization: TIP4P - other atoms
- * Calculate forces: yes
- */
-void nb_kernel333(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real fijD,fijR;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx1,jy1,jz1,fjx1,fjy1,fjz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated VdW interaction - dispersion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw6 = c6*VV;
- fijD = c6*FF;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw12 = c12*VV;
- fijR = c12*FF;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
- fscal = -((fijD+fijR)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- fjx1 = faction[j3+0] - tx;
- fjy1 = faction[j3+1] - ty;
- fjz1 = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv21;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx21;
- ty = fscal*dy21;
- tz = fscal*dz21;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv31;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx31;
- ty = fscal*dy31;
- tz = fscal*dz31;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx1 = fjx1 - tx;
- fjy1 = fjy1 - ty;
- fjz1 = fjz1 - tz;
-
- /* Load parameters for j atom */
- qq = qM*jq;
-
- /* Calculate table index */
- r = rsq41*rinv41;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv41;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx41;
- ty = fscal*dy41;
- tz = fscal*dz41;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = fjx1 - tx;
- faction[j3+1] = fjy1 - ty;
- faction[j3+2] = fjz1 - tz;
-
- /* Inner loop uses 179 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 38 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel333nf
- * Coulomb interaction: Tabulated
- * VdW interaction: Tabulated
- * water optimization: TIP4P - other atoms
- * Calculate forces: no
- */
-void nb_kernel333nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real jq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx21,dy21,dz21,rsq21,rinv21;
- real dx31,dy31,dz31,rsq31,rinv31;
- real dx41,dy41,dz41,rsq41,rinv41;
- real qH,qM;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = facel*charge[ii+1];
- qM = facel*charge[ii+3];
- nti = 2*ntype*type[ii];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx21 = ix2 - jx1;
- dy21 = iy2 - jy1;
- dz21 = iz2 - jz1;
- rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
- dx31 = ix3 - jx1;
- dy31 = iy3 - jy1;
- dz31 = iz3 - jz1;
- rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
- dx41 = ix4 - jx1;
- dy41 = iy4 - jy1;
- dz41 = iz4 - jz1;
- rsq41 = dx41*dx41+dy41*dy41+dz41*dz41;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv21 = gmx_invsqrt(rsq21);
- rinv31 = gmx_invsqrt(rsq31);
- rinv41 = gmx_invsqrt(rsq41);
-
- /* Load parameters for j atom */
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated VdW interaction - dispersion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw6 = c6*VV;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw12 = c12*VV;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
-
- /* Load parameters for j atom */
- jq = charge[jnr+0];
- qq = qH*jq;
-
- /* Calculate table index */
- r = rsq21*rinv21;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
-
- /* Calculate table index */
- r = rsq31*rinv31;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qM*jq;
-
- /* Calculate table index */
- r = rsq41*rinv41;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Inner loop uses 110 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 14 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL333_H_
-#define _NBKERNEL333_H_
-
-/*! \file nb_kernel333.h
- * \brief Nonbonded kernel 333 (Tab Coul + Tab VdW, TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 333 with forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel333
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 333 without forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> TIP4p - other atoms <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel333nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL333_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-#include "nb_kernel334.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel334
- * Coulomb interaction: Tabulated
- * VdW interaction: Tabulated
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: yes
- */
-void nb_kernel334(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real qq,vcoul,vctot;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real fijD,fijR;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real ix2,iy2,iz2,fix2,fiy2,fiz2;
- real ix3,iy3,iz3,fix3,fiy3,fiz3;
- real ix4,iy4,iz4,fix4,fiy4,fiz4;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2,fjx2,fjy2,fjz2;
- real jx3,jy3,jz3,fjx3,fjy3,fjz3;
- real jx4,jy4,jz4,fjx4,fjy4,fjz4;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
- fix2 = 0;
- fiy2 = 0;
- fiz2 = 0;
- fix3 = 0;
- fiy3 = 0;
- fiz3 = 0;
- fix4 = 0;
- fiy4 = 0;
- fiz4 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated VdW interaction - dispersion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw6 = c6*VV;
- fijD = c6*FF;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw12 = c12*VV;
- fijR = c12*FF;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
- fscal = -((fijD+fijR)*tabscale)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq22*rinv22;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv22;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx22;
- ty = fscal*dy22;
- tz = fscal*dz22;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx2 = faction[j3+3] - tx;
- fjy2 = faction[j3+4] - ty;
- fjz2 = faction[j3+5] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq23*rinv23;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv23;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx23;
- ty = fscal*dy23;
- tz = fscal*dz23;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx3 = faction[j3+6] - tx;
- fjy3 = faction[j3+7] - ty;
- fjz3 = faction[j3+8] - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq24*rinv24;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv24;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx24;
- ty = fscal*dy24;
- tz = fscal*dz24;
-
- /* Increment i atom force */
- fix2 = fix2 + tx;
- fiy2 = fiy2 + ty;
- fiz2 = fiz2 + tz;
-
- /* Decrement j atom force */
- fjx4 = faction[j3+9] - tx;
- fjy4 = faction[j3+10] - ty;
- fjz4 = faction[j3+11] - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq32*rinv32;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv32;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx32;
- ty = fscal*dy32;
- tz = fscal*dz32;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx2 = fjx2 - tx;
- fjy2 = fjy2 - ty;
- fjz2 = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq33*rinv33;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv33;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx33;
- ty = fscal*dy33;
- tz = fscal*dz33;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx3 = fjx3 - tx;
- fjy3 = fjy3 - ty;
- fjz3 = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq34*rinv34;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv34;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx34;
- ty = fscal*dy34;
- tz = fscal*dz34;
-
- /* Increment i atom force */
- fix3 = fix3 + tx;
- fiy3 = fiy3 + ty;
- fiz3 = fiz3 + tz;
-
- /* Decrement j atom force */
- fjx4 = fjx4 - tx;
- fjy4 = fjy4 - ty;
- fjz4 = fjz4 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq42*rinv42;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv42;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx42;
- ty = fscal*dy42;
- tz = fscal*dz42;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+3] = fjx2 - tx;
- faction[j3+4] = fjy2 - ty;
- faction[j3+5] = fjz2 - tz;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq43*rinv43;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv43;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx43;
- ty = fscal*dy43;
- tz = fscal*dz43;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+6] = fjx3 - tx;
- faction[j3+7] = fjy3 - ty;
- faction[j3+8] = fjz3 - tz;
-
- /* Load parameters for j atom */
- qq = qqMM;
-
- /* Calculate table index */
- r = rsq44*rinv44;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vcoul = qq*VV;
- fijC = qq*FF;
- vctot = vctot + vcoul;
- fscal = -((fijC)*tabscale)*rinv44;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx44;
- ty = fscal*dy44;
- tz = fscal*dz44;
-
- /* Increment i atom force */
- fix4 = fix4 + tx;
- fiy4 = fiy4 + ty;
- fiz4 = fiz4 + tz;
-
- /* Decrement j atom force */
- faction[j3+9] = fjx4 - tx;
- faction[j3+10] = fjy4 - ty;
- faction[j3+11] = fjz4 - tz;
-
- /* Inner loop uses 423 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- faction[ii3+3] = faction[ii3+3] + fix2;
- faction[ii3+4] = faction[ii3+4] + fiy2;
- faction[ii3+5] = faction[ii3+5] + fiz2;
- faction[ii3+6] = faction[ii3+6] + fix3;
- faction[ii3+7] = faction[ii3+7] + fiy3;
- faction[ii3+8] = faction[ii3+8] + fiz3;
- faction[ii3+9] = faction[ii3+9] + fix4;
- faction[ii3+10] = faction[ii3+10] + fiy4;
- faction[ii3+11] = faction[ii3+11] + fiz4;
- fshift[is3] = fshift[is3]+fix1+fix2+fix3+fix4;
- fshift[is3+1] = fshift[is3+1]+fiy1+fiy2+fiy3+fiy4;
- fshift[is3+2] = fshift[is3+2]+fiz1+fiz2+fiz3+fiz4;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 38 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel334nf
- * Coulomb interaction: Tabulated
- * VdW interaction: Tabulated
- * water optimization: pairs of TIP4P interactions
- * Calculate forces: no
- */
-void nb_kernel334nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real qq,vcoul,vctot;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real ix1,iy1,iz1;
- real ix2,iy2,iz2;
- real ix3,iy3,iz3;
- real ix4,iy4,iz4;
- real jx1,jy1,jz1;
- real jx2,jy2,jz2;
- real jx3,jy3,jz3;
- real jx4,jy4,jz4;
- real dx11,dy11,dz11,rsq11,rinv11;
- real dx22,dy22,dz22,rsq22,rinv22;
- real dx23,dy23,dz23,rsq23,rinv23;
- real dx24,dy24,dz24,rsq24,rinv24;
- real dx32,dy32,dz32,rsq32,rinv32;
- real dx33,dy33,dz33,rsq33,rinv33;
- real dx34,dy34,dz34,rsq34,rinv34;
- real dx42,dy42,dz42,rsq42,rinv42;
- real dx43,dy43,dz43,rsq43,rinv43;
- real dx44,dy44,dz44,rsq44,rinv44;
- real qH,qM,qqMM,qqMH,qqHH;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
-
- /* Initialize water data */
- ii = iinr[0];
- qH = charge[ii+1];
- qM = charge[ii+3];
- qqMM = facel*qM*qM;
- qqMH = facel*qM*qH;
- qqHH = facel*qH*qH;
- tj = 2*(ntype+1)*type[ii];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
- ix2 = shX + pos[ii3+3];
- iy2 = shY + pos[ii3+4];
- iz2 = shZ + pos[ii3+5];
- ix3 = shX + pos[ii3+6];
- iy3 = shY + pos[ii3+7];
- iz3 = shZ + pos[ii3+8];
- ix4 = shX + pos[ii3+9];
- iy4 = shY + pos[ii3+10];
- iz4 = shZ + pos[ii3+11];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
- jx2 = pos[j3+3];
- jy2 = pos[j3+4];
- jz2 = pos[j3+5];
- jx3 = pos[j3+6];
- jy3 = pos[j3+7];
- jz3 = pos[j3+8];
- jx4 = pos[j3+9];
- jy4 = pos[j3+10];
- jz4 = pos[j3+11];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
- dx22 = ix2 - jx2;
- dy22 = iy2 - jy2;
- dz22 = iz2 - jz2;
- rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
- dx23 = ix2 - jx3;
- dy23 = iy2 - jy3;
- dz23 = iz2 - jz3;
- rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
- dx24 = ix2 - jx4;
- dy24 = iy2 - jy4;
- dz24 = iz2 - jz4;
- rsq24 = dx24*dx24+dy24*dy24+dz24*dz24;
- dx32 = ix3 - jx2;
- dy32 = iy3 - jy2;
- dz32 = iz3 - jz2;
- rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
- dx33 = ix3 - jx3;
- dy33 = iy3 - jy3;
- dz33 = iz3 - jz3;
- rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
- dx34 = ix3 - jx4;
- dy34 = iy3 - jy4;
- dz34 = iz3 - jz4;
- rsq34 = dx34*dx34+dy34*dy34+dz34*dz34;
- dx42 = ix4 - jx2;
- dy42 = iy4 - jy2;
- dz42 = iz4 - jz2;
- rsq42 = dx42*dx42+dy42*dy42+dz42*dz42;
- dx43 = ix4 - jx3;
- dy43 = iy4 - jy3;
- dz43 = iz4 - jz3;
- rsq43 = dx43*dx43+dy43*dy43+dz43*dz43;
- dx44 = ix4 - jx4;
- dy44 = iy4 - jy4;
- dz44 = iz4 - jz4;
- rsq44 = dx44*dx44+dy44*dy44+dz44*dz44;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
- rinv22 = gmx_invsqrt(rsq22);
- rinv23 = gmx_invsqrt(rsq23);
- rinv24 = gmx_invsqrt(rsq24);
- rinv32 = gmx_invsqrt(rsq32);
- rinv33 = gmx_invsqrt(rsq33);
- rinv34 = gmx_invsqrt(rsq34);
- rinv42 = gmx_invsqrt(rsq42);
- rinv43 = gmx_invsqrt(rsq43);
- rinv44 = gmx_invsqrt(rsq44);
-
- /* Load parameters for j atom */
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated VdW interaction - dispersion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw6 = c6*VV;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw12 = c12*VV;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq22*rinv22;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq23*rinv23;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq24*rinv24;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq32*rinv32;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqHH;
-
- /* Calculate table index */
- r = rsq33*rinv33;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq34*rinv34;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq42*rinv42;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqMH;
-
- /* Calculate table index */
- r = rsq43*rinv43;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Load parameters for j atom */
- qq = qqMM;
-
- /* Calculate table index */
- r = rsq44*rinv44;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 12*n0;
-
- /* Tabulated coulomb interaction */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vcoul = qq*VV;
- vctot = vctot + vcoul;
-
- /* Inner loop uses 258 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 14 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL334_H_
-#define _NBKERNEL334_H_
-
-/*! \file nb_kernel334.h
- * \brief Nonbonded kernel 334 (Tab Coul + Tab VdW, TIP4p-TIP4p)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 334 with forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel334
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 334 without forces.
- *
- * <b>Coulomb interaction:</b> Tabulated <br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> TIP4p - TIP4p <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel334nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL334_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-/* get gmx_gbdata_t */
-#include "../nb_kerneltype.h"
-
-#include "nb_kernel400.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel400
- * Coulomb interaction: Generalized-Born
- * VdW interaction: Not calculated
- * water optimization: No
- * Calculate forces: yes
- */
-void nb_kernel400(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real iq;
- real qq,vcoul,vctot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real isai,isaj,isaprod,gbscale,vgb,vgbtot;
- real dvdasum,dvdatmp,dvdaj,fgb;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- gmx_gbdata_t *gbdata;
- real * gpol;
- real scale_gb;
-
- gbdata = (gmx_gbdata_t *)work;
- gpol = gbdata->gpol;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- scale_gb = (1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent);
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
- gbtabscale = *p_gbtabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- isai = invsqrta[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- vgbtot = 0;
- dvdasum = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- isaj = invsqrta[jnr];
- isaprod = isai*isaj;
- qq = iq*charge[jnr];
- vcoul = qq*rinv11;
- fscal = vcoul*rinv11;
- qq = isaprod*(-qq)*scale_gb;
- gbscale = isaprod*gbtabscale;
-
- /* Tabulated Generalized-Born interaction */
- dvdaj = dvda[jnr];
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*gbscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
- Y = GBtab[nnn];
- F = GBtab[nnn+1];
- Geps = eps*GBtab[nnn+2];
- Heps2 = eps2*GBtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vgb = qq*VV;
- fijC = qq*FF*gbscale;
- dvdatmp = -0.5*(vgb+fijC*r);
- dvdasum = dvdasum + dvdatmp;
- dvda[jnr] = dvdaj+dvdatmp*isaj*isaj;
- vctot = vctot + vcoul;
- vgbtot = vgbtot + vgb;
- fscal = -(fijC-fscal)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Inner loop uses 49 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- fshift[is3] = fshift[is3]+fix1;
- fshift[is3+1] = fshift[is3+1]+fiy1;
- fshift[is3+2] = fshift[is3+2]+fiz1;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- gpol[ggid] = gpol[ggid] + vgbtot;
- dvda[ii] = dvda[ii] + dvdasum*isai*isai;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 12 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel400nf
- * Coulomb interaction: Generalized-Born
- * VdW interaction: Not calculated
- * water optimization: No
- * Calculate forces: no
- */
-void nb_kernel400nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real iq;
- real qq,vcoul,vctot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real isai,isaj,isaprod,gbscale,vgb;
- real ix1,iy1,iz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
- gbtabscale = *p_gbtabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- isai = invsqrta[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- isaj = invsqrta[jnr];
- isaprod = isai*isaj;
- qq = iq*charge[jnr];
- vcoul = qq*rinv11;
- qq = isaprod*(-qq);
- gbscale = isaprod*gbtabscale;
-
- /* Tabulated Generalized-Born interaction */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*gbscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
- Y = GBtab[nnn];
- F = GBtab[nnn+1];
- Geps = eps*GBtab[nnn+2];
- Heps2 = eps2*GBtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vgb = qq*VV;
- vctot = vctot + vcoul;
-
- /* Inner loop uses 29 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 5 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL400_H_
-#define _NBKERNEL400_H_
-
-/*! \file nb_kernel400.h
- * \brief Nonbonded kernel 400 (GB Coul)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 400 with forces.
- *
- * <b>Coulomb interaction:</b> Generalized Born<br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel400
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 400 without forces.
- *
- * <b>Coulomb interaction:</b> Generalized Born<br>
- * <b>VdW interaction:</b> No <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel400nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL400_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-/* get gmx_gbdata_t */
-#include "../nb_kerneltype.h"
-
-#include "nb_kernel410.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel410
- * Coulomb interaction: Generalized-Born
- * VdW interaction: Lennard-Jones
- * water optimization: No
- * Calculate forces: yes
- */
-void nb_kernel410(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real isai,isaj,isaprod,gbscale,vgb,vgbtot;
- real dvdasum,dvdatmp,dvdaj,fgb;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,c12;
- gmx_gbdata_t *gbdata;
- real * gpol;
- real scale_gb;
-
- gbdata = (gmx_gbdata_t *)work;
- gpol = gbdata->gpol;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- scale_gb = (1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent);
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
- gbtabscale = *p_gbtabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- isai = invsqrta[ii];
- nti = 2*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
- vgbtot = 0;
- dvdasum = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- isaj = invsqrta[jnr];
- isaprod = isai*isaj;
- qq = iq*charge[jnr];
- vcoul = qq*rinv11;
- fscal = vcoul*rinv11;
- qq = isaprod*(-qq)*scale_gb;
- gbscale = isaprod*gbtabscale;
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
- rinvsq = rinv11*rinv11;
-
- /* Tabulated Generalized-Born interaction */
- dvdaj = dvda[jnr];
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*gbscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
- Y = GBtab[nnn];
- F = GBtab[nnn+1];
- Geps = eps*GBtab[nnn+2];
- Heps2 = eps2*GBtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vgb = qq*VV;
- fijC = qq*FF*gbscale;
- dvdatmp = -0.5*(vgb+fijC*r);
- dvdasum = dvdasum + dvdatmp;
- dvda[jnr] = dvdaj+dvdatmp*isaj*isaj;
- vctot = vctot + vcoul;
- vgbtot = vgbtot + vgb;
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
- fscal = (12.0*Vvdw12-6.0*Vvdw6)*rinvsq-(fijC-fscal)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Inner loop uses 62 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- fshift[is3] = fshift[is3]+fix1;
- fshift[is3+1] = fshift[is3+1]+fiy1;
- fshift[is3+2] = fshift[is3+2]+fiz1;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- gpol[ggid] = gpol[ggid] + vgbtot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
- dvda[ii] = dvda[ii] + dvdasum*isai*isai;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 13 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel410nf
- * Coulomb interaction: Generalized-Born
- * VdW interaction: Lennard-Jones
- * water optimization: No
- * Calculate forces: no
- */
-void nb_kernel410nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real isai,isaj,isaprod,gbscale,vgb;
- real ix1,iy1,iz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
- gbtabscale = *p_gbtabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- isai = invsqrta[ii];
- nti = 2*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- isaj = invsqrta[jnr];
- isaprod = isai*isaj;
- qq = iq*charge[jnr];
- vcoul = qq*rinv11;
- qq = isaprod*(-qq);
- gbscale = isaprod*gbtabscale;
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
- rinvsq = rinv11*rinv11;
-
- /* Tabulated Generalized-Born interaction */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*gbscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
- Y = GBtab[nnn];
- F = GBtab[nnn+1];
- Geps = eps*GBtab[nnn+2];
- Heps2 = eps2*GBtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vgb = qq*VV;
- vctot = vctot + vcoul;
-
- /* Lennard-Jones interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- Vvdw12 = c12*rinvsix*rinvsix;
- Vvdwtot = Vvdwtot+Vvdw12-Vvdw6;
-
- /* Inner loop uses 37 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 6 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL410_H_
-#define _NBKERNEL410_H_
-
-/*! \file nb_kernel410.h
- * \brief Nonbonded kernel 410 (GB Coul + LJ)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 410 with forces.
- *
- * <b>Coulomb interaction:</b> Generalized Born<br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel410
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 410 without forces.
- *
- * <b>Coulomb interaction:</b> Generalized Born<br>
- * <b>VdW interaction:</b> Lennard-Jones <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel410nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL410_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-/* get gmx_gbdata_t */
-#include "../nb_kerneltype.h"
-
-#include "nb_kernel420.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel420
- * Coulomb interaction: Generalized-Born
- * VdW interaction: Buckingham
- * water optimization: No
- * Calculate forces: yes
- */
-void nb_kernel420(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real rinvsq;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real isai,isaj,isaprod,gbscale,vgb;
- real dvdasum,dvdatmp,dvdaj,fgb;
- real Vvdwexp,br;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
- gbtabscale = *p_gbtabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- isai = invsqrta[ii];
- nti = 3*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
- dvdasum = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- isaj = invsqrta[jnr];
- isaprod = isai*isaj;
- qq = iq*charge[jnr];
- vcoul = qq*rinv11;
- fscal = vcoul*rinv11;
- qq = isaprod*(-qq);
- gbscale = isaprod*gbtabscale;
- tj = nti+3*type[jnr];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
- rinvsq = rinv11*rinv11;
-
- /* Tabulated Generalized-Born interaction */
- dvdaj = dvda[jnr];
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*gbscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
- Y = GBtab[nnn];
- F = GBtab[nnn+1];
- Geps = eps*GBtab[nnn+2];
- Heps2 = eps2*GBtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vgb = qq*VV;
- fijC = qq*FF*gbscale;
- dvdatmp = -0.5*(vgb+fijC*r);
- dvdasum = dvdasum + dvdatmp;
- dvda[jnr] = dvdaj+dvdatmp*isaj*isaj;
- vctot = vctot + vcoul;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
- fscal = (br*Vvdwexp-6.0*Vvdw6)*rinvsq-(fijC-fscal)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Inner loop uses 88 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- fshift[is3] = fshift[is3]+fix1;
- fshift[is3+1] = fshift[is3+1]+fiy1;
- fshift[is3+2] = fshift[is3+2]+fiz1;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
- dvda[ii] = dvda[ii] + dvdasum*isai*isai;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 13 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel420nf
- * Coulomb interaction: Generalized-Born
- * VdW interaction: Buckingham
- * water optimization: No
- * Calculate forces: no
- */
-void nb_kernel420nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real rinvsq;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real rinvsix;
- real Vvdw6,Vvdwtot;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real isai,isaj,isaprod,gbscale,vgb;
- real Vvdwexp,br;
- real ix1,iy1,iz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,cexp1,cexp2;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
- gbtabscale = *p_gbtabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- isai = invsqrta[ii];
- nti = 3*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- isaj = invsqrta[jnr];
- isaprod = isai*isaj;
- qq = iq*charge[jnr];
- vcoul = qq*rinv11;
- qq = isaprod*(-qq);
- gbscale = isaprod*gbtabscale;
- tj = nti+3*type[jnr];
- c6 = vdwparam[tj];
- cexp1 = vdwparam[tj+1];
- cexp2 = vdwparam[tj+2];
- rinvsq = rinv11*rinv11;
-
- /* Tabulated Generalized-Born interaction */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*gbscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
- Y = GBtab[nnn];
- F = GBtab[nnn+1];
- Geps = eps*GBtab[nnn+2];
- Heps2 = eps2*GBtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vgb = qq*VV;
- vctot = vctot + vcoul;
-
- /* Buckingham interaction */
- rinvsix = rinvsq*rinvsq*rinvsq;
- Vvdw6 = c6*rinvsix;
- br = cexp2*rsq11*rinv11;
- Vvdwexp = cexp1*exp(-br);
- Vvdwtot = Vvdwtot+Vvdwexp-Vvdw6;
-
- /* Inner loop uses 64 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 6 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL420_H_
-#define _NBKERNEL420_H_
-
-/*! \file nb_kernel420.h
- * \brief Nonbonded kernel 420 (GB Coul + Bham)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 420 with forces.
- *
- * <b>Coulomb interaction:</b> Generalized Born<br>
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel420
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real * work);
-
-
-/*! \brief Nonbonded kernel 420 without forces.
- *
- * \internal Generated at compile time in either C or Fortran
- * <b>VdW interaction:</b> Buckingham <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel420nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real * work);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL420_H_ */
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <math.h>
-
-#include "vec.h"
-#ifdef GMX_THREAD_SHM_FDECOMP
-#include "thread_mpi.h"
-#endif
-
-/* get gmx_gbdata_t */
-#include "../nb_kerneltype.h"
-
-#include "nb_kernel430.h"
-
-/*
- * Gromacs nonbonded kernel nb_kernel430
- * Coulomb interaction: Generalized-Born
- * VdW interaction: Tabulated
- * water optimization: No
- * Calculate forces: yes
- */
-void nb_kernel430(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real fscal,tx,ty,tz;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real FF;
- real fijC;
- real fijD,fijR;
- real isai,isaj,isaprod,gbscale,vgb,vgbtot;
- real dvdasum,dvdatmp,dvdaj,fgb;
- real ix1,iy1,iz1,fix1,fiy1,fiz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,c12;
- gmx_gbdata_t *gbdata;
- real * gpol;
- real scale_gb;
-
- gbdata = (gmx_gbdata_t *)work;
- gpol = gbdata->gpol;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- scale_gb = (1.0/gbdata->epsilon_r) - (1.0/gbdata->gb_epsilon_solvent);
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
- gbtabscale = *p_gbtabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- isai = invsqrta[ii];
- nti = 2*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
- dvdasum = 0;
- vgbtot = 0;
-
- /* Clear i atom forces */
- fix1 = 0;
- fiy1 = 0;
- fiz1 = 0;
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- isaj = invsqrta[jnr];
- isaprod = isai*isaj;
- qq = iq*charge[jnr];
- vcoul = qq*rinv11;
- fscal = vcoul*rinv11;
- qq = isaprod*(-qq)*scale_gb;
- gbscale = isaprod*gbtabscale;
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Tabulated Generalized-Born interaction */
- dvdaj = dvda[jnr];
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*gbscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
- Y = GBtab[nnn];
- F = GBtab[nnn+1];
- Geps = eps*GBtab[nnn+2];
- Heps2 = eps2*GBtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- vgb = qq*VV;
- fijC = qq*FF*gbscale;
- dvdatmp = -0.5*(vgb+fijC*r);
- dvdasum = dvdasum + dvdatmp;
- dvda[jnr] = dvdaj+dvdatmp*isaj*isaj;
- vctot = vctot + vcoul;
- vgbtot = vgbtot + vgb;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw6 = c6*VV;
- fijD = c6*FF;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- FF = Fp+Geps+2.0*Heps2;
- Vvdw12 = c12*VV;
- fijR = c12*FF;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
- fscal = -((fijD+fijR)*tabscale+fijC-fscal)*rinv11;
-
- /* Calculate temporary vectorial force */
- tx = fscal*dx11;
- ty = fscal*dy11;
- tz = fscal*dz11;
-
- /* Increment i atom force */
- fix1 = fix1 + tx;
- fiy1 = fiy1 + ty;
- fiz1 = fiz1 + tz;
-
- /* Decrement j atom force */
- faction[j3+0] = faction[j3+0] - tx;
- faction[j3+1] = faction[j3+1] - ty;
- faction[j3+2] = faction[j3+2] - tz;
-
- /* Inner loop uses 80 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
- faction[ii3+0] = faction[ii3+0] + fix1;
- faction[ii3+1] = faction[ii3+1] + fiy1;
- faction[ii3+2] = faction[ii3+2] + fiz1;
- fshift[is3] = fshift[is3]+fix1;
- fshift[is3+1] = fshift[is3+1]+fiy1;
- fshift[is3+2] = fshift[is3+2]+fiz1;
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
- gpol[ggid] = gpol[ggid] + vgbtot;
- dvda[ii] = dvda[ii] + dvdasum*isai*isai;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 13 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
-
-
-
-/*
- * Gromacs nonbonded kernel nb_kernel430nf
- * Coulomb interaction: Generalized-Born
- * VdW interaction: Tabulated
- * water optimization: No
- * Calculate forces: no
- */
-void nb_kernel430nf(
- int * p_nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * p_facel,
- real * p_krf,
- real * p_crf,
- real * Vc,
- int * type,
- int * p_ntype,
- real * vdwparam,
- real * Vvdw,
- real * p_tabscale,
- real * VFtab,
- real * invsqrta,
- real * dvda,
- real * p_gbtabscale,
- real * GBtab,
- int * p_nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work)
-{
- int nri,ntype,nthreads;
- real facel,krf,crf,tabscale,gbtabscale;
- int n,ii,is3,ii3,k,nj0,nj1,jnr,j3,ggid;
- int nn0,nn1,nouter,ninner;
- real shX,shY,shZ;
- real iq;
- real qq,vcoul,vctot;
- int nti;
- int tj;
- real Vvdw6,Vvdwtot;
- real Vvdw12;
- real r,rt,eps,eps2;
- int n0,nnn;
- real Y,F,Geps,Heps2,Fp,VV;
- real isai,isaj,isaprod,gbscale,vgb;
- real ix1,iy1,iz1;
- real jx1,jy1,jz1;
- real dx11,dy11,dz11,rsq11,rinv11;
- real c6,c12;
-
- nri = *p_nri;
- ntype = *p_ntype;
- nthreads = *p_nthreads;
- facel = *p_facel;
- krf = *p_krf;
- crf = *p_crf;
- tabscale = *p_tabscale;
- gbtabscale = *p_gbtabscale;
-
- /* Reset outer and inner iteration counters */
- nouter = 0;
- ninner = 0;
-
- /* Loop over thread workunits */
-
- do
- {
-#ifdef GMX_THREAD_SHM_FDECOMP
- tMPI_Thread_mutex_lock((tMPI_Thread_mutex_t *)mtx);
- nn0 = *count;
-
- /* Take successively smaller chunks (at least 10 lists) */
- nn1 = nn0+(nri-nn0)/(2*nthreads)+10;
- *count = nn1;
- tMPI_Thread_mutex_unlock((tMPI_Thread_mutex_t *)mtx);
- if(nn1>nri) nn1=nri;
-#else
- nn0 = 0;
- nn1 = nri;
-#endif
- /* Start outer loop over neighborlists */
-
- for(n=nn0; (n<nn1); n++)
- {
-
- /* Load shift vector for this list */
- is3 = 3*shift[n];
- shX = shiftvec[is3];
- shY = shiftvec[is3+1];
- shZ = shiftvec[is3+2];
-
- /* Load limits for loop over neighbors */
- nj0 = jindex[n];
- nj1 = jindex[n+1];
-
- /* Get outer coordinate index */
- ii = iinr[n];
- ii3 = 3*ii;
-
- /* Load i atom data, add shift vector */
- ix1 = shX + pos[ii3+0];
- iy1 = shY + pos[ii3+1];
- iz1 = shZ + pos[ii3+2];
-
- /* Load parameters for i atom */
- iq = facel*charge[ii];
- isai = invsqrta[ii];
- nti = 2*ntype*type[ii];
-
- /* Zero the potential energy for this list */
- vctot = 0;
- Vvdwtot = 0;
-
- /* Clear i atom forces */
-
- for(k=nj0; (k<nj1); k++)
- {
-
- /* Get j neighbor index, and coordinate index */
- jnr = jjnr[k];
- j3 = 3*jnr;
-
- /* load j atom coordinates */
- jx1 = pos[j3+0];
- jy1 = pos[j3+1];
- jz1 = pos[j3+2];
-
- /* Calculate distance */
- dx11 = ix1 - jx1;
- dy11 = iy1 - jy1;
- dz11 = iz1 - jz1;
- rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
-
- /* Calculate 1/r and 1/r2 */
- rinv11 = gmx_invsqrt(rsq11);
-
- /* Load parameters for j atom */
- isaj = invsqrta[jnr];
- isaprod = isai*isaj;
- qq = iq*charge[jnr];
- vcoul = qq*rinv11;
- qq = isaprod*(-qq);
- gbscale = isaprod*gbtabscale;
- tj = nti+2*type[jnr];
- c6 = vdwparam[tj];
- c12 = vdwparam[tj+1];
-
- /* Tabulated Generalized-Born interaction */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*gbscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 4*n0;
- Y = GBtab[nnn];
- F = GBtab[nnn+1];
- Geps = eps*GBtab[nnn+2];
- Heps2 = eps2*GBtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- vgb = qq*VV;
- vctot = vctot + vcoul;
-
- /* Calculate table index */
- r = rsq11*rinv11;
-
- /* Calculate table index */
- rt = r*tabscale;
- n0 = rt;
- eps = rt-n0;
- eps2 = eps*eps;
- nnn = 8*n0;
-
- /* Tabulated VdW interaction - dispersion */
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw6 = c6*VV;
-
- /* Tabulated VdW interaction - repulsion */
- nnn = nnn+4;
- Y = VFtab[nnn];
- F = VFtab[nnn+1];
- Geps = eps*VFtab[nnn+2];
- Heps2 = eps2*VFtab[nnn+3];
- Fp = F+Geps+Heps2;
- VV = Y+eps*Fp;
- Vvdw12 = c12*VV;
- Vvdwtot = Vvdwtot+ Vvdw6 + Vvdw12;
-
- /* Inner loop uses 49 flops/iteration */
- }
-
-
- /* Add i forces to mem and shifted force list */
-
- /* Add potential energies to the group for this list */
- ggid = gid[n];
- Vc[ggid] = Vc[ggid] + vctot;
- Vvdw[ggid] = Vvdw[ggid] + Vvdwtot;
-
- /* Increment number of inner iterations */
- ninner = ninner + nj1 - nj0;
-
- /* Outer loop uses 6 flops/iteration */
- }
-
-
- /* Increment number of outer iterations */
- nouter = nouter + nn1 - nn0;
- }
- while (nn1<nri);
-
-
- /* Write outer/inner iteration count to pointers */
- *outeriter = nouter;
- *inneriter = ninner;
-}
-
-
+++ /dev/null
-/*
- * This source code is part of
- *
- * G R O M A C S
- *
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
- *
- * Gromacs is a library for molecular simulation and trajectory analysis,
- * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
- * a full list of developers and information, check out http://www.gromacs.org
- *
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
- * later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
- *
- * To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL430_H_
-#define _NBKERNEL430_H_
-
-/*! \file nb_kernel430.h
- * \brief Nonbonded kernel 430 (GB Coul + Tab VdW)
- *
- * \internal
- */
-
-#include "types/simple.h"
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-}
-#endif
-
-
-/*! \brief Nonbonded kernel 430 with forces.
- *
- * <b>Coulomb interaction:</b> Generalized Born<br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> Yes <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel430
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-/*! \brief Nonbonded kernel 430 without forces.
- *
- * <b>Coulomb interaction:</b> Generalized Born<br>
- * <b>VdW interaction:</b> Tabulated <br>
- * <b>Water optimization:</b> No <br>
- * <b>Forces calculated:</b> No <br>
- *
- * \note All level1 and level2 nonbonded kernels use the same
- * call sequence. Parameters are documented in nb_kernel.h
- */
-void
-nb_kernel430nf
- (int * nri, int iinr[],
- int jindex[], int jjnr[],
- int shift[], real shiftvec[],
- real fshift[], int gid[],
- real pos[], real faction[],
- real charge[], real * facel,
- real * krf, real * crf,
- real Vc[], int type[],
- int * ntype, real vdwparam[],
- real Vvdw[], real * tabscale,
- real VFtab[], real invsqrta[],
- real dvda[], real * gbtabscale,
- real GBtab[], int * nthreads,
- int * count, void * mtx,
- int * outeriter, int * inneriter,
- real work[]);
-
-
-#ifdef __cplusplus
-}
-#endif
-
-#endif /* _NBKERNEL430_H_ */
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwBham_GeomP1P1_VF_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCSTab_VdwBham_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 81 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 15 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*81);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwBham_GeomP1P1_F_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCSTab_VdwBham_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 74 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*74);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwBham_GeomW3P1_VF_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCSTab_VdwBham_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq10*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq20*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 165 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*165);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwBham_GeomW3P1_F_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCSTab_VdwBham_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 150 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*150);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwBham_GeomW3W3_VF_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCSTab_VdwBham_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r01 = rsq01*rinv01;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r01*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq01*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq01*FF*vftabscale*rinv01;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r02 = rsq02*rinv02;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r02*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq02*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq02*FF*vftabscale*rinv02;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq10*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r11*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq11*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq11*FF*vftabscale*rinv11;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r12*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq12*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq12*FF*vftabscale*rinv12;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq20*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r21*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq21*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq21*FF*vftabscale*rinv21;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r22*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq22*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq22*FF*vftabscale*rinv22;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 408 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*408);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwBham_GeomW3W3_F_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCSTab_VdwBham_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r01 = rsq01*rinv01;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r01*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq01*FF*vftabscale*rinv01;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r02 = rsq02*rinv02;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r02*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq02*FF*vftabscale*rinv02;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r11*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq11*FF*vftabscale*rinv11;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r12*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq12*FF*vftabscale*rinv12;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r21*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq21*FF*vftabscale*rinv21;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r22*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq22*FF*vftabscale*rinv22;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 369 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*369);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwBham_GeomW4P1_VF_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCSTab_VdwBham_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq10*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq20*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r30*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq30*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq30*FF*vftabscale*rinv30;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 187 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*187);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwBham_GeomW4P1_F_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCSTab_VdwBham_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r30*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq30*FF*vftabscale*rinv30;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 172 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*172);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwBham_GeomW4W4_VF_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCSTab_VdwBham_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r11*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq11*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq11*FF*vftabscale*rinv11;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r12*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq12*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq12*FF*vftabscale*rinv12;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r13 = rsq13*rinv13;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r13*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq13*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq13*FF*vftabscale*rinv13;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r21*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq21*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq21*FF*vftabscale*rinv21;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r22*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq22*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq22*FF*vftabscale*rinv22;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r23 = rsq23*rinv23;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r23*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq23*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq23*FF*vftabscale*rinv23;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r31 = rsq31*rinv31;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r31*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq31*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq31*FF*vftabscale*rinv31;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r32 = rsq32*rinv32;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r32*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq32*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq32*FF*vftabscale*rinv32;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r33 = rsq33*rinv33;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r33*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq33*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq33*FF*vftabscale*rinv33;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 430 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_VF,outeriter*41 + inneriter*430);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwBham_GeomW4W4_F_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCSTab_VdwBham_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r11*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq11*FF*vftabscale*rinv11;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r12*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq12*FF*vftabscale*rinv12;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r13 = rsq13*rinv13;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r13*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq13*FF*vftabscale*rinv13;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r21*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq21*FF*vftabscale*rinv21;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r22*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq22*FF*vftabscale*rinv22;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r23 = rsq23*rinv23;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r23*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq23*FF*vftabscale*rinv23;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r31 = rsq31*rinv31;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r31*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq31*FF*vftabscale*rinv31;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r32 = rsq32*rinv32;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r32*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq32*FF*vftabscale*rinv32;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r33 = rsq33*rinv33;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r33*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq33*FF*vftabscale*rinv33;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 391 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_F,outeriter*39 + inneriter*391);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: CubicSplineTable
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec_vdw->data;
+ vftabscale = kernel_data->table_elec_vdw->scale;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 4;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 73 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 15 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*73);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: CubicSplineTable
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec_vdw->data;
+ vftabscale = kernel_data->table_elec_vdw->scale;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 4;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 61 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*61);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec_vdw->data;
+ vftabscale = kernel_data->table_elec_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 4;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq10*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq20*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 157 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*157);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec_vdw->data;
+ vftabscale = kernel_data->table_elec_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 4;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 137 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*137);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec_vdw->data;
+ vftabscale = kernel_data->table_elec_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 4;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r01 = rsq01*rinv01;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r01*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq01*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq01*FF*vftabscale*rinv01;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r02 = rsq02*rinv02;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r02*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq02*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq02*FF*vftabscale*rinv02;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq10*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r11*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq11*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq11*FF*vftabscale*rinv11;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r12*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq12*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq12*FF*vftabscale*rinv12;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq20*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r21*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq21*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq21*FF*vftabscale*rinv21;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r22*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq22*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq22*FF*vftabscale*rinv22;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 400 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*400);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec_vdw->data;
+ vftabscale = kernel_data->table_elec_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 4;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r01 = rsq01*rinv01;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r01*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq01*FF*vftabscale*rinv01;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r02 = rsq02*rinv02;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r02*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq02*FF*vftabscale*rinv02;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r11*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq11*FF*vftabscale*rinv11;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r12*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq12*FF*vftabscale*rinv12;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r21*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq21*FF*vftabscale*rinv21;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r22*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq22*FF*vftabscale*rinv22;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 356 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*356);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec_vdw->data;
+ vftabscale = kernel_data->table_elec_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 4;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq10*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq20*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r30*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq30*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq30*FF*vftabscale*rinv30;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 181 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*181);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec_vdw->data;
+ vftabscale = kernel_data->table_elec_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 4;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r30*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq30*FF*vftabscale*rinv30;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 161 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*161);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec_vdw->data;
+ vftabscale = kernel_data->table_elec_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 4;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r11*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq11*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq11*FF*vftabscale*rinv11;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r12*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq12*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq12*FF*vftabscale*rinv12;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r13 = rsq13*rinv13;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r13*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq13*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq13*FF*vftabscale*rinv13;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r21*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq21*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq21*FF*vftabscale*rinv21;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r22*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq22*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq22*FF*vftabscale*rinv22;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r23 = rsq23*rinv23;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r23*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq23*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq23*FF*vftabscale*rinv23;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r31 = rsq31*rinv31;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r31*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq31*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq31*FF*vftabscale*rinv31;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r32 = rsq32*rinv32;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r32*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq32*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq32*FF*vftabscale*rinv32;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r33 = rsq33*rinv33;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r33*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq33*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq33*FF*vftabscale*rinv33;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 424 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_VF,outeriter*41 + inneriter*424);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec_vdw->data;
+ vftabscale = kernel_data->table_elec_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 4;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r11*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq11*FF*vftabscale*rinv11;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r12*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq12*FF*vftabscale*rinv12;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r13 = rsq13*rinv13;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r13*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq13*FF*vftabscale*rinv13;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r21*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq21*FF*vftabscale*rinv21;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r22*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq22*FF*vftabscale*rinv22;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r23 = rsq23*rinv23;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r23*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq23*FF*vftabscale*rinv23;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r31 = rsq31*rinv31;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r31*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq31*FF*vftabscale*rinv31;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r32 = rsq32*rinv32;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r32*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq32*FF*vftabscale*rinv32;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r33 = rsq33*rinv33;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r33*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 3*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq33*FF*vftabscale*rinv33;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 380 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_F,outeriter*39 + inneriter*380);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 55 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 15 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*55);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 46 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*46);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq10*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq20*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 139 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*139);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 122 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*122);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r01 = rsq01*rinv01;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r01*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq01*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq01*FF*vftabscale*rinv01;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r02 = rsq02*rinv02;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r02*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq02*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq02*FF*vftabscale*rinv02;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq10*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r11*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq11*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq11*FF*vftabscale*rinv11;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r12*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq12*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq12*FF*vftabscale*rinv12;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq20*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r21*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq21*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq21*FF*vftabscale*rinv21;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r22*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq22*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq22*FF*vftabscale*rinv22;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 382 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*382);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r01 = rsq01*rinv01;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r01*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq01*FF*vftabscale*rinv01;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r02 = rsq02*rinv02;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r02*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq02*FF*vftabscale*rinv02;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r11*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq11*FF*vftabscale*rinv11;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r12*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq12*FF*vftabscale*rinv12;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r21*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq21*FF*vftabscale*rinv21;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r22*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq22*FF*vftabscale*rinv22;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 341 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*341);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = 1.0/rsq00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq10*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq20*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r30*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq30*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq30*FF*vftabscale*rinv30;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 158 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*158);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = 1.0/rsq00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r30*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq30*FF*vftabscale*rinv30;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 141 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*141);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = 1.0/rsq00;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r11*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq11*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq11*FF*vftabscale*rinv11;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r12*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq12*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq12*FF*vftabscale*rinv12;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r13 = rsq13*rinv13;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r13*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq13*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq13*FF*vftabscale*rinv13;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r21*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq21*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq21*FF*vftabscale*rinv21;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r22*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq22*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq22*FF*vftabscale*rinv22;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r23 = rsq23*rinv23;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r23*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq23*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq23*FF*vftabscale*rinv23;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r31 = rsq31*rinv31;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r31*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq31*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq31*FF*vftabscale*rinv31;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r32 = rsq32*rinv32;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r32*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq32*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq32*FF*vftabscale*rinv32;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r33 = rsq33*rinv33;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r33*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq33*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq33*FF*vftabscale*rinv33;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 401 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_VF,outeriter*41 + inneriter*401);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = 1.0/rsq00;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r11*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq11*FF*vftabscale*rinv11;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r12*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq12*FF*vftabscale*rinv12;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r13 = rsq13*rinv13;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r13*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq13*FF*vftabscale*rinv13;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r21*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq21*FF*vftabscale*rinv21;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r22*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq22*FF*vftabscale*rinv22;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r23 = rsq23*rinv23;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r23*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq23*FF*vftabscale*rinv23;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r31 = rsq31*rinv31;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r31*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq31*FF*vftabscale*rinv31;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r32 = rsq32*rinv32;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r32*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq32*FF*vftabscale*rinv32;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r33 = rsq33*rinv33;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r33*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq33*FF*vftabscale*rinv33;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 360 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_F,outeriter*39 + inneriter*360);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: None
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 42 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 14 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*14 + inneriter*42);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: None
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 38 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*13 + inneriter*38);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: None
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq10*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq20*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 126 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3_VF,outeriter*31 + inneriter*126);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: None
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 114 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3_F,outeriter*30 + inneriter*114);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: None
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ qq00 = iq0*jq0;
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r01 = rsq01*rinv01;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r01*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq01*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq01*FF*vftabscale*rinv01;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r02 = rsq02*rinv02;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r02*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq02*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq02*FF*vftabscale*rinv02;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq10*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r11*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq11*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq11*FF*vftabscale*rinv11;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r12*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq12*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq12*FF*vftabscale*rinv12;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq20*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r21*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq21*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq21*FF*vftabscale*rinv21;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r22*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq22*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq22*FF*vftabscale*rinv22;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 369 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3W3_VF,outeriter*31 + inneriter*369);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: None
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ qq00 = iq0*jq0;
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq00*FF*vftabscale*rinv00;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r01 = rsq01*rinv01;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r01*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq01*FF*vftabscale*rinv01;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r02 = rsq02*rinv02;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r02*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq02*FF*vftabscale*rinv02;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r11*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq11*FF*vftabscale*rinv11;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r12*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq12*FF*vftabscale*rinv12;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r21*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq21*FF*vftabscale*rinv21;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r22*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq22*FF*vftabscale*rinv22;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 333 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3W3_F,outeriter*30 + inneriter*333);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: None
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq10*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq20*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r30*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq30*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq30*FF*vftabscale*rinv30;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 126 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4_VF,outeriter*31 + inneriter*126);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: None
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r10*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq10*FF*vftabscale*rinv10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r20*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq20*FF*vftabscale*rinv20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r30*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq30*FF*vftabscale*rinv30;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 114 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4_F,outeriter*30 + inneriter*114);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: None
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r11*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq11*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq11*FF*vftabscale*rinv11;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r12*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq12*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq12*FF*vftabscale*rinv12;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r13 = rsq13*rinv13;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r13*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq13*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq13*FF*vftabscale*rinv13;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r21*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq21*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq21*FF*vftabscale*rinv21;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r22*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq22*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq22*FF*vftabscale*rinv22;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r23 = rsq23*rinv23;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r23*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq23*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq23*FF*vftabscale*rinv23;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r31 = rsq31*rinv31;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r31*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq31*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq31*FF*vftabscale*rinv31;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r32 = rsq32*rinv32;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r32*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq32*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq32*FF*vftabscale*rinv32;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r33 = rsq33*rinv33;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r33*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ velec = qq33*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq33*FF*vftabscale*rinv33;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 369 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4W4_VF,outeriter*31 + inneriter*369);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_c
+ * Electrostatics interaction: CubicSplineTable
+ * VdW interaction: None
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r11*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq11*FF*vftabscale*rinv11;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r12*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq12*FF*vftabscale*rinv12;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r13 = rsq13*rinv13;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r13*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq13*FF*vftabscale*rinv13;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r21*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq21*FF*vftabscale*rinv21;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r22*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq22*FF*vftabscale*rinv22;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r23 = rsq23*rinv23;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r23*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq23*FF*vftabscale*rinv23;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r31 = rsq31*rinv31;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r31*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq31*FF*vftabscale*rinv31;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r32 = rsq32*rinv32;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r32*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq32*FF*vftabscale*rinv32;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r33 = rsq33*rinv33;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r33*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 1*4*vfitab;
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq33*FF*vftabscale*rinv33;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 333 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4W4_F,outeriter*30 + inneriter*333);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwBham_GeomP1P1_VF_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCoul_VdwBham_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 67 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 15 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*67);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwBham_GeomP1P1_F_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCoul_VdwBham_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 63 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*63);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwBham_GeomW3P1_VF_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCoul_VdwBham_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 123 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*123);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwBham_GeomW3P1_F_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCoul_VdwBham_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 117 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*117);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwBham_GeomW3W3_VF_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCoul_VdwBham_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq01*rinv01;
+ felec = velec*rinvsq01;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq02*rinv02;
+ felec = velec*rinvsq02;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq11*rinv11;
+ felec = velec*rinvsq11;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq12*rinv12;
+ felec = velec*rinvsq12;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq21*rinv21;
+ felec = velec*rinvsq21;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq22*rinv22;
+ felec = velec*rinvsq22;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 282 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*282);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwBham_GeomW3W3_F_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCoul_VdwBham_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq01*rinv01;
+ felec = velec*rinvsq01;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq02*rinv02;
+ felec = velec*rinvsq02;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq11*rinv11;
+ felec = velec*rinvsq11;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq12*rinv12;
+ felec = velec*rinvsq12;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq21*rinv21;
+ felec = velec*rinvsq21;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq22*rinv22;
+ felec = velec*rinvsq22;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 270 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*270);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwBham_GeomW4P1_VF_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCoul_VdwBham_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq30 = iq3*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq30*rinv30;
+ felec = velec*rinvsq30;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 145 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*145);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwBham_GeomW4P1_F_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCoul_VdwBham_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq30 = iq3*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq30*rinv30;
+ felec = velec*rinvsq30;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 139 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*139);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwBham_GeomW4W4_VF_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCoul_VdwBham_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq11*rinv11;
+ felec = velec*rinvsq11;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq12*rinv12;
+ felec = velec*rinvsq12;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq13*rinv13;
+ felec = velec*rinvsq13;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq21*rinv21;
+ felec = velec*rinvsq21;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq22*rinv22;
+ felec = velec*rinvsq22;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq23*rinv23;
+ felec = velec*rinvsq23;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq31*rinv31;
+ felec = velec*rinvsq31;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq32*rinv32;
+ felec = velec*rinvsq32;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq33*rinv33;
+ felec = velec*rinvsq33;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 304 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_VF,outeriter*41 + inneriter*304);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwBham_GeomW4W4_F_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCoul_VdwBham_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq11*rinv11;
+ felec = velec*rinvsq11;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq12*rinv12;
+ felec = velec*rinvsq12;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq13*rinv13;
+ felec = velec*rinvsq13;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq21*rinv21;
+ felec = velec*rinvsq21;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq22*rinv22;
+ felec = velec*rinvsq22;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq23*rinv23;
+ felec = velec*rinvsq23;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq31*rinv31;
+ felec = velec*rinvsq31;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq32*rinv32;
+ felec = velec*rinvsq32;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq33*rinv33;
+ felec = velec*rinvsq33;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 292 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_F,outeriter*39 + inneriter*292);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: CubicSplineTable
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 62 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 15 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*62);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: CubicSplineTable
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 53 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*53);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 118 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*118);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 107 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*107);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq01*rinv01;
+ felec = velec*rinvsq01;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq02*rinv02;
+ felec = velec*rinvsq02;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq11*rinv11;
+ felec = velec*rinvsq11;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq12*rinv12;
+ felec = velec*rinvsq12;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq21*rinv21;
+ felec = velec*rinvsq21;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq22*rinv22;
+ felec = velec*rinvsq22;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 277 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*277);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq01*rinv01;
+ felec = velec*rinvsq01;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq02*rinv02;
+ felec = velec*rinvsq02;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq11*rinv11;
+ felec = velec*rinvsq11;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq12*rinv12;
+ felec = velec*rinvsq12;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq21*rinv21;
+ felec = velec*rinvsq21;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq22*rinv22;
+ felec = velec*rinvsq22;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 260 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*260);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq30 = iq3*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq30*rinv30;
+ felec = velec*rinvsq30;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 139 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*139);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq30 = iq3*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq30*rinv30;
+ felec = velec*rinvsq30;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 128 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*128);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq11*rinv11;
+ felec = velec*rinvsq11;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq12*rinv12;
+ felec = velec*rinvsq12;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq13*rinv13;
+ felec = velec*rinvsq13;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq21*rinv21;
+ felec = velec*rinvsq21;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq22*rinv22;
+ felec = velec*rinvsq22;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq23*rinv23;
+ felec = velec*rinvsq23;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq31*rinv31;
+ felec = velec*rinvsq31;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq32*rinv32;
+ felec = velec*rinvsq32;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq33*rinv33;
+ felec = velec*rinvsq33;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 298 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_VF,outeriter*41 + inneriter*298);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq11*rinv11;
+ felec = velec*rinvsq11;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq12*rinv12;
+ felec = velec*rinvsq12;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq13*rinv13;
+ felec = velec*rinvsq13;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq21*rinv21;
+ felec = velec*rinvsq21;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq22*rinv22;
+ felec = velec*rinvsq22;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq23*rinv23;
+ felec = velec*rinvsq23;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq31*rinv31;
+ felec = velec*rinvsq31;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq32*rinv32;
+ felec = velec*rinvsq32;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq33*rinv33;
+ felec = velec*rinvsq33;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 281 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_F,outeriter*39 + inneriter*281);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 40 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 15 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*40);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 34 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*34);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 96 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*96);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 88 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*88);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq01*rinv01;
+ felec = velec*rinvsq01;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq02*rinv02;
+ felec = velec*rinvsq02;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq11*rinv11;
+ felec = velec*rinvsq11;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq12*rinv12;
+ felec = velec*rinvsq12;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq21*rinv21;
+ felec = velec*rinvsq21;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq22*rinv22;
+ felec = velec*rinvsq22;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 255 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*255);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq01*rinv01;
+ felec = velec*rinvsq01;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq02*rinv02;
+ felec = velec*rinvsq02;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq11*rinv11;
+ felec = velec*rinvsq11;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq12*rinv12;
+ felec = velec*rinvsq12;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq21*rinv21;
+ felec = velec*rinvsq21;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq22*rinv22;
+ felec = velec*rinvsq22;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 241 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*241);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = 1.0/rsq00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq30 = iq3*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq30*rinv30;
+ felec = velec*rinvsq30;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 116 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*116);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = 1.0/rsq00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq30 = iq3*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq30*rinv30;
+ felec = velec*rinvsq30;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 108 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*108);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = 1.0/rsq00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq11*rinv11;
+ felec = velec*rinvsq11;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq12*rinv12;
+ felec = velec*rinvsq12;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq13*rinv13;
+ felec = velec*rinvsq13;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq21*rinv21;
+ felec = velec*rinvsq21;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq22*rinv22;
+ felec = velec*rinvsq22;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq23*rinv23;
+ felec = velec*rinvsq23;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq31*rinv31;
+ felec = velec*rinvsq31;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq32*rinv32;
+ felec = velec*rinvsq32;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq33*rinv33;
+ felec = velec*rinvsq33;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 275 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_VF,outeriter*41 + inneriter*275);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = 1.0/rsq00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq11*rinv11;
+ felec = velec*rinvsq11;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq12*rinv12;
+ felec = velec*rinvsq12;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq13*rinv13;
+ felec = velec*rinvsq13;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq21*rinv21;
+ felec = velec*rinvsq21;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq22*rinv22;
+ felec = velec*rinvsq22;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq23*rinv23;
+ felec = velec*rinvsq23;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq31*rinv31;
+ felec = velec*rinvsq31;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq32*rinv32;
+ felec = velec*rinvsq32;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq33*rinv33;
+ felec = velec*rinvsq33;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 261 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_F,outeriter*39 + inneriter*261);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: None
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq00 = iq0*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 28 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 14 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*14 + inneriter*28);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: None
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq00 = iq0*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 27 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*13 + inneriter*27);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: None
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq00 = iq0*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 84 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3_VF,outeriter*31 + inneriter*84);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: None
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq00 = iq0*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 81 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3_F,outeriter*30 + inneriter*81);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: None
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ qq00 = iq0*jq0;
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq01*rinv01;
+ felec = velec*rinvsq01;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq02*rinv02;
+ felec = velec*rinvsq02;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq11*rinv11;
+ felec = velec*rinvsq11;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq12*rinv12;
+ felec = velec*rinvsq12;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq21*rinv21;
+ felec = velec*rinvsq21;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq22*rinv22;
+ felec = velec*rinvsq22;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 243 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3W3_VF,outeriter*31 + inneriter*243);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: None
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ qq00 = iq0*jq0;
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq00*rinv00;
+ felec = velec*rinvsq00;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq01*rinv01;
+ felec = velec*rinvsq01;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq02*rinv02;
+ felec = velec*rinvsq02;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq11*rinv11;
+ felec = velec*rinvsq11;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq12*rinv12;
+ felec = velec*rinvsq12;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq21*rinv21;
+ felec = velec*rinvsq21;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq22*rinv22;
+ felec = velec*rinvsq22;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 234 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3W3_F,outeriter*30 + inneriter*234);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: None
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq30 = iq3*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq30*rinv30;
+ felec = velec*rinvsq30;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 84 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4_VF,outeriter*31 + inneriter*84);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: None
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq10*rinv10;
+ felec = velec*rinvsq10;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq20*rinv20;
+ felec = velec*rinvsq20;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq30 = iq3*jq0;
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq30*rinv30;
+ felec = velec*rinvsq30;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 81 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4_F,outeriter*30 + inneriter*81);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: None
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq11*rinv11;
+ felec = velec*rinvsq11;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq12*rinv12;
+ felec = velec*rinvsq12;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq13*rinv13;
+ felec = velec*rinvsq13;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq21*rinv21;
+ felec = velec*rinvsq21;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq22*rinv22;
+ felec = velec*rinvsq22;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq23*rinv23;
+ felec = velec*rinvsq23;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq31*rinv31;
+ felec = velec*rinvsq31;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq32*rinv32;
+ felec = velec*rinvsq32;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq33*rinv33;
+ felec = velec*rinvsq33;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 243 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4W4_VF,outeriter*31 + inneriter*243);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_c
+ * Electrostatics interaction: Coulomb
+ * VdW interaction: None
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq11*rinv11;
+ felec = velec*rinvsq11;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq12*rinv12;
+ felec = velec*rinvsq12;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq13*rinv13;
+ felec = velec*rinvsq13;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq21*rinv21;
+ felec = velec*rinvsq21;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq22*rinv22;
+ felec = velec*rinvsq22;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq23*rinv23;
+ felec = velec*rinvsq23;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq31*rinv31;
+ felec = velec*rinvsq31;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq32*rinv32;
+ felec = velec*rinvsq32;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq33*rinv33;
+ felec = velec*rinvsq33;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 234 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4W4_F,outeriter*30 + inneriter*234);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*((rinv00-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = (vvdwexp-cexp1_00*exp(-cexp2_00*rvdw)) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 111 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 15 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*111);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 69 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*69);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*((rinv00-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = (vvdwexp-cexp1_00*exp(-cexp2_00*rvdw)) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*((rinv10-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*((rinv20-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 195 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*195);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 137 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*137);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*((rinv00-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = (vvdwexp-cexp1_00*exp(-cexp2_00*rvdw)) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ r01 = rsq01*rinv01;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r01*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq01*((rinv01-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq01*rinv01*(rinvsq01-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ r02 = rsq02*rinv02;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r02*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq02*((rinv02-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq02*rinv02*(rinvsq02-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*((rinv10-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*((rinv11-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*((rinv12-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*((rinv20-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*((rinv21-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*((rinv22-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 438 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*438);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ r01 = rsq01*rinv01;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r01*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq01*rinv01*(rinvsq01-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ r02 = rsq02*rinv02;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r02*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq02*rinv02*(rinvsq02-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 332 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*332);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = (vvdwexp-cexp1_00*exp(-cexp2_00*rvdw)) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*((rinv10-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*((rinv20-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r30*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq30*((rinv30-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq30*rinv30*(rinvsq30-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 218 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*218);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r30*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq30*rinv30*(rinvsq30-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 160 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*160);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = (vvdwexp-cexp1_00*exp(-cexp2_00*rvdw)) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*((rinv11-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*((rinv12-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ r13 = rsq13*rinv13;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r13*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq13*((rinv13-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq13*rinv13*(rinvsq13-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*((rinv21-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*((rinv22-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ r23 = rsq23*rinv23;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r23*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq23*((rinv23-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq23*rinv23*(rinvsq23-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ r31 = rsq31*rinv31;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r31*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq31*((rinv31-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq31*rinv31*(rinvsq31-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ r32 = rsq32*rinv32;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r32*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq32*((rinv32-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq32*rinv32*(rinvsq32-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ r33 = rsq33*rinv33;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r33*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq33*((rinv33-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq33*rinv33*(rinvsq33-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 461 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_VF,outeriter*41 + inneriter*461);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ r13 = rsq13*rinv13;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r13*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq13*rinv13*(rinvsq13-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ r23 = rsq23*rinv23;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r23*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq23*rinv23*(rinvsq23-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ r31 = rsq31*rinv31;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r31*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq31*rinv31*(rinvsq31-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ r32 = rsq32*rinv32;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r32*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq32*rinv32*(rinvsq32-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ r33 = rsq33*rinv33;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r33*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq33*rinv33*(rinvsq33-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 355 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_F,outeriter*39 + inneriter*355);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*((rinv00-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = (vvdw12 - c12_00*sh_vdw_invrcut6*sh_vdw_invrcut6)*(1.0/12.0) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 59 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 15 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*59);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 41 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*41);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*((rinv00-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = (vvdw12 - c12_00*sh_vdw_invrcut6*sh_vdw_invrcut6)*(1.0/12.0) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*((rinv10-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*((rinv20-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 143 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*143);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 109 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*109);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*((rinv00-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = (vvdw12 - c12_00*sh_vdw_invrcut6*sh_vdw_invrcut6)*(1.0/12.0) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ r01 = rsq01*rinv01;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r01*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq01*((rinv01-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq01*rinv01*(rinvsq01-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ r02 = rsq02*rinv02;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r02*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq02*((rinv02-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq02*rinv02*(rinvsq02-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*((rinv10-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*((rinv11-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*((rinv12-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*((rinv20-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*((rinv21-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*((rinv22-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 386 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*386);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ r01 = rsq01*rinv01;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r01*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq01*rinv01*(rinvsq01-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ r02 = rsq02*rinv02;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r02*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq02*rinv02*(rinvsq02-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 304 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*304);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = 1.0/rsq00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = (vvdw12 - c12_00*sh_vdw_invrcut6*sh_vdw_invrcut6)*(1.0/12.0) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*((rinv10-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*((rinv20-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r30*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq30*((rinv30-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq30*rinv30*(rinvsq30-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 163 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*163);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = 1.0/rsq00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r30*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq30*rinv30*(rinvsq30-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 129 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*129);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = 1.0/rsq00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = (vvdw12 - c12_00*sh_vdw_invrcut6*sh_vdw_invrcut6)*(1.0/12.0) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*((rinv11-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*((rinv12-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ r13 = rsq13*rinv13;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r13*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq13*((rinv13-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq13*rinv13*(rinvsq13-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*((rinv21-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*((rinv22-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ r23 = rsq23*rinv23;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r23*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq23*((rinv23-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq23*rinv23*(rinvsq23-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ r31 = rsq31*rinv31;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r31*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq31*((rinv31-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq31*rinv31*(rinvsq31-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ r32 = rsq32*rinv32;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r32*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq32*((rinv32-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq32*rinv32*(rinvsq32-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ r33 = rsq33*rinv33;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r33*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq33*((rinv33-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq33*rinv33*(rinvsq33-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 406 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_VF,outeriter*41 + inneriter*406);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = 1.0/rsq00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ r13 = rsq13*rinv13;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r13*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq13*rinv13*(rinvsq13-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ r23 = rsq23*rinv23;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r23*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq23*rinv23*(rinvsq23-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ r31 = rsq31*rinv31;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r31*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq31*rinv31*(rinvsq31-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ r32 = rsq32*rinv32;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r32*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq32*rinv32*(rinvsq32-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ r33 = rsq33*rinv33;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r33*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq33*rinv33*(rinvsq33-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 324 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_F,outeriter*39 + inneriter*324);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwNone_GeomP1P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSh_VdwNone_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*((rinv00-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 42 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 14 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*14 + inneriter*42);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwNone_GeomP1P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSh_VdwNone_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 34 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*13 + inneriter*34);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwNone_GeomW3P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSh_VdwNone_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*((rinv00-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*((rinv10-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*((rinv20-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 126 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3_VF,outeriter*31 + inneriter*126);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwNone_GeomW3P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSh_VdwNone_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 102 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3_F,outeriter*30 + inneriter*102);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwNone_GeomW3W3_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSh_VdwNone_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ qq00 = iq0*jq0;
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*((rinv00-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ r01 = rsq01*rinv01;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r01*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq01*((rinv01-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq01*rinv01*(rinvsq01-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ r02 = rsq02*rinv02;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r02*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq02*((rinv02-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq02*rinv02*(rinvsq02-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*((rinv10-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*((rinv11-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*((rinv12-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*((rinv20-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*((rinv21-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*((rinv22-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 369 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3W3_VF,outeriter*31 + inneriter*369);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwNone_GeomW3W3_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSh_VdwNone_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ qq00 = iq0*jq0;
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ r01 = rsq01*rinv01;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r01*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq01*rinv01*(rinvsq01-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ r02 = rsq02*rinv02;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r02*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq02*rinv02*(rinvsq02-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 297 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3W3_F,outeriter*30 + inneriter*297);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwNone_GeomW4P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSh_VdwNone_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*((rinv10-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*((rinv20-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r30*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq30*((rinv30-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq30*rinv30*(rinvsq30-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 126 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4_VF,outeriter*31 + inneriter*126);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwNone_GeomW4P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSh_VdwNone_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r30*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq30*rinv30*(rinvsq30-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 102 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4_F,outeriter*30 + inneriter*102);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwNone_GeomW4W4_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSh_VdwNone_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*((rinv11-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*((rinv12-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ r13 = rsq13*rinv13;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r13*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq13*((rinv13-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq13*rinv13*(rinvsq13-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*((rinv21-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*((rinv22-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ r23 = rsq23*rinv23;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r23*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq23*((rinv23-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq23*rinv23*(rinvsq23-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ r31 = rsq31*rinv31;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r31*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq31*((rinv31-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq31*rinv31*(rinvsq31-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ r32 = rsq32*rinv32;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r32*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq32*((rinv32-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq32*rinv32*(rinvsq32-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ r33 = rsq33*rinv33;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r33*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq33*((rinv33-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq33*rinv33*(rinvsq33-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 369 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4W4_VF,outeriter*31 + inneriter*369);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSh_VdwNone_GeomW4W4_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSh_VdwNone_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ r13 = rsq13*rinv13;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r13*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq13*rinv13*(rinvsq13-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ r23 = rsq23*rinv23;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r23*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq23*rinv23*(rinvsq23-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ r31 = rsq31*rinv31;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r31*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq31*rinv31*(rinvsq31-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ r32 = rsq32*rinv32;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r32*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq32*rinv32*(rinvsq32-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ r33 = rsq33*rinv33;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r33*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq33*rinv33*(rinvsq33-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 297 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4W4_F,outeriter*30 + inneriter*297);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ vvdw *= sw;
+ felec = felec*sw + velec*dsw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 101 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 15 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*101);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 97 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*97);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ vvdw *= sw;
+ felec = felec*sw + velec*dsw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ d = r10-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ d = r20-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 219 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*219);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ d = r10-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ d = r20-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 211 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*211);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ vvdw *= sw;
+ felec = felec*sw + velec*dsw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ r01 = rsq01*rinv01;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r01*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq01*(rinv01-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq01*rinv01*(rinvsq01-felec);
+
+ d = r01-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ r02 = rsq02*rinv02;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r02*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq02*(rinv02-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq02*rinv02*(rinvsq02-felec);
+
+ d = r02-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ d = r10-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*(rinv11-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ d = r11-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*(rinv12-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ d = r12-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ d = r20-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*(rinv21-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ d = r21-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*(rinv22-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ d = r22-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 564 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*564);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ r01 = rsq01*rinv01;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r01*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq01*(rinv01-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq01*rinv01*(rinvsq01-felec);
+
+ d = r01-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ r02 = rsq02*rinv02;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r02*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq02*(rinv02-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq02*rinv02*(rinvsq02-felec);
+
+ d = r02-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ d = r10-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*(rinv11-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ d = r11-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*(rinv12-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ d = r12-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ d = r20-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*(rinv21-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ d = r21-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*(rinv22-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ d = r22-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 544 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*544);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ vvdw *= sw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ d = r10-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ d = r20-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r30*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq30*(rinv30-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq30*rinv30*(rinvsq30-felec);
+
+ d = r30-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 256 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*256);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ d = r10-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ d = r20-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r30*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq30*(rinv30-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq30*rinv30*(rinvsq30-felec);
+
+ d = r30-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 248 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*248);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ vvdw *= sw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*(rinv11-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ d = r11-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*(rinv12-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ d = r12-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ r13 = rsq13*rinv13;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r13*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq13*(rinv13-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq13*rinv13*(rinvsq13-felec);
+
+ d = r13-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*(rinv21-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ d = r21-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*(rinv22-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ d = r22-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ r23 = rsq23*rinv23;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r23*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq23*(rinv23-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq23*rinv23*(rinvsq23-felec);
+
+ d = r23-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ r31 = rsq31*rinv31;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r31*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq31*(rinv31-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq31*rinv31*(rinvsq31-felec);
+
+ d = r31-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ r32 = rsq32*rinv32;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r32*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq32*(rinv32-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq32*rinv32*(rinvsq32-felec);
+
+ d = r32-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ r33 = rsq33*rinv33;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r33*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq33*(rinv33-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq33*rinv33*(rinvsq33-felec);
+
+ d = r33-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 601 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_VF,outeriter*41 + inneriter*601);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*(rinv11-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ d = r11-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*(rinv12-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ d = r12-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ r13 = rsq13*rinv13;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r13*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq13*(rinv13-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq13*rinv13*(rinvsq13-felec);
+
+ d = r13-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*(rinv21-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ d = r21-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*(rinv22-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ d = r22-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ r23 = rsq23*rinv23;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r23*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq23*(rinv23-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq23*rinv23*(rinvsq23-felec);
+
+ d = r23-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ r31 = rsq31*rinv31;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r31*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq31*(rinv31-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq31*rinv31*(rinvsq31-felec);
+
+ d = r31-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ r32 = rsq32*rinv32;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r32*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq32*(rinv32-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq32*rinv32*(rinvsq32-felec);
+
+ d = r32-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ r33 = rsq33*rinv33;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r33*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq33*(rinv33-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq33*rinv33*(rinvsq33-felec);
+
+ d = r33-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 581 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_F,outeriter*39 + inneriter*581);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ vvdw *= sw;
+ felec = felec*sw + velec*dsw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 75 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 15 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*75);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 71 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*71);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ vvdw *= sw;
+ felec = felec*sw + velec*dsw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ d = r10-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ d = r20-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 193 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*193);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ d = r10-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ d = r20-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 185 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*185);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ vvdw *= sw;
+ felec = felec*sw + velec*dsw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ r01 = rsq01*rinv01;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r01*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq01*(rinv01-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq01*rinv01*(rinvsq01-felec);
+
+ d = r01-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ r02 = rsq02*rinv02;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r02*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq02*(rinv02-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq02*rinv02*(rinvsq02-felec);
+
+ d = r02-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ d = r10-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*(rinv11-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ d = r11-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*(rinv12-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ d = r12-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ d = r20-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*(rinv21-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ d = r21-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*(rinv22-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ d = r22-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 538 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*538);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ r01 = rsq01*rinv01;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r01*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq01*(rinv01-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq01*rinv01*(rinvsq01-felec);
+
+ d = r01-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ r02 = rsq02*rinv02;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r02*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq02*(rinv02-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq02*rinv02*(rinvsq02-felec);
+
+ d = r02-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ d = r10-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*(rinv11-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ d = r11-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*(rinv12-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ d = r12-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ d = r20-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*(rinv21-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ d = r21-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*(rinv22-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ d = r22-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 518 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*518);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ vvdw *= sw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ d = r10-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ d = r20-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r30*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq30*(rinv30-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq30*rinv30*(rinvsq30-felec);
+
+ d = r30-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 230 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*230);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ d = r10-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ d = r20-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r30*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq30*(rinv30-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq30*rinv30*(rinvsq30-felec);
+
+ d = r30-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 222 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*222);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ vvdw *= sw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*(rinv11-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ d = r11-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*(rinv12-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ d = r12-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ r13 = rsq13*rinv13;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r13*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq13*(rinv13-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq13*rinv13*(rinvsq13-felec);
+
+ d = r13-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*(rinv21-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ d = r21-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*(rinv22-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ d = r22-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ r23 = rsq23*rinv23;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r23*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq23*(rinv23-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq23*rinv23*(rinvsq23-felec);
+
+ d = r23-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ r31 = rsq31*rinv31;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r31*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq31*(rinv31-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq31*rinv31*(rinvsq31-felec);
+
+ d = r31-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ r32 = rsq32*rinv32;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r32*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq32*(rinv32-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq32*rinv32*(rinvsq32-felec);
+
+ d = r32-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ r33 = rsq33*rinv33;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r33*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq33*(rinv33-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq33*rinv33*(rinvsq33-felec);
+
+ d = r33-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 575 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_VF,outeriter*41 + inneriter*575);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*(rinv11-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ d = r11-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*(rinv12-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ d = r12-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ r13 = rsq13*rinv13;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r13*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq13*(rinv13-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq13*rinv13*(rinvsq13-felec);
+
+ d = r13-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*(rinv21-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ d = r21-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*(rinv22-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ d = r22-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ r23 = rsq23*rinv23;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r23*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq23*(rinv23-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq23*rinv23*(rinvsq23-felec);
+
+ d = r23-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ r31 = rsq31*rinv31;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r31*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq31*(rinv31-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq31*rinv31*(rinvsq31-felec);
+
+ d = r31-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ r32 = rsq32*rinv32;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r32*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq32*(rinv32-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq32*rinv32*(rinvsq32-felec);
+
+ d = r32-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ r33 = rsq33*rinv33;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r33*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq33*(rinv33-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq33*rinv33*(rinvsq33-felec);
+
+ d = r33-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 555 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_F,outeriter*39 + inneriter*555);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwNone_GeomP1P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSw_VdwNone_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 59 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 14 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*14 + inneriter*59);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwNone_GeomP1P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSw_VdwNone_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 57 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*13 + inneriter*57);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwNone_GeomW3P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSw_VdwNone_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ d = r10-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ d = r20-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 177 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3_VF,outeriter*31 + inneriter*177);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwNone_GeomW3P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSw_VdwNone_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ d = r10-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ d = r20-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 171 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3_F,outeriter*30 + inneriter*171);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwNone_GeomW3W3_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSw_VdwNone_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ qq00 = iq0*jq0;
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ r01 = rsq01*rinv01;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r01*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq01*(rinv01-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq01*rinv01*(rinvsq01-felec);
+
+ d = r01-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ r02 = rsq02*rinv02;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r02*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq02*(rinv02-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq02*rinv02*(rinvsq02-felec);
+
+ d = r02-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ d = r10-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*(rinv11-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ d = r11-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*(rinv12-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ d = r12-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ d = r20-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*(rinv21-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ d = r21-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*(rinv22-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ d = r22-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 522 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3W3_VF,outeriter*31 + inneriter*522);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwNone_GeomW3W3_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSw_VdwNone_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ qq00 = iq0*jq0;
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ r01 = rsq01*rinv01;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r01*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq01*(rinv01-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq01*rinv01*(rinvsq01-felec);
+
+ d = r01-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ r02 = rsq02*rinv02;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r02*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq02*(rinv02-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq02*rinv02*(rinvsq02-felec);
+
+ d = r02-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ d = r10-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*(rinv11-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ d = r11-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*(rinv12-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ d = r12-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ d = r20-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*(rinv21-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ d = r21-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*(rinv22-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ d = r22-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 504 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3W3_F,outeriter*30 + inneriter*504);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwNone_GeomW4P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSw_VdwNone_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ d = r10-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ d = r20-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r30*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq30*(rinv30-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq30*rinv30*(rinvsq30-felec);
+
+ d = r30-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 177 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4_VF,outeriter*31 + inneriter*177);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ d = r10-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ d = r20-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r30*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq30*(rinv30-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq30*rinv30*(rinvsq30-felec);
+
+ d = r30-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 171 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4_F,outeriter*30 + inneriter*171);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*(rinv11-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ d = r11-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*(rinv12-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ d = r12-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ r13 = rsq13*rinv13;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r13*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq13*(rinv13-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq13*rinv13*(rinvsq13-felec);
+
+ d = r13-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*(rinv21-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ d = r21-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*(rinv22-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ d = r22-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ r23 = rsq23*rinv23;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r23*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq23*(rinv23-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq23*rinv23*(rinvsq23-felec);
+
+ d = r23-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ r31 = rsq31*rinv31;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r31*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq31*(rinv31-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq31*rinv31*(rinvsq31-felec);
+
+ d = r31-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ r32 = rsq32*rinv32;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r32*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq32*(rinv32-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq32*rinv32*(rinvsq32-felec);
+
+ d = r32-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ r33 = rsq33*rinv33;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r33*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq33*(rinv33-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq33*rinv33*(rinvsq33-felec);
+
+ d = r33-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ velec *= sw;
+ felec = felec*sw + velec*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 522 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4W4_VF,outeriter*31 + inneriter*522);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rcoulomb_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*(rinv11-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ d = r11-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*(rinv12-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ d = r12-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ r13 = rsq13*rinv13;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r13*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq13*(rinv13-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq13*rinv13*(rinvsq13-felec);
+
+ d = r13-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*(rinv21-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ d = r21-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*(rinv22-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ d = r22-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ r23 = rsq23*rinv23;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r23*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq23*(rinv23-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq23*rinv23*(rinvsq23-felec);
+
+ d = r23-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ r31 = rsq31*rinv31;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r31*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq31*(rinv31-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq31*rinv31*(rinvsq31-felec);
+
+ d = r31-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ r32 = rsq32*rinv32;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r32*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq32*(rinv32-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq32*rinv32*(rinvsq32-felec);
+
+ d = r32-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ r33 = rsq33*rinv33;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r33*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq33*(rinv33-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq33*rinv33*(rinvsq33-felec);
+
+ d = r33-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ felec = felec*sw + velec*dsw;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 504 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4W4_F,outeriter*30 + inneriter*504);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwBham_GeomP1P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEw_VdwBham_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 79 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 15 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*79);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwBham_GeomP1P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEw_VdwBham_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 69 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*69);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwBham_GeomW3P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEw_VdwBham_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 161 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*161);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwBham_GeomW3P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEw_VdwBham_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 137 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*137);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwBham_GeomW3W3_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEw_VdwBham_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r01 = rsq01*rinv01;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r01*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq01*(rinv01-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq01*rinv01*(rinvsq01-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r02 = rsq02*rinv02;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r02*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq02*(rinv02-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq02*rinv02*(rinvsq02-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*(rinv11-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*(rinv12-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*(rinv21-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*(rinv22-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 398 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*398);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwBham_GeomW3W3_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEw_VdwBham_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r01 = rsq01*rinv01;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r01*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq01*rinv01*(rinvsq01-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r02 = rsq02*rinv02;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r02*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq02*rinv02*(rinvsq02-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 332 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*332);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwBham_GeomW4P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEw_VdwBham_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r30*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq30*(rinv30-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq30*rinv30*(rinvsq30-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 184 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*184);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwBham_GeomW4P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEw_VdwBham_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r30*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq30*rinv30*(rinvsq30-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 160 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*160);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwBham_GeomW4W4_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEw_VdwBham_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*(rinv11-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*(rinv12-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r13 = rsq13*rinv13;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r13*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq13*(rinv13-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq13*rinv13*(rinvsq13-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*(rinv21-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*(rinv22-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r23 = rsq23*rinv23;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r23*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq23*(rinv23-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq23*rinv23*(rinvsq23-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r31 = rsq31*rinv31;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r31*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq31*(rinv31-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq31*rinv31*(rinvsq31-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r32 = rsq32*rinv32;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r32*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq32*(rinv32-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq32*rinv32*(rinvsq32-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r33 = rsq33*rinv33;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r33*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq33*(rinv33-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq33*rinv33*(rinvsq33-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 421 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_VF,outeriter*41 + inneriter*421);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwBham_GeomW4W4_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEw_VdwBham_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r13 = rsq13*rinv13;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r13*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq13*rinv13*(rinvsq13-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r23 = rsq23*rinv23;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r23*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq23*rinv23*(rinvsq23-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r31 = rsq31*rinv31;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r31*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq31*rinv31*(rinvsq31-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r32 = rsq32*rinv32;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r32*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq32*rinv32*(rinvsq32-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r33 = rsq33*rinv33;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r33*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq33*rinv33*(rinvsq33-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 355 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_F,outeriter*39 + inneriter*355);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwCSTab_GeomP1P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: CubicSplineTable
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEw_VdwCSTab_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 74 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 15 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*74);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwCSTab_GeomP1P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: CubicSplineTable
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEw_VdwCSTab_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 59 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*59);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwCSTab_GeomW3P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEw_VdwCSTab_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 156 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*156);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwCSTab_GeomW3P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEw_VdwCSTab_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 127 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*127);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwCSTab_GeomW3W3_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEw_VdwCSTab_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r01 = rsq01*rinv01;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r01*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq01*(rinv01-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq01*rinv01*(rinvsq01-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r02 = rsq02*rinv02;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r02*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq02*(rinv02-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq02*rinv02*(rinvsq02-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*(rinv11-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*(rinv12-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*(rinv21-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*(rinv22-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 393 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*393);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwCSTab_GeomW3W3_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEw_VdwCSTab_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r01 = rsq01*rinv01;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r01*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq01*rinv01*(rinvsq01-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r02 = rsq02*rinv02;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r02*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq02*rinv02*(rinvsq02-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 322 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*322);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwCSTab_GeomW4P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEw_VdwCSTab_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r30*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq30*(rinv30-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq30*rinv30*(rinvsq30-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 178 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*178);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwCSTab_GeomW4P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEw_VdwCSTab_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r30*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq30*rinv30*(rinvsq30-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 149 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*149);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwCSTab_GeomW4W4_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEw_VdwCSTab_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*(rinv11-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*(rinv12-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r13 = rsq13*rinv13;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r13*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq13*(rinv13-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq13*rinv13*(rinvsq13-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*(rinv21-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*(rinv22-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r23 = rsq23*rinv23;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r23*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq23*(rinv23-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq23*rinv23*(rinvsq23-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r31 = rsq31*rinv31;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r31*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq31*(rinv31-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq31*rinv31*(rinvsq31-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r32 = rsq32*rinv32;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r32*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq32*(rinv32-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq32*rinv32*(rinvsq32-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r33 = rsq33*rinv33;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r33*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq33*(rinv33-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq33*rinv33*(rinvsq33-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 415 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_VF,outeriter*41 + inneriter*415);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwCSTab_GeomW4W4_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEw_VdwCSTab_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r13 = rsq13*rinv13;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r13*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq13*rinv13*(rinvsq13-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r23 = rsq23*rinv23;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r23*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq23*rinv23*(rinvsq23-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r31 = rsq31*rinv31;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r31*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq31*rinv31*(rinvsq31-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r32 = rsq32*rinv32;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r32*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq32*rinv32*(rinvsq32-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r33 = rsq33*rinv33;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r33*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq33*rinv33*(rinvsq33-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 344 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_F,outeriter*39 + inneriter*344);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwLJ_GeomP1P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEw_VdwLJ_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 53 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 15 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*53);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwLJ_GeomP1P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEw_VdwLJ_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 41 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*41);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwLJ_GeomW3P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEw_VdwLJ_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 135 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*135);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwLJ_GeomW3P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEw_VdwLJ_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 109 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*109);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwLJ_GeomW3W3_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEw_VdwLJ_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r01 = rsq01*rinv01;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r01*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq01*(rinv01-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq01*rinv01*(rinvsq01-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r02 = rsq02*rinv02;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r02*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq02*(rinv02-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq02*rinv02*(rinvsq02-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*(rinv11-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*(rinv12-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*(rinv21-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*(rinv22-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 372 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*372);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwLJ_GeomW3W3_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEw_VdwLJ_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r01 = rsq01*rinv01;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r01*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq01*rinv01*(rinvsq01-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r02 = rsq02*rinv02;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r02*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq02*rinv02*(rinvsq02-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 304 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*304);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwLJ_GeomW4P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEw_VdwLJ_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = 1.0/rsq00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r30*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq30*(rinv30-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq30*rinv30*(rinvsq30-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 155 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*155);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwLJ_GeomW4P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEw_VdwLJ_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = 1.0/rsq00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r30*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq30*rinv30*(rinvsq30-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 129 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*129);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwLJ_GeomW4W4_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEw_VdwLJ_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = 1.0/rsq00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*(rinv11-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*(rinv12-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r13 = rsq13*rinv13;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r13*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq13*(rinv13-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq13*rinv13*(rinvsq13-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*(rinv21-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*(rinv22-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r23 = rsq23*rinv23;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r23*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq23*(rinv23-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq23*rinv23*(rinvsq23-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r31 = rsq31*rinv31;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r31*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq31*(rinv31-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq31*rinv31*(rinvsq31-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r32 = rsq32*rinv32;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r32*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq32*(rinv32-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq32*rinv32*(rinvsq32-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r33 = rsq33*rinv33;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r33*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq33*(rinv33-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq33*rinv33*(rinvsq33-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 392 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_VF,outeriter*41 + inneriter*392);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwLJ_GeomW4W4_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEw_VdwLJ_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = 1.0/rsq00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r13 = rsq13*rinv13;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r13*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq13*rinv13*(rinvsq13-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r23 = rsq23*rinv23;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r23*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq23*rinv23*(rinvsq23-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r31 = rsq31*rinv31;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r31*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq31*rinv31*(rinvsq31-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r32 = rsq32*rinv32;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r32*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq32*rinv32*(rinvsq32-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r33 = rsq33*rinv33;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r33*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq33*rinv33*(rinvsq33-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 324 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_F,outeriter*39 + inneriter*324);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwNone_GeomP1P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEw_VdwNone_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 41 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 14 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*14 + inneriter*41);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwNone_GeomP1P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEw_VdwNone_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 34 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*13 + inneriter*34);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwNone_GeomW3P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEw_VdwNone_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 123 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3_VF,outeriter*31 + inneriter*123);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwNone_GeomW3P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEw_VdwNone_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 102 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3_F,outeriter*30 + inneriter*102);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwNone_GeomW3W3_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEw_VdwNone_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ qq00 = iq0*jq0;
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq00*(rinv00-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r01 = rsq01*rinv01;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r01*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq01*(rinv01-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq01*rinv01*(rinvsq01-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r02 = rsq02*rinv02;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r02*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq02*(rinv02-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq02*rinv02*(rinvsq02-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*(rinv11-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*(rinv12-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*(rinv21-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*(rinv22-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 360 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3W3_VF,outeriter*31 + inneriter*360);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwNone_GeomW3W3_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEw_VdwNone_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ qq00 = iq0*jq0;
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r00*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq00*rinv00*(rinvsq00-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r01 = rsq01*rinv01;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r01*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq01*rinv01*(rinvsq01-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r02 = rsq02*rinv02;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r02*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq02*rinv02*(rinvsq02-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 297 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3W3_F,outeriter*30 + inneriter*297);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwNone_GeomW4P1_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEw_VdwNone_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq10*(rinv10-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq20*(rinv20-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r30*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq30*(rinv30-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq30*rinv30*(rinvsq30-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 123 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4_VF,outeriter*31 + inneriter*123);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwNone_GeomW4P1_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEw_VdwNone_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r10 = rsq10*rinv10;
+
+ qq10 = iq1*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r10*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq10*rinv10*(rinvsq10-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r20 = rsq20*rinv20;
+
+ qq20 = iq2*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r20*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq20*rinv20*(rinvsq20-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r30 = rsq30*rinv30;
+
+ qq30 = iq3*jq0;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r30*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq30*rinv30*(rinvsq30-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 102 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4_F,outeriter*30 + inneriter*102);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwNone_GeomW4W4_VF_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecEw_VdwNone_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq11*(rinv11-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq12*(rinv12-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r13 = rsq13*rinv13;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r13*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq13*(rinv13-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq13*rinv13*(rinvsq13-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq21*(rinv21-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq22*(rinv22-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r23 = rsq23*rinv23;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r23*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq23*(rinv23-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq23*rinv23*(rinvsq23-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r31 = rsq31*rinv31;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r31*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq31*(rinv31-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq31*rinv31*(rinvsq31-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r32 = rsq32*rinv32;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r32*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq32*(rinv32-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq32*rinv32*(rinvsq32-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r33 = rsq33*rinv33;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r33*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ velec = qq33*(rinv33-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ felec = qq33*rinv33*(rinvsq33-felec);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 360 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4W4_VF,outeriter*31 + inneriter*360);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecEw_VdwNone_GeomW4W4_F_c
+ * Electrostatics interaction: Ewald
+ * VdW interaction: None
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecEw_VdwNone_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ sh_ewald = fr->ic->sh_ewald;
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r11 = rsq11*rinv11;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r11*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq11*rinv11*(rinvsq11-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r12 = rsq12*rinv12;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r12*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq12*rinv12*(rinvsq12-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r13 = rsq13*rinv13;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r13*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq13*rinv13*(rinvsq13-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r21 = rsq21*rinv21;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r21*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq21*rinv21*(rinvsq21-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r22 = rsq22*rinv22;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r22*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq22*rinv22*(rinvsq22-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r23 = rsq23*rinv23;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r23*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq23*rinv23*(rinvsq23-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r31 = rsq31*rinv31;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r31*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq31*rinv31*(rinvsq31-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r32 = rsq32*rinv32;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r32*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq32*rinv32*(rinvsq32-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r33 = rsq33*rinv33;
+
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r33*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq33*rinv33*(rinvsq33-felec);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 297 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4W4_F,outeriter*30 + inneriter*297);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwBham_GeomP1P1_VF_c
+ * Electrostatics interaction: GeneralizedBorn
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecGB_VdwBham_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int gbitab;
+ real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
+ real *invsqrta,*dvda,*gbtab;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ invsqrta = fr->invsqrta;
+ dvda = fr->dvda;
+ gbtabscale = fr->gbtab.scale;
+ gbtab = fr->gbtab.data;
+ gbinvepsdiff = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ isai0 = invsqrta[inr+0];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vgbsum = 0.0;
+ vvdwsum = 0.0;
+ dvdasum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ isaj0 = invsqrta[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
+ isaprod = isai0*isaj0;
+ gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
+ gbscale = isaprod*gbtabscale;
+ dvdaj = dvda[jnr+0];
+
+ /* Calculate generalized born table index - this is a separate table from the normal one,
+ * but we use the same procedure by multiplying r with scale and truncating to integer.
+ */
+ rt = r00*gbscale;
+ gbitab = rt;
+ gbeps = rt-gbitab;
+ gbitab = 4*gbitab;
+
+ Y = gbtab[gbitab];
+ F = gbtab[gbitab+1];
+ Geps = gbeps*gbtab[gbitab+2];
+ Heps2 = gbeps*gbeps*gbtab[gbitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+gbeps*Fp;
+ vgb = gbqqfactor*VV;
+
+ FF = Fp+Geps+2.0*Heps2;
+ fgb = gbqqfactor*FF*gbscale;
+ dvdatmp = -0.5*(vgb+fgb*r00);
+ dvdasum = dvdasum + dvdatmp;
+ dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
+ velec = qq00*rinv00;
+ felec = (velec*rinv00-fgb)*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vgbsum += vgb;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 97 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_polarization[ggid] += vgbsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+ dvda[nri] = dvda[nri] + dvdasum*isai0*isai0;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 16 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*16 + inneriter*97);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwBham_GeomP1P1_F_c
+ * Electrostatics interaction: GeneralizedBorn
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecGB_VdwBham_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int gbitab;
+ real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
+ real *invsqrta,*dvda,*gbtab;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ invsqrta = fr->invsqrta;
+ dvda = fr->dvda;
+ gbtabscale = fr->gbtab.scale;
+ gbtab = fr->gbtab.data;
+ gbinvepsdiff = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ isai0 = invsqrta[inr+0];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ dvdasum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ isaj0 = invsqrta[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
+ isaprod = isai0*isaj0;
+ gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
+ gbscale = isaprod*gbtabscale;
+ dvdaj = dvda[jnr+0];
+
+ /* Calculate generalized born table index - this is a separate table from the normal one,
+ * but we use the same procedure by multiplying r with scale and truncating to integer.
+ */
+ rt = r00*gbscale;
+ gbitab = rt;
+ gbeps = rt-gbitab;
+ gbitab = 4*gbitab;
+
+ Y = gbtab[gbitab];
+ F = gbtab[gbitab+1];
+ Geps = gbeps*gbtab[gbitab+2];
+ Heps2 = gbeps*gbeps*gbtab[gbitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+gbeps*Fp;
+ vgb = gbqqfactor*VV;
+
+ FF = Fp+Geps+2.0*Heps2;
+ fgb = gbqqfactor*FF*gbscale;
+ dvdatmp = -0.5*(vgb+fgb*r00);
+ dvdasum = dvdasum + dvdatmp;
+ dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
+ velec = qq00*rinv00;
+ felec = (velec*rinv00-fgb)*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 92 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ dvda[nri] = dvda[nri] + dvdasum*isai0*isai0;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*92);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_c
+ * Electrostatics interaction: GeneralizedBorn
+ * VdW interaction: CubicSplineTable
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int gbitab;
+ real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
+ real *invsqrta,*dvda,*gbtab;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ invsqrta = fr->invsqrta;
+ dvda = fr->dvda;
+ gbtabscale = fr->gbtab.scale;
+ gbtab = fr->gbtab.data;
+ gbinvepsdiff = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ isai0 = invsqrta[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vgbsum = 0.0;
+ vvdwsum = 0.0;
+ dvdasum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ isaj0 = invsqrta[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
+ isaprod = isai0*isaj0;
+ gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
+ gbscale = isaprod*gbtabscale;
+ dvdaj = dvda[jnr+0];
+
+ /* Calculate generalized born table index - this is a separate table from the normal one,
+ * but we use the same procedure by multiplying r with scale and truncating to integer.
+ */
+ rt = r00*gbscale;
+ gbitab = rt;
+ gbeps = rt-gbitab;
+ gbitab = 4*gbitab;
+
+ Y = gbtab[gbitab];
+ F = gbtab[gbitab+1];
+ Geps = gbeps*gbtab[gbitab+2];
+ Heps2 = gbeps*gbeps*gbtab[gbitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+gbeps*Fp;
+ vgb = gbqqfactor*VV;
+
+ FF = Fp+Geps+2.0*Heps2;
+ fgb = gbqqfactor*FF*gbscale;
+ dvdatmp = -0.5*(vgb+fgb*r00);
+ dvdasum = dvdasum + dvdatmp;
+ dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
+ velec = qq00*rinv00;
+ felec = (velec*rinv00-fgb)*rinv00;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vgbsum += vgb;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 91 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_polarization[ggid] += vgbsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+ dvda[nri] = dvda[nri] + dvdasum*isai0*isai0;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 16 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*16 + inneriter*91);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_c
+ * Electrostatics interaction: GeneralizedBorn
+ * VdW interaction: CubicSplineTable
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int gbitab;
+ real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
+ real *invsqrta,*dvda,*gbtab;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ invsqrta = fr->invsqrta;
+ dvda = fr->dvda;
+ gbtabscale = fr->gbtab.scale;
+ gbtab = fr->gbtab.data;
+ gbinvepsdiff = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ isai0 = invsqrta[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ dvdasum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ isaj0 = invsqrta[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
+ isaprod = isai0*isaj0;
+ gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
+ gbscale = isaprod*gbtabscale;
+ dvdaj = dvda[jnr+0];
+
+ /* Calculate generalized born table index - this is a separate table from the normal one,
+ * but we use the same procedure by multiplying r with scale and truncating to integer.
+ */
+ rt = r00*gbscale;
+ gbitab = rt;
+ gbeps = rt-gbitab;
+ gbitab = 4*gbitab;
+
+ Y = gbtab[gbitab];
+ F = gbtab[gbitab+1];
+ Geps = gbeps*gbtab[gbitab+2];
+ Heps2 = gbeps*gbeps*gbtab[gbitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+gbeps*Fp;
+ vgb = gbqqfactor*VV;
+
+ FF = Fp+Geps+2.0*Heps2;
+ fgb = gbqqfactor*FF*gbscale;
+ dvdatmp = -0.5*(vgb+fgb*r00);
+ dvdasum = dvdasum + dvdatmp;
+ dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
+ velec = qq00*rinv00;
+ felec = (velec*rinv00-fgb)*rinv00;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 81 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ dvda[nri] = dvda[nri] + dvdasum*isai0*isai0;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*81);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_c
+ * Electrostatics interaction: GeneralizedBorn
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int gbitab;
+ real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
+ real *invsqrta,*dvda,*gbtab;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ invsqrta = fr->invsqrta;
+ dvda = fr->dvda;
+ gbtabscale = fr->gbtab.scale;
+ gbtab = fr->gbtab.data;
+ gbinvepsdiff = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ isai0 = invsqrta[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vgbsum = 0.0;
+ vvdwsum = 0.0;
+ dvdasum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ isaj0 = invsqrta[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
+ isaprod = isai0*isaj0;
+ gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
+ gbscale = isaprod*gbtabscale;
+ dvdaj = dvda[jnr+0];
+
+ /* Calculate generalized born table index - this is a separate table from the normal one,
+ * but we use the same procedure by multiplying r with scale and truncating to integer.
+ */
+ rt = r00*gbscale;
+ gbitab = rt;
+ gbeps = rt-gbitab;
+ gbitab = 4*gbitab;
+
+ Y = gbtab[gbitab];
+ F = gbtab[gbitab+1];
+ Geps = gbeps*gbtab[gbitab+2];
+ Heps2 = gbeps*gbeps*gbtab[gbitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+gbeps*Fp;
+ vgb = gbqqfactor*VV;
+
+ FF = Fp+Geps+2.0*Heps2;
+ fgb = gbqqfactor*FF*gbscale;
+ dvdatmp = -0.5*(vgb+fgb*r00);
+ dvdasum = dvdasum + dvdatmp;
+ dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
+ velec = qq00*rinv00;
+ felec = (velec*rinv00-fgb)*rinv00;
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vgbsum += vgb;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 71 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_polarization[ggid] += vgbsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+ dvda[nri] = dvda[nri] + dvdasum*isai0*isai0;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 16 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*16 + inneriter*71);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_c
+ * Electrostatics interaction: GeneralizedBorn
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int gbitab;
+ real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
+ real *invsqrta,*dvda,*gbtab;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ invsqrta = fr->invsqrta;
+ dvda = fr->dvda;
+ gbtabscale = fr->gbtab.scale;
+ gbtab = fr->gbtab.data;
+ gbinvepsdiff = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ isai0 = invsqrta[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ dvdasum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ isaj0 = invsqrta[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
+ isaprod = isai0*isaj0;
+ gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
+ gbscale = isaprod*gbtabscale;
+ dvdaj = dvda[jnr+0];
+
+ /* Calculate generalized born table index - this is a separate table from the normal one,
+ * but we use the same procedure by multiplying r with scale and truncating to integer.
+ */
+ rt = r00*gbscale;
+ gbitab = rt;
+ gbeps = rt-gbitab;
+ gbitab = 4*gbitab;
+
+ Y = gbtab[gbitab];
+ F = gbtab[gbitab+1];
+ Geps = gbeps*gbtab[gbitab+2];
+ Heps2 = gbeps*gbeps*gbtab[gbitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+gbeps*Fp;
+ vgb = gbqqfactor*VV;
+
+ FF = Fp+Geps+2.0*Heps2;
+ fgb = gbqqfactor*FF*gbscale;
+ dvdatmp = -0.5*(vgb+fgb*r00);
+ dvdasum = dvdasum + dvdatmp;
+ dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
+ velec = qq00*rinv00;
+ felec = (velec*rinv00-fgb)*rinv00;
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 64 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ dvda[nri] = dvda[nri] + dvdasum*isai0*isai0;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*64);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_c
+ * Electrostatics interaction: GeneralizedBorn
+ * VdW interaction: None
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int gbitab;
+ real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
+ real *invsqrta,*dvda,*gbtab;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ invsqrta = fr->invsqrta;
+ dvda = fr->dvda;
+ gbtabscale = fr->gbtab.scale;
+ gbtab = fr->gbtab.data;
+ gbinvepsdiff = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ isai0 = invsqrta[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vgbsum = 0.0;
+ dvdasum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ isaj0 = invsqrta[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+
+ /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
+ isaprod = isai0*isaj0;
+ gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
+ gbscale = isaprod*gbtabscale;
+ dvdaj = dvda[jnr+0];
+
+ /* Calculate generalized born table index - this is a separate table from the normal one,
+ * but we use the same procedure by multiplying r with scale and truncating to integer.
+ */
+ rt = r00*gbscale;
+ gbitab = rt;
+ gbeps = rt-gbitab;
+ gbitab = 4*gbitab;
+
+ Y = gbtab[gbitab];
+ F = gbtab[gbitab+1];
+ Geps = gbeps*gbtab[gbitab+2];
+ Heps2 = gbeps*gbeps*gbtab[gbitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+gbeps*Fp;
+ vgb = gbqqfactor*VV;
+
+ FF = Fp+Geps+2.0*Heps2;
+ fgb = gbqqfactor*FF*gbscale;
+ dvdatmp = -0.5*(vgb+fgb*r00);
+ dvdasum = dvdasum + dvdatmp;
+ dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
+ velec = qq00*rinv00;
+ felec = (velec*rinv00-fgb)*rinv00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vgbsum += vgb;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 58 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_polarization[ggid] += vgbsum;
+ dvda[nri] = dvda[nri] + dvdasum*isai0*isai0;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 15 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*15 + inneriter*58);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecGB_VdwNone_GeomP1P1_F_c
+ * Electrostatics interaction: GeneralizedBorn
+ * VdW interaction: None
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecGB_VdwNone_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int gbitab;
+ real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
+ real *invsqrta,*dvda,*gbtab;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+
+ invsqrta = fr->invsqrta;
+ dvda = fr->dvda;
+ gbtabscale = fr->gbtab.scale;
+ gbtab = fr->gbtab.data;
+ gbinvepsdiff = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ isai0 = invsqrta[inr+0];
+
+ dvdasum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ isaj0 = invsqrta[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+
+ /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
+ isaprod = isai0*isaj0;
+ gbqqfactor = isaprod*(-qq00)*gbinvepsdiff;
+ gbscale = isaprod*gbtabscale;
+ dvdaj = dvda[jnr+0];
+
+ /* Calculate generalized born table index - this is a separate table from the normal one,
+ * but we use the same procedure by multiplying r with scale and truncating to integer.
+ */
+ rt = r00*gbscale;
+ gbitab = rt;
+ gbeps = rt-gbitab;
+ gbitab = 4*gbitab;
+
+ Y = gbtab[gbitab];
+ F = gbtab[gbitab+1];
+ Geps = gbeps*gbtab[gbitab+2];
+ Heps2 = gbeps*gbeps*gbtab[gbitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+gbeps*Fp;
+ vgb = gbqqfactor*VV;
+
+ FF = Fp+Geps+2.0*Heps2;
+ fgb = gbqqfactor*FF*gbscale;
+ dvdatmp = -0.5*(vgb+fgb*r00);
+ dvdasum = dvdasum + dvdatmp;
+ dvda[jnr] = dvdaj+dvdatmp*isaj0*isaj0;
+ velec = qq00*rinv00;
+ felec = (velec*rinv00-fgb)*rinv00;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 56 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ dvda[nri] = dvda[nri] + dvdasum*isai0*isai0;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*13 + inneriter*56);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_VF_c
+ * Electrostatics interaction: None
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ rcutoff = fr->rvdw;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = (vvdwexp-cexp1_00*exp(-cexp2_00*rvdw)) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 92 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_VDW_VF,outeriter*13 + inneriter*92);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_F_c
+ * Electrostatics interaction: None
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ rcutoff = fr->rvdw;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 58 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 12 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_VDW_F,outeriter*12 + inneriter*58);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_VF_c
+ * Electrostatics interaction: None
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ rcutoff = fr->rvdw;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ vvdw *= sw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 79 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_VDW_VF,outeriter*13 + inneriter*79);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_F_c
+ * Electrostatics interaction: None
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ rcutoff = fr->rvdw;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 77 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 12 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_VDW_F,outeriter*12 + inneriter*77);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwBham_GeomP1P1_VF_c
+ * Electrostatics interaction: None
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecNone_VdwBham_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 61 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_VDW_VF,outeriter*13 + inneriter*61);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwBham_GeomP1P1_F_c
+ * Electrostatics interaction: None
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecNone_VdwBham_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 58 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 12 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_VDW_F,outeriter*12 + inneriter*58);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_c
+ * Electrostatics interaction: None
+ * VdW interaction: CubicSplineTable
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ /* Load parameters for j particles */
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 55 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_VDW_VF,outeriter*13 + inneriter*55);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_c
+ * Electrostatics interaction: None
+ * VdW interaction: CubicSplineTable
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ /* Load parameters for j particles */
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 47 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 12 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_VDW_F,outeriter*12 + inneriter*47);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwLJSh_GeomP1P1_VF_c
+ * Electrostatics interaction: None
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecNone_VdwLJSh_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ rcutoff = fr->rvdw;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinvsq00 = 1.0/rsq00;
+
+ /* Load parameters for j particles */
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = (vvdw12 - c12_00*sh_vdw_invrcut6*sh_vdw_invrcut6)*(1.0/12.0) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 37 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_VDW_VF,outeriter*13 + inneriter*37);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwLJSh_GeomP1P1_F_c
+ * Electrostatics interaction: None
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecNone_VdwLJSh_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ rcutoff = fr->rvdw;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinvsq00 = 1.0/rsq00;
+
+ /* Load parameters for j particles */
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 27 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 12 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_VDW_F,outeriter*12 + inneriter*27);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwLJSw_GeomP1P1_VF_c
+ * Electrostatics interaction: None
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecNone_VdwLJSw_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ rcutoff = fr->rvdw;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ vvdw *= sw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 53 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_VDW_VF,outeriter*13 + inneriter*53);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_c
+ * Electrostatics interaction: None
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ rcutoff = fr->rvdw;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 51 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 12 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_VDW_F,outeriter*12 + inneriter*51);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_c
+ * Electrostatics interaction: None
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinvsq00 = 1.0/rsq00;
+
+ /* Load parameters for j particles */
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 32 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_VDW_VF,outeriter*13 + inneriter*32);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_c
+ * Electrostatics interaction: None
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinvsq00 = 1.0/rsq00;
+
+ /* Load parameters for j particles */
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 27 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 12 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_VDW_F,outeriter*12 + inneriter*27);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = (vvdwexp-cexp1_00*exp(-cexp2_00*rvdw)) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 102 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 15 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*102);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 63 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*63);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = (vvdwexp-cexp1_00*exp(-cexp2_00*rvdw)) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 166 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*166);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 117 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*117);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = (vvdwexp-cexp1_00*exp(-cexp2_00*rvdw)) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq01*(rinv01+krf*rsq01-crf);
+ felec = qq01*(rinv01*rinvsq01-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq02*(rinv02+krf*rsq02-crf);
+ felec = qq02*(rinv02*rinvsq02-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq11*(rinv11+krf*rsq11-crf);
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq12*(rinv12+krf*rsq12-crf);
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq21*(rinv21+krf*rsq21-crf);
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq22*(rinv22+krf*rsq22-crf);
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 349 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*349);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq01*(rinv01*rinvsq01-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq02*(rinv02*rinvsq02-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 270 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*270);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = (vvdwexp-cexp1_00*exp(-cexp2_00*rvdw)) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ qq30 = iq3*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq30*(rinv30+krf*rsq30-crf);
+ felec = qq30*(rinv30*rinvsq30-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 188 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*188);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ qq30 = iq3*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq30*(rinv30*rinvsq30-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 139 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*139);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = (vvdwexp-cexp1_00*exp(-cexp2_00*rvdw)) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq11*(rinv11+krf*rsq11-crf);
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq12*(rinv12+krf*rsq12-crf);
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq13*(rinv13+krf*rsq13-crf);
+ felec = qq13*(rinv13*rinvsq13-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq21*(rinv21+krf*rsq21-crf);
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq22*(rinv22+krf*rsq22-crf);
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq23*(rinv23+krf*rsq23-crf);
+ felec = qq23*(rinv23*rinvsq23-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq31*(rinv31+krf*rsq31-crf);
+ felec = qq31*(rinv31*rinvsq31-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq32*(rinv32+krf*rsq32-crf);
+ felec = qq32*(rinv32*rinvsq32-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq33*(rinv33+krf*rsq33-crf);
+ felec = qq33*(rinv33*rinvsq33-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 371 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_VF,outeriter*41 + inneriter*371);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq13*(rinv13*rinvsq13-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq23*(rinv23*rinvsq23-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq31*(rinv31*rinvsq31-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq32*(rinv32*rinvsq32-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq33*(rinv33*rinvsq33-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 292 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_F,outeriter*39 + inneriter*292);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ vvdw *= sw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 89 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 15 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*89);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 82 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*82);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ vvdw *= sw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 153 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*153);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 136 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*136);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ vvdw *= sw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq01*(rinv01+krf*rsq01-crf);
+ felec = qq01*(rinv01*rinvsq01-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq02*(rinv02+krf*rsq02-crf);
+ felec = qq02*(rinv02*rinvsq02-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq11*(rinv11+krf*rsq11-crf);
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq12*(rinv12+krf*rsq12-crf);
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq21*(rinv21+krf*rsq21-crf);
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq22*(rinv22+krf*rsq22-crf);
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 336 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*336);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq01*(rinv01*rinvsq01-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq02*(rinv02*rinvsq02-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 289 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*289);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ vvdw *= sw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ qq30 = iq3*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq30*(rinv30+krf*rsq30-crf);
+ felec = qq30*(rinv30*rinvsq30-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 175 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*175);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ qq30 = iq3*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq30*(rinv30*rinvsq30-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 158 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*158);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ vvdw *= sw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq11*(rinv11+krf*rsq11-crf);
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq12*(rinv12+krf*rsq12-crf);
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq13*(rinv13+krf*rsq13-crf);
+ felec = qq13*(rinv13*rinvsq13-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq21*(rinv21+krf*rsq21-crf);
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq22*(rinv22+krf*rsq22-crf);
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq23*(rinv23+krf*rsq23-crf);
+ felec = qq23*(rinv23*rinvsq23-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq31*(rinv31+krf*rsq31-crf);
+ felec = qq31*(rinv31*rinvsq31-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq32*(rinv32+krf*rsq32-crf);
+ felec = qq32*(rinv32*rinvsq32-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq33*(rinv33+krf*rsq33-crf);
+ felec = qq33*(rinv33*rinvsq33-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 358 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_VF,outeriter*41 + inneriter*358);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq13*(rinv13*rinvsq13-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq23*(rinv23*rinvsq23-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq31*(rinv31*rinvsq31-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq32*(rinv32*rinvsq32-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq33*(rinv33*rinvsq33-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 311 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_F,outeriter*39 + inneriter*311);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: CubicSplineTable
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 66 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 15 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*66);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: CubicSplineTable
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 53 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*53);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 130 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*130);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 107 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*107);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq01*(rinv01+krf*rsq01-crf);
+ felec = qq01*(rinv01*rinvsq01-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq02*(rinv02+krf*rsq02-crf);
+ felec = qq02*(rinv02*rinvsq02-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq11*(rinv11+krf*rsq11-crf);
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq12*(rinv12+krf*rsq12-crf);
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq21*(rinv21+krf*rsq21-crf);
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq22*(rinv22+krf*rsq22-crf);
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 313 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*313);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq01*(rinv01*rinvsq01-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq02*(rinv02*rinvsq02-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 260 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*260);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ qq30 = iq3*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq30*(rinv30+krf*rsq30-crf);
+ felec = qq30*(rinv30*rinvsq30-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 151 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*151);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ qq30 = iq3*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq30*(rinv30*rinvsq30-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 128 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*128);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq11*(rinv11+krf*rsq11-crf);
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq12*(rinv12+krf*rsq12-crf);
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq13*(rinv13+krf*rsq13-crf);
+ felec = qq13*(rinv13*rinvsq13-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq21*(rinv21+krf*rsq21-crf);
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq22*(rinv22+krf*rsq22-crf);
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq23*(rinv23+krf*rsq23-crf);
+ felec = qq23*(rinv23*rinvsq23-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq31*(rinv31+krf*rsq31-crf);
+ felec = qq31*(rinv31*rinvsq31-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq32*(rinv32+krf*rsq32-crf);
+ felec = qq32*(rinv32*rinvsq32-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq33*(rinv33+krf*rsq33-crf);
+ felec = qq33*(rinv33*rinvsq33-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 334 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_VF,outeriter*41 + inneriter*334);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq13*(rinv13*rinvsq13-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq23*(rinv23*rinvsq23-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq31*(rinv31*rinvsq31-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq32*(rinv32*rinvsq32-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq33*(rinv33*rinvsq33-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 281 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_F,outeriter*39 + inneriter*281);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = (vvdw12 - c12_00*sh_vdw_invrcut6*sh_vdw_invrcut6)*(1.0/12.0) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 49 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 15 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*49);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 34 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*34);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = (vvdw12 - c12_00*sh_vdw_invrcut6*sh_vdw_invrcut6)*(1.0/12.0) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 113 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*113);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 88 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*88);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = (vvdw12 - c12_00*sh_vdw_invrcut6*sh_vdw_invrcut6)*(1.0/12.0) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq01*(rinv01+krf*rsq01-crf);
+ felec = qq01*(rinv01*rinvsq01-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq02*(rinv02+krf*rsq02-crf);
+ felec = qq02*(rinv02*rinvsq02-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq11*(rinv11+krf*rsq11-crf);
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq12*(rinv12+krf*rsq12-crf);
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq21*(rinv21+krf*rsq21-crf);
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq22*(rinv22+krf*rsq22-crf);
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 296 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*296);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq01*(rinv01*rinvsq01-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq02*(rinv02*rinvsq02-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 241 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*241);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = 1.0/rsq00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = (vvdw12 - c12_00*sh_vdw_invrcut6*sh_vdw_invrcut6)*(1.0/12.0) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ qq30 = iq3*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq30*(rinv30+krf*rsq30-crf);
+ felec = qq30*(rinv30*rinvsq30-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 133 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*133);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = 1.0/rsq00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ qq30 = iq3*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq30*(rinv30*rinvsq30-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 108 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*108);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = 1.0/rsq00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = (vvdw12 - c12_00*sh_vdw_invrcut6*sh_vdw_invrcut6)*(1.0/12.0) - (vvdw6 - c6_00*sh_vdw_invrcut6)*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq11*(rinv11+krf*rsq11-crf);
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq12*(rinv12+krf*rsq12-crf);
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq13*(rinv13+krf*rsq13-crf);
+ felec = qq13*(rinv13*rinvsq13-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq21*(rinv21+krf*rsq21-crf);
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq22*(rinv22+krf*rsq22-crf);
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq23*(rinv23+krf*rsq23-crf);
+ felec = qq23*(rinv23*rinvsq23-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq31*(rinv31+krf*rsq31-crf);
+ felec = qq31*(rinv31*rinvsq31-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq32*(rinv32+krf*rsq32-crf);
+ felec = qq32*(rinv32*rinvsq32-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq33*(rinv33+krf*rsq33-crf);
+ felec = qq33*(rinv33*rinvsq33-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 316 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_VF,outeriter*41 + inneriter*316);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = 1.0/rsq00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq13*(rinv13*rinvsq13-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq23*(rinv23*rinvsq23-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq31*(rinv31*rinvsq31-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq32*(rinv32*rinvsq32-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq33*(rinv33*rinvsq33-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 261 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_F,outeriter*39 + inneriter*261);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ vvdw *= sw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 63 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 15 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*63);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 56 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*56);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ vvdw *= sw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 127 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*127);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 110 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*110);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ vvdw *= sw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq01*(rinv01+krf*rsq01-crf);
+ felec = qq01*(rinv01*rinvsq01-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq02*(rinv02+krf*rsq02-crf);
+ felec = qq02*(rinv02*rinvsq02-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq11*(rinv11+krf*rsq11-crf);
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq12*(rinv12+krf*rsq12-crf);
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq21*(rinv21+krf*rsq21-crf);
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq22*(rinv22+krf*rsq22-crf);
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 310 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*310);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq01*(rinv01*rinvsq01-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq02*(rinv02*rinvsq02-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 263 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*263);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ vvdw *= sw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ qq30 = iq3*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq30*(rinv30+krf*rsq30-crf);
+ felec = qq30*(rinv30*rinvsq30-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 149 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*149);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ qq30 = iq3*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq30*(rinv30*rinvsq30-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 132 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*132);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ vvdw *= sw;
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq11*(rinv11+krf*rsq11-crf);
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq12*(rinv12+krf*rsq12-crf);
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq13*(rinv13+krf*rsq13-crf);
+ felec = qq13*(rinv13*rinvsq13-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq21*(rinv21+krf*rsq21-crf);
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq22*(rinv22+krf*rsq22-crf);
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq23*(rinv23+krf*rsq23-crf);
+ felec = qq23*(rinv23*rinvsq23-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq31*(rinv31+krf*rsq31-crf);
+ felec = qq31*(rinv31*rinvsq31-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq32*(rinv32+krf*rsq32-crf);
+ felec = qq32*(rinv32*rinvsq32-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq33*(rinv33+krf*rsq33-crf);
+ felec = qq33*(rinv33*rinvsq33-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 332 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_VF,outeriter*41 + inneriter*332);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ rswitch = fr->rvdw_switch;
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ r00 = rsq00*rinv00;
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ d = r00-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+
+ /* Evaluate switch function */
+ fvdw = fvdw*sw + vvdw*dsw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq13*(rinv13*rinvsq13-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq23*(rinv23*rinvsq23-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq31*(rinv31*rinvsq31-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq32*(rinv32*rinvsq32-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq33*(rinv33*rinvsq33-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 285 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_F,outeriter*39 + inneriter*285);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwNone_GeomP1P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: None
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwNone_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ qq00 = iq0*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 32 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 14 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*14 + inneriter*32);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwNone_GeomP1P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: None
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwNone_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ qq00 = iq0*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 27 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*13 + inneriter*27);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwNone_GeomW3P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: None
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwNone_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ qq00 = iq0*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 96 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3_VF,outeriter*31 + inneriter*96);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwNone_GeomW3P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: None
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwNone_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ qq00 = iq0*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 81 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3_F,outeriter*30 + inneriter*81);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwNone_GeomW3W3_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: None
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwNone_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ qq00 = iq0*jq0;
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq01*(rinv01+krf*rsq01-crf);
+ felec = qq01*(rinv01*rinvsq01-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq02*(rinv02+krf*rsq02-crf);
+ felec = qq02*(rinv02*rinvsq02-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq11*(rinv11+krf*rsq11-crf);
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq12*(rinv12+krf*rsq12-crf);
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq21*(rinv21+krf*rsq21-crf);
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq22*(rinv22+krf*rsq22-crf);
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 279 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3W3_VF,outeriter*31 + inneriter*279);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwNone_GeomW3W3_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: None
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwNone_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ qq00 = iq0*jq0;
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq00<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq01<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq01*(rinv01*rinvsq01-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq02<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq02*(rinv02*rinvsq02-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 234 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3W3_F,outeriter*30 + inneriter*234);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwNone_GeomW4P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: None
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwNone_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ qq30 = iq3*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq30*(rinv30+krf*rsq30-crf);
+ felec = qq30*(rinv30*rinvsq30-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 96 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4_VF,outeriter*31 + inneriter*96);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwNone_GeomW4P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: None
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwNone_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq10<rcutoff2)
+ {
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq20<rcutoff2)
+ {
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq30<rcutoff2)
+ {
+
+ qq30 = iq3*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq30*(rinv30*rinvsq30-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 81 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4_F,outeriter*30 + inneriter*81);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwNone_GeomW4W4_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: None
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRFCut_VdwNone_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq11*(rinv11+krf*rsq11-crf);
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq12*(rinv12+krf*rsq12-crf);
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq13*(rinv13+krf*rsq13-crf);
+ felec = qq13*(rinv13*rinvsq13-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq21*(rinv21+krf*rsq21-crf);
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq22*(rinv22+krf*rsq22-crf);
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq23*(rinv23+krf*rsq23-crf);
+ felec = qq23*(rinv23*rinvsq23-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq31*(rinv31+krf*rsq31-crf);
+ felec = qq31*(rinv31*rinvsq31-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq32*(rinv32+krf*rsq32-crf);
+ felec = qq32*(rinv32*rinvsq32-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq33*(rinv33+krf*rsq33-crf);
+ felec = qq33*(rinv33*rinvsq33-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 279 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4W4_VF,outeriter*31 + inneriter*279);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRFCut_VdwNone_GeomW4W4_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: None
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRFCut_VdwNone_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ rcutoff2 = rcutoff*rcutoff;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq11<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq12<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq13<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq13*(rinv13*rinvsq13-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq21<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq22<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq23<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq23*(rinv23*rinvsq23-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq31<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq31*(rinv31*rinvsq31-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq32<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq32*(rinv32*rinvsq32-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ }
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ if (rsq33<rcutoff2)
+ {
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq33*(rinv33*rinvsq33-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ }
+
+ /* Inner loop uses 234 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4W4_F,outeriter*30 + inneriter*234);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwBham_GeomP1P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRF_VdwBham_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 71 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 15 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*71);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwBham_GeomP1P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRF_VdwBham_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 63 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*63);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwBham_GeomW3P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRF_VdwBham_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 135 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*135);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwBham_GeomW3P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRF_VdwBham_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 117 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*117);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwBham_GeomW3W3_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRF_VdwBham_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq01*(rinv01+krf*rsq01-crf);
+ felec = qq01*(rinv01*rinvsq01-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq02*(rinv02+krf*rsq02-crf);
+ felec = qq02*(rinv02*rinvsq02-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq11*(rinv11+krf*rsq11-crf);
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq12*(rinv12+krf*rsq12-crf);
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq21*(rinv21+krf*rsq21-crf);
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq22*(rinv22+krf*rsq22-crf);
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 318 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*318);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwBham_GeomW3W3_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRF_VdwBham_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq01*(rinv01*rinvsq01-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq02*(rinv02*rinvsq02-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 270 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*270);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwBham_GeomW4P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRF_VdwBham_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq30 = iq3*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq30*(rinv30+krf*rsq30-crf);
+ felec = qq30*(rinv30*rinvsq30-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 157 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*157);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwBham_GeomW4P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRF_VdwBham_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 3*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq30 = iq3*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq30*(rinv30*rinvsq30-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 139 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*139);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwBham_GeomW4W4_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRF_VdwBham_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq11*(rinv11+krf*rsq11-crf);
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq12*(rinv12+krf*rsq12-crf);
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq13*(rinv13+krf*rsq13-crf);
+ felec = qq13*(rinv13*rinvsq13-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq21*(rinv21+krf*rsq21-crf);
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq22*(rinv22+krf*rsq22-crf);
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq23*(rinv23+krf*rsq23-crf);
+ felec = qq23*(rinv23*rinvsq23-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq31*(rinv31+krf*rsq31-crf);
+ felec = qq31*(rinv31*rinvsq31-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq32*(rinv32+krf*rsq32-crf);
+ felec = qq32*(rinv32*rinvsq32-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq33*(rinv33+krf*rsq33-crf);
+ felec = qq33*(rinv33*rinvsq33-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 340 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_VF,outeriter*41 + inneriter*340);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwBham_GeomW4W4_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: Buckingham
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRF_VdwBham_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 3*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 3*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ cexp1_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ cexp2_00 = vdwparam[vdwioffset0+vdwjidx0+2];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ br = cexp2_00*r00;
+ vvdwexp = cexp1_00*exp(-br);
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq13*(rinv13*rinvsq13-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq23*(rinv23*rinvsq23-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq31*(rinv31*rinvsq31-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq32*(rinv32*rinvsq32-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq33*(rinv33*rinvsq33-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 292 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_F,outeriter*39 + inneriter*292);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwCSTab_GeomP1P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: CubicSplineTable
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRF_VdwCSTab_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 66 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 15 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*66);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwCSTab_GeomP1P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: CubicSplineTable
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRF_VdwCSTab_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 53 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*53);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwCSTab_GeomW3P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRF_VdwCSTab_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 130 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*130);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwCSTab_GeomW3P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRF_VdwCSTab_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 107 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*107);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwCSTab_GeomW3W3_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRF_VdwCSTab_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq01*(rinv01+krf*rsq01-crf);
+ felec = qq01*(rinv01*rinvsq01-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq02*(rinv02+krf*rsq02-crf);
+ felec = qq02*(rinv02*rinvsq02-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq11*(rinv11+krf*rsq11-crf);
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq12*(rinv12+krf*rsq12-crf);
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq21*(rinv21+krf*rsq21-crf);
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq22*(rinv22+krf*rsq22-crf);
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 313 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*313);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwCSTab_GeomW3W3_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRF_VdwCSTab_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq01*(rinv01*rinvsq01-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq02*(rinv02*rinvsq02-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 260 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*260);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq30 = iq3*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq30*(rinv30+krf*rsq30-crf);
+ felec = qq30*(rinv30*rinvsq30-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 151 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*151);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq30 = iq3*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq30*(rinv30*rinvsq30-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 128 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*128);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_00*VV;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ vvdw = vvdw12+vvdw6;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq11*(rinv11+krf*rsq11-crf);
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq12*(rinv12+krf*rsq12-crf);
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq13*(rinv13+krf*rsq13-crf);
+ felec = qq13*(rinv13*rinvsq13-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq21*(rinv21+krf*rsq21-crf);
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq22*(rinv22+krf*rsq22-crf);
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq23*(rinv23+krf*rsq23-crf);
+ felec = qq23*(rinv23*rinvsq23-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq31*(rinv31+krf*rsq31-crf);
+ felec = qq31*(rinv31*rinvsq31-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq32*(rinv32+krf*rsq32-crf);
+ felec = qq32*(rinv32*rinvsq32-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq33*(rinv33+krf*rsq33-crf);
+ felec = qq33*(rinv33*rinvsq33-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 334 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_VF,outeriter*41 + inneriter*334);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: CubicSplineTable
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ r00 = rsq00*rinv00;
+
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r00*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = 2*4*vfitab;
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += 0;
+ Y = vftab[vfitab];
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_00*FF;
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ Y = vftab[vfitab+4];
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_00*FF;
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq13*(rinv13*rinvsq13-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq23*(rinv23*rinvsq23-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq31*(rinv31*rinvsq31-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq32*(rinv32*rinvsq32-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq33*(rinv33*rinvsq33-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 281 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_F,outeriter*39 + inneriter*281);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwLJ_GeomP1P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRF_VdwLJ_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 44 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 15 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,outeriter*15 + inneriter*44);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwLJ_GeomP1P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRF_VdwLJ_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 34 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_F,outeriter*13 + inneriter*34);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwLJ_GeomW3P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRF_VdwLJ_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 108 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_VF,outeriter*32 + inneriter*108);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwLJ_GeomW3P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRF_VdwLJ_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 88 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3_F,outeriter*30 + inneriter*88);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwLJ_GeomW3W3_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRF_VdwLJ_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+ vvdwsum += vvdw;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq01*(rinv01+krf*rsq01-crf);
+ felec = qq01*(rinv01*rinvsq01-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq02*(rinv02+krf*rsq02-crf);
+ felec = qq02*(rinv02*rinvsq02-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq11*(rinv11+krf*rsq11-crf);
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq12*(rinv12+krf*rsq12-crf);
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq21*(rinv21+krf*rsq21-crf);
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq22*(rinv22+krf*rsq22-crf);
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 291 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 32 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_VF,outeriter*32 + inneriter*291);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwLJ_GeomW3W3_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRF_VdwLJ_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ qq00 = iq0*jq0;
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = felec+fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq01*(rinv01*rinvsq01-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq02*(rinv02*rinvsq02-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 241 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W3W3_F,outeriter*30 + inneriter*241);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwLJ_GeomW4P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRF_VdwLJ_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = 1.0/rsq00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq30 = iq3*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq30*(rinv30+krf*rsq30-crf);
+ felec = qq30*(rinv30*rinvsq30-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 128 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_VF,outeriter*41 + inneriter*128);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwLJ_GeomW4P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRF_VdwLJ_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq00 = 1.0/rsq00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+ vdwjidx0 = 2*vdwtype[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq30 = iq3*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq30*(rinv30*rinvsq30-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 108 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4_F,outeriter*39 + inneriter*108);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwLJ_GeomW4W4_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRF_VdwLJ_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+ vvdwsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = 1.0/rsq00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ vvdw6 = c6_00*rinvsix;
+ vvdw12 = c12_00*rinvsix*rinvsix;
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ fvdw = (vvdw12-vvdw6)*rinvsq00;
+
+ /* Update potential sums from outer loop */
+ vvdwsum += vvdw;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq11*(rinv11+krf*rsq11-crf);
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq12*(rinv12+krf*rsq12-crf);
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq13*(rinv13+krf*rsq13-crf);
+ felec = qq13*(rinv13*rinvsq13-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq21*(rinv21+krf*rsq21-crf);
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq22*(rinv22+krf*rsq22-crf);
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq23*(rinv23+krf*rsq23-crf);
+ felec = qq23*(rinv23*rinvsq23-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq31*(rinv31+krf*rsq31-crf);
+ felec = qq31*(rinv31*rinvsq31-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq32*(rinv32+krf*rsq32-crf);
+ felec = qq32*(rinv32*rinvsq32-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq33*(rinv33+krf*rsq33-crf);
+ felec = qq33*(rinv33*rinvsq33-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 311 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 41 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_VF,outeriter*41 + inneriter*311);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwLJ_GeomW4W4_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: LennardJones
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRF_VdwLJ_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+ vdwioffset0 = 2*nvdwtype*vdwtype[inr+0];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ vdwjidx0 = 2*vdwtype[inr+0];
+ c6_00 = vdwparam[vdwioffset0+vdwjidx0];
+ c12_00 = vdwparam[vdwioffset0+vdwjidx0+1];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq00 = 1.0/rsq00;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq00*rinvsq00*rinvsq00;
+ fvdw = (c12_00*rinvsix-c6_00)*rinvsix*rinvsq00;
+
+ fscal = fvdw;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq13*(rinv13*rinvsq13-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq23*(rinv23*rinvsq23-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq31*(rinv31*rinvsq31-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq32*(rinv32*rinvsq32-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq33*(rinv33*rinvsq33-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 261 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 39 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_W4W4_F,outeriter*39 + inneriter*261);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwNone_GeomP1P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: None
+ * Geometry: Particle-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRF_VdwNone_GeomP1P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq00 = iq0*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 32 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 14 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VF,outeriter*14 + inneriter*32);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwNone_GeomP1P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: None
+ * Geometry: Particle-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRF_VdwNone_GeomP1P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+
+ /* Load parameters for i particles */
+ iq0 = facel*charge[inr+0];
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+
+ rinv00 = gmx_invsqrt(rsq00);
+
+ rinvsq00 = rinv00*rinv00;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq00 = iq0*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 27 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 13 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_F,outeriter*13 + inneriter*27);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwNone_GeomW3P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: None
+ * Geometry: Water3-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRF_VdwNone_GeomW3P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq00 = iq0*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 96 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3_VF,outeriter*31 + inneriter*96);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwNone_GeomW3P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: None
+ * Geometry: Water3-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRF_VdwNone_GeomW3P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq00 = iq0*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 81 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3_F,outeriter*30 + inneriter*81);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwNone_GeomW3W3_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: None
+ * Geometry: Water3-Water3
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRF_VdwNone_GeomW3W3_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ qq00 = iq0*jq0;
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq00*(rinv00+krf*rsq00-crf);
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq01*(rinv01+krf*rsq01-crf);
+ felec = qq01*(rinv01*rinvsq01-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq02*(rinv02+krf*rsq02-crf);
+ felec = qq02*(rinv02*rinvsq02-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq11*(rinv11+krf*rsq11-crf);
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq12*(rinv12+krf*rsq12-crf);
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq21*(rinv21+krf*rsq21-crf);
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq22*(rinv22+krf*rsq22-crf);
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 279 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3W3_VF,outeriter*31 + inneriter*279);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwNone_GeomW3W3_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: None
+ * Geometry: Water3-Water3
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRF_VdwNone_GeomW3W3_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset0;
+ real ix0,iy0,iz0,fix0,fiy0,fiz0,iq0,isai0;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ real dx00,dy00,dz00,rsq00,rinv00,rinvsq00,r00,qq00,c6_00,c12_00,cexp1_00,cexp2_00;
+ real dx01,dy01,dz01,rsq01,rinv01,rinvsq01,r01,qq01,c6_01,c12_01,cexp1_01,cexp2_01;
+ real dx02,dy02,dz02,rsq02,rinv02,rinvsq02,r02,qq02,c6_02,c12_02,cexp1_02,cexp2_02;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq0 = facel*charge[inr+0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+
+ jq0 = charge[inr+0];
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ qq00 = iq0*jq0;
+ qq01 = iq0*jq1;
+ qq02 = iq0*jq2;
+ qq10 = iq1*jq0;
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq20 = iq2*jq0;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix0 = shX + x[i_coord_offset+DIM*0+XX];
+ iy0 = shY + x[i_coord_offset+DIM*0+YY];
+ iz0 = shZ + x[i_coord_offset+DIM*0+ZZ];
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+
+ fix0 = 0.0;
+ fiy0 = 0.0;
+ fiz0 = 0.0;
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+
+ /* Calculate displacement vector */
+ dx00 = ix0 - jx0;
+ dy00 = iy0 - jy0;
+ dz00 = iz0 - jz0;
+ dx01 = ix0 - jx1;
+ dy01 = iy0 - jy1;
+ dz01 = iz0 - jz1;
+ dx02 = ix0 - jx2;
+ dy02 = iy0 - jy2;
+ dz02 = iz0 - jz2;
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+
+ /* Calculate squared distance and things based on it */
+ rsq00 = dx00*dx00+dy00*dy00+dz00*dz00;
+ rsq01 = dx01*dx01+dy01*dy01+dz01*dz01;
+ rsq02 = dx02*dx02+dy02*dy02+dz02*dz02;
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+
+ rinv00 = gmx_invsqrt(rsq00);
+ rinv01 = gmx_invsqrt(rsq01);
+ rinv02 = gmx_invsqrt(rsq02);
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+
+ rinvsq00 = rinv00*rinv00;
+ rinvsq01 = rinv01*rinv01;
+ rinvsq02 = rinv02*rinv02;
+ rinvsq10 = rinv10*rinv10;
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq00*(rinv00*rinvsq00-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx00;
+ ty = fscal*dy00;
+ tz = fscal*dz00;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq01*(rinv01*rinvsq01-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx01;
+ ty = fscal*dy01;
+ tz = fscal*dz01;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq02*(rinv02*rinvsq02-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx02;
+ ty = fscal*dy02;
+ tz = fscal*dz02;
+
+ /* Update vectorial force */
+ fix0 += tx;
+ fiy0 += ty;
+ fiz0 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /* Inner loop uses 234 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*0+XX] += fix0;
+ f[i_coord_offset+DIM*0+YY] += fiy0;
+ f[i_coord_offset+DIM*0+ZZ] += fiz0;
+ tx += fix0;
+ ty += fiy0;
+ tz += fiz0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W3W3_F,outeriter*30 + inneriter*234);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwNone_GeomW4P1_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: None
+ * Geometry: Water4-Particle
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRF_VdwNone_GeomW4P1_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq10*(rinv10+krf*rsq10-crf);
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq20*(rinv20+krf*rsq20-crf);
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq30 = iq3*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq30*(rinv30+krf*rsq30-crf);
+ felec = qq30*(rinv30*rinvsq30-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 96 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4_VF,outeriter*31 + inneriter*96);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwNone_GeomW4P1_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: None
+ * Geometry: Water4-Particle
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRF_VdwNone_GeomW4P1_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx0;
+ real jx0,jy0,jz0,fjx0,fjy0,fjz0,jq0,isaj0;
+ real dx10,dy10,dz10,rsq10,rinv10,rinvsq10,r10,qq10,c6_10,c12_10,cexp1_10,cexp2_10;
+ real dx20,dy20,dz20,rsq20,rinv20,rinvsq20,r20,qq20,c6_20,c12_20,cexp1_20,cexp2_20;
+ real dx30,dy30,dz30,rsq30,rinv30,rinvsq30,r30,qq30,c6_30,c12_30,cexp1_30,cexp2_30;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx0 = x[j_coord_offset+DIM*0+XX];
+ jy0 = x[j_coord_offset+DIM*0+YY];
+ jz0 = x[j_coord_offset+DIM*0+ZZ];
+
+ /* Calculate displacement vector */
+ dx10 = ix1 - jx0;
+ dy10 = iy1 - jy0;
+ dz10 = iz1 - jz0;
+ dx20 = ix2 - jx0;
+ dy20 = iy2 - jy0;
+ dz20 = iz2 - jz0;
+ dx30 = ix3 - jx0;
+ dy30 = iy3 - jy0;
+ dz30 = iz3 - jz0;
+
+ /* Calculate squared distance and things based on it */
+ rsq10 = dx10*dx10+dy10*dy10+dz10*dz10;
+ rsq20 = dx20*dx20+dy20*dy20+dz20*dz20;
+ rsq30 = dx30*dx30+dy30*dy30+dz30*dz30;
+
+ rinv10 = gmx_invsqrt(rsq10);
+ rinv20 = gmx_invsqrt(rsq20);
+ rinv30 = gmx_invsqrt(rsq30);
+
+ rinvsq10 = rinv10*rinv10;
+ rinvsq20 = rinv20*rinv20;
+ rinvsq30 = rinv30*rinv30;
+
+ /* Load parameters for j particles */
+ jq0 = charge[jnr+0];
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq10 = iq1*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq10*(rinv10*rinvsq10-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx10;
+ ty = fscal*dy10;
+ tz = fscal*dz10;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq20 = iq2*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq20*(rinv20*rinvsq20-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx20;
+ ty = fscal*dy20;
+ tz = fscal*dz20;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ qq30 = iq3*jq0;
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq30*(rinv30*rinvsq30-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx30;
+ ty = fscal*dy30;
+ tz = fscal*dz30;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*0+XX] -= tx;
+ f[j_coord_offset+DIM*0+YY] -= ty;
+ f[j_coord_offset+DIM*0+ZZ] -= tz;
+
+ /* Inner loop uses 81 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4_F,outeriter*30 + inneriter*81);
+}
--- /dev/null
+/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * Copyright (c) 2001-2012, The GROMACS Development Team
+ *
+ * Gromacs is a library for molecular simulation and trajectory analysis,
+ * written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
+ * a full list of developers and information, check out http://www.gromacs.org
+ *
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
+ * later version.
+ *
+ * To help fund GROMACS development, we humbly ask that you cite
+ * the papers people have written on it - you can find them on the website.
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwNone_GeomW4W4_VF_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: None
+ * Geometry: Water4-Water4
+ * Calculate force/pot: PotentialAndForce
+ */
+void
+nb_kernel_ElecRF_VdwNone_GeomW4W4_VF_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Reset potential sums */
+ velecsum = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq11*(rinv11+krf*rsq11-crf);
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq12*(rinv12+krf*rsq12-crf);
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq13*(rinv13+krf*rsq13-crf);
+ felec = qq13*(rinv13*rinvsq13-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq21*(rinv21+krf*rsq21-crf);
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq22*(rinv22+krf*rsq22-crf);
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq23*(rinv23+krf*rsq23-crf);
+ felec = qq23*(rinv23*rinvsq23-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq31*(rinv31+krf*rsq31-crf);
+ felec = qq31*(rinv31*rinvsq31-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq32*(rinv32+krf*rsq32-crf);
+ felec = qq32*(rinv32*rinvsq32-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ velec = qq33*(rinv33+krf*rsq33-crf);
+ felec = qq33*(rinv33*rinvsq33-krf2);
+
+ /* Update potential sums from outer loop */
+ velecsum += velec;
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 279 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ ggid = gid[iidx];
+ /* Update potential energies */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 31 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4W4_VF,outeriter*31 + inneriter*279);
+}
+/*
+ * Gromacs nonbonded kernel: nb_kernel_ElecRF_VdwNone_GeomW4W4_F_c
+ * Electrostatics interaction: ReactionField
+ * VdW interaction: None
+ * Geometry: Water4-Water4
+ * Calculate force/pot: Force
+ */
+void
+nb_kernel_ElecRF_VdwNone_GeomW4W4_F_c
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ int vdwioffset1;
+ real ix1,iy1,iz1,fix1,fiy1,fiz1,iq1,isai1;
+ int vdwioffset2;
+ real ix2,iy2,iz2,fix2,fiy2,fiz2,iq2,isai2;
+ int vdwioffset3;
+ real ix3,iy3,iz3,fix3,fiy3,fiz3,iq3,isai3;
+ int vdwjidx1;
+ real jx1,jy1,jz1,fjx1,fjy1,fjz1,jq1,isaj1;
+ int vdwjidx2;
+ real jx2,jy2,jz2,fjx2,fjy2,fjz2,jq2,isaj2;
+ int vdwjidx3;
+ real jx3,jy3,jz3,fjx3,fjy3,fjz3,jq3,isaj3;
+ real dx11,dy11,dz11,rsq11,rinv11,rinvsq11,r11,qq11,c6_11,c12_11,cexp1_11,cexp2_11;
+ real dx12,dy12,dz12,rsq12,rinv12,rinvsq12,r12,qq12,c6_12,c12_12,cexp1_12,cexp2_12;
+ real dx13,dy13,dz13,rsq13,rinv13,rinvsq13,r13,qq13,c6_13,c12_13,cexp1_13,cexp2_13;
+ real dx21,dy21,dz21,rsq21,rinv21,rinvsq21,r21,qq21,c6_21,c12_21,cexp1_21,cexp2_21;
+ real dx22,dy22,dz22,rsq22,rinv22,rinvsq22,r22,qq22,c6_22,c12_22,cexp1_22,cexp2_22;
+ real dx23,dy23,dz23,rsq23,rinv23,rinvsq23,r23,qq23,c6_23,c12_23,cexp1_23,cexp2_23;
+ real dx31,dy31,dz31,rsq31,rinv31,rinvsq31,r31,qq31,c6_31,c12_31,cexp1_31,cexp2_31;
+ real dx32,dy32,dz32,rsq32,rinv32,rinvsq32,r32,qq32,c6_32,c12_32,cexp1_32,cexp2_32;
+ real dx33,dy33,dz33,rsq33,rinv33,rinvsq33,r33,qq33,c6_33,c12_33,cexp1_33,cexp2_33;
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ iq1 = facel*charge[inr+1];
+ iq2 = facel*charge[inr+2];
+ iq3 = facel*charge[inr+3];
+
+ jq1 = charge[inr+1];
+ jq2 = charge[inr+2];
+ jq3 = charge[inr+3];
+ qq11 = iq1*jq1;
+ qq12 = iq1*jq2;
+ qq13 = iq1*jq3;
+ qq21 = iq2*jq1;
+ qq22 = iq2*jq2;
+ qq23 = iq2*jq3;
+ qq31 = iq3*jq1;
+ qq32 = iq3*jq2;
+ qq33 = iq3*jq3;
+
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ ix1 = shX + x[i_coord_offset+DIM*1+XX];
+ iy1 = shY + x[i_coord_offset+DIM*1+YY];
+ iz1 = shZ + x[i_coord_offset+DIM*1+ZZ];
+ ix2 = shX + x[i_coord_offset+DIM*2+XX];
+ iy2 = shY + x[i_coord_offset+DIM*2+YY];
+ iz2 = shZ + x[i_coord_offset+DIM*2+ZZ];
+ ix3 = shX + x[i_coord_offset+DIM*3+XX];
+ iy3 = shY + x[i_coord_offset+DIM*3+YY];
+ iz3 = shZ + x[i_coord_offset+DIM*3+ZZ];
+
+ fix1 = 0.0;
+ fiy1 = 0.0;
+ fiz1 = 0.0;
+ fix2 = 0.0;
+ fiy2 = 0.0;
+ fiz2 = 0.0;
+ fix3 = 0.0;
+ fiy3 = 0.0;
+ fiz3 = 0.0;
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ jx1 = x[j_coord_offset+DIM*1+XX];
+ jy1 = x[j_coord_offset+DIM*1+YY];
+ jz1 = x[j_coord_offset+DIM*1+ZZ];
+ jx2 = x[j_coord_offset+DIM*2+XX];
+ jy2 = x[j_coord_offset+DIM*2+YY];
+ jz2 = x[j_coord_offset+DIM*2+ZZ];
+ jx3 = x[j_coord_offset+DIM*3+XX];
+ jy3 = x[j_coord_offset+DIM*3+YY];
+ jz3 = x[j_coord_offset+DIM*3+ZZ];
+
+ /* Calculate displacement vector */
+ dx11 = ix1 - jx1;
+ dy11 = iy1 - jy1;
+ dz11 = iz1 - jz1;
+ dx12 = ix1 - jx2;
+ dy12 = iy1 - jy2;
+ dz12 = iz1 - jz2;
+ dx13 = ix1 - jx3;
+ dy13 = iy1 - jy3;
+ dz13 = iz1 - jz3;
+ dx21 = ix2 - jx1;
+ dy21 = iy2 - jy1;
+ dz21 = iz2 - jz1;
+ dx22 = ix2 - jx2;
+ dy22 = iy2 - jy2;
+ dz22 = iz2 - jz2;
+ dx23 = ix2 - jx3;
+ dy23 = iy2 - jy3;
+ dz23 = iz2 - jz3;
+ dx31 = ix3 - jx1;
+ dy31 = iy3 - jy1;
+ dz31 = iz3 - jz1;
+ dx32 = ix3 - jx2;
+ dy32 = iy3 - jy2;
+ dz32 = iz3 - jz2;
+ dx33 = ix3 - jx3;
+ dy33 = iy3 - jy3;
+ dz33 = iz3 - jz3;
+
+ /* Calculate squared distance and things based on it */
+ rsq11 = dx11*dx11+dy11*dy11+dz11*dz11;
+ rsq12 = dx12*dx12+dy12*dy12+dz12*dz12;
+ rsq13 = dx13*dx13+dy13*dy13+dz13*dz13;
+ rsq21 = dx21*dx21+dy21*dy21+dz21*dz21;
+ rsq22 = dx22*dx22+dy22*dy22+dz22*dz22;
+ rsq23 = dx23*dx23+dy23*dy23+dz23*dz23;
+ rsq31 = dx31*dx31+dy31*dy31+dz31*dz31;
+ rsq32 = dx32*dx32+dy32*dy32+dz32*dz32;
+ rsq33 = dx33*dx33+dy33*dy33+dz33*dz33;
+
+ rinv11 = gmx_invsqrt(rsq11);
+ rinv12 = gmx_invsqrt(rsq12);
+ rinv13 = gmx_invsqrt(rsq13);
+ rinv21 = gmx_invsqrt(rsq21);
+ rinv22 = gmx_invsqrt(rsq22);
+ rinv23 = gmx_invsqrt(rsq23);
+ rinv31 = gmx_invsqrt(rsq31);
+ rinv32 = gmx_invsqrt(rsq32);
+ rinv33 = gmx_invsqrt(rsq33);
+
+ rinvsq11 = rinv11*rinv11;
+ rinvsq12 = rinv12*rinv12;
+ rinvsq13 = rinv13*rinv13;
+ rinvsq21 = rinv21*rinv21;
+ rinvsq22 = rinv22*rinv22;
+ rinvsq23 = rinv23*rinv23;
+ rinvsq31 = rinv31*rinv31;
+ rinvsq32 = rinv32*rinv32;
+ rinvsq33 = rinv33*rinv33;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq11*(rinv11*rinvsq11-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx11;
+ ty = fscal*dy11;
+ tz = fscal*dz11;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq12*(rinv12*rinvsq12-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx12;
+ ty = fscal*dy12;
+ tz = fscal*dz12;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq13*(rinv13*rinvsq13-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx13;
+ ty = fscal*dy13;
+ tz = fscal*dz13;
+
+ /* Update vectorial force */
+ fix1 += tx;
+ fiy1 += ty;
+ fiz1 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq21*(rinv21*rinvsq21-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx21;
+ ty = fscal*dy21;
+ tz = fscal*dz21;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq22*(rinv22*rinvsq22-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx22;
+ ty = fscal*dy22;
+ tz = fscal*dz22;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq23*(rinv23*rinvsq23-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx23;
+ ty = fscal*dy23;
+ tz = fscal*dz23;
+
+ /* Update vectorial force */
+ fix2 += tx;
+ fiy2 += ty;
+ fiz2 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq31*(rinv31*rinvsq31-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx31;
+ ty = fscal*dy31;
+ tz = fscal*dz31;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*1+XX] -= tx;
+ f[j_coord_offset+DIM*1+YY] -= ty;
+ f[j_coord_offset+DIM*1+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq32*(rinv32*rinvsq32-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx32;
+ ty = fscal*dy32;
+ tz = fscal*dz32;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*2+XX] -= tx;
+ f[j_coord_offset+DIM*2+YY] -= ty;
+ f[j_coord_offset+DIM*2+ZZ] -= tz;
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ felec = qq33*(rinv33*rinvsq33-krf2);
+
+ fscal = felec;
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx33;
+ ty = fscal*dy33;
+ tz = fscal*dz33;
+
+ /* Update vectorial force */
+ fix3 += tx;
+ fiy3 += ty;
+ fiz3 += tz;
+ f[j_coord_offset+DIM*3+XX] -= tx;
+ f[j_coord_offset+DIM*3+YY] -= ty;
+ f[j_coord_offset+DIM*3+ZZ] -= tz;
+
+ /* Inner loop uses 234 flops */
+ }
+ /* End of innermost loop */
+
+ tx = ty = tz = 0;
+ f[i_coord_offset+DIM*1+XX] += fix1;
+ f[i_coord_offset+DIM*1+YY] += fiy1;
+ f[i_coord_offset+DIM*1+ZZ] += fiz1;
+ tx += fix1;
+ ty += fiy1;
+ tz += fiz1;
+ f[i_coord_offset+DIM*2+XX] += fix2;
+ f[i_coord_offset+DIM*2+YY] += fiy2;
+ f[i_coord_offset+DIM*2+ZZ] += fiz2;
+ tx += fix2;
+ ty += fiy2;
+ tz += fiz2;
+ f[i_coord_offset+DIM*3+XX] += fix3;
+ f[i_coord_offset+DIM*3+YY] += fiy3;
+ f[i_coord_offset+DIM*3+ZZ] += fiz3;
+ tx += fix3;
+ ty += fiy3;
+ tz += fiz3;
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses 30 flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_W4W4_F,outeriter*30 + inneriter*234);
+}
#include "smalloc.h"
#include "nb_kernel_allvsall.h"
+#include "nrnb.h"
typedef struct
{
void
-nb_kernel_allvsall(t_forcerec * fr,
- t_mdatoms * mdatoms,
- t_blocka * excl,
- real * x,
- real * f,
- real * Vc,
- real * Vvdw,
- int * outeriter,
- int * inneriter,
- void * work)
+nb_kernel_allvsall(t_nblist * nlist,
+ rvec * xx,
+ rvec * ff,
+ t_forcerec * fr,
+ t_mdatoms * mdatoms,
+ nb_kernel_data_t * kernel_data,
+ t_nrnb * nrnb)
{
gmx_allvsall_data_t *aadata;
int natoms;
real vcoul,vctot;
real c6,c12,Vvdw6,Vvdw12,Vvdwtot;
real fscal;
-
+ t_blocka * excl;
+ real * f;
+ real * x;
+ real * Vvdw;
+ real * Vc;
+
+ x = xx[0];
+ f = ff[0];
charge = mdatoms->chargeA;
type = mdatoms->typeA;
facel = fr->epsfac;
natoms = mdatoms->nr;
ni0 = mdatoms->start;
ni1 = mdatoms->start+mdatoms->homenr;
-
- aadata = *((gmx_allvsall_data_t **)work);
+ aadata = fr->AllvsAll_work;
+ excl = kernel_data->exclusions;
+
+ Vc = kernel_data->energygrp_elec;
+ Vvdw = kernel_data->energygrp_vdw;
if(aadata==NULL)
{
setup_aadata(&aadata,excl,natoms,type,fr->ntype,fr->nbfp);
- *((gmx_allvsall_data_t **)work) = aadata;
+ fr->AllvsAll_work = aadata;
}
for(i=ni0; i<ni1; i++)
/* Outer loop uses 6 flops/iteration */
}
- /* Write outer/inner iteration count to pointers */
- *outeriter = ni1-ni0;
- *inneriter = (ni1-ni0)*natoms/2;
+ /* 12 flops per outer iteration
+ * 19 flops per inner iteration
+ */
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,(ni1-ni0)*12 + ((ni1-ni0)*natoms/2)*19);
}
#include "types/simple.h"
#include "typedefs.h"
+#include "../nb_kernel.h"
void
-nb_kernel_allvsall(t_forcerec * fr,
- t_mdatoms * mdatoms,
- t_blocka * excl,
- real * x,
- real * f,
- real * Vc,
- real * Vvdw,
- int * outeriter,
- int * inneriter,
- void * work);
+nb_kernel_allvsall(t_nblist * nlist,
+ rvec * x,
+ rvec * f,
+ t_forcerec * fr,
+ t_mdatoms * mdatoms,
+ nb_kernel_data_t * kernel_data,
+ t_nrnb * nrnb);
+
#endif
#include "smalloc.h"
#include "nb_kernel_allvsallgb.h"
+#include "nrnb.h"
typedef struct
{
void
-nb_kernel_allvsallgb(t_forcerec * fr,
- t_mdatoms * mdatoms,
- t_blocka * excl,
- real * x,
- real * f,
- real * Vc,
- real * Vvdw,
- real * vpol,
- int * outeriter,
- int * inneriter,
- void * work)
+nb_kernel_allvsallgb(t_nblist * nlist,
+ rvec * xx,
+ rvec * ff,
+ t_forcerec * fr,
+ t_mdatoms * mdatoms,
+ nb_kernel_data_t * kernel_data,
+ t_nrnb * nrnb)
{
gmx_allvsall_data_t *aadata;
int natoms;
real fscal,dvdatmp,fijC,vgb;
real Y,F,Fp,Geps,Heps2,VV,FF,eps,eps2,r,rt;
real dvdaj,gbscale,isaprod,isai,isaj,gbtabscale;
-
+ real * f;
+ real * x;
+ t_blocka * excl;
+ real * Vvdw;
+ real * Vc;
+ real * vpol;
+
+ x = xx[0];
+ f = ff[0];
charge = mdatoms->chargeA;
type = mdatoms->typeA;
gbfactor = ((1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent));
facel = fr->epsfac;
- GBtab = fr->gbtab.tab;
+ GBtab = fr->gbtab.data;
gbtabscale = fr->gbtab.scale;
invsqrta = fr->invsqrta;
dvda = fr->dvda;
-
+ vpol = kernel_data->energygrp_polarization;
+
natoms = mdatoms->nr;
ni0 = mdatoms->start;
ni1 = mdatoms->start+mdatoms->homenr;
- aadata = *((gmx_allvsall_data_t **)work);
+ aadata = fr->AllvsAll_work;
+ excl = kernel_data->exclusions;
+
+ Vc = kernel_data->energygrp_elec;
+ Vvdw = kernel_data->energygrp_vdw;
if(aadata==NULL)
{
setup_aadata(&aadata,excl,natoms,type,fr->ntype,fr->nbfp);
- *((gmx_allvsall_data_t **)work) = aadata;
+ fr->AllvsAll_work = aadata;
}
for(i=ni0; i<ni1; i++)
/* Outer loop uses 6 flops/iteration */
}
- /* Write outer/inner iteration count to pointers */
- *outeriter = ni1-ni0;
- *inneriter = (ni1-ni0)*natoms/2;
+ /* 12 flops per outer iteration
+ * 19 flops per inner iteration
+ */
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW_VF,(ni1-ni0)*12 + ((ni1-ni0)*natoms/2)*19);
}
#include "types/simple.h"
#include "typedefs.h"
+#include "../nb_kernel.h"
void
-nb_kernel_allvsallgb(t_forcerec * fr,
- t_mdatoms * mdatoms,
- t_blocka * excl,
- real * x,
- real * f,
- real * Vc,
- real * Vvdw,
- real * vpol,
- int * outeriter,
- int * inneriter,
- void * work);
+nb_kernel_allvsallgb(t_nblist * nlist,
+ rvec * x,
+ rvec * f,
+ t_forcerec * fr,
+ t_mdatoms * mdatoms,
+ nb_kernel_data_t * kernel_data,
+ t_nrnb * nrnb);
#endif
/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
* This source code is part of
*
* G R O M A C S
*
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
+ * Copyright (c) 2001-2012, The GROMACS Development Team
*
* Gromacs is a library for molecular simulation and trajectory analysis,
* written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
* a full list of developers and information, check out http://www.gromacs.org
*
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
* later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
*
* To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
+ * the papers people have written on it - you can find them on the website.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
-#include <stdio.h>
-
-#include "types/nrnb.h"
-#include "nb_kernel_c.h"
-#include "../nb_kerneltype.h"
+#ifndef nb_kernel_c_h
+#define nb_kernel_c_h
+#include "../nb_kernel.h"
-/* Include standard kernel headers in local directory */
-#include "nb_kernel010.h"
-#include "nb_kernel020.h"
-#include "nb_kernel030.h"
-#include "nb_kernel100.h"
-#include "nb_kernel101.h"
-#include "nb_kernel102.h"
-#include "nb_kernel103.h"
-#include "nb_kernel104.h"
-#include "nb_kernel110.h"
-#include "nb_kernel111.h"
-#include "nb_kernel112.h"
-#include "nb_kernel113.h"
-#include "nb_kernel114.h"
-#include "nb_kernel120.h"
-#include "nb_kernel121.h"
-#include "nb_kernel122.h"
-#include "nb_kernel123.h"
-#include "nb_kernel124.h"
-#include "nb_kernel130.h"
-#include "nb_kernel131.h"
-#include "nb_kernel132.h"
-#include "nb_kernel133.h"
-#include "nb_kernel134.h"
-#include "nb_kernel200.h"
-#include "nb_kernel201.h"
-#include "nb_kernel202.h"
-#include "nb_kernel203.h"
-#include "nb_kernel204.h"
-#include "nb_kernel210.h"
-#include "nb_kernel211.h"
-#include "nb_kernel212.h"
-#include "nb_kernel213.h"
-#include "nb_kernel214.h"
-#include "nb_kernel220.h"
-#include "nb_kernel221.h"
-#include "nb_kernel222.h"
-#include "nb_kernel223.h"
-#include "nb_kernel224.h"
-#include "nb_kernel230.h"
-#include "nb_kernel231.h"
-#include "nb_kernel232.h"
-#include "nb_kernel233.h"
-#include "nb_kernel234.h"
-#include "nb_kernel300.h"
-#include "nb_kernel301.h"
-#include "nb_kernel302.h"
-#include "nb_kernel303.h"
-#include "nb_kernel304.h"
-#include "nb_kernel310.h"
-#include "nb_kernel311.h"
-#include "nb_kernel312.h"
-#include "nb_kernel313.h"
-#include "nb_kernel314.h"
-#include "nb_kernel320.h"
-#include "nb_kernel321.h"
-#include "nb_kernel322.h"
-#include "nb_kernel323.h"
-#include "nb_kernel324.h"
-#include "nb_kernel330.h"
-#include "nb_kernel331.h"
-#include "nb_kernel332.h"
-#include "nb_kernel333.h"
-#include "nb_kernel334.h"
-#include "nb_kernel400.h"
-#include "nb_kernel410.h"
-#include "nb_kernel420.h"
-#include "nb_kernel430.h"
+nb_kernel_t nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecNone_VdwLJSh_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecNone_VdwLJSh_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecNone_VdwLJSw_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecNone_VdwBham_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecNone_VdwBham_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecEw_VdwLJ_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecEw_VdwLJ_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecEw_VdwLJ_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecEw_VdwLJ_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecEw_VdwLJ_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecEw_VdwLJ_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecEw_VdwLJ_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecEw_VdwLJ_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecEw_VdwLJ_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecEw_VdwLJ_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecEw_VdwNone_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecEw_VdwNone_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecEw_VdwNone_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecEw_VdwNone_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecEw_VdwNone_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecEw_VdwNone_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecEw_VdwNone_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecEw_VdwNone_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecEw_VdwNone_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecEw_VdwNone_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecEw_VdwCSTab_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecEw_VdwCSTab_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecEw_VdwCSTab_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecEw_VdwCSTab_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecEw_VdwCSTab_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecEw_VdwCSTab_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecEw_VdwCSTab_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecEw_VdwCSTab_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecEw_VdwCSTab_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecEw_VdwCSTab_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecEw_VdwBham_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecEw_VdwBham_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecEw_VdwBham_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecEw_VdwBham_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecEw_VdwBham_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecEw_VdwBham_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecEw_VdwBham_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecEw_VdwBham_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecEw_VdwBham_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecEw_VdwBham_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwNone_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwNone_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwNone_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwNone_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwNone_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwNone_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwNone_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwNone_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwNone_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwNone_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecCoul_VdwBham_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecCSTab_VdwBham_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecGB_VdwNone_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecGB_VdwBham_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecGB_VdwBham_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwNone_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwNone_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwNone_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwNone_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwNone_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwNone_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwNone_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwNone_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwNone_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwNone_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecRF_VdwLJ_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecRF_VdwLJ_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecRF_VdwLJ_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecRF_VdwLJ_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecRF_VdwLJ_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecRF_VdwLJ_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecRF_VdwLJ_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecRF_VdwLJ_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecRF_VdwLJ_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecRF_VdwLJ_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecRF_VdwNone_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecRF_VdwNone_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecRF_VdwNone_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecRF_VdwNone_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecRF_VdwNone_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecRF_VdwNone_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecRF_VdwNone_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecRF_VdwNone_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecRF_VdwNone_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecRF_VdwNone_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_c;
+nb_kernel_t nb_kernel_ElecRF_VdwBham_GeomP1P1_VF_c;
+nb_kernel_t nb_kernel_ElecRF_VdwBham_GeomP1P1_F_c;
+nb_kernel_t nb_kernel_ElecRF_VdwBham_GeomW3P1_VF_c;
+nb_kernel_t nb_kernel_ElecRF_VdwBham_GeomW3P1_F_c;
+nb_kernel_t nb_kernel_ElecRF_VdwBham_GeomW3W3_VF_c;
+nb_kernel_t nb_kernel_ElecRF_VdwBham_GeomW3W3_F_c;
+nb_kernel_t nb_kernel_ElecRF_VdwBham_GeomW4P1_VF_c;
+nb_kernel_t nb_kernel_ElecRF_VdwBham_GeomW4P1_F_c;
+nb_kernel_t nb_kernel_ElecRF_VdwBham_GeomW4W4_VF_c;
+nb_kernel_t nb_kernel_ElecRF_VdwBham_GeomW4W4_F_c;
-static nb_kernel_t *
-kernellist[eNR_NBKERNEL_NR] =
+nb_kernel_info_t
+kernellist_c[] =
{
- nb_kernel010,
- nb_kernel020,
- nb_kernel030,
- nb_kernel100,
- nb_kernel101,
- nb_kernel102,
- nb_kernel103,
- nb_kernel104,
- nb_kernel110,
- nb_kernel111,
- nb_kernel112,
- nb_kernel113,
- nb_kernel114,
- nb_kernel120,
- nb_kernel121,
- nb_kernel122,
- nb_kernel123,
- nb_kernel124,
- nb_kernel130,
- nb_kernel131,
- nb_kernel132,
- nb_kernel133,
- nb_kernel134,
- nb_kernel200,
- nb_kernel201,
- nb_kernel202,
- nb_kernel203,
- nb_kernel204,
- nb_kernel210,
- nb_kernel211,
- nb_kernel212,
- nb_kernel213,
- nb_kernel214,
- nb_kernel220,
- nb_kernel221,
- nb_kernel222,
- nb_kernel223,
- nb_kernel224,
- nb_kernel230,
- nb_kernel231,
- nb_kernel232,
- nb_kernel233,
- nb_kernel234,
- nb_kernel300,
- nb_kernel301,
- nb_kernel302,
- nb_kernel303,
- nb_kernel304,
- nb_kernel310,
- nb_kernel311,
- nb_kernel312,
- nb_kernel313,
- nb_kernel314,
- nb_kernel320,
- nb_kernel321,
- nb_kernel322,
- nb_kernel323,
- nb_kernel324,
- nb_kernel330,
- nb_kernel331,
- nb_kernel332,
- nb_kernel333,
- nb_kernel334,
- nb_kernel400,
- nb_kernel410,
- nb_kernel430,
- nb_kernel010nf,
- nb_kernel020nf,
- nb_kernel030nf,
- nb_kernel100nf,
- nb_kernel101nf,
- nb_kernel102nf,
- nb_kernel103nf,
- nb_kernel104nf,
- nb_kernel110nf,
- nb_kernel111nf,
- nb_kernel112nf,
- nb_kernel113nf,
- nb_kernel114nf,
- nb_kernel120nf,
- nb_kernel121nf,
- nb_kernel122nf,
- nb_kernel123nf,
- nb_kernel124nf,
- nb_kernel130nf,
- nb_kernel131nf,
- nb_kernel132nf,
- nb_kernel133nf,
- nb_kernel134nf,
- nb_kernel200nf,
- nb_kernel201nf,
- nb_kernel202nf,
- nb_kernel203nf,
- nb_kernel204nf,
- nb_kernel210nf,
- nb_kernel211nf,
- nb_kernel212nf,
- nb_kernel213nf,
- nb_kernel214nf,
- nb_kernel220nf,
- nb_kernel221nf,
- nb_kernel222nf,
- nb_kernel223nf,
- nb_kernel224nf,
- nb_kernel230nf,
- nb_kernel231nf,
- nb_kernel232nf,
- nb_kernel233nf,
- nb_kernel234nf,
- nb_kernel300nf,
- nb_kernel301nf,
- nb_kernel302nf,
- nb_kernel303nf,
- nb_kernel304nf,
- nb_kernel310nf,
- nb_kernel311nf,
- nb_kernel312nf,
- nb_kernel313nf,
- nb_kernel314nf,
- nb_kernel320nf,
- nb_kernel321nf,
- nb_kernel322nf,
- nb_kernel323nf,
- nb_kernel324nf,
- nb_kernel330nf,
- nb_kernel331nf,
- nb_kernel332nf,
- nb_kernel333nf,
- nb_kernel334nf,
- nb_kernel400nf,
- nb_kernel410nf,
- nb_kernel430nf,
+ { nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_c, "nb_kernel_ElecNone_VdwLJ_GeomP1P1_VF_c", "c", "None", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_c, "nb_kernel_ElecNone_VdwLJ_GeomP1P1_F_c", "c", "None", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecNone_VdwLJSh_GeomP1P1_VF_c, "nb_kernel_ElecNone_VdwLJSh_GeomP1P1_VF_c", "c", "None", "None", "LennardJones", "PotentialShift", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecNone_VdwLJSh_GeomP1P1_F_c, "nb_kernel_ElecNone_VdwLJSh_GeomP1P1_F_c", "c", "None", "None", "LennardJones", "PotentialShift", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecNone_VdwLJSw_GeomP1P1_VF_c, "nb_kernel_ElecNone_VdwLJSw_GeomP1P1_VF_c", "c", "None", "None", "LennardJones", "PotentialSwitch", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_c, "nb_kernel_ElecNone_VdwLJSw_GeomP1P1_F_c", "c", "None", "None", "LennardJones", "PotentialSwitch", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_c, "nb_kernel_ElecNone_VdwCSTab_GeomP1P1_VF_c", "c", "None", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_c, "nb_kernel_ElecNone_VdwCSTab_GeomP1P1_F_c", "c", "None", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecNone_VdwBham_GeomP1P1_VF_c, "nb_kernel_ElecNone_VdwBham_GeomP1P1_VF_c", "c", "None", "None", "Buckingham", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecNone_VdwBham_GeomP1P1_F_c, "nb_kernel_ElecNone_VdwBham_GeomP1P1_F_c", "c", "None", "None", "Buckingham", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_VF_c, "nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_VF_c", "c", "None", "None", "Buckingham", "PotentialShift", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_F_c, "nb_kernel_ElecNone_VdwBhamSh_GeomP1P1_F_c", "c", "None", "None", "Buckingham", "PotentialShift", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_VF_c, "nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_VF_c", "c", "None", "None", "Buckingham", "PotentialSwitch", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_F_c, "nb_kernel_ElecNone_VdwBhamSw_GeomP1P1_F_c", "c", "None", "None", "Buckingham", "PotentialSwitch", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecEw_VdwLJ_GeomP1P1_VF_c, "nb_kernel_ElecEw_VdwLJ_GeomP1P1_VF_c", "c", "Ewald", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEw_VdwLJ_GeomP1P1_F_c, "nb_kernel_ElecEw_VdwLJ_GeomP1P1_F_c", "c", "Ewald", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecEw_VdwLJ_GeomW3P1_VF_c, "nb_kernel_ElecEw_VdwLJ_GeomW3P1_VF_c", "c", "Ewald", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEw_VdwLJ_GeomW3P1_F_c, "nb_kernel_ElecEw_VdwLJ_GeomW3P1_F_c", "c", "Ewald", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecEw_VdwLJ_GeomW3W3_VF_c, "nb_kernel_ElecEw_VdwLJ_GeomW3W3_VF_c", "c", "Ewald", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecEw_VdwLJ_GeomW3W3_F_c, "nb_kernel_ElecEw_VdwLJ_GeomW3W3_F_c", "c", "Ewald", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecEw_VdwLJ_GeomW4P1_VF_c, "nb_kernel_ElecEw_VdwLJ_GeomW4P1_VF_c", "c", "Ewald", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEw_VdwLJ_GeomW4P1_F_c, "nb_kernel_ElecEw_VdwLJ_GeomW4P1_F_c", "c", "Ewald", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecEw_VdwLJ_GeomW4W4_VF_c, "nb_kernel_ElecEw_VdwLJ_GeomW4W4_VF_c", "c", "Ewald", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecEw_VdwLJ_GeomW4W4_F_c, "nb_kernel_ElecEw_VdwLJ_GeomW4W4_F_c", "c", "Ewald", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecEw_VdwNone_GeomP1P1_VF_c, "nb_kernel_ElecEw_VdwNone_GeomP1P1_VF_c", "c", "Ewald", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEw_VdwNone_GeomP1P1_F_c, "nb_kernel_ElecEw_VdwNone_GeomP1P1_F_c", "c", "Ewald", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecEw_VdwNone_GeomW3P1_VF_c, "nb_kernel_ElecEw_VdwNone_GeomW3P1_VF_c", "c", "Ewald", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEw_VdwNone_GeomW3P1_F_c, "nb_kernel_ElecEw_VdwNone_GeomW3P1_F_c", "c", "Ewald", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecEw_VdwNone_GeomW3W3_VF_c, "nb_kernel_ElecEw_VdwNone_GeomW3W3_VF_c", "c", "Ewald", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecEw_VdwNone_GeomW3W3_F_c, "nb_kernel_ElecEw_VdwNone_GeomW3W3_F_c", "c", "Ewald", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecEw_VdwNone_GeomW4P1_VF_c, "nb_kernel_ElecEw_VdwNone_GeomW4P1_VF_c", "c", "Ewald", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEw_VdwNone_GeomW4P1_F_c, "nb_kernel_ElecEw_VdwNone_GeomW4P1_F_c", "c", "Ewald", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecEw_VdwNone_GeomW4W4_VF_c, "nb_kernel_ElecEw_VdwNone_GeomW4W4_VF_c", "c", "Ewald", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecEw_VdwNone_GeomW4W4_F_c, "nb_kernel_ElecEw_VdwNone_GeomW4W4_F_c", "c", "Ewald", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecEw_VdwCSTab_GeomP1P1_VF_c, "nb_kernel_ElecEw_VdwCSTab_GeomP1P1_VF_c", "c", "Ewald", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEw_VdwCSTab_GeomP1P1_F_c, "nb_kernel_ElecEw_VdwCSTab_GeomP1P1_F_c", "c", "Ewald", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecEw_VdwCSTab_GeomW3P1_VF_c, "nb_kernel_ElecEw_VdwCSTab_GeomW3P1_VF_c", "c", "Ewald", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEw_VdwCSTab_GeomW3P1_F_c, "nb_kernel_ElecEw_VdwCSTab_GeomW3P1_F_c", "c", "Ewald", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecEw_VdwCSTab_GeomW3W3_VF_c, "nb_kernel_ElecEw_VdwCSTab_GeomW3W3_VF_c", "c", "Ewald", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecEw_VdwCSTab_GeomW3W3_F_c, "nb_kernel_ElecEw_VdwCSTab_GeomW3W3_F_c", "c", "Ewald", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecEw_VdwCSTab_GeomW4P1_VF_c, "nb_kernel_ElecEw_VdwCSTab_GeomW4P1_VF_c", "c", "Ewald", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEw_VdwCSTab_GeomW4P1_F_c, "nb_kernel_ElecEw_VdwCSTab_GeomW4P1_F_c", "c", "Ewald", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecEw_VdwCSTab_GeomW4W4_VF_c, "nb_kernel_ElecEw_VdwCSTab_GeomW4W4_VF_c", "c", "Ewald", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecEw_VdwCSTab_GeomW4W4_F_c, "nb_kernel_ElecEw_VdwCSTab_GeomW4W4_F_c", "c", "Ewald", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecEw_VdwBham_GeomP1P1_VF_c, "nb_kernel_ElecEw_VdwBham_GeomP1P1_VF_c", "c", "Ewald", "None", "Buckingham", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEw_VdwBham_GeomP1P1_F_c, "nb_kernel_ElecEw_VdwBham_GeomP1P1_F_c", "c", "Ewald", "None", "Buckingham", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecEw_VdwBham_GeomW3P1_VF_c, "nb_kernel_ElecEw_VdwBham_GeomW3P1_VF_c", "c", "Ewald", "None", "Buckingham", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEw_VdwBham_GeomW3P1_F_c, "nb_kernel_ElecEw_VdwBham_GeomW3P1_F_c", "c", "Ewald", "None", "Buckingham", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecEw_VdwBham_GeomW3W3_VF_c, "nb_kernel_ElecEw_VdwBham_GeomW3W3_VF_c", "c", "Ewald", "None", "Buckingham", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecEw_VdwBham_GeomW3W3_F_c, "nb_kernel_ElecEw_VdwBham_GeomW3W3_F_c", "c", "Ewald", "None", "Buckingham", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecEw_VdwBham_GeomW4P1_VF_c, "nb_kernel_ElecEw_VdwBham_GeomW4P1_VF_c", "c", "Ewald", "None", "Buckingham", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEw_VdwBham_GeomW4P1_F_c, "nb_kernel_ElecEw_VdwBham_GeomW4P1_F_c", "c", "Ewald", "None", "Buckingham", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecEw_VdwBham_GeomW4W4_VF_c, "nb_kernel_ElecEw_VdwBham_GeomW4W4_VF_c", "c", "Ewald", "None", "Buckingham", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecEw_VdwBham_GeomW4W4_F_c, "nb_kernel_ElecEw_VdwBham_GeomW4W4_F_c", "c", "Ewald", "None", "Buckingham", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_VF_c, "nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_VF_c", "c", "Ewald", "PotentialShift", "LennardJones", "PotentialShift", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_F_c, "nb_kernel_ElecEwSh_VdwLJSh_GeomP1P1_F_c", "c", "Ewald", "PotentialShift", "LennardJones", "PotentialShift", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_VF_c, "nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_VF_c", "c", "Ewald", "PotentialShift", "LennardJones", "PotentialShift", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_F_c, "nb_kernel_ElecEwSh_VdwLJSh_GeomW3P1_F_c", "c", "Ewald", "PotentialShift", "LennardJones", "PotentialShift", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_VF_c, "nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_VF_c", "c", "Ewald", "PotentialShift", "LennardJones", "PotentialShift", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_F_c, "nb_kernel_ElecEwSh_VdwLJSh_GeomW3W3_F_c", "c", "Ewald", "PotentialShift", "LennardJones", "PotentialShift", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_VF_c, "nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_VF_c", "c", "Ewald", "PotentialShift", "LennardJones", "PotentialShift", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_F_c, "nb_kernel_ElecEwSh_VdwLJSh_GeomW4P1_F_c", "c", "Ewald", "PotentialShift", "LennardJones", "PotentialShift", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_VF_c, "nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_VF_c", "c", "Ewald", "PotentialShift", "LennardJones", "PotentialShift", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_F_c, "nb_kernel_ElecEwSh_VdwLJSh_GeomW4W4_F_c", "c", "Ewald", "PotentialShift", "LennardJones", "PotentialShift", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecEwSh_VdwNone_GeomP1P1_VF_c, "nb_kernel_ElecEwSh_VdwNone_GeomP1P1_VF_c", "c", "Ewald", "PotentialShift", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSh_VdwNone_GeomP1P1_F_c, "nb_kernel_ElecEwSh_VdwNone_GeomP1P1_F_c", "c", "Ewald", "PotentialShift", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecEwSh_VdwNone_GeomW3P1_VF_c, "nb_kernel_ElecEwSh_VdwNone_GeomW3P1_VF_c", "c", "Ewald", "PotentialShift", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSh_VdwNone_GeomW3P1_F_c, "nb_kernel_ElecEwSh_VdwNone_GeomW3P1_F_c", "c", "Ewald", "PotentialShift", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecEwSh_VdwNone_GeomW3W3_VF_c, "nb_kernel_ElecEwSh_VdwNone_GeomW3W3_VF_c", "c", "Ewald", "PotentialShift", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSh_VdwNone_GeomW3W3_F_c, "nb_kernel_ElecEwSh_VdwNone_GeomW3W3_F_c", "c", "Ewald", "PotentialShift", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecEwSh_VdwNone_GeomW4P1_VF_c, "nb_kernel_ElecEwSh_VdwNone_GeomW4P1_VF_c", "c", "Ewald", "PotentialShift", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSh_VdwNone_GeomW4P1_F_c, "nb_kernel_ElecEwSh_VdwNone_GeomW4P1_F_c", "c", "Ewald", "PotentialShift", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecEwSh_VdwNone_GeomW4W4_VF_c, "nb_kernel_ElecEwSh_VdwNone_GeomW4W4_VF_c", "c", "Ewald", "PotentialShift", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSh_VdwNone_GeomW4W4_F_c, "nb_kernel_ElecEwSh_VdwNone_GeomW4W4_F_c", "c", "Ewald", "PotentialShift", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_VF_c, "nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_VF_c", "c", "Ewald", "PotentialShift", "Buckingham", "PotentialShift", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_F_c, "nb_kernel_ElecEwSh_VdwBhamSh_GeomP1P1_F_c", "c", "Ewald", "PotentialShift", "Buckingham", "PotentialShift", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_VF_c, "nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_VF_c", "c", "Ewald", "PotentialShift", "Buckingham", "PotentialShift", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_F_c, "nb_kernel_ElecEwSh_VdwBhamSh_GeomW3P1_F_c", "c", "Ewald", "PotentialShift", "Buckingham", "PotentialShift", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_VF_c, "nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_VF_c", "c", "Ewald", "PotentialShift", "Buckingham", "PotentialShift", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_F_c, "nb_kernel_ElecEwSh_VdwBhamSh_GeomW3W3_F_c", "c", "Ewald", "PotentialShift", "Buckingham", "PotentialShift", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_VF_c, "nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_VF_c", "c", "Ewald", "PotentialShift", "Buckingham", "PotentialShift", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_F_c, "nb_kernel_ElecEwSh_VdwBhamSh_GeomW4P1_F_c", "c", "Ewald", "PotentialShift", "Buckingham", "PotentialShift", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_VF_c, "nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_VF_c", "c", "Ewald", "PotentialShift", "Buckingham", "PotentialShift", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_F_c, "nb_kernel_ElecEwSh_VdwBhamSh_GeomW4W4_F_c", "c", "Ewald", "PotentialShift", "Buckingham", "PotentialShift", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_VF_c, "nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_VF_c", "c", "Ewald", "PotentialSwitch", "LennardJones", "PotentialSwitch", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_F_c, "nb_kernel_ElecEwSw_VdwLJSw_GeomP1P1_F_c", "c", "Ewald", "PotentialSwitch", "LennardJones", "PotentialSwitch", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_VF_c, "nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_VF_c", "c", "Ewald", "PotentialSwitch", "LennardJones", "PotentialSwitch", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_F_c, "nb_kernel_ElecEwSw_VdwLJSw_GeomW3P1_F_c", "c", "Ewald", "PotentialSwitch", "LennardJones", "PotentialSwitch", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_VF_c, "nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_VF_c", "c", "Ewald", "PotentialSwitch", "LennardJones", "PotentialSwitch", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_F_c, "nb_kernel_ElecEwSw_VdwLJSw_GeomW3W3_F_c", "c", "Ewald", "PotentialSwitch", "LennardJones", "PotentialSwitch", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_VF_c, "nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_VF_c", "c", "Ewald", "PotentialSwitch", "LennardJones", "PotentialSwitch", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_F_c, "nb_kernel_ElecEwSw_VdwLJSw_GeomW4P1_F_c", "c", "Ewald", "PotentialSwitch", "LennardJones", "PotentialSwitch", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_VF_c, "nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_VF_c", "c", "Ewald", "PotentialSwitch", "LennardJones", "PotentialSwitch", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_F_c, "nb_kernel_ElecEwSw_VdwLJSw_GeomW4W4_F_c", "c", "Ewald", "PotentialSwitch", "LennardJones", "PotentialSwitch", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecEwSw_VdwNone_GeomP1P1_VF_c, "nb_kernel_ElecEwSw_VdwNone_GeomP1P1_VF_c", "c", "Ewald", "PotentialSwitch", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSw_VdwNone_GeomP1P1_F_c, "nb_kernel_ElecEwSw_VdwNone_GeomP1P1_F_c", "c", "Ewald", "PotentialSwitch", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecEwSw_VdwNone_GeomW3P1_VF_c, "nb_kernel_ElecEwSw_VdwNone_GeomW3P1_VF_c", "c", "Ewald", "PotentialSwitch", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSw_VdwNone_GeomW3P1_F_c, "nb_kernel_ElecEwSw_VdwNone_GeomW3P1_F_c", "c", "Ewald", "PotentialSwitch", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecEwSw_VdwNone_GeomW3W3_VF_c, "nb_kernel_ElecEwSw_VdwNone_GeomW3W3_VF_c", "c", "Ewald", "PotentialSwitch", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSw_VdwNone_GeomW3W3_F_c, "nb_kernel_ElecEwSw_VdwNone_GeomW3W3_F_c", "c", "Ewald", "PotentialSwitch", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecEwSw_VdwNone_GeomW4P1_VF_c, "nb_kernel_ElecEwSw_VdwNone_GeomW4P1_VF_c", "c", "Ewald", "PotentialSwitch", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_c, "nb_kernel_ElecEwSw_VdwNone_GeomW4P1_F_c", "c", "Ewald", "PotentialSwitch", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_c, "nb_kernel_ElecEwSw_VdwNone_GeomW4W4_VF_c", "c", "Ewald", "PotentialSwitch", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_c, "nb_kernel_ElecEwSw_VdwNone_GeomW4W4_F_c", "c", "Ewald", "PotentialSwitch", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_VF_c, "nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_VF_c", "c", "Ewald", "PotentialSwitch", "Buckingham", "PotentialSwitch", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_F_c, "nb_kernel_ElecEwSw_VdwBhamSw_GeomP1P1_F_c", "c", "Ewald", "PotentialSwitch", "Buckingham", "PotentialSwitch", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_VF_c, "nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_VF_c", "c", "Ewald", "PotentialSwitch", "Buckingham", "PotentialSwitch", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_F_c, "nb_kernel_ElecEwSw_VdwBhamSw_GeomW3P1_F_c", "c", "Ewald", "PotentialSwitch", "Buckingham", "PotentialSwitch", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_VF_c, "nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_VF_c", "c", "Ewald", "PotentialSwitch", "Buckingham", "PotentialSwitch", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_F_c, "nb_kernel_ElecEwSw_VdwBhamSw_GeomW3W3_F_c", "c", "Ewald", "PotentialSwitch", "Buckingham", "PotentialSwitch", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_VF_c, "nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_VF_c", "c", "Ewald", "PotentialSwitch", "Buckingham", "PotentialSwitch", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_F_c, "nb_kernel_ElecEwSw_VdwBhamSw_GeomW4P1_F_c", "c", "Ewald", "PotentialSwitch", "Buckingham", "PotentialSwitch", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_VF_c, "nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_VF_c", "c", "Ewald", "PotentialSwitch", "Buckingham", "PotentialSwitch", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_F_c, "nb_kernel_ElecEwSw_VdwBhamSw_GeomW4W4_F_c", "c", "Ewald", "PotentialSwitch", "Buckingham", "PotentialSwitch", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_c, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_VF_c", "c", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_c, "nb_kernel_ElecCoul_VdwLJ_GeomP1P1_F_c", "c", "Coulomb", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_c, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_VF_c", "c", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_c, "nb_kernel_ElecCoul_VdwLJ_GeomW3P1_F_c", "c", "Coulomb", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_c, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_VF_c", "c", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_c, "nb_kernel_ElecCoul_VdwLJ_GeomW3W3_F_c", "c", "Coulomb", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_c, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_VF_c", "c", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_c, "nb_kernel_ElecCoul_VdwLJ_GeomW4P1_F_c", "c", "Coulomb", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_c, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_VF_c", "c", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_c, "nb_kernel_ElecCoul_VdwLJ_GeomW4W4_F_c", "c", "Coulomb", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_c, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_VF_c", "c", "Coulomb", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_c, "nb_kernel_ElecCoul_VdwNone_GeomP1P1_F_c", "c", "Coulomb", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_c, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_VF_c", "c", "Coulomb", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_c, "nb_kernel_ElecCoul_VdwNone_GeomW3P1_F_c", "c", "Coulomb", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_c, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_VF_c", "c", "Coulomb", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_c, "nb_kernel_ElecCoul_VdwNone_GeomW3W3_F_c", "c", "Coulomb", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_c, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_VF_c", "c", "Coulomb", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_c, "nb_kernel_ElecCoul_VdwNone_GeomW4P1_F_c", "c", "Coulomb", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_c, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_VF_c", "c", "Coulomb", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_c, "nb_kernel_ElecCoul_VdwNone_GeomW4W4_F_c", "c", "Coulomb", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_c, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_VF_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_c, "nb_kernel_ElecCoul_VdwCSTab_GeomP1P1_F_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_VF_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW3P1_F_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_VF_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW3W3_F_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_VF_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW4P1_F_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_VF_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_c, "nb_kernel_ElecCoul_VdwCSTab_GeomW4W4_F_c", "c", "Coulomb", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCoul_VdwBham_GeomP1P1_VF_c, "nb_kernel_ElecCoul_VdwBham_GeomP1P1_VF_c", "c", "Coulomb", "None", "Buckingham", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwBham_GeomP1P1_F_c, "nb_kernel_ElecCoul_VdwBham_GeomP1P1_F_c", "c", "Coulomb", "None", "Buckingham", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwBham_GeomW3P1_VF_c, "nb_kernel_ElecCoul_VdwBham_GeomW3P1_VF_c", "c", "Coulomb", "None", "Buckingham", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwBham_GeomW3P1_F_c, "nb_kernel_ElecCoul_VdwBham_GeomW3P1_F_c", "c", "Coulomb", "None", "Buckingham", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwBham_GeomW3W3_VF_c, "nb_kernel_ElecCoul_VdwBham_GeomW3W3_VF_c", "c", "Coulomb", "None", "Buckingham", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwBham_GeomW3W3_F_c, "nb_kernel_ElecCoul_VdwBham_GeomW3W3_F_c", "c", "Coulomb", "None", "Buckingham", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCoul_VdwBham_GeomW4P1_VF_c, "nb_kernel_ElecCoul_VdwBham_GeomW4P1_VF_c", "c", "Coulomb", "None", "Buckingham", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwBham_GeomW4P1_F_c, "nb_kernel_ElecCoul_VdwBham_GeomW4P1_F_c", "c", "Coulomb", "None", "Buckingham", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCoul_VdwBham_GeomW4W4_VF_c, "nb_kernel_ElecCoul_VdwBham_GeomW4W4_VF_c", "c", "Coulomb", "None", "Buckingham", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCoul_VdwBham_GeomW4W4_F_c, "nb_kernel_ElecCoul_VdwBham_GeomW4W4_F_c", "c", "Coulomb", "None", "Buckingham", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_c, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_VF_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_c, "nb_kernel_ElecCSTab_VdwLJ_GeomP1P1_F_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_VF_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW3P1_F_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_VF_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW3W3_F_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_VF_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW4P1_F_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_VF_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_c, "nb_kernel_ElecCSTab_VdwLJ_GeomW4W4_F_c", "c", "CubicSplineTable", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_c, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_VF_c", "c", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_c, "nb_kernel_ElecCSTab_VdwNone_GeomP1P1_F_c", "c", "CubicSplineTable", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_c, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_VF_c", "c", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_c, "nb_kernel_ElecCSTab_VdwNone_GeomW3P1_F_c", "c", "CubicSplineTable", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_c, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_VF_c", "c", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_c, "nb_kernel_ElecCSTab_VdwNone_GeomW3W3_F_c", "c", "CubicSplineTable", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_c, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_VF_c", "c", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_c, "nb_kernel_ElecCSTab_VdwNone_GeomW4P1_F_c", "c", "CubicSplineTable", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_c, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_VF_c", "c", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_c, "nb_kernel_ElecCSTab_VdwNone_GeomW4W4_F_c", "c", "CubicSplineTable", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_VF_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomP1P1_F_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_VF_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3P1_F_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_VF_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW3W3_F_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_VF_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4P1_F_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_VF_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_c, "nb_kernel_ElecCSTab_VdwCSTab_GeomW4W4_F_c", "c", "CubicSplineTable", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwBham_GeomP1P1_VF_c, "nb_kernel_ElecCSTab_VdwBham_GeomP1P1_VF_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwBham_GeomP1P1_F_c, "nb_kernel_ElecCSTab_VdwBham_GeomP1P1_F_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwBham_GeomW3P1_VF_c, "nb_kernel_ElecCSTab_VdwBham_GeomW3P1_VF_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwBham_GeomW3P1_F_c, "nb_kernel_ElecCSTab_VdwBham_GeomW3P1_F_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwBham_GeomW3W3_VF_c, "nb_kernel_ElecCSTab_VdwBham_GeomW3W3_VF_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwBham_GeomW3W3_F_c, "nb_kernel_ElecCSTab_VdwBham_GeomW3W3_F_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwBham_GeomW4P1_VF_c, "nb_kernel_ElecCSTab_VdwBham_GeomW4P1_VF_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwBham_GeomW4P1_F_c, "nb_kernel_ElecCSTab_VdwBham_GeomW4P1_F_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecCSTab_VdwBham_GeomW4W4_VF_c, "nb_kernel_ElecCSTab_VdwBham_GeomW4W4_VF_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecCSTab_VdwBham_GeomW4W4_F_c, "nb_kernel_ElecCSTab_VdwBham_GeomW4W4_F_c", "c", "CubicSplineTable", "None", "Buckingham", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_c, "nb_kernel_ElecGB_VdwLJ_GeomP1P1_VF_c", "c", "GeneralizedBorn", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_c, "nb_kernel_ElecGB_VdwLJ_GeomP1P1_F_c", "c", "GeneralizedBorn", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_c, "nb_kernel_ElecGB_VdwNone_GeomP1P1_VF_c", "c", "GeneralizedBorn", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecGB_VdwNone_GeomP1P1_F_c, "nb_kernel_ElecGB_VdwNone_GeomP1P1_F_c", "c", "GeneralizedBorn", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_c, "nb_kernel_ElecGB_VdwCSTab_GeomP1P1_VF_c", "c", "GeneralizedBorn", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_c, "nb_kernel_ElecGB_VdwCSTab_GeomP1P1_F_c", "c", "GeneralizedBorn", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecGB_VdwBham_GeomP1P1_VF_c, "nb_kernel_ElecGB_VdwBham_GeomP1P1_VF_c", "c", "GeneralizedBorn", "None", "Buckingham", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecGB_VdwBham_GeomP1P1_F_c, "nb_kernel_ElecGB_VdwBham_GeomP1P1_F_c", "c", "GeneralizedBorn", "None", "Buckingham", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_c, "nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_VF_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_c, "nb_kernel_ElecRFCut_VdwLJSh_GeomP1P1_F_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_c, "nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_VF_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_F_c, "nb_kernel_ElecRFCut_VdwLJSh_GeomW3P1_F_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_VF_c, "nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_VF_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_F_c, "nb_kernel_ElecRFCut_VdwLJSh_GeomW3W3_F_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_VF_c, "nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_VF_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_F_c, "nb_kernel_ElecRFCut_VdwLJSh_GeomW4P1_F_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_VF_c, "nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_VF_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_F_c, "nb_kernel_ElecRFCut_VdwLJSh_GeomW4W4_F_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialShift", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_VF_c, "nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_VF_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialSwitch", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_F_c, "nb_kernel_ElecRFCut_VdwLJSw_GeomP1P1_F_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialSwitch", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_VF_c, "nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_VF_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialSwitch", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_F_c, "nb_kernel_ElecRFCut_VdwLJSw_GeomW3P1_F_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialSwitch", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_VF_c, "nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_VF_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialSwitch", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_F_c, "nb_kernel_ElecRFCut_VdwLJSw_GeomW3W3_F_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialSwitch", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_VF_c, "nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_VF_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialSwitch", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_F_c, "nb_kernel_ElecRFCut_VdwLJSw_GeomW4P1_F_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialSwitch", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_VF_c, "nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_VF_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialSwitch", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_F_c, "nb_kernel_ElecRFCut_VdwLJSw_GeomW4W4_F_c", "c", "ReactionField", "ExactCutoff", "LennardJones", "PotentialSwitch", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwNone_GeomP1P1_VF_c, "nb_kernel_ElecRFCut_VdwNone_GeomP1P1_VF_c", "c", "ReactionField", "ExactCutoff", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwNone_GeomP1P1_F_c, "nb_kernel_ElecRFCut_VdwNone_GeomP1P1_F_c", "c", "ReactionField", "ExactCutoff", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwNone_GeomW3P1_VF_c, "nb_kernel_ElecRFCut_VdwNone_GeomW3P1_VF_c", "c", "ReactionField", "ExactCutoff", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwNone_GeomW3P1_F_c, "nb_kernel_ElecRFCut_VdwNone_GeomW3P1_F_c", "c", "ReactionField", "ExactCutoff", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwNone_GeomW3W3_VF_c, "nb_kernel_ElecRFCut_VdwNone_GeomW3W3_VF_c", "c", "ReactionField", "ExactCutoff", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwNone_GeomW3W3_F_c, "nb_kernel_ElecRFCut_VdwNone_GeomW3W3_F_c", "c", "ReactionField", "ExactCutoff", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwNone_GeomW4P1_VF_c, "nb_kernel_ElecRFCut_VdwNone_GeomW4P1_VF_c", "c", "ReactionField", "ExactCutoff", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwNone_GeomW4P1_F_c, "nb_kernel_ElecRFCut_VdwNone_GeomW4P1_F_c", "c", "ReactionField", "ExactCutoff", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwNone_GeomW4W4_VF_c, "nb_kernel_ElecRFCut_VdwNone_GeomW4W4_VF_c", "c", "ReactionField", "ExactCutoff", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwNone_GeomW4W4_F_c, "nb_kernel_ElecRFCut_VdwNone_GeomW4W4_F_c", "c", "ReactionField", "ExactCutoff", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_VF_c, "nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_VF_c", "c", "ReactionField", "ExactCutoff", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_F_c, "nb_kernel_ElecRFCut_VdwCSTab_GeomP1P1_F_c", "c", "ReactionField", "ExactCutoff", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_VF_c, "nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_VF_c", "c", "ReactionField", "ExactCutoff", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_F_c, "nb_kernel_ElecRFCut_VdwCSTab_GeomW3P1_F_c", "c", "ReactionField", "ExactCutoff", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_VF_c, "nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_VF_c", "c", "ReactionField", "ExactCutoff", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_F_c, "nb_kernel_ElecRFCut_VdwCSTab_GeomW3W3_F_c", "c", "ReactionField", "ExactCutoff", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_VF_c, "nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_VF_c", "c", "ReactionField", "ExactCutoff", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_F_c, "nb_kernel_ElecRFCut_VdwCSTab_GeomW4P1_F_c", "c", "ReactionField", "ExactCutoff", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_VF_c, "nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_VF_c", "c", "ReactionField", "ExactCutoff", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_F_c, "nb_kernel_ElecRFCut_VdwCSTab_GeomW4W4_F_c", "c", "ReactionField", "ExactCutoff", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_VF_c, "nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_VF_c", "c", "ReactionField", "ExactCutoff", "Buckingham", "PotentialShift", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_F_c, "nb_kernel_ElecRFCut_VdwBhamSh_GeomP1P1_F_c", "c", "ReactionField", "ExactCutoff", "Buckingham", "PotentialShift", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_VF_c, "nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_VF_c", "c", "ReactionField", "ExactCutoff", "Buckingham", "PotentialShift", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_F_c, "nb_kernel_ElecRFCut_VdwBhamSh_GeomW3P1_F_c", "c", "ReactionField", "ExactCutoff", "Buckingham", "PotentialShift", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_VF_c, "nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_VF_c", "c", "ReactionField", "ExactCutoff", "Buckingham", "PotentialShift", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_F_c, "nb_kernel_ElecRFCut_VdwBhamSh_GeomW3W3_F_c", "c", "ReactionField", "ExactCutoff", "Buckingham", "PotentialShift", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_VF_c, "nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_VF_c", "c", "ReactionField", "ExactCutoff", "Buckingham", "PotentialShift", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_F_c, "nb_kernel_ElecRFCut_VdwBhamSh_GeomW4P1_F_c", "c", "ReactionField", "ExactCutoff", "Buckingham", "PotentialShift", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_VF_c, "nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_VF_c", "c", "ReactionField", "ExactCutoff", "Buckingham", "PotentialShift", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_F_c, "nb_kernel_ElecRFCut_VdwBhamSh_GeomW4W4_F_c", "c", "ReactionField", "ExactCutoff", "Buckingham", "PotentialShift", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_VF_c, "nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_VF_c", "c", "ReactionField", "ExactCutoff", "Buckingham", "PotentialSwitch", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_F_c, "nb_kernel_ElecRFCut_VdwBhamSw_GeomP1P1_F_c", "c", "ReactionField", "ExactCutoff", "Buckingham", "PotentialSwitch", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_VF_c, "nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_VF_c", "c", "ReactionField", "ExactCutoff", "Buckingham", "PotentialSwitch", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_F_c, "nb_kernel_ElecRFCut_VdwBhamSw_GeomW3P1_F_c", "c", "ReactionField", "ExactCutoff", "Buckingham", "PotentialSwitch", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_VF_c, "nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_VF_c", "c", "ReactionField", "ExactCutoff", "Buckingham", "PotentialSwitch", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_F_c, "nb_kernel_ElecRFCut_VdwBhamSw_GeomW3W3_F_c", "c", "ReactionField", "ExactCutoff", "Buckingham", "PotentialSwitch", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_VF_c, "nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_VF_c", "c", "ReactionField", "ExactCutoff", "Buckingham", "PotentialSwitch", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_F_c, "nb_kernel_ElecRFCut_VdwBhamSw_GeomW4P1_F_c", "c", "ReactionField", "ExactCutoff", "Buckingham", "PotentialSwitch", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_VF_c, "nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_VF_c", "c", "ReactionField", "ExactCutoff", "Buckingham", "PotentialSwitch", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_F_c, "nb_kernel_ElecRFCut_VdwBhamSw_GeomW4W4_F_c", "c", "ReactionField", "ExactCutoff", "Buckingham", "PotentialSwitch", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecRF_VdwLJ_GeomP1P1_VF_c, "nb_kernel_ElecRF_VdwLJ_GeomP1P1_VF_c", "c", "ReactionField", "None", "LennardJones", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRF_VdwLJ_GeomP1P1_F_c, "nb_kernel_ElecRF_VdwLJ_GeomP1P1_F_c", "c", "ReactionField", "None", "LennardJones", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecRF_VdwLJ_GeomW3P1_VF_c, "nb_kernel_ElecRF_VdwLJ_GeomW3P1_VF_c", "c", "ReactionField", "None", "LennardJones", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRF_VdwLJ_GeomW3P1_F_c, "nb_kernel_ElecRF_VdwLJ_GeomW3P1_F_c", "c", "ReactionField", "None", "LennardJones", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecRF_VdwLJ_GeomW3W3_VF_c, "nb_kernel_ElecRF_VdwLJ_GeomW3W3_VF_c", "c", "ReactionField", "None", "LennardJones", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecRF_VdwLJ_GeomW3W3_F_c, "nb_kernel_ElecRF_VdwLJ_GeomW3W3_F_c", "c", "ReactionField", "None", "LennardJones", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecRF_VdwLJ_GeomW4P1_VF_c, "nb_kernel_ElecRF_VdwLJ_GeomW4P1_VF_c", "c", "ReactionField", "None", "LennardJones", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRF_VdwLJ_GeomW4P1_F_c, "nb_kernel_ElecRF_VdwLJ_GeomW4P1_F_c", "c", "ReactionField", "None", "LennardJones", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecRF_VdwLJ_GeomW4W4_VF_c, "nb_kernel_ElecRF_VdwLJ_GeomW4W4_VF_c", "c", "ReactionField", "None", "LennardJones", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecRF_VdwLJ_GeomW4W4_F_c, "nb_kernel_ElecRF_VdwLJ_GeomW4W4_F_c", "c", "ReactionField", "None", "LennardJones", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecRF_VdwNone_GeomP1P1_VF_c, "nb_kernel_ElecRF_VdwNone_GeomP1P1_VF_c", "c", "ReactionField", "None", "None", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRF_VdwNone_GeomP1P1_F_c, "nb_kernel_ElecRF_VdwNone_GeomP1P1_F_c", "c", "ReactionField", "None", "None", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecRF_VdwNone_GeomW3P1_VF_c, "nb_kernel_ElecRF_VdwNone_GeomW3P1_VF_c", "c", "ReactionField", "None", "None", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRF_VdwNone_GeomW3P1_F_c, "nb_kernel_ElecRF_VdwNone_GeomW3P1_F_c", "c", "ReactionField", "None", "None", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecRF_VdwNone_GeomW3W3_VF_c, "nb_kernel_ElecRF_VdwNone_GeomW3W3_VF_c", "c", "ReactionField", "None", "None", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecRF_VdwNone_GeomW3W3_F_c, "nb_kernel_ElecRF_VdwNone_GeomW3W3_F_c", "c", "ReactionField", "None", "None", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecRF_VdwNone_GeomW4P1_VF_c, "nb_kernel_ElecRF_VdwNone_GeomW4P1_VF_c", "c", "ReactionField", "None", "None", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRF_VdwNone_GeomW4P1_F_c, "nb_kernel_ElecRF_VdwNone_GeomW4P1_F_c", "c", "ReactionField", "None", "None", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecRF_VdwNone_GeomW4W4_VF_c, "nb_kernel_ElecRF_VdwNone_GeomW4W4_VF_c", "c", "ReactionField", "None", "None", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecRF_VdwNone_GeomW4W4_F_c, "nb_kernel_ElecRF_VdwNone_GeomW4W4_F_c", "c", "ReactionField", "None", "None", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecRF_VdwCSTab_GeomP1P1_VF_c, "nb_kernel_ElecRF_VdwCSTab_GeomP1P1_VF_c", "c", "ReactionField", "None", "CubicSplineTable", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRF_VdwCSTab_GeomP1P1_F_c, "nb_kernel_ElecRF_VdwCSTab_GeomP1P1_F_c", "c", "ReactionField", "None", "CubicSplineTable", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecRF_VdwCSTab_GeomW3P1_VF_c, "nb_kernel_ElecRF_VdwCSTab_GeomW3P1_VF_c", "c", "ReactionField", "None", "CubicSplineTable", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRF_VdwCSTab_GeomW3P1_F_c, "nb_kernel_ElecRF_VdwCSTab_GeomW3P1_F_c", "c", "ReactionField", "None", "CubicSplineTable", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecRF_VdwCSTab_GeomW3W3_VF_c, "nb_kernel_ElecRF_VdwCSTab_GeomW3W3_VF_c", "c", "ReactionField", "None", "CubicSplineTable", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecRF_VdwCSTab_GeomW3W3_F_c, "nb_kernel_ElecRF_VdwCSTab_GeomW3W3_F_c", "c", "ReactionField", "None", "CubicSplineTable", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_c, "nb_kernel_ElecRF_VdwCSTab_GeomW4P1_VF_c", "c", "ReactionField", "None", "CubicSplineTable", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_c, "nb_kernel_ElecRF_VdwCSTab_GeomW4P1_F_c", "c", "ReactionField", "None", "CubicSplineTable", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_c, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_VF_c", "c", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_c, "nb_kernel_ElecRF_VdwCSTab_GeomW4W4_F_c", "c", "ReactionField", "None", "CubicSplineTable", "None", "Water4Water4", "", "Force" },
+ { nb_kernel_ElecRF_VdwBham_GeomP1P1_VF_c, "nb_kernel_ElecRF_VdwBham_GeomP1P1_VF_c", "c", "ReactionField", "None", "Buckingham", "None", "ParticleParticle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRF_VdwBham_GeomP1P1_F_c, "nb_kernel_ElecRF_VdwBham_GeomP1P1_F_c", "c", "ReactionField", "None", "Buckingham", "None", "ParticleParticle", "", "Force" },
+ { nb_kernel_ElecRF_VdwBham_GeomW3P1_VF_c, "nb_kernel_ElecRF_VdwBham_GeomW3P1_VF_c", "c", "ReactionField", "None", "Buckingham", "None", "Water3Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRF_VdwBham_GeomW3P1_F_c, "nb_kernel_ElecRF_VdwBham_GeomW3P1_F_c", "c", "ReactionField", "None", "Buckingham", "None", "Water3Particle", "", "Force" },
+ { nb_kernel_ElecRF_VdwBham_GeomW3W3_VF_c, "nb_kernel_ElecRF_VdwBham_GeomW3W3_VF_c", "c", "ReactionField", "None", "Buckingham", "None", "Water3Water3", "", "PotentialAndForce" },
+ { nb_kernel_ElecRF_VdwBham_GeomW3W3_F_c, "nb_kernel_ElecRF_VdwBham_GeomW3W3_F_c", "c", "ReactionField", "None", "Buckingham", "None", "Water3Water3", "", "Force" },
+ { nb_kernel_ElecRF_VdwBham_GeomW4P1_VF_c, "nb_kernel_ElecRF_VdwBham_GeomW4P1_VF_c", "c", "ReactionField", "None", "Buckingham", "None", "Water4Particle", "", "PotentialAndForce" },
+ { nb_kernel_ElecRF_VdwBham_GeomW4P1_F_c, "nb_kernel_ElecRF_VdwBham_GeomW4P1_F_c", "c", "ReactionField", "None", "Buckingham", "None", "Water4Particle", "", "Force" },
+ { nb_kernel_ElecRF_VdwBham_GeomW4W4_VF_c, "nb_kernel_ElecRF_VdwBham_GeomW4W4_VF_c", "c", "ReactionField", "None", "Buckingham", "None", "Water4Water4", "", "PotentialAndForce" },
+ { nb_kernel_ElecRF_VdwBham_GeomW4W4_F_c, "nb_kernel_ElecRF_VdwBham_GeomW4W4_F_c", "c", "ReactionField", "None", "Buckingham", "None", "Water4Water4", "", "Force" }
};
+int
+kernellist_c_size = sizeof(kernellist_c)/sizeof(kernellist_c[0]);
-void
-nb_kernel_setup(FILE *log,nb_kernel_t **list)
-{
- int i;
- nb_kernel_t *p;
-
- if(NULL != log)
- fprintf(log,"Configuring standard C nonbonded kernels...\n");
-
- for(i=0;i<eNR_NBKERNEL_NR;i++)
- {
- p = kernellist[i];
- if(p!=NULL)
- list[i] = p;
- }
-}
+#endif
/*
+ * Note: this file was generated by the Gromacs c kernel generator.
+ *
* This source code is part of
*
* G R O M A C S
*
- * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2009, The GROMACS Development Team
+ * Copyright (c) 2001-2012, The GROMACS Development Team
*
* Gromacs is a library for molecular simulation and trajectory analysis,
* written by Erik Lindahl, David van der Spoel, Berk Hess, and others - for
* a full list of developers and information, check out http://www.gromacs.org
*
- * This program is free software; you can redistribute it and/or modify it under
- * the terms of the GNU Lesser General Public License as published by the Free
- * Software Foundation; either version 2 of the License, or (at your option) any
+ * This program is free software; you can redistribute it and/or modify it under
+ * the terms of the GNU Lesser General Public License as published by the Free
+ * Software Foundation; either version 2 of the License, or (at your option) any
* later version.
- * As a special exception, you may use this file as part of a free software
- * library without restriction. Specifically, if other files instantiate
- * templates or use macros or inline functions from this file, or you compile
- * this file and link it with other files to produce an executable, this
- * file does not by itself cause the resulting executable to be covered by
- * the GNU Lesser General Public License.
- *
- * In plain-speak: do not worry about classes/macros/templates either - only
- * changes to the library have to be LGPL, not an application linking with it.
*
* To help fund GROMACS development, we humbly ask that you cite
- * the papers people have written on it - you can find them on the website!
- */
-#ifndef _NBKERNEL_H_
-#define _NBKERNEL_H_
-
-/** \file
- * \brief The vanilla nonbonded Gromacs kernels (portable, written in C).
- *
- * \internal
+ * the papers people have written on it - you can find them on the website.
*/
+#ifndef nb_kernel_c_h
+#define nb_kernel_c_h
-#include <stdio.h>
+#include "../nb_kernel.h"
-#include "../nb_kerneltype.h"
-#include "nb_kernel_allvsall.h"
-#include "nb_kernel_allvsallgb.h"
-void
-nb_kernel_setup(FILE *fplog,nb_kernel_t **list);
+/* List of kernels for this architecture with metadata about them */
+extern nb_kernel_info_t
+kernellist_c[];
-#endif /* _NBKERNEL_H_ */
+/* Length of kernellist_c */
+extern int
+kernellist_c_size;
+#endif
--- /dev/null
+/* #if 0 */
+#error This file must be processed with the Gromacs pre-preprocessor
+/* #endif */
+/* #if INCLUDE_HEADER */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include <math.h>
+
+#include "../nb_kernel.h"
+#include "types/simple.h"
+#include "vec.h"
+#include "nrnb.h"
+/* #endif */
+
+/* ## List of variables set by the generating script: */
+/* ## */
+/* ## Setttings that apply to the entire kernel: */
+/* ## KERNEL_ELEC: String, choice for electrostatic interactions */
+/* ## KERNEL_VDW: String, choice for van der Waals interactions */
+/* ## KERNEL_NAME: String, name of this kernel */
+/* ## KERNEL_VF: String telling if we calculate potential, force, or both */
+/* ## GEOMETRY_I/GEOMETRY_J: String, name of each geometry, e.g. 'Water3' or '1Particle' */
+/* ## */
+/* ## Setttings that apply to particles in the outer (I) or inner (J) loops: */
+/* ## PARTICLES_I[]/ Arrays with lists of i/j particles to use in kernel. It is */
+/* ## PARTICLES_J[]: just [0] for particle geometry, but can be longer for water */
+/* ## PARTICLES_ELEC_I[]/ Arrays with lists of i/j particle that have electrostatics */
+/* ## PARTICLES_ELEC_J[]: interactions that should be calculated in this kernel. */
+/* ## PARTICLES_VDW_I[]/ Arrays with the list of i/j particle that have VdW */
+/* ## PARTICLES_VDW_J[]: interactions that should be calculated in this kernel. */
+/* ## */
+/* ## Setttings for pairs of interactions (e.g. 2nd i particle against 1st j particle) */
+/* ## PAIRS_IJ[]: Array with (i,j) tuples of pairs for which interactions */
+/* ## should be calculated in this kernel. Zero-charge particles */
+/* ## do not have interactions with particles without vdw, and */
+/* ## Vdw-only interactions are not evaluated in a no-vdw-kernel. */
+/* ## INTERACTION_FLAGS[][]: 2D matrix, dimension e.g. 3*3 for water-water interactions. */
+/* ## For each i-j pair, the element [I][J] is a list of strings */
+/* ## defining properties/flags of this interaction. Examples */
+/* ## include 'electrostatics'/'vdw' if that type of interaction */
+/* ## should be evaluated, 'rsq'/'rinv'/'rinvsq' if those values */
+/* ## are needed, and 'exactcutoff' or 'shift','switch' to */
+/* ## decide if the force/potential should be modified. This way */
+/* ## we only calculate values absolutely needed for each case. */
+
+/* ## Calculate the size and offset for (merged/interleaved) table data */
+
+/* #if ('CubicSplineTable' in [KERNEL_ELEC,KERNEL_VDW]) or KERNEL_VF=='PotentialAndForce' */
+/* #define TABLE_POINT_SIZE 4 */
+/* #else */
+/* #define TABLE_POINT_SIZE 2 */
+/* #endif */
+
+/* #if 'Table' in KERNEL_ELEC and 'Table' in KERNEL_VDW */
+/* #define TABLE_NINTERACTIONS 3 */
+/* #define TABLE_VDW_OFFSET TABLE_POINT_SIZE */
+/* #elif 'Table' in KERNEL_ELEC */
+/* #define TABLE_NINTERACTIONS 1 */
+/* #elif 'Table' in KERNEL_VDW */
+/* #define TABLE_NINTERACTIONS 2 */
+/* #define TABLE_VDW_OFFSET 0 */
+/* #else */
+/* #define TABLE_NINTERACTIONS 0 */
+/* #endif */
+
+/* #if 'Buckingham' in KERNEL_VDW */
+/* #define NVDWPARAM 3 */
+/* #else */
+/* #define NVDWPARAM 2 */
+/* #endif */
+
+/*
+ * Gromacs nonbonded kernel: {KERNEL_NAME}
+ * Electrostatics interaction: {KERNEL_ELEC}
+ * VdW interaction: {KERNEL_VDW}
+ * Geometry: {GEOMETRY_I}-{GEOMETRY_J}
+ * Calculate force/pot: {KERNEL_VF}
+ */
+void
+{KERNEL_NAME}
+ (t_nblist * gmx_restrict nlist,
+ rvec * gmx_restrict xx,
+ rvec * gmx_restrict ff,
+ t_forcerec * gmx_restrict fr,
+ t_mdatoms * gmx_restrict mdatoms,
+ nb_kernel_data_t * gmx_restrict kernel_data,
+ t_nrnb * gmx_restrict nrnb)
+{
+ /* ## Not all variables are used for all kernels, but any optimizing compiler fixes that, */
+ /* ## so there is no point in going to extremes to exclude variables that are not needed. */
+ int i_shift_offset,i_coord_offset,j_coord_offset;
+ int j_index_start,j_index_end;
+ int nri,inr,ggid,iidx,jidx,jnr,outeriter,inneriter;
+ real shX,shY,shZ,tx,ty,tz,fscal,rcutoff,rcutoff2;
+ int *iinr,*jindex,*jjnr,*shiftidx,*gid;
+ real *shiftvec,*fshift,*x,*f;
+ /* #for I in PARTICLES_I */
+ int vdwioffset{I};
+ real ix{I},iy{I},iz{I},fix{I},fiy{I},fiz{I},iq{I},isai{I};
+ /* #endfor */
+ /* #for J in PARTICLES_J */
+ int vdwjidx{J};
+ real jx{J},jy{J},jz{J},fjx{J},fjy{J},fjz{J},jq{J},isaj{J};
+ /* #endfor */
+ /* #for I,J in PAIRS_IJ */
+ real dx{I}{J},dy{I}{J},dz{I}{J},rsq{I}{J},rinv{I}{J},rinvsq{I}{J},r{I}{J},qq{I}{J},c6_{I}{J},c12_{I}{J},cexp1_{I}{J},cexp2_{I}{J};
+ /* #endfor */
+ /* #if KERNEL_ELEC != 'None' */
+ real velec,felec,velecsum,facel,crf,krf,krf2;
+ real *charge;
+ /* #endif */
+ /* #if 'GeneralizedBorn' in KERNEL_ELEC */
+ int gbitab;
+ real vgb,fgb,vgbsum,dvdasum,gbscale,gbtabscale,isaprod,gbqqfactor,gbinvepsdiff,dvdaj,gbeps,dvdatmp;
+ real *invsqrta,*dvda,*gbtab;
+ /* #endif */
+ /* #if KERNEL_VDW != 'None' */
+ int nvdwtype;
+ real rinvsix,rvdw,vvdw,vvdw6,vvdw12,fvdw,fvdw6,fvdw12,vvdwsum,br,vvdwexp,sh_vdw_invrcut6;
+ int *vdwtype;
+ real *vdwparam;
+ /* #endif */
+ /* #if 'Table' in KERNEL_ELEC or 'GeneralizedBorn' in KERNEL_ELEC or 'Table' in KERNEL_VDW */
+ int vfitab;
+ real rt,vfeps,vftabscale,Y,F,Geps,Heps2,Fp,VV,FF;
+ real *vftab;
+ /* #endif */
+ /* #if 'Ewald' in KERNEL_ELEC */
+ int ewitab;
+ real ewtabscale,eweps,sh_ewald,ewrt,ewtabhalfspace;
+ real *ewtab;
+ /* #endif */
+ /* #if 'PotentialSwitch' in [KERNEL_MOD_ELEC,KERNEL_MOD_VDW] */
+ real rswitch,swV3,swV4,swV5,swF2,swF3,swF4,d,d2,sw,dsw;
+ /* #endif */
+
+ x = xx[0];
+ f = ff[0];
+
+ nri = nlist->nri;
+ iinr = nlist->iinr;
+ jindex = nlist->jindex;
+ jjnr = nlist->jjnr;
+ shiftidx = nlist->shift;
+ gid = nlist->gid;
+ shiftvec = fr->shift_vec[0];
+ fshift = fr->fshift[0];
+ /* #if KERNEL_ELEC != 'None' */
+ facel = fr->epsfac;
+ charge = mdatoms->chargeA;
+ /* #if 'ReactionField' in KERNEL_ELEC */
+ krf = fr->ic->k_rf;
+ krf2 = krf*2.0;
+ crf = fr->ic->c_rf;
+ /* #endif */
+ /* #endif */
+ /* #if KERNEL_VDW != 'None' */
+ nvdwtype = fr->ntype;
+ vdwparam = fr->nbfp;
+ vdwtype = mdatoms->typeA;
+ /* #endif */
+
+ /* #if 'Table' in KERNEL_ELEC and 'Table' in KERNEL_VDW */
+ vftab = kernel_data->table_elec_vdw->data;
+ vftabscale = kernel_data->table_elec_vdw->scale;
+ /* #elif 'Table' in KERNEL_ELEC */
+ vftab = kernel_data->table_elec->data;
+ vftabscale = kernel_data->table_elec->scale;
+ /* #elif 'Table' in KERNEL_VDW */
+ vftab = kernel_data->table_vdw->data;
+ vftabscale = kernel_data->table_vdw->scale;
+ /* #endif */
+
+ /* #if 'Ewald' in KERNEL_ELEC */
+ sh_ewald = fr->ic->sh_ewald;
+ /* #if KERNEL_VF=='Force' */
+ ewtab = fr->ic->tabq_coul_F;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+ /* #else */
+ ewtab = fr->ic->tabq_coul_FDV0;
+ ewtabscale = fr->ic->tabq_scale;
+ ewtabhalfspace = 0.5/ewtabscale;
+ /* #endif */
+ /* #endif */
+
+ /* #if KERNEL_ELEC=='GeneralizedBorn' */
+ invsqrta = fr->invsqrta;
+ dvda = fr->dvda;
+ gbtabscale = fr->gbtab.scale;
+ gbtab = fr->gbtab.data;
+ gbinvepsdiff = (1.0/fr->epsilon_r) - (1.0/fr->gb_epsilon_solvent);
+ /* #endif */
+
+ /* #if 'Water' in GEOMETRY_I */
+ /* Setup water-specific parameters */
+ inr = nlist->iinr[0];
+ /* #for I in PARTICLES_ELEC_I */
+ iq{I} = facel*charge[inr+{I}];
+ /* #endfor */
+ /* #for I in PARTICLES_VDW_I */
+ vdwioffset{I} = {NVDWPARAM}*nvdwtype*vdwtype[inr+{I}];
+ /* #endfor */
+ /* #endif */
+
+ /* #if 'Water' in GEOMETRY_J */
+ /* #for J in PARTICLES_ELEC_J */
+ jq{J} = charge[inr+{J}];
+ /* #endfor */
+ /* #for J in PARTICLES_VDW_J */
+ vdwjidx{J} = {NVDWPARAM}*vdwtype[inr+{J}];
+ /* #endfor */
+ /* #for I,J in PAIRS_IJ */
+ /* #if 'electrostatics' in INTERACTION_FLAGS[I][J] */
+ qq{I}{J} = iq{I}*jq{J};
+ /* #endif */
+ /* #if 'vdw' in INTERACTION_FLAGS[I][J] */
+ /* #if 'Buckingham' in KERNEL_VDW */
+ c6_{I}{J} = vdwparam[vdwioffset{I}+vdwjidx{J}];
+ cexp1_{I}{J} = vdwparam[vdwioffset{I}+vdwjidx{J}+1];
+ cexp2_{I}{J} = vdwparam[vdwioffset{I}+vdwjidx{J}+2];
+ /* #else */
+ c6_{I}{J} = vdwparam[vdwioffset{I}+vdwjidx{J}];
+ c12_{I}{J} = vdwparam[vdwioffset{I}+vdwjidx{J}+1];
+ /* #endif */
+ /* #endif */
+ /* #endfor */
+ /* #endif */
+
+ /* #if KERNEL_MOD_ELEC!='None' or KERNEL_MOD_VDW!='None' */
+ /* #if KERNEL_ELEC!='None' */
+ /* When we use explicit cutoffs the value must be identical for elec and VdW, so use elec as an arbitrary choice */
+ rcutoff = fr->rcoulomb;
+ /* #else */
+ rcutoff = fr->rvdw;
+ /* #endif */
+ rcutoff2 = rcutoff*rcutoff;
+ /* #endif */
+
+ /* #if KERNEL_MOD_VDW=='PotentialShift' */
+ sh_vdw_invrcut6 = fr->ic->sh_invrc6;
+ rvdw = fr->rvdw;
+ /* #endif */
+
+ /* #if 'PotentialSwitch' in [KERNEL_MOD_ELEC,KERNEL_MOD_VDW] */
+ /* #if KERNEL_MOD_ELEC=='PotentialSwitch' */
+ rswitch = fr->rcoulomb_switch;
+ /* #else */
+ rswitch = fr->rvdw_switch;
+ /* #endif */
+ /* Setup switch parameters */
+ d = rcutoff-rswitch;
+ swV3 = -10.0/(d*d*d);
+ swV4 = 15.0/(d*d*d*d);
+ swV5 = -6.0/(d*d*d*d*d);
+ /* #if 'Force' in KERNEL_VF */
+ swF2 = -30.0/(d*d*d);
+ swF3 = 60.0/(d*d*d*d);
+ swF4 = -30.0/(d*d*d*d*d);
+ /* #endif */
+ /* #endif */
+
+ /* ## Keep track of the floating point operations we issue for reporting! */
+ /* #define OUTERFLOPS 0 */
+ /* #define INNERFLOPS 0 */
+ outeriter = 0;
+ inneriter = 0;
+
+ /* Start outer loop over neighborlists */
+ for(iidx=0; iidx<nri; iidx++)
+ {
+ /* Load shift vector for this list */
+ i_shift_offset = DIM*shiftidx[iidx];
+ shX = shiftvec[i_shift_offset+XX];
+ shY = shiftvec[i_shift_offset+YY];
+ shZ = shiftvec[i_shift_offset+ZZ];
+
+ /* Load limits for loop over neighbors */
+ j_index_start = jindex[iidx];
+ j_index_end = jindex[iidx+1];
+
+ /* Get outer coordinate index */
+ inr = iinr[iidx];
+ i_coord_offset = DIM*inr;
+
+ /* Load i particle coords and add shift vector */
+ /* ## Loop over i particles, but only include ones that we use - skip e.g. vdw-only sites for elec-only kernel */
+ /* #for I in PARTICLES_I */
+ ix{I} = shX + x[i_coord_offset+DIM*{I}+XX];
+ iy{I} = shY + x[i_coord_offset+DIM*{I}+YY];
+ iz{I} = shZ + x[i_coord_offset+DIM*{I}+ZZ];
+ /* #define OUTERFLOPS OUTERFLOPS+3 */
+ /* #endfor */
+
+ /* #if 'Force' in KERNEL_VF */
+ /* #for I in PARTICLES_I */
+ fix{I} = 0.0;
+ fiy{I} = 0.0;
+ fiz{I} = 0.0;
+ /* #endfor */
+ /* #endif */
+
+ /* ## For water we already preloaded parameters at the start of the kernel */
+ /* #if not 'Water' in GEOMETRY_I */
+ /* Load parameters for i particles */
+ /* #for I in PARTICLES_ELEC_I */
+ iq{I} = facel*charge[inr+{I}];
+ /* #define OUTERFLOPS OUTERFLOPS+1 */
+ /* #if KERNEL_ELEC=='GeneralizedBorn' */
+ isai{I} = invsqrta[inr+{I}];
+ /* #endif */
+ /* #endfor */
+ /* #for I in PARTICLES_VDW_I */
+ vdwioffset{I} = {NVDWPARAM}*nvdwtype*vdwtype[inr+{I}];
+ /* #endfor */
+ /* #endif */
+
+ /* #if 'Potential' in KERNEL_VF */
+ /* Reset potential sums */
+ /* #if KERNEL_ELEC != 'None' */
+ velecsum = 0.0;
+ /* #endif */
+ /* #if 'GeneralizedBorn' in KERNEL_ELEC */
+ vgbsum = 0.0;
+ /* #endif */
+ /* #if KERNEL_VDW != 'None' */
+ vvdwsum = 0.0;
+ /* #endif */
+ /* #endif */
+ /* #if 'GeneralizedBorn' in KERNEL_ELEC and 'Force' in KERNEL_VF */
+ dvdasum = 0.0;
+ /* #endif */
+
+ /* Start inner kernel loop */
+ for(jidx=j_index_start; jidx<j_index_end; jidx++)
+ {
+ /* Get j neighbor index, and coordinate index */
+ jnr = jjnr[jidx];
+ j_coord_offset = DIM*jnr;
+
+ /* load j atom coordinates */
+ /* #for J in PARTICLES_J */
+ jx{J} = x[j_coord_offset+DIM*{J}+XX];
+ jy{J} = x[j_coord_offset+DIM*{J}+YY];
+ jz{J} = x[j_coord_offset+DIM*{J}+ZZ];
+ /* #endfor */
+
+ /* Calculate displacement vector */
+ /* #for I,J in PAIRS_IJ */
+ dx{I}{J} = ix{I} - jx{J};
+ dy{I}{J} = iy{I} - jy{J};
+ dz{I}{J} = iz{I} - jz{J};
+ /* #define INNERFLOPS INNERFLOPS+3 */
+ /* #endfor */
+
+ /* Calculate squared distance and things based on it */
+ /* #for I,J in PAIRS_IJ */
+ rsq{I}{J} = dx{I}{J}*dx{I}{J}+dy{I}{J}*dy{I}{J}+dz{I}{J}*dz{I}{J};
+ /* #define INNERFLOPS INNERFLOPS+5 */
+ /* #endfor */
+
+ /* #for I,J in PAIRS_IJ */
+ /* #if 'rinv' in INTERACTION_FLAGS[I][J] */
+ rinv{I}{J} = gmx_invsqrt(rsq{I}{J});
+ /* #define INNERFLOPS INNERFLOPS+5 */
+ /* #endif */
+ /* #endfor */
+
+ /* #for I,J in PAIRS_IJ */
+ /* #if 'rinvsq' in INTERACTION_FLAGS[I][J] */
+ /* # if 'rinv' not in INTERACTION_FLAGS[I][J] */
+ rinvsq{I}{J} = 1.0/rsq{I}{J};
+ /* #define INNERFLOPS INNERFLOPS+4 */
+ /* #else */
+ rinvsq{I}{J} = rinv{I}{J}*rinv{I}{J};
+ /* #define INNERFLOPS INNERFLOPS+1 */
+ /* #endif */
+ /* #endif */
+ /* #endfor */
+
+ /* #if not 'Water' in GEOMETRY_J */
+ /* Load parameters for j particles */
+ /* #for J in PARTICLES_ELEC_J */
+ jq{J} = charge[jnr+{J}];
+ /* #if KERNEL_ELEC=='GeneralizedBorn' */
+ isaj{J} = invsqrta[jnr+{J}];
+ /* #endif */
+ /* #endfor */
+ /* #for J in PARTICLES_VDW_J */
+ vdwjidx{J} = {NVDWPARAM}*vdwtype[jnr+{J}];
+ /* #endfor */
+ /* #endif */
+
+ /* #for I,J in PAIRS_IJ */
+
+ /**************************
+ * CALCULATE INTERACTIONS *
+ **************************/
+
+ /* #if 'exactcutoff' in INTERACTION_FLAGS[I][J] */
+ /* ## We always calculate rinv/rinvsq above to enable pipelineing in compilers (performance tested on x86) */
+ if (rsq{I}{J}<rcutoff2)
+ {
+ /* #if 0 ## this and the next two lines is a hack to maintain auto-indentation in template file */
+ }
+ /* #endif */
+ /* #endif */
+
+ /* #if 'r' in INTERACTION_FLAGS[I][J] */
+ r{I}{J} = rsq{I}{J}*rinv{I}{J};
+ /* #define INNERFLOPS INNERFLOPS+1 */
+ /* #endif */
+
+ /* ## For water geometries we already loaded parameters at the start of the kernel */
+ /* #if not 'Water' in GEOMETRY_J */
+ /* #if 'electrostatics' in INTERACTION_FLAGS[I][J] */
+ qq{I}{J} = iq{I}*jq{J};
+ /* #define INNERFLOPS INNERFLOPS+1 */
+ /* #endif */
+ /* #if 'vdw' in INTERACTION_FLAGS[I][J] */
+ /* #if KERNEL_VDW=='Buckingham' */
+ c6_{I}{J} = vdwparam[vdwioffset{I}+vdwjidx{J}];
+ cexp1_{I}{J} = vdwparam[vdwioffset{I}+vdwjidx{J}+1];
+ cexp2_{I}{J} = vdwparam[vdwioffset{I}+vdwjidx{J}+2];
+ /* #else */
+ c6_{I}{J} = vdwparam[vdwioffset{I}+vdwjidx{J}];
+ c12_{I}{J} = vdwparam[vdwioffset{I}+vdwjidx{J}+1];
+ /* #endif */
+ /* #endif */
+ /* #endif */
+
+ /* #if 'table' in INTERACTION_FLAGS[I][J] */
+ /* Calculate table index by multiplying r with table scale and truncate to integer */
+ rt = r{I}{J}*vftabscale;
+ vfitab = rt;
+ vfeps = rt-vfitab;
+ vfitab = {TABLE_NINTERACTIONS}*{TABLE_POINT_SIZE}*vfitab;
+ /* #define INNERFLOPS INNERFLOPS+2 */
+ /* #endif */
+
+ /* ## ELECTROSTATIC INTERACTIONS */
+ /* #if 'electrostatics' in INTERACTION_FLAGS[I][J] */
+
+ /* #if KERNEL_ELEC=='Coulomb' */
+
+ /* COULOMB ELECTROSTATICS */
+ velec = qq{I}{J}*rinv{I}{J};
+ /* #define INNERFLOPS INNERFLOPS+1 */
+ /* #if 'Force' in KERNEL_VF */
+ felec = velec*rinvsq{I}{J};
+ /* #define INNERFLOPS INNERFLOPS+2 */
+ /* #endif */
+
+ /* #elif KERNEL_ELEC=='ReactionField' */
+
+ /* REACTION-FIELD ELECTROSTATICS */
+ /* #if 'Potential' in KERNEL_VF */
+ velec = qq{I}{J}*(rinv{I}{J}+krf*rsq{I}{J}-crf);
+ /* #define INNERFLOPS INNERFLOPS+4 */
+ /* #endif */
+ /* #if 'Force' in KERNEL_VF */
+ felec = qq{I}{J}*(rinv{I}{J}*rinvsq{I}{J}-krf2);
+ /* #define INNERFLOPS INNERFLOPS+3 */
+ /* #endif */
+
+ /* #elif KERNEL_ELEC=='GeneralizedBorn' */
+
+ /* GENERALIZED BORN AND COULOMB ELECTROSTATICS */
+ isaprod = isai{I}*isaj{J};
+ gbqqfactor = isaprod*(-qq{I}{J})*gbinvepsdiff;
+ gbscale = isaprod*gbtabscale;
+ dvdaj = dvda[jnr+{J}];
+ /* #define INNERFLOPS INNERFLOPS+5 */
+
+ /* Calculate generalized born table index - this is a separate table from the normal one,
+ * but we use the same procedure by multiplying r with scale and truncating to integer.
+ */
+ rt = r{I}{J}*gbscale;
+ gbitab = rt;
+ gbeps = rt-gbitab;
+ gbitab = 4*gbitab;
+
+ Y = gbtab[gbitab];
+ F = gbtab[gbitab+1];
+ Geps = gbeps*gbtab[gbitab+2];
+ Heps2 = gbeps*gbeps*gbtab[gbitab+3];
+ Fp = F+Geps+Heps2;
+ VV = Y+gbeps*Fp;
+ vgb = gbqqfactor*VV;
+ /* #define INNERFLOPS INNERFLOPS+10 */
+
+ /* #if 'Force' in KERNEL_VF */
+ FF = Fp+Geps+2.0*Heps2;
+ fgb = gbqqfactor*FF*gbscale;
+ dvdatmp = -0.5*(vgb+fgb*r{I}{J});
+ dvdasum = dvdasum + dvdatmp;
+ dvda[jnr] = dvdaj+dvdatmp*isaj{J}*isaj{J};
+ /* #define INNERFLOPS INNERFLOPS+13 */
+ /* #endif */
+ velec = qq{I}{J}*rinv{I}{J};
+ /* #define INNERFLOPS INNERFLOPS+1 */
+ /* #if 'Force' in KERNEL_VF */
+ felec = (velec*rinv{I}{J}-fgb)*rinv{I}{J};
+ /* #define INNERFLOPS INNERFLOPS+3 */
+ /* #endif */
+
+ /* #elif KERNEL_ELEC=='Ewald' */
+ /* EWALD ELECTROSTATICS */
+
+ /* Calculate Ewald table index by multiplying r with scale and truncate to integer */
+ ewrt = r{I}{J}*ewtabscale;
+ ewitab = ewrt;
+ eweps = ewrt-ewitab;
+ /* #define INNERFLOPS INNERFLOPS+2 */
+ /* #if 'Potential' in KERNEL_VF or KERNEL_MOD_ELEC=='PotentialSwitch' */
+ ewitab = 4*ewitab;
+ felec = ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ /* #define INNERFLOPS INNERFLOPS+4 */
+ /* #if KERNEL_MOD_ELEC=='PotentialShift' */
+ velec = qq{I}{J}*((rinv{I}{J}-sh_ewald)-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ /* #define INNERFLOPS INNERFLOPS+7 */
+ /* #else */
+ velec = qq{I}{J}*(rinv{I}{J}-(ewtab[ewitab+2]-ewtabhalfspace*eweps*(ewtab[ewitab]+felec)));
+ /* #define INNERFLOPS INNERFLOPS+6 */
+ /* #endif */
+ /* #if 'Force' in KERNEL_VF */
+ felec = qq{I}{J}*rinv{I}{J}*(rinvsq{I}{J}-felec);
+ /* #define INNERFLOPS INNERFLOPS+3 */
+ /* #endif */
+ /* #elif KERNEL_VF=='Force' */
+ felec = (1.0-eweps)*ewtab[ewitab]+eweps*ewtab[ewitab+1];
+ felec = qq{I}{J}*rinv{I}{J}*(rinvsq{I}{J}-felec);
+ /* #define INNERFLOPS INNERFLOPS+7 */
+ /* #endif */
+
+ /* #elif KERNEL_ELEC=='CubicSplineTable' */
+
+ /* CUBIC SPLINE TABLE ELECTROSTATICS */
+ /* #if 'Force' in KERNEL_VF */
+ Y = vftab[vfitab];
+ /* #endif */
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ /* #define INNERFLOPS INNERFLOPS+5 */
+ /* #if 'Potential' in KERNEL_VF */
+ VV = Y+vfeps*Fp;
+ velec = qq{I}{J}*VV;
+ /* #define INNERFLOPS INNERFLOPS+3 */
+ /* #endif */
+ /* #if 'Force' in KERNEL_VF */
+ FF = Fp+Geps+2.0*Heps2;
+ felec = -qq{I}{J}*FF*vftabscale*rinv{I}{J};
+ /* #define INNERFLOPS INNERFLOPS+7 */
+ /* #endif */
+ /* #endif */
+ /* ## End of check for electrostatics interaction forms */
+ /* #endif */
+ /* ## END OF ELECTROSTATIC INTERACTION CHECK FOR PAIR I-J */
+
+ /* #if 'vdw' in INTERACTION_FLAGS[I][J] */
+
+ /* #if KERNEL_VDW=='LennardJones' */
+
+ /* LENNARD-JONES DISPERSION/REPULSION */
+
+ rinvsix = rinvsq{I}{J}*rinvsq{I}{J}*rinvsq{I}{J};
+ /* #define INNERFLOPS INNERFLOPS+2 */
+ /* #if 'Potential' in KERNEL_VF or KERNEL_MOD_VDW=='PotentialSwitch' */
+ vvdw6 = c6_{I}{J}*rinvsix;
+ vvdw12 = c12_{I}{J}*rinvsix*rinvsix;
+ /* #define INNERFLOPS INNERFLOPS+3 */
+ /* #if KERNEL_MOD_VDW=='PotentialShift' */
+ vvdw = (vvdw12 - c12_{I}{J}*sh_vdw_invrcut6*sh_vdw_invrcut6)*(1.0/12.0) - (vvdw6 - c6_{I}{J}*sh_vdw_invrcut6)*(1.0/6.0);
+ /* #define INNERFLOPS INNERFLOPS+8 */
+ /* #else */
+ vvdw = vvdw12*(1.0/12.0) - vvdw6*(1.0/6.0);
+ /* #define INNERFLOPS INNERFLOPS+3 */
+ /* #endif */
+ /* ## Check for force inside potential check, i.e. this means we already did the potential part */
+ /* #if 'Force' in KERNEL_VF */
+ fvdw = (vvdw12-vvdw6)*rinvsq{I}{J};
+ /* #define INNERFLOPS INNERFLOPS+2 */
+ /* #endif */
+ /* #elif KERNEL_VF=='Force' */
+ /* ## Force-only LennardJones makes it possible to save 1 flop (they do add up...) */
+ fvdw = (c12_{I}{J}*rinvsix-c6_{I}{J})*rinvsix*rinvsq{I}{J};
+ /* #define INNERFLOPS INNERFLOPS+4 */
+ /* #endif */
+
+ /* #elif KERNEL_VDW=='Buckingham' */
+
+ /* BUCKINGHAM DISPERSION/REPULSION */
+ rinvsix = rinvsq{I}{J}*rinvsq{I}{J}*rinvsq{I}{J};
+ vvdw6 = c6_{I}{J}*rinvsix;
+ br = cexp2_{I}{J}*r{I}{J};
+ vvdwexp = cexp1_{I}{J}*exp(-br);
+ /* ## Estimate exp() to 25 flops */
+ /* #define INNERFLOPS INNERFLOPS+31 */
+ /* #if 'Potential' in KERNEL_VF or KERNEL_MOD_VDW=='PotentialSwitch' */
+ /* #if KERNEL_MOD_VDW=='PotentialShift' */
+ vvdw = (vvdwexp-cexp1_{I}{J}*exp(-cexp2_{I}{J}*rvdw)) - (vvdw6 - c6_{I}{J}*sh_vdw_invrcut6)*(1.0/6.0);
+ /* #define INNERFLOPS INNERFLOPS+33 */
+ /* #else */
+ vvdw = vvdwexp - vvdw6*(1.0/6.0);
+ /* #define INNERFLOPS INNERFLOPS+2 */
+ /* #endif */
+ /* #endif */
+ /* #if 'Force' in KERNEL_VF */
+ fvdw = (br*vvdwexp-vvdw6)*rinvsq{I}{J};
+ /* #define INNERFLOPS INNERFLOPS+3 */
+ /* #endif */
+
+ /* #elif KERNEL_VDW=='CubicSplineTable' */
+
+ /* CUBIC SPLINE TABLE DISPERSION */
+ vfitab += {TABLE_VDW_OFFSET};
+ /* #if 'Force' in KERNEL_VF */
+ Y = vftab[vfitab];
+ /* #endif */
+ F = vftab[vfitab+1];
+ Geps = vfeps*vftab[vfitab+2];
+ Heps2 = vfeps*vfeps*vftab[vfitab+3];
+ Fp = F+Geps+Heps2;
+ /* #define INNERFLOPS INNERFLOPS+5 */
+ /* #if 'Potential' in KERNEL_VF */
+ VV = Y+vfeps*Fp;
+ vvdw6 = c6_{I}{J}*VV;
+ /* #define INNERFLOPS INNERFLOPS+3 */
+ /* #endif */
+ /* #if 'Force' in KERNEL_VF */
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw6 = c6_{I}{J}*FF;
+ /* #define INNERFLOPS INNERFLOPS+4 */
+ /* #endif */
+
+ /* CUBIC SPLINE TABLE REPULSION */
+ /* #if 'Force' in KERNEL_VF */
+ Y = vftab[vfitab+4];
+ /* #endif */
+ F = vftab[vfitab+5];
+ Geps = vfeps*vftab[vfitab+6];
+ Heps2 = vfeps*vfeps*vftab[vfitab+7];
+ Fp = F+Geps+Heps2;
+ /* #define INNERFLOPS INNERFLOPS+5 */
+ /* #if 'Potential' in KERNEL_VF */
+ VV = Y+vfeps*Fp;
+ vvdw12 = c12_{I}{J}*VV;
+ /* #define INNERFLOPS INNERFLOPS+3 */
+ /* #endif */
+ /* #if 'Force' in KERNEL_VF */
+ FF = Fp+Geps+2.0*Heps2;
+ fvdw12 = c12_{I}{J}*FF;
+ /* #define INNERFLOPS INNERFLOPS+4 */
+ /* #endif */
+ /* #if 'Potential' in KERNEL_VF */
+ vvdw = vvdw12+vvdw6;
+ /* #define INNERFLOPS INNERFLOPS+1 */
+ /* #endif */
+ /* #if 'Force' in KERNEL_VF */
+ fvdw = -(fvdw6+fvdw12)*vftabscale*rinv{I}{J};
+ /* #define INNERFLOPS INNERFLOPS+4 */
+ /* #endif */
+ /* #endif */
+ /* ## End of check for vdw interaction forms */
+ /* #endif */
+ /* ## END OF VDW INTERACTION CHECK FOR PAIR I-J */
+
+ /* #if 'switch' in INTERACTION_FLAGS[I][J] */
+ d = r{I}{J}-rswitch;
+ d = (d>0.0) ? d : 0.0;
+ d2 = d*d;
+ sw = 1.0+d2*d*(swV3+d*(swV4+d*swV5));
+ /* #define INNERFLOPS INNERFLOPS+9 */
+
+ /* #if 'Force' in KERNEL_VF */
+ dsw = d2*(swF2+d*(swF3+d*swF4));
+ /* #define INNERFLOPS INNERFLOPS+5 */
+ /* #endif */
+
+ /* Evaluate switch function */
+ /* #if 'Potential' in KERNEL_VF */
+ /* #if 'electrostatics' in INTERACTION_FLAGS[I][J] and KERNEL_MOD_ELEC=='PotentialSwitch' */
+ velec *= sw;
+ /* #define INNERFLOPS INNERFLOPS+1 */
+ /* #endif */
+ /* #if 'vdw' in INTERACTION_FLAGS[I][J] and KERNEL_MOD_VDW=='PotentialSwitch' */
+ vvdw *= sw;
+ /* #define INNERFLOPS INNERFLOPS+1 */
+ /* #endif */
+ /* #endif */
+ /* #if 'Force' in KERNEL_VF */
+ /* #if 'electrostatics' in INTERACTION_FLAGS[I][J] and KERNEL_MOD_ELEC=='PotentialSwitch' */
+ felec = felec*sw + velec*dsw;
+ /* #define INNERFLOPS INNERFLOPS+3 */
+ /* #endif */
+ /* #if 'vdw' in INTERACTION_FLAGS[I][J] and KERNEL_MOD_VDW=='PotentialSwitch' */
+ fvdw = fvdw*sw + vvdw*dsw;
+ /* #define INNERFLOPS INNERFLOPS+3 */
+ /* #endif */
+ /* #endif */
+ /* #endif */
+
+ /* #if 'Potential' in KERNEL_VF */
+ /* Update potential sums from outer loop */
+ /* #if 'electrostatics' in INTERACTION_FLAGS[I][J] */
+ velecsum += velec;
+ /* #define INNERFLOPS INNERFLOPS+1 */
+ /* #if KERNEL_ELEC=='GeneralizedBorn' */
+ vgbsum += vgb;
+ /* #define INNERFLOPS INNERFLOPS+1 */
+ /* #endif */
+ /* #endif */
+ /* #if 'vdw' in INTERACTION_FLAGS[I][J] */
+ vvdwsum += vvdw;
+ /* #define INNERFLOPS INNERFLOPS+1 */
+ /* #endif */
+ /* #endif */
+
+ /* #if 'Force' in KERNEL_VF */
+
+ /* #if 'electrostatics' in INTERACTION_FLAGS[I][J] and 'vdw' in INTERACTION_FLAGS[I][J] */
+ fscal = felec+fvdw;
+ /* #define INNERFLOPS INNERFLOPS+1 */
+ /* #elif 'electrostatics' in INTERACTION_FLAGS[I][J] */
+ fscal = felec;
+ /* #elif 'vdw' in INTERACTION_FLAGS[I][J] */
+ fscal = fvdw;
+ /* #endif */
+
+ /* Calculate temporary vectorial force */
+ tx = fscal*dx{I}{J};
+ ty = fscal*dy{I}{J};
+ tz = fscal*dz{I}{J};
+
+ /* Update vectorial force */
+ fix{I} += tx;
+ fiy{I} += ty;
+ fiz{I} += tz;
+ f[j_coord_offset+DIM*{J}+XX] -= tx;
+ f[j_coord_offset+DIM*{J}+YY] -= ty;
+ f[j_coord_offset+DIM*{J}+ZZ] -= tz;
+
+ /* #define INNERFLOPS INNERFLOPS+9 */
+ /* #endif */
+
+ /* #if 'exactcutoff' in INTERACTION_FLAGS[I][J] */
+ /* #if 0 ## This and next two lines is a hack to maintain indentation in template file */
+ {
+ /* #endif */
+ }
+ /* #endif */
+ /* ## End of check for the interaction being outside the cutoff */
+
+ /* #endfor */
+ /* ## End of loop over i-j interaction pairs */
+
+ /* Inner loop uses {INNERFLOPS} flops */
+ }
+ /* End of innermost loop */
+
+ /* #if 'Force' in KERNEL_VF */
+ tx = ty = tz = 0;
+ /* #for I in PARTICLES_I */
+ f[i_coord_offset+DIM*{I}+XX] += fix{I};
+ f[i_coord_offset+DIM*{I}+YY] += fiy{I};
+ f[i_coord_offset+DIM*{I}+ZZ] += fiz{I};
+ tx += fix{I};
+ ty += fiy{I};
+ tz += fiz{I};
+ /* #define OUTERFLOPS OUTERFLOPS+6 */
+ /* #endfor */
+ fshift[i_shift_offset+XX] += tx;
+ fshift[i_shift_offset+YY] += ty;
+ fshift[i_shift_offset+ZZ] += tz;
+ /* #define OUTERFLOPS OUTERFLOPS+3 */
+ /* #endif */
+
+ /* #if 'Potential' in KERNEL_VF */
+ ggid = gid[iidx];
+ /* Update potential energies */
+ /* #if KERNEL_ELEC != 'None' */
+ kernel_data->energygrp_elec[ggid] += velecsum;
+ /* #define OUTERFLOPS OUTERFLOPS+1 */
+ /* #endif */
+ /* #if 'GeneralizedBorn' in KERNEL_ELEC */
+ kernel_data->energygrp_polarization[ggid] += vgbsum;
+ /* #define OUTERFLOPS OUTERFLOPS+1 */
+ /* #endif */
+ /* #if KERNEL_VDW != 'None' */
+ kernel_data->energygrp_vdw[ggid] += vvdwsum;
+ /* #define OUTERFLOPS OUTERFLOPS+1 */
+ /* #endif */
+ /* #endif */
+ /* #if 'GeneralizedBorn' in KERNEL_ELEC and 'Force' in KERNEL_VF */
+ dvda[nri] = dvda[nri] + dvdasum*isai{I}*isai{I};
+ /* #endif */
+
+ /* Increment number of inner iterations */
+ inneriter += j_index_end - j_index_start;
+
+ /* Outer loop uses {OUTERFLOPS} flops */
+ }
+
+ /* Increment number of outer iterations */
+ outeriter += nri;
+
+ /* Update outer/inner flops */
+ /* ## NB: This is not important, it just affects the flopcount. However, since our preprocessor is */
+ /* ## primitive and replaces aggressively even in strings inside these directives, we need to */
+ /* ## assemble the main part of the name (containing KERNEL/ELEC/VDW) directly in the source. */
+ /* #if GEOMETRY_I == 'Water3' */
+ /* #define ISUFFIX '_W3' */
+ /* #elif GEOMETRY_I == 'Water4' */
+ /* #define ISUFFIX '_W4' */
+ /* #else */
+ /* #define ISUFFIX '' */
+ /* #endif */
+ /* #if GEOMETRY_J == 'Water3' */
+ /* #define JSUFFIX 'W3' */
+ /* #elif GEOMETRY_J == 'Water4' */
+ /* #define JSUFFIX 'W4' */
+ /* #else */
+ /* #define JSUFFIX '' */
+ /* #endif */
+ /* #if 'PotentialAndForce' in KERNEL_VF */
+ /* #define VFSUFFIX '_VF' */
+ /* #elif 'Potential' in KERNEL_VF */
+ /* #define VFSUFFIX '_V' */
+ /* #else */
+ /* #define VFSUFFIX '_F' */
+ /* #endif */
+
+ /* #if KERNEL_ELEC != 'None' and KERNEL_VDW != 'None' */
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC_VDW{ISUFFIX}{JSUFFIX}{VFSUFFIX},outeriter*{OUTERFLOPS} + inneriter*{INNERFLOPS});
+ /* #elif KERNEL_ELEC != 'None' */
+ inc_nrnb(nrnb,eNR_NBKERNEL_ELEC{ISUFFIX}{JSUFFIX}{VFSUFFIX},outeriter*{OUTERFLOPS} + inneriter*{INNERFLOPS});
+ /* #else */
+ inc_nrnb(nrnb,eNR_NBKERNEL_VDW{ISUFFIX}{JSUFFIX}{VFSUFFIX},outeriter*{OUTERFLOPS} + inneriter*{INNERFLOPS});
+ /* #endif */
+}
#include "types/nrnb.h"
#include "nb_kernel_f77_double.h"
-#include "../nb_kerneltype.h"
+#include "../nb_kernel.h"
/* Include standard kernel headers in local directory */
#include <stdio.h>
-#include "../nb_kerneltype.h"
+#include "../nb_kernel.h"
void
nb_kernel_setup_f77_double(FILE *fplog,nb_kernel_t **list);
#include "types/nrnb.h"
#include "nb_kernel_f77_single.h"
-#include "../nb_kerneltype.h"
+#include "../nb_kernel.h"
/* Include standard kernel headers in local directory */
#include <stdio.h>
-#include "../nb_kerneltype.h"
+#include "../nb_kernel.h"
void
nb_kernel_setup_f77_single(FILE *fplog,nb_kernel_t **list);
#include "types/nrnb.h"
#include "nb_kernel_power6.h"
-#include "../nb_kerneltype.h"
+#include "../nb_kernel.h"
/* Include standard kernel headers in local directory */
#include <stdio.h>
-#include "../nb_kerneltype.h"
+#include "../nb_kernel.h"
void
nb_kernel_setup_power6(FILE *fplog,nb_kernel_t **list);
#include <gmx_sse2_double.h>
/* get gmx_gbdata_t */
-#include "../nb_kerneltype.h"
+#include "../nb_kernel.h"
void nb_kernel400_sse2_double(int * p_nri,
#include <gmx_sse2_double.h>
/* get gmx_gbdata_t */
-#include "../nb_kerneltype.h"
+#include "../nb_kernel.h"
#include <gmx_sse2_double.h>
/* get gmx_gbdata_t */
-#include "../nb_kerneltype.h"
+#include "../nb_kernel.h"
void nb_kernel430_sse2_double(int * p_nri,
#include <stdlib.h>
#include <stdio.h>
-#include "../nb_kerneltype.h"
+#include "../nb_kernel.h"
#include "nb_kernel_sse2_double.h"
static nb_kernel_t *
#include <types/simple.h>
-#include "../nb_kerneltype.h"
+#include "../nb_kernel.h"
#ifdef __cplusplus
extern "C" {
#include <gmx_sse2_single.h>
/* get gmx_gbdata_t */
-#include "../nb_kerneltype.h"
+#include "../nb_kernel.h"
void nb_kernel400_sse2_single(int * p_nri,
#include <gmx_sse2_single.h>
/* get gmx_gbdata_t */
-#include "../nb_kerneltype.h"
+#include "../nb_kernel.h"
void nb_kernel410_sse2_single(int * p_nri,
#include <gmx_sse2_single.h>
/* get gmx_gbdata_t */
-#include "../nb_kerneltype.h"
+#include "../nb_kernel.h"
void nb_kernel430_sse2_single(int * p_nri,
#include <intrin.h>
#endif
-#include "../nb_kerneltype.h"
+#include "../nb_kernel.h"
#include "nb_kernel_sse2_single.h"
static nb_kernel_t *
#include <types/simple.h>
-#include "../nb_kerneltype.h"
+#include "../nb_kernel.h"
#include "nb_kernel_allvsall_sse2_single.h"
#include "nb_kernel_allvsallgb_sse2_single.h"
+++ /dev/null
-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
- *
- * Gromacs 4.0 Copyright (c) 1991-2003
- * David van der Spoel, Erik Lindahl, University of Groningen.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org
- *
- * And Hey:
- * Gnomes, ROck Monsters And Chili Sauce
- */
-
-#ifndef _NB_KERNEL_H_
-#define _NB_KERNEL_H_
-
-#include <types/simple.h>
-
-/** \file
- * \brief Function interfaces and nonbonded kernel meta-data.
- *
- * \internal
- *
- * This file contains the definitions of the call sequences and
- * parameter documetation for the nonbonded kernels, both the
- * optimized level1/level2 kernels in Fortran or C, and the more
- * general level0 normal and free energy kernels.
- * It also defines an information structure used to record
- * data about nonbonded kernels, their type of call sequence,
- * and the number of flops used in the outer and inner loops.
- */
-
-#ifdef __cplusplus
-extern "C" {
-#endif
-#if 0
-} /* fixes auto-indentation problems */
-#endif
-
-
-
-
-/* Temporary structure to be able to pass 2 GB data through the
- * work data pointer argument.
- */
-typedef struct
-{
- real gb_epsilon_solvent; /* Epsilon for solvent */
- real epsilon_r; /* Epsilon for inner dielectric */
- real * gpol; /* Polarization energy group */
-} gmx_gbdata_t;
-
-
-/** Interface to level1 optimized nonbonded kernels.
- *
- * \internal
- *
- * To simplify the jungle of nonbonded function calls in earlier
- * versions of Gromacs, we have changed most nonbonded kernels
- * to use the same call sequence, even if some of the parameters
- * are ununsed in a particular kernel.
- *
- * This function call sequence is used by all level1 kernels. When this is
- * written it is actually used by the level2 kernels too, but that might
- * change in the future - don't assume they are identical.
- * All arguments are passed as pointers to make to interface identical across
- * the Fortran and C implementations. For the same reason (Fortran & assembly)
- * we cannot use structures.
- *
- * The nonbonded kernels should never be called directly - use
- * the setup and wrapper routines in gmx_nonbonded.h instead.
- *
- * \param nri Number of neighborlists/i-particles/outer-particles.
- * The outer loop of the nonbonded kernel will iterate
- * over these indices. This number must always
- * be provided,
- * \param iinr Atom number (starting on 0) for each index 0..(nri-1)
- * in the outer loop. These are the 'owner'/'parent'
- * particles of each neighborlist. It is quite common
- * that a particle occurs several times with different
- * shift indices. This is the field 'ilist' in
- * the neighborlist. This array must always be provided.
- * \param jindex This array specifies the index of the first j neighbor
- * in the array jjnr[] which belongs to the corresponding
- * i atom. The j neighbors for all lists are merged into
- * one continous array, so we also get the first index for
- * the next list in the next element. The size of this list
- * is nri+1, and the last position contains the number of
- * entries in the j list. Confused? It is actually pretty
- * straightforward; for index <tt>i</tt> the i atom is
- * <tt>iinr[i]</tt>, and the atom indices of the neighbors
- * to interact with are in positions <tt>jindex[i]</tt>
- * through <tt>(jindex[i+1]-1)</tt> in <tt>jjnr[]</tt>.
- * This corresponds to ilist_jindex in the neighborlist.
- * This array must always be provided.
- * \param jjnr Array with the j particle neighbors of list i in positions
- * <tt>jindex[i]</tt> through <tt>(jindex[i+1]-1)</tt>. This
- * field is called jlist in the neighborlist structure.
- * This array must always be provided.
- * \param shift Array with shift vector index corresponding to each
- * iinr neighborlist. In most codes, periodic boundary
- * conditions are applied by checking pairwise distances
- * of particles, and correcting differences of more than
- * half a box. This is costly (latencies) and unnecessary
- * since we already decided which periodic copy to use during
- * neighborsearching. We solve this by introducing
- * \a shiftvectors and a \a shiftindex. The shiftvectors is
- * normally an array of 3*3*3 vectors, corresponding to
- * displacements +- one box unit in one or more directions.
- * The central box (no displacement) is always in the middle,
- * index 13 in the case of 3*3*3 shift vectors.
- * Imagine a particle interacting with two particles in the
- * current box, and three particles in the box to the left.
- * We represent this with two ilist entries, one with shift
- * index=13 (central box) and one with shift index=12.
- * all neighbors in each sublist will have the same shift,
- * so in the nonbonded interaction, we only have to add the
- * shift vector to the outer (i) particle coordinates before
- * starting the loop over neighbors. This extracts periodic
- * boundary condition calculations from the inner loops,
- * increasing performance significantly. This array must
- * always be provided, but if you do not use any periodic
- * boundary conditions you could set all elements to zero
- * and provide a shiftvec array of length three, with all
- * elements there too being zero.
- * \param shiftvec The shift vectors for each index. Since the code needs to
- * interface with Fortran or assembly, we have to use
- * pointers to float/double instead of the gmx_rvec_t type.
- * The x/y/z shift distances for shift index idx are in
- * <tt>shiftvec[3*idx]</tt>, <tt>shiftvec[3*idx+1]</tt>,
- * and <tt>shiftvec[3*idx+2]</tt>. This is fully binary
- * compatible with an array of gmx_rvec_t, so you can simply
- * use a typecast when calling. The length of the array is
- * three times the number of shift indices. This array
- * must be provided, but see the comment for shift.
- * \param fshift Forces from 'other periodic boxes' for each shift index.
- * The shift concept does not affect the forces on individual
- * atoms, but it will have an effect on the virial. To
- * account for this, we add the total force on the i particle
- * in each outer loop to the current shift index in this
- * array, which has exactly the same dimensions as the
- * shiftvec array above. The Gromacs manual describes how
- * this is used to calculate the effect in the virial.
- * Dimension is identical to shiftvec.
- * For kernels that do not calculate forces this can be NULL.
- * \param gid Energy group index for each i neighborlist index; this
- * corresponds to ilist_groupindex in the neighborlist and is
- * used to decompose energies into groupwise contributions.
- * If an i particle belongs to group A, and has interactions
- * both with groups A,B, and C, you will get three different
- * i list entries with energy group indices corresponding to
- * A-A, A-B, and A-C neighbors, in addition to possible
- * copies due to different shift indices. The energies will
- * be added to this index (i.e. index=gid[i]) in the vc and
- * vnb arrays. This array must always be provided.
- * If you don't want to decompose energies all groups should
- * be set to index 0 (length or the array nri).
- * \param pos Coordinates of atoms, starting on 0 as all arrays. To
- * interface with fortran and assembly this is a simple list
- * of floats, with x/y/z of atom n in positions
- * <tt>pos[3*n]</tt>, <tt>pos[3*n+1]</tt>, and
- * <tt>pos[3*n+2]</tt>. This is binary compatible with,
- * and can be typecast from, an array of gmx_rvec_t.
- * This array must always be provided.
- * \param faction Forces of atoms. To interface with fortran and assembly
- * this is a simple list of floats, with x/y/z of atom n in
- * positions <tt>pos[3*n]</tt>, <tt>pos[3*n+1]</tt>, and
- * <tt>pos[3*n+2]</tt>. This is binary compatible with,
- * and can be typecast from, an array of gmx_rvec_t.
- * For kernels that do not calculate forces this can be NULL.
- * \param charge Array with the charge of atom n in position n.
- * If you are calling a kernel without coulomb interaction
- * this parameter can safely be set to NULL.
- * \param facel Factor to multiply all electrostatic interactions with;
- * this is essentially 1/(4*pi*epsilon). For kernels without
- * coulomb interaction the value will not be used. In the
- * fortran version (pass-by-reference) it can be NULL in
- * that case.
- * \param krf The 'k' constant for reaction-field electrostatic
- * interactions. Can be zero/NULL for non-RF interactions.
- * \param crf The 'c' constant for reaction-field electrostatic
- * interactions. Can be zero/NULL for non-RF interactions.
- * \param vc List of Coulomb energies, the length is equal to the
- * number of energy group combinations. As described for
- * gid above, the coulomb energy of each outer/i-particle
- * list will be added to vc[gid[i]]. Can be NULL for
- * kernels without electrostatic interaction.
- * \param type Array with the index of the Van der Waals type for each
- * atom, starting on 0 . This is used to look up the VdW
- * parameters. When no VdW interactions are calculated
- * (i.e. only Coulomb), this can be set to NULL.
- * \param ntype Number of VdW types, used to look up the VdW parameters.
- * This parameter can be zero (NULL for pass-by-reference)
- * if the kernel does not include VdW interactions.
- * \param vdwparam Array with Van der Waals parameters. The contents and
- * size depends on the number of parameters required for
- * the selected VdW interaction (3 for B-ham, 2 for LJ, etc).
- * There are a total of ntype*ntype pair combinations, and
- * the size of this array is the number of such pairs times
- * the number of parameters.
- * With 'nparam' parameters, and 'ntype' types in total,
- * the first parameter for interactions between atoms of VdW
- * type 'ti' and VdW type 'tj' is located in
- * <tt>vdwparam[nparam*(ntype*ti+tj)]</tt>, and the
- * additional parameters follow directly in the next
- * position(s). Note that the array corresponds to a
- * symmetric matrix - you should get the same parameters if
- * you swap ti and tj. This parameter can be NULL
- * if the kernel does not include VdW interactions.
- * \param vvdw List of Van der Waals energies, the length is equal to
- * the number of energy group combinations. As described
- * for gid above, the coulomb energy of each outer list
- * will be added to vc[gid[i]]. Can be NULL for
- * kernels without electrostatic interaction.
- * \param tabscale Distance between table points in the vftab table.
- * This is always the same for Coulomb and VdW when both
- * are tabulated. If the kernel does not include any
- * tabulated interactions it can be zero, or NULL when
- * passed-by-reference.
- * \param vftab Table data for Coulomb and/or VdW interactions.
- * Each 'point' in the table consists of the four
- * floating-point numbers Y,F,G,H as described in the
- * Gromacs manual. If the kernel only tabulates the
- * Coulomb interaction this is followed by the next
- * point. If both Coulomb and Van der Waals interactions
- * are tabulated it is instead followed by another
- * four numbers for the dispersion table at the same
- * point, and then finally the repulsion table, i.e.
- * a total of 12 numbers per table point. If only
- * Van der Waals interactions are tabulated the
- * Dispersion and Repulsion table (in that order) use
- * a total of 8 floating-point numbers per point.
- * This array only needs to be provided for kernels with
- * tabulated interactions - otherwise it can be NULL.
- * \param invsqrta Array with the inverse square root of the born radius
- * of each atom. This can safely be NULL when the kernel
- * does not calculate Generalized Born interactions.
- * \param dvda Array where the derivative of the potential with respect
- * to the born radius for each atom will be written. This
- * is necessary to calculate the effect of born radius
- * derivatives on forces. However, just as for the force
- * arrays it must be provided even when not calculating
- * forces, since an implementation might not provide a
- * non-force version of the routine. When the kernel does
- * not calculate Generalized Born interactions it can
- * safely be set to NULL, though.
- * \param gbtabscale Distance between (scaled) table points for tabulated
- * Generalized Born interactions. If the kernel does not
- * calculate Generalized Born interactions it can be zero,
- * or NULL when passed-by-reference. Note that this is
- * usually different from the standard (non-GB) table scale.
- * \param gbtab Table data for Generalized Born Coulomb interactions.
- * Since these interactions contain parameters that
- * enter in a non-trivial way I have introduced a trick
- * where the tabulated interaction is a function of
- * the distance scaled with the square roots of the two
- * born radii. Apart from this it contains similar
- * data (Y,F,G,H) as the normal Coulomb/VdW tables.
- * See comments in the table code for details. This
- * can safely be set to NULL if you are not using
- * Generalized Born interactions.
- * \param nthreads Number of threads calling the kernel concurrently.
- * This value is only used to optimize the chunk size
- * of the neighborlists processed by each thread, so
- * it won't cause incorrect results if you get it wrong.
- * \param count Pointer to a common counter to synchronize
- * multithreaded execution. This is normally the counter
- * in the neighborlist. It must be set to zero before
- * calling the kernel to get correct results. Note that
- * this is necessary even for a single thread if Gromacs
- * is compiled with thread support (meaning it is
- * a mandatory parameter).
- * \param mtx Pointer to a mutex protecting the counter, masked as
- * a pointer-to-void since thread support is optional.
- * However, if Gromacs is compiled with threads you \a must
- * provide a mutex - it would hurt performance to check
- * it for each iteration in the nonbonded kernel. The
- * mutex is normally created automatically by the
- * neighborlist initialization routine gmx_nlist_init().
- * (Yet another reason not to call kernels directly).
- * \param outeriter The number of iterations performed in the outer loop
- * of the kernel will be written to this integer. If
- * multiple threads are calling the loop this will be
- * the part of nri handled by this thread.
- * This value is only used to get accurate flop accounting.
- * Since we cannot check for NULL pointers in Fortran it must
- * always be provided, but you can discard
- * the result if you don't need it.
- * \param inneriter The number of iterations performed in the inner loop
- * of the kernel will be written to this integer; compare
- * with nouter. Since we cannot check for NULL pointers in
- * Fortran it must always be provided, but you can discard
- * the result if you don't need it.
- * \param work Double precision work array - to be used for optimization.
- *
- * \warning There is \a very little error control inside
- * the nonbonded kernels in order to maximize performance.
- * It cannot be overemphasized that you should never call
- * them directly, but rely on the higher-level routines.
- */
-typedef void
-nb_kernel_t(int * nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * facel,
- real * krf,
- real * crf,
- real * vc,
- int * type,
- int * ntype,
- real * vdwparam,
- real * vvdw,
- real * tabscale,
- real * vftab,
- real * invsqrta,
- real * dvda,
- real * gbtabscale,
- real * gbtab,
- int * nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real * work);
-
-
-
-typedef void
-nb_adress_kernel_t(int * nri,
- int * iinr,
- int * jindex,
- int * jjnr,
- int * shift,
- real * shiftvec,
- real * fshift,
- int * gid,
- real * pos,
- real * faction,
- real * charge,
- real * facel,
- real * krf,
- real * crf,
- real * vc,
- int * type,
- int * ntype,
- real * vdwparam,
- real * vvdw,
- real * tabscale,
- real * vftab,
- real * invsqrta,
- real * dvda,
- real * gbtabscale,
- real * gbtab,
- int * nthreads,
- int * count,
- void * mtx,
- int * outeriter,
- int * inneriter,
- real force_cap,
- real * wf);
-
-
-
-#ifdef __cplusplus
-}
-#endif
-
-
-#endif /* _NB_KERNEL_H_ */
#include <config.h>
#endif
-#ifdef GMX_THREAD_SHM_FDECOMP
+#ifdef GMX_THREAD_MPI
#include <thread_mpi.h>
#endif
-
#include <stdio.h>
#include <stdlib.h>
#include "typedefs.h"
#include "vec.h"
#include "maths.h"
#include "macros.h"
+#include "string2.h"
#include "force.h"
#include "names.h"
#include "main.h"
#include "smalloc.h"
#include "nonbonded.h"
+#include "nb_kernel.h"
#include "nb_kernel_c/nb_kernel_c.h"
-#include "nb_kernel_adress_c/nb_kernel_c_adress.h"
+
#include "nb_free_energy.h"
#include "nb_generic.h"
#include "nb_generic_cg.h"
#include "nb_generic_adress.h"
-/* 1,4 interactions uses kernel 330 directly */
-#include "nb_kernel_c/nb_kernel330.h"
-#include "nb_kernel_adress_c/nb_kernel330_adress.h"
-
-
-
-#if 0 && defined (GMX_X86_SSE2)
-# ifdef GMX_DOUBLE
-# include "nb_kernel_sse2_double/nb_kernel_sse2_double.h"
-# else
-# include "nb_kernel_sse2_single/nb_kernel_sse2_single.h"
-# endif
-#endif
-#if defined(GMX_FORTRAN)
-# ifdef GMX_DOUBLE
-# include "nb_kernel_f77_double/nb_kernel_f77_double.h"
-# else
-# include "nb_kernel_f77_single/nb_kernel_f77_single.h"
-# endif
+#ifdef GMX_THREAD_MPI
+static tMPI_Thread_mutex_t nonbonded_setup_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
#endif
+static gmx_bool nonbonded_setup_done = FALSE;
-#ifdef GMX_POWER6
-#include "nb_kernel_power6/nb_kernel_power6.h"
+void
+gmx_nonbonded_setup(FILE * fplog,
+ t_forcerec * fr,
+ gmx_bool bGenericKernelOnly)
+{
+#ifdef GMX_THREAD_MPI
+ tMPI_Thread_mutex_lock(&nonbonded_setup_mutex);
#endif
+ /* Here we are guaranteed only one thread made it. */
+ if(nonbonded_setup_done==FALSE)
+ {
+ if(bGenericKernelOnly==FALSE)
+ {
+ /* Add the generic kernels to the structure stored statically in nb_kernel.c */
-#ifdef GMX_BLUEGENE
-#include "nb_kernel_bluegene/nb_kernel_bluegene.h"
-#endif
+ /* Add interaction-specific C kernels */
+ nb_kernel_list_add_kernels(kernellist_c,kernellist_c_size);
+ /* Add interaction-specific accelerated SSE kernels, etc. here */
+ }
+ /* Create a hash for faster lookups */
+ nb_kernel_list_hash_init();
+ nonbonded_setup_done=TRUE;
+ }
+#ifdef GMX_THREAD_MPI
+ tMPI_Thread_mutex_unlock(&nonbonded_setup_mutex);
+#endif
+}
-enum { TABLE_NONE, TABLE_COMBINED, TABLE_COUL, TABLE_VDW, TABLE_NR };
-/* Table version for each kernel.
- */
-static const int
-nb_kernel_table[eNR_NBKERNEL_NR] =
+void
+gmx_nonbonded_set_kernel_pointers(FILE *log, t_nblist *nl)
{
- TABLE_NONE, /* kernel010 */
- TABLE_NONE, /* kernel020 */
- TABLE_VDW, /* kernel030 */
- TABLE_NONE, /* kernel100 */
- TABLE_NONE, /* kernel101 */
- TABLE_NONE, /* kernel102 */
- TABLE_NONE, /* kernel103 */
- TABLE_NONE, /* kernel104 */
- TABLE_NONE, /* kernel110 */
- TABLE_NONE, /* kernel111 */
- TABLE_NONE, /* kernel112 */
- TABLE_NONE, /* kernel113 */
- TABLE_NONE, /* kernel114 */
- TABLE_NONE, /* kernel120 */
- TABLE_NONE, /* kernel121 */
- TABLE_NONE, /* kernel122 */
- TABLE_NONE, /* kernel123 */
- TABLE_NONE, /* kernel124 */
- TABLE_VDW, /* kernel130 */
- TABLE_VDW, /* kernel131 */
- TABLE_VDW, /* kernel132 */
- TABLE_VDW, /* kernel133 */
- TABLE_VDW, /* kernel134 */
- TABLE_NONE, /* kernel200 */
- TABLE_NONE, /* kernel201 */
- TABLE_NONE, /* kernel202 */
- TABLE_NONE, /* kernel203 */
- TABLE_NONE, /* kernel204 */
- TABLE_NONE, /* kernel210 */
- TABLE_NONE, /* kernel211 */
- TABLE_NONE, /* kernel212 */
- TABLE_NONE, /* kernel213 */
- TABLE_NONE, /* kernel214 */
- TABLE_NONE, /* kernel220 */
- TABLE_NONE, /* kernel221 */
- TABLE_NONE, /* kernel222 */
- TABLE_NONE, /* kernel223 */
- TABLE_NONE, /* kernel224 */
- TABLE_VDW, /* kernel230 */
- TABLE_VDW, /* kernel231 */
- TABLE_VDW, /* kernel232 */
- TABLE_VDW, /* kernel233 */
- TABLE_VDW, /* kernel234 */
- TABLE_COUL, /* kernel300 */
- TABLE_COUL, /* kernel301 */
- TABLE_COUL, /* kernel302 */
- TABLE_COUL, /* kernel303 */
- TABLE_COUL, /* kernel304 */
- TABLE_COUL, /* kernel310 */
- TABLE_COUL, /* kernel311 */
- TABLE_COUL, /* kernel312 */
- TABLE_COUL, /* kernel313 */
- TABLE_COUL, /* kernel314 */
- TABLE_COUL, /* kernel320 */
- TABLE_COUL, /* kernel321 */
- TABLE_COUL, /* kernel322 */
- TABLE_COUL, /* kernel323 */
- TABLE_COUL, /* kernel324 */
- TABLE_COMBINED, /* kernel330 */
- TABLE_COMBINED, /* kernel331 */
- TABLE_COMBINED, /* kernel332 */
- TABLE_COMBINED, /* kernel333 */
- TABLE_COMBINED, /* kernel334 */
- TABLE_NONE, /* kernel400 */
- TABLE_NONE, /* kernel410 */
- TABLE_VDW /* kernel430 */
-};
-
+ const char * elec;
+ const char * elec_mod;
+ const char * vdw;
+ const char * vdw_mod;
+ const char * geom;
+ const char * other;
+ const char * vf;
+
+ const char * archs[] = { "c" };
+ int i;
+
+ if(nonbonded_setup_done==FALSE)
+ {
+ /* We typically call this setup routine before starting timers,
+ * but if that has not been done for whatever reason we do it now.
+ */
+ gmx_nonbonded_setup(NULL,NULL,FALSE);
+ }
+ /* Not used yet */
+ other="";
-static nb_kernel_t **
-nb_kernel_list = NULL;
+ nl->kernelptr_vf = NULL;
+ nl->kernelptr_v = NULL;
+ nl->kernelptr_f = NULL;
-static nb_adress_kernel_t **
-nb_kernel_list_adress = NULL;
+ elec = gmx_nbkernel_elec_names[nl->ielec];
+ elec_mod = eintmod_names[nl->ielecmod];
+ vdw = gmx_nbkernel_vdw_names[nl->ivdw];
+ vdw_mod = eintmod_names[nl->ivdwmod];
+ geom = gmx_nblist_geometry_names[nl->igeometry];
-void
-gmx_setup_kernels(FILE *fplog,t_forcerec *fr,gmx_bool bGenericKernelOnly)
-{
- int i;
-
- snew(nb_kernel_list,eNR_NBKERNEL_NR);
-
- /* Note that later calls overwrite earlier, so the preferred (fastest)
- * version should be at the end. For instance, we call SSE after 3DNow.
- */
-
- for(i=0; i<eNR_NBKERNEL_NR; i++)
- {
- nb_kernel_list[i] = NULL;
- }
-
- if (bGenericKernelOnly)
- {
- return;
- }
-
- if(fplog)
+ if(nl->free_energy)
{
- fprintf(fplog,"Configuring nonbonded kernels...\n");
+ nl->kernelptr_vf = gmx_nb_free_energy_kernel;
+ nl->kernelptr_f = gmx_nb_free_energy_kernel;
}
-
- nb_kernel_setup(fplog,nb_kernel_list);
-
- if(fr->use_cpu_acceleration==FALSE)
+ else if(!gmx_strcasecmp_min(geom,"CG-CG"))
{
- return;
+ nl->kernelptr_vf = gmx_nb_generic_cg_kernel;
+ nl->kernelptr_f = gmx_nb_generic_cg_kernel;
}
-
- /* Setup kernels. The last called setup routine will overwrite earlier assignments,
- * so we should e.g. test SSE3 support _after_ SSE2 support,
- * and call e.g. Fortran setup before SSE.
- */
-
-#if defined(GMX_FORTRAN) && defined(GMX_DOUBLE)
- nb_kernel_setup_f77_double(fplog,nb_kernel_list);
-#endif
-
-#if defined(GMX_FORTRAN) && !defined(GMX_DOUBLE)
- nb_kernel_setup_f77_single(fplog,nb_kernel_list);
-#endif
-
-#ifdef GMX_BLUEGENE
- nb_kernel_setup_bluegene(fplog,nb_kernel_list);
-#endif
-
-#ifdef GMX_POWER6
- nb_kernel_setup_power6(fplog,nb_kernel_list);
-#endif
-
- if(fplog)
+ else
{
- fprintf(fplog,"\n\n");
- }
-}
-
-void
-gmx_setup_adress_kernels(FILE *fplog,gmx_bool bGenericKernelOnly) {
- int i;
+ /* Try to find a specific kernel first */
- snew(nb_kernel_list_adress, eNR_NBKERNEL_NR);
-
- for (i = 0; i < eNR_NBKERNEL_NR; i++) {
- nb_kernel_list_adress[i] = NULL;
- }
+ for(i=0;i<asize(archs) && nl->kernelptr_vf==NULL ;i++)
+ {
+ nl->kernelptr_vf = nb_kernel_list_findkernel(log,archs[i],elec,elec_mod,vdw,vdw_mod,geom,other,"PotentialAndForce");
+ }
+ for(i=0;i<asize(archs) && nl->kernelptr_f==NULL ;i++)
+ {
+ nl->kernelptr_f = nb_kernel_list_findkernel(log,archs[i],elec,elec_mod,vdw,vdw_mod,geom,other,"Force");
+ /* If there is not force-only optimized kernel, is there a potential & force one? */
+ if(nl->kernelptr_f == NULL)
+ {
+ nl->kernelptr_f = nb_kernel_list_findkernel(NULL,archs[i],elec,elec_mod,vdw,vdw_mod,geom,other,"PotentialAndForce");
+ }
+ }
- if (bGenericKernelOnly)
- {
- return;
+ /* Give up, pick a generic one instead */
+ if(nl->kernelptr_vf==NULL)
+ {
+ nl->kernelptr_vf = gmx_nb_generic_kernel;
+ nl->kernelptr_f = gmx_nb_generic_kernel;
+ if(log)
+ {
+ fprintf(log,
+ "WARNING - Slow generic NB kernel used for neighborlist with\n"
+ " Elec: '%s', Modifier: '%s'\n"
+ " Vdw: '%s', Modifier: '%s'\n"
+ " Geom: '%s', Other: '%s'\n\n",
+ elec,elec_mod,vdw,vdw_mod,geom,other);
+ }
+ }
}
- nb_kernel_setup_adress(fplog, nb_kernel_list_adress);
+ return;
}
void do_nonbonded(t_commrec *cr,t_forcerec *fr,
- rvec x[],rvec f[],t_mdatoms *mdatoms,t_blocka *excl,
- real egnb[],real egcoul[],real egpol[],rvec box_size,
+ rvec x[],rvec f_shortrange[],rvec f_longrange[],t_mdatoms *mdatoms,t_blocka *excl,
+ gmx_grppairener_t *grppener,rvec box_size,
t_nrnb *nrnb,real *lambda, real *dvdl,
int nls,int eNL,int flags)
{
- gmx_bool bLR,bDoForces,bForeignLambda;
- t_nblist * nlist;
- real * fshift;
- int n,n0,n1,i,i0,i1,nrnb_ind,sz;
- t_nblists *nblists;
- gmx_bool bWater;
- FILE * fp;
- int fac=0;
- int nthreads = 1;
- int tabletype;
- int outeriter,inneriter;
- real * tabledata = NULL;
- gmx_gbdata_t gbdata;
-
- nb_kernel_t *kernelptr=NULL;
- nb_adress_kernel_t *adresskernelptr=NULL;
+ t_nblist * nlist;
+ int n,n0,n1,i,i0,i1,sz,range;
+ t_nblists * nblists;
+ nb_kernel_data_t kernel_data;
+ nb_kernel_t * kernelptr=NULL;
+ rvec * f;
- gmx_bool bCG; /* for AdresS */
- int k;/* for AdresS */
-
- bLR = (flags & GMX_DONB_LR);
- bDoForces = (flags & GMX_DONB_FORCES);
- bForeignLambda = (flags & GMX_DONB_FOREIGNLAMBDA);
-
- bCG = FALSE; /* for AdresS */
-
- gbdata.gb_epsilon_solvent = fr->gb_epsilon_solvent;
- gbdata.epsilon_r = fr->epsilon_r;
- gbdata.gpol = egpol;
+ kernel_data.flags = flags;
+ kernel_data.exclusions = excl;
+ kernel_data.lambda = lambda;
+ kernel_data.dvdl = dvdl;
- if (!fr->adress_type==eAdressOff && !bDoForces){
- gmx_fatal(FARGS,"No force kernels not implemeted for adress");
- }
-
- if(fr->bAllvsAll)
+ if(fr->bAllvsAll)
{
- if(fr->bGB)
- {
-#if 0 && defined (GMX_X86_SSE2)
-# ifdef GMX_DOUBLE
- if(fr->use_cpu_acceleration)
- {
- nb_kernel_allvsallgb_sse2_double(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,egpol,
- &outeriter,&inneriter,&fr->AllvsAll_work);
- }
- else
- {
- nb_kernel_allvsallgb(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,egpol,
- &outeriter,&inneriter,&fr->AllvsAll_work);
- }
-# else /* not double */
- if(fr->use_cpu_acceleration)
- {
- nb_kernel_allvsallgb_sse2_single(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,egpol,
- &outeriter,&inneriter,&fr->AllvsAll_work);
- }
- else
- {
- nb_kernel_allvsallgb(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,egpol,
- &outeriter,&inneriter,&fr->AllvsAll_work);
- }
-# endif /* double/single alt. */
-#else /* no SSE support compiled in */
- nb_kernel_allvsallgb(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,egpol,
- &outeriter,&inneriter,&fr->AllvsAll_work);
-#endif
- inc_nrnb(nrnb,eNR_NBKERNEL_ALLVSALLGB,inneriter);
- }
- else
- {
-#if 0 && defined (GMX_X86_SSE2)
-# ifdef GMX_DOUBLE
- if(fr->use_cpu_acceleration)
- {
- nb_kernel_allvsall_sse2_double(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,
- &outeriter,&inneriter,&fr->AllvsAll_work);
- }
- else
- {
- nb_kernel_allvsall(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,
- &outeriter,&inneriter,&fr->AllvsAll_work);
- }
-
-# else /* not double */
- if(fr->use_cpu_acceleration)
- {
- nb_kernel_allvsall_sse2_single(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,
- &outeriter,&inneriter,&fr->AllvsAll_work);
- }
- else
- {
- nb_kernel_allvsall(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,
- &outeriter,&inneriter,&fr->AllvsAll_work);
- }
-
-# endif /* double/single check */
-#else /* No SSE2 support compiled in */
- nb_kernel_allvsall(fr,mdatoms,excl,x[0],f[0],egcoul,egnb,
- &outeriter,&inneriter,&fr->AllvsAll_work);
-#endif
-
- inc_nrnb(nrnb,eNR_NBKERNEL_ALLVSALL,inneriter);
- }
- inc_nrnb(nrnb,eNR_NBKERNEL_OUTER,outeriter);
return;
}
- if (eNL >= 0)
+ if (eNL >= 0)
{
i0 = eNL;
i1 = i0+1;
i1 = eNL_NR;
}
- if (nls >= 0)
+ if (nls >= 0)
{
n0 = nls;
n1 = nls+1;
}
- else
+ else
{
n0 = 0;
n1 = fr->nnblists;
}
-
- if(nb_kernel_list == NULL)
- {
- gmx_fatal(FARGS,"gmx_setup_kernels has not been called");
- }
-
- fshift = fr->fshift[0];
-
- for(n=n0; (n<n1); n++)
+
+ for(n=n0; (n<n1); n++)
{
nblists = &fr->nblists[n];
- for(i=i0; (i<i1); i++)
- {
- outeriter = inneriter = 0;
-
- if (bLR)
- {
- nlist = &(nblists->nlist_lr[i]);
- }
- else
- {
- nlist = &(nblists->nlist_sr[i]);
- }
-
- if (nlist->nri > 0)
- {
- nrnb_ind = nlist->il_code;
-
- if(nrnb_ind==eNR_NBKERNEL_FREE_ENERGY)
- {
- /* generic free energy, use combined table */
- tabledata = nblists->tab.tab;
- }
- else
- {
- if (bForeignLambda)
- {
- /* We don't need the non-perturbed interactions */
- continue;
- }
- tabletype = nb_kernel_table[nrnb_ind];
-
- /* normal kernels, not free energy */
- if (!bDoForces)
- {
- nrnb_ind += eNR_NBKERNEL_NR/2;
- }
-
- if(tabletype == TABLE_COMBINED)
- {
- tabledata = nblists->tab.tab;
- }
- else if(tabletype == TABLE_COUL)
- {
- tabledata = nblists->coultab;
- }
- else if(tabletype == TABLE_VDW)
- {
- tabledata = nblists->vdwtab;
- }
- else
- {
- tabledata = NULL;
- }
- }
-
- nlist->count = 0;
-
- if(nlist->free_energy)
- {
- if(nlist->ivdw==enbvdwBHAM)
- {
- gmx_fatal(FARGS,"Cannot do free energy Buckingham interactions.");
- }
-
- gmx_nb_free_energy_kernel(nlist->icoul,
- nlist->ivdw,
- nlist->nri,
- nlist->iinr,
- nlist->jindex,
- nlist->jjnr,
- nlist->shift,
- fr->shift_vec[0],
- fshift,
- nlist->gid,
- x[0],
- f[0],
- mdatoms->chargeA,
- mdatoms->chargeB,
- fr->epsfac,
- fr->k_rf,
- fr->c_rf,
- fr->ewaldcoeff,
- egcoul,
- mdatoms->typeA,
- mdatoms->typeB,
- fr->ntype,
- fr->nbfp,
- egnb,
- nblists->tab.scale,
- tabledata,
- lambda[efptCOUL],
- lambda[efptVDW],
- dvdl,
- fr->sc_alphacoul,
- fr->sc_alphavdw,
- fr->sc_power,
- fr->sc_r_power,
- fr->sc_sigma6_def,
- fr->sc_sigma6_min,
- bDoForces,
- &outeriter,
- &inneriter);
- }
- else if (nlist->enlist == enlistCG_CG)
- {
- if (fr->adress_type==eAdressOff){
- /* Call the charge group based inner loop */
- gmx_nb_generic_cg_kernel(nlist,
- fr,
- mdatoms,
- x[0],
- f[0],
- fshift,
- egcoul,
- egnb,
- nblists->tab.scale,
- tabledata,
- &outeriter,
- &inneriter);
- }
- else
- {
- /*gmx_nb_generic_adress_kernel(nlist,
- fr,
- mdatoms,
- x[0],
- f[0],
- fshift,
- egcoul,
- egnb,
- nblists->tab.scale,
- tabledata,
- &outeriter,
- &inneriter);*/
- gmx_fatal(FARGS,"Death & horror! Adress cgcg kernel not implemented anymore.\n");
+ kernel_data.table_elec = &nblists->table_elec;
+ kernel_data.table_vdw = &nblists->table_vdw;
+ kernel_data.table_elec_vdw = &nblists->table_elec_vdw;
- }
+ for(range=0;range<2;range++)
+ {
+ /* Are we doing short/long-range? */
+ if(range==0)
+ {
+ /* Short-range */
+ if(!(flags & GMX_NONBONDED_DO_SR))
+ {
+ continue;
}
- else
+ kernel_data.energygrp_elec = grppener->ener[egCOULSR];
+ kernel_data.energygrp_vdw = grppener->ener[fr->bBHAM ? egBHAMSR : egLJSR];
+ kernel_data.energygrp_polarization = grppener->ener[egGB];
+ nlist = nblists->nlist_sr;
+ f = f_shortrange;
+ }
+ else if(range==1)
+ {
+ /* Long-range */
+ if(!(flags & GMX_NONBONDED_DO_LR))
{
- /* AdresS*/
- /* for adress we need to determine for each energy group wether it is explicit or coarse-grained */
- if (!fr->adress_type == eAdressOff) {
- bCG = FALSE;
- if ( !fr->adress_group_explicit[ mdatoms->cENER[nlist->iinr[0]] ] ){
- bCG=TRUE;
- }
- /* If this processor has only explicit atoms (w=1)
- skip the coarse grained force calculation. Same for
- only coarsegrained atoms and explicit interactions.
- Last condition is to make sure that generic kernel is not
- skipped*/
- if (mdatoms->pureex && bCG && nb_kernel_list[nrnb_ind] != NULL) continue;
- if (mdatoms->purecg && !bCG && nb_kernel_list[nrnb_ind] != NULL) continue;
- }
-
- if (fr->adress_type == eAdressOff ||
- mdatoms->pureex ||
- mdatoms->purecg){
- /* if we only have to calculate pure cg/ex interactions
- we can use the faster standard gromacs kernels*/
- kernelptr = nb_kernel_list[nrnb_ind];
- }else{
- /* This processor has hybrid interactions which means
- * we have to
- * use our own kernels. We have two kernel types: one that
- * calculates the forces with the explicit prefactor w1*w2
- * and one for coarse-grained with (1-w1*w2)
- * explicit kernels are the second part of the kernel
- * list */
- if (!bCG) nrnb_ind += eNR_NBKERNEL_NR/2;
- adresskernelptr = nb_kernel_list_adress[nrnb_ind];
- }
-
- if (kernelptr == NULL && adresskernelptr == NULL)
- {
- /* Call a generic nonbonded kernel */
-
- /* If you want to hack/test your own interactions,
- * do it in this routine and make sure it is called
- * by setting the environment variable GMX_NB_GENERIC.
- */
- if (fr->adress_type==eAdressOff){
-
- gmx_nb_generic_kernel(nlist,
- fr,
- mdatoms,
- x[0],
- f[0],
- fshift,
- egcoul,
- egnb,
- nblists->tab.scale,
- tabledata,
- &outeriter,
- &inneriter);
- }else /* do generic AdResS kernels (slow)*/
- {
-
- gmx_nb_generic_adress_kernel(nlist,
- fr,
- mdatoms,
- x[0],
- f[0],
- fshift,
- egcoul,
- egnb,
- nblists->tab.scale,
- tabledata,
- &outeriter,
- &inneriter,
- bCG);
- }
-
+ continue;
+ }
+ kernel_data.energygrp_elec = grppener->ener[egCOULLR];
+ kernel_data.energygrp_vdw = grppener->ener[fr->bBHAM ? egBHAMLR : egLJLR];
+ kernel_data.energygrp_polarization = grppener->ener[egGB];
+ nlist = nblists->nlist_lr;
+ f = f_longrange;
+ }
+ for(i=i0; (i<i1); i++)
+ {
+ if (nlist[i].nri > 0)
+ {
+ if(flags & GMX_NONBONDED_DO_POTENTIAL)
+ {
+ /* Potential and force */
+ kernelptr = (nb_kernel_t *)nlist[i].kernelptr_vf;
}
else
{
- /* Call nonbonded kernel from function pointer */
- if (kernelptr!=NULL){
- (*kernelptr)( &(nlist->nri),
- nlist->iinr,
- nlist->jindex,
- nlist->jjnr,
- nlist->shift,
- fr->shift_vec[0],
- fshift,
- nlist->gid,
- x[0],
- f[0],
- mdatoms->chargeA,
- &(fr->epsfac),
- &(fr->k_rf),
- &(fr->c_rf),
- egcoul,
- mdatoms->typeA,
- &(fr->ntype),
- fr->nbfp,
- egnb,
- &(nblists->tab.scale),
- tabledata,
- fr->invsqrta,
- fr->dvda,
- &(fr->gbtabscale),
- fr->gbtab.tab,
- &nthreads,
- &(nlist->count),
- nlist->mtx,
- &outeriter,
- &inneriter,
- (real *)&gbdata);
- }else if (adresskernelptr != NULL)
- { /* Adress kernels */
- (*adresskernelptr)( &(nlist->nri),
- nlist->iinr,
- nlist->jindex,
- nlist->jjnr,
- nlist->shift,
- fr->shift_vec[0],
- fshift,
- nlist->gid,
- x[0],
- f[0],
- mdatoms->chargeA,
- &(fr->epsfac),
- &(fr->k_rf),
- &(fr->c_rf),
- egcoul,
- mdatoms->typeA,
- &(fr->ntype),
- fr->nbfp,
- egnb,
- &(nblists->tab.scale),
- tabledata,
- fr->invsqrta,
- fr->dvda,
- &(fr->gbtabscale),
- fr->gbtab.tab,
- &nthreads,
- &(nlist->count),
- nlist->mtx,
- &outeriter,
- &inneriter,
- fr->adress_ex_forcecap,
- mdatoms->wf);
- }
+ /* Force only, no potential */
+ kernelptr = (nb_kernel_t *)nlist[i].kernelptr_f;
}
- }
-
- /* Update flop accounting */
-
- /* Outer loop in kernel */
- switch (nlist->enlist) {
- case enlistATOM_ATOM: fac = 1; break;
- case enlistSPC_ATOM: fac = 3; break;
- case enlistSPC_SPC: fac = 9; break;
- case enlistTIP4P_ATOM: fac = 4; break;
- case enlistTIP4P_TIP4P: fac = 16; break;
- case enlistCG_CG: fac = 1; break;
- }
- inc_nrnb(nrnb,eNR_NBKERNEL_OUTER,fac*outeriter);
- /* inner loop in kernel */
- inc_nrnb(nrnb,nrnb_ind,inneriter);
+ if(nlist[i].free_energy==0 && (flags & GMX_NONBONDED_DO_FOREIGNLAMBDA))
+ {
+ /* We don't need the non-perturbed interactions */
+ continue;
+ }
+ (*kernelptr)(&(nlist[i]),x,f,fr,mdatoms,&kernel_data,nrnb);
+ }
}
}
}
}
+static void
+nb_listed_warning_rlimit(const rvec *x,int ai, int aj,int * global_atom_index,real r, real rlimit)
+{
+ gmx_warning("Listed nonbonded interaction between particles %d and %d\n"
+ "at distance %.3f which is larger than the table limit %.3f nm.\n\n"
+ "This is likely either a 1,4 interaction, or a listed interaction inside\n"
+ "a smaller molecule you are decoupling during a free energy calculation.\n"
+ "Since interactions at distances beyond the table cannot be computed,\n"
+ "they are skipped until they are inside the table limit again. You will\n"
+ "only see this message once, even if it occurs for several interactions.\n\n"
+ "IMPORTANT: This should not happen in a stable simulation, so there is\n"
+ "probably something wrong with your system. Only change the table-extension\n"
+ "distance in the mdp file if you are really sure that is the reason.\n",
+ glatnr(global_atom_index,ai),glatnr(global_atom_index,aj),r,rlimit);
+
+ if (debug)
+ {
+ fprintf(debug,
+ "%8f %8f %8f\n%8f %8f %8f\n1-4 (%d,%d) interaction not within cut-off! r=%g. Ignored\n",
+ x[ai][XX],x[ai][YY],x[ai][ZZ],x[aj][XX],x[aj][YY],x[aj][ZZ],
+ glatnr(global_atom_index,ai),glatnr(global_atom_index,aj),r);
+ }
+}
+
+
-real
-do_listed_vdw_q(int ftype,int nbonds,
+/* This might logically belong better in the nb_generic.c module, but it is only
+ * used in do_nonbonded_listed(), and we want it to be inlined there to avoid an
+ * extra functional call for every single pair listed in the topology.
+ */
+static real
+nb_evaluate_single(real r2, real tabscale,real *vftab,
+ real qq, real c6, real c12, real *velec, real *vvdw)
+{
+ real rinv,r,rtab,eps,eps2,Y,F,Geps,Heps2,Fp,VVe,FFe,VVd,FFd,VVr,FFr,fscal;
+ int ntab;
+
+ /* Do the tabulated interactions - first table lookup */
+ rinv = gmx_invsqrt(r2);
+ r = r2*rinv;
+ rtab = r*tabscale;
+ ntab = rtab;
+ eps = rtab-ntab;
+ eps2 = eps*eps;
+ ntab = 12*ntab;
+ /* Electrostatics */
+ Y = vftab[ntab];
+ F = vftab[ntab+1];
+ Geps = eps*vftab[ntab+2];
+ Heps2 = eps2*vftab[ntab+3];
+ Fp = F+Geps+Heps2;
+ VVe = Y+eps*Fp;
+ FFe = Fp+Geps+2.0*Heps2;
+ /* Dispersion */
+ Y = vftab[ntab+4];
+ F = vftab[ntab+5];
+ Geps = eps*vftab[ntab+6];
+ Heps2 = eps2*vftab[ntab+7];
+ Fp = F+Geps+Heps2;
+ VVd = Y+eps*Fp;
+ FFd = Fp+Geps+2.0*Heps2;
+ /* Repulsion */
+ Y = vftab[ntab+8];
+ F = vftab[ntab+9];
+ Geps = eps*vftab[ntab+10];
+ Heps2 = eps2*vftab[ntab+11];
+ Fp = F+Geps+Heps2;
+ VVr = Y+eps*Fp;
+ FFr = Fp+Geps+2.0*Heps2;
+
+ *velec = qq*VVe;
+ *vvdw = c6*VVd+c12*VVr;
+
+ fscal = -(qq*FFe+c6*FFd+c12*FFr)*tabscale*rinv;
+
+ return fscal;
+}
+
+
+real
+do_nonbonded_listed(int ftype,int nbonds,
const t_iatom iatoms[],const t_iparams iparams[],
const rvec x[],rvec f[],rvec fshift[],
const t_pbc *pbc,const t_graph *g,
const t_forcerec *fr,gmx_grppairener_t *grppener,
int *global_atom_index)
{
- static gmx_bool bWarn=FALSE;
- real eps,r2,*tab,rtab2=0;
- rvec dx,x14[2],f14[2];
- int i,ai,aj,itype;
- int typeA[2]={0,0},typeB[2]={0,1};
- real chargeA[2]={0,0},chargeB[2];
- int gid,shift_vir,shift_f;
- int j_index[] = { 0, 1 };
- int i0=0,i1=1,i2=2;
- ivec dt;
- int outeriter,inneriter;
- int nthreads = 1;
- int count;
- real krf,crf,tabscale;
- int ntype=0;
- real *nbfp=NULL;
- real *egnb=NULL,*egcoul=NULL;
- t_nblist tmplist;
- int icoul,ivdw;
- gmx_bool bMolPBC,bFreeEnergy;
+ int ielec,ivdw;
+ real qq,c6,c12;
+ rvec dx;
+ ivec dt;
+ int i,j,itype,ai,aj,gid;
+ int fshift_index;
+ real r2,rinv;
+ real fscal,velec,vvdw;
+ real * energygrp_elec;
+ real * energygrp_vdw;
+ static gmx_bool warned_rlimit=FALSE;
+ /* Free energy stuff */
+ gmx_bool bFreeEnergy;
+ real LFC[2],LFV[2],DLF[2],lfac_coul[2],lfac_vdw[2],dlfac_coul[2],dlfac_vdw[2];
+ real qqB,c6B,c12B,sigma2_def,sigma2_min;
- gmx_bool bCG; /* AdResS*/
- real wf14[2]={0,0}; /* AdResS*/
-
-#if GMX_THREAD_SHM_FDECOMP
- pthread_mutex_t mtx;
-#else
- void * mtx = NULL;
-#endif
-
-#if GMX_THREAD_SHM_FDECOMP
- pthread_mutex_initialize(&mtx);
-#endif
-
- bMolPBC = fr->bMolPBC;
-
switch (ftype) {
- case F_LJ14:
- case F_LJC14_Q:
- eps = fr->epsfac*fr->fudgeQQ;
- ntype = 1;
- egnb = grppener->ener[egLJ14];
- egcoul = grppener->ener[egCOUL14];
- break;
- case F_LJC_PAIRS_NB:
- eps = fr->epsfac;
- ntype = 1;
- egnb = grppener->ener[egLJSR];
- egcoul = grppener->ener[egCOULSR];
- break;
- default:
- gmx_fatal(FARGS,"Unknown function type %d in do_nonbonded14",
- ftype);
- }
- tab = fr->tab14.tab;
- rtab2 = sqr(fr->tab14.r);
- tabscale = fr->tab14.scale;
-
- krf = fr->k_rf;
- crf = fr->c_rf;
-
- /* Determine the values for icoul/ivdw. */
- if (fr->bEwald) {
- icoul = enbcoulOOR;
- }
- else if(fr->bcoultab)
- {
- icoul = enbcoulTAB;
- }
- else if(fr->eeltype == eelRF_NEC)
- {
- icoul = enbcoulRF;
- }
- else
- {
- icoul = enbcoulOOR;
+ case F_LJ14:
+ case F_LJC14_Q:
+ energygrp_elec = grppener->ener[egCOUL14];
+ energygrp_vdw = grppener->ener[egLJ14];
+ break;
+ case F_LJC_PAIRS_NB:
+ energygrp_elec = grppener->ener[egCOULSR];
+ energygrp_vdw = grppener->ener[egLJSR];
+ break;
+ default:
+ energygrp_elec = NULL; /* Keep compiler happy */
+ energygrp_vdw = NULL; /* Keep compiler happy */
+ gmx_fatal(FARGS,"Unknown function type %d in do_nonbonded14",ftype);
+ break;
}
- if(fr->bvdwtab)
+ if(fr->efep != efepNO)
{
- ivdw = enbvdwTAB;
+ /* Lambda factor for state A=1-lambda and B=lambda */
+ LFC[0] = 1.0 - lambda[efptCOUL];
+ LFV[0] = 1.0 - lambda[efptVDW];
+ LFC[1] = lambda[efptCOUL];
+ LFV[1] = lambda[efptVDW];
+
+ /*derivative of the lambda factor for state A and B */
+ DLF[0] = -1;
+ DLF[1] = 1;
+
+ /* precalculate */
+ sigma2_def = pow(fr->sc_sigma6_def,1.0/3.0);
+ sigma2_min = pow(fr->sc_sigma6_min,1.0/3.0);
+
+ for (i=0;i<2;i++)
+ {
+ lfac_coul[i] = (fr->sc_power==2 ? (1-LFC[i])*(1-LFC[i]) : (1-LFC[i]));
+ dlfac_coul[i] = DLF[i]*fr->sc_power/fr->sc_r_power*(fr->sc_power==2 ? (1-LFC[i]) : 1);
+ lfac_vdw[i] = (fr->sc_power==2 ? (1-LFV[i])*(1-LFV[i]) : (1-LFV[i]));
+ dlfac_vdw[i] = DLF[i]*fr->sc_power/fr->sc_r_power*(fr->sc_power==2 ? (1-LFV[i]) : 1);
+ }
}
else
{
- ivdw = enbvdwLJ;
+ sigma2_min = sigma2_def = 0;
}
-
-
- bCG = FALSE; /*Adres*/
- /* We don't do SSE or altivec here, due to large overhead for 4-fold
- * unrolling on short lists
- */
-
+
bFreeEnergy = FALSE;
- for(i=0; (i<nbonds); )
+ for(i=0; (i<nbonds); )
{
itype = iatoms[i++];
ai = iatoms[i++];
aj = iatoms[i++];
gid = GID(md->cENER[ai],md->cENER[aj],md->nenergrp);
- if (!fr->adress_type == eAdressOff) {
- if (fr->adress_group_explicit[md->cENER[ai]] != fr->adress_group_explicit[md->cENER[aj]]){
- /*exclude cg-ex interaction*/
- continue;
- }
- bCG = !fr->adress_group_explicit[md->cENER[ai]];
- wf14[0] = md->wf[ai];
- wf14[1] = md->wf[aj];
- }
+ /* Get parameters */
switch (ftype) {
- case F_LJ14:
- bFreeEnergy =
+ case F_LJ14:
+ bFreeEnergy =
(fr->efep != efepNO &&
((md->nPerturbed && (md->bPerturbed[ai] || md->bPerturbed[aj])) ||
iparams[itype].lj14.c6A != iparams[itype].lj14.c6B ||
iparams[itype].lj14.c12A != iparams[itype].lj14.c12B));
- chargeA[0] = md->chargeA[ai];
- chargeA[1] = md->chargeA[aj];
- nbfp = (real *)&(iparams[itype].lj14.c6A);
- break;
- case F_LJC14_Q:
- eps = fr->epsfac*iparams[itype].ljc14.fqq;
- chargeA[0] = iparams[itype].ljc14.qi;
- chargeA[1] = iparams[itype].ljc14.qj;
- nbfp = (real *)&(iparams[itype].ljc14.c6);
- break;
- case F_LJC_PAIRS_NB:
- chargeA[0] = iparams[itype].ljcnb.qi;
- chargeA[1] = iparams[itype].ljcnb.qj;
- nbfp = (real *)&(iparams[itype].ljcnb.c6);
- break;
+ qq = md->chargeA[ai]*md->chargeA[aj]*fr->epsfac*fr->fudgeQQ;
+ c6 = iparams[itype].lj14.c6A;
+ c12 = iparams[itype].lj14.c12A;
+ break;
+ case F_LJC14_Q:
+ qq = iparams[itype].ljc14.qi*iparams[itype].ljc14.qj*fr->epsfac*iparams[itype].ljc14.fqq;
+ c6 = iparams[itype].ljc14.c6;
+ c12 = iparams[itype].ljc14.c12;
+ break;
+ case F_LJC_PAIRS_NB:
+ qq = iparams[itype].ljcnb.qi*iparams[itype].ljcnb.qj*fr->epsfac;
+ c6 = iparams[itype].ljcnb.c6;
+ c12 = iparams[itype].ljcnb.c12;
+ break;
+ default:
+ /* Cannot happen since we called gmx_fatal() above in this case */
+ qq = c6 = c12 = 0; /* Keep compiler happy */
+ break;
}
- if (!bMolPBC)
+ /* To save flops in the optimized kernels, c6/c12 have 6.0/12.0 derivative prefactors
+ * included in the general nfbp array now. This means the tables are scaled down by the
+ * same factor, so when we use the original c6/c12 parameters from iparams[] they must
+ * be scaled up.
+ */
+ c6 *= 6.0;
+ c12 *= 12.0;
+
+ /* Do we need to apply full periodic boundary conditions? */
+ if(fr->bMolPBC==TRUE)
{
- /* This is a bonded interaction, atoms are in the same box */
- shift_f = CENTRAL;
- r2 = distance2(x[ai],x[aj]);
+ fshift_index = pbc_dx_aiuc(pbc,x[ai],x[aj],dx);
}
- else
+ else
{
- /* Apply full periodic boundary conditions */
- shift_f = pbc_dx_aiuc(pbc,x[ai],x[aj],dx);
- r2 = norm2(dx);
+ fshift_index = CENTRAL;
+ rvec_sub(x[ai],x[aj],dx);
}
+ r2 = norm2(dx);
- if (r2 >= rtab2)
+ if(r2>=fr->tab14.r*fr->tab14.r)
{
- if (!bWarn)
+ if(warned_rlimit==FALSE)
{
- fprintf(stderr,"Warning: 1-4 interaction between %d and %d "
- "at distance %.3f which is larger than the 1-4 table size %.3f nm\n",
- glatnr(global_atom_index,ai),
- glatnr(global_atom_index,aj),
- sqrt(r2), sqrt(rtab2));
- fprintf(stderr,"These are ignored for the rest of the simulation\n");
- fprintf(stderr,"This usually means your system is exploding,\n"
- "if not, you should increase table-extension in your mdp file\n"
- "or with user tables increase the table size\n");
- bWarn = TRUE;
+ nb_listed_warning_rlimit(x,ai,aj,global_atom_index,sqrt(r2),fr->tab14.r);
+ warned_rlimit=TRUE;
}
- if (debug)
- fprintf(debug,"%8f %8f %8f\n%8f %8f %8f\n1-4 (%d,%d) interaction not within cut-off! r=%g. Ignored\n",
- x[ai][XX],x[ai][YY],x[ai][ZZ],
- x[aj][XX],x[aj][YY],x[aj][ZZ],
- glatnr(global_atom_index,ai),
- glatnr(global_atom_index,aj),
- sqrt(r2));
+ continue;
}
- else
+
+ if (bFreeEnergy)
{
- copy_rvec(x[ai],x14[0]);
- copy_rvec(x[aj],x14[1]);
- clear_rvec(f14[0]);
- clear_rvec(f14[1]);
-#ifdef DEBUG
- fprintf(debug,"LJ14: grp-i=%2d, grp-j=%2d, ngrp=%2d, GID=%d\n",
- md->cENER[ai],md->cENER[aj],md->nenergrp,gid);
-#endif
-
- outeriter = inneriter = count = 0;
- if (bFreeEnergy)
+ /* Currently free energy is only supported for F_LJ14, so no need to check for that if we got here */
+ qqB = md->chargeB[ai]*md->chargeB[aj]*fr->epsfac*fr->fudgeQQ;
+ c6B = iparams[itype].lj14.c6B*6.0;
+ c12B = iparams[itype].lj14.c12B*12.0;
+
+ fscal = nb_free_energy_evaluate_single(r2,fr->sc_r_power,fr->sc_alphacoul,fr->sc_alphavdw,
+ fr->tab14.scale,fr->tab14.data,qq,c6,c12,qqB,c6B,c12B,
+ LFC,LFV,DLF,lfac_coul,lfac_vdw,dlfac_coul,dlfac_vdw,
+ fr->sc_sigma6_def,fr->sc_sigma6_min,sigma2_def,sigma2_min,&velec,&vvdw,dvdl);
+ }
+ else
{
- chargeB[0] = md->chargeB[ai];
- chargeB[1] = md->chargeB[aj];
- /* We pass &(iparams[itype].lj14.c6A) as LJ parameter matrix
- * to the innerloops.
- * Here we use that the LJ-14 parameters are stored in iparams
- * as c6A,c12A,c6B,c12B, which are referenced correctly
- * in the innerloops if we assign type combinations 0-0 and 0-1
- * to atom pair ai-aj in topologies A and B respectively.
- */
-
- /* need to do a bit of a kludge here -- the way it is set up,
- if the charges change, but the vdw do not, then even though bFreeEnergy is on,
- it won't work, because all the bonds are perturbed.
- */
- if(ivdw==enbvdwBHAM)
- {
- gmx_fatal(FARGS,"Cannot do free energy Buckingham interactions.");
- }
- count = 0;
- gmx_nb_free_energy_kernel(icoul,
- ivdw,
- i1,
- &i0,
- j_index,
- &i1,
- &shift_f,
- fr->shift_vec[0],
- fshift[0],
- &gid,
- x14[0],
- f14[0],
- chargeA,
- chargeB,
- eps,
- krf,
- crf,
- fr->ewaldcoeff,
- egcoul,
- typeA,
- typeB,
- ntype,
- nbfp,
- egnb,
- tabscale,
- tab,
- lambda[efptCOUL],
- lambda[efptVDW],
- dvdl,
- fr->sc_alphacoul,
- fr->sc_alphavdw,
- fr->sc_power,
- 6.0, /* for 1-4's use the 6 power always - 48 power too high because of where they are forced to be */
- fr->sc_sigma6_def,
- fr->sc_sigma6_min,
- TRUE,
- &outeriter,
- &inneriter);
+ /* Evaluate tabulated interaction without free energy */
+ fscal = nb_evaluate_single(r2,fr->tab14.scale,fr->tab14.data,qq,c6,c12,&velec,&vvdw);
}
- else
- {
- if (fr->adress_type==eAdressOff || !fr->adress_do_hybridpairs){
- /* Not perturbed - call kernel 330 */
- nb_kernel330
- ( &i1,
- &i0,
- j_index,
- &i1,
- &shift_f,
- fr->shift_vec[0],
- fshift[0],
- &gid,
- x14[0],
- f14[0],
- chargeA,
- &eps,
- &krf,
- &crf,
- egcoul,
- typeA,
- &ntype,
- nbfp,
- egnb,
- &tabscale,
- tab,
- NULL,
- NULL,
- NULL,
- NULL,
- &nthreads,
- &count,
- (void *)&mtx,
- &outeriter,
- &inneriter,
- NULL);
- } else {
- if (bCG) {
- nb_kernel330_adress_cg(&i1,
- &i0,
- j_index,
- &i1,
- &shift_f,
- fr->shift_vec[0],
- fshift[0],
- &gid,
- x14[0],
- f14[0],
- chargeA,
- &eps,
- &krf,
- &crf,
- egcoul,
- typeA,
- &ntype,
- nbfp,
- egnb,
- &tabscale,
- tab,
- NULL,
- NULL,
- NULL,
- NULL,
- &nthreads,
- &count,
- (void *) &mtx,
- &outeriter,
- &inneriter,
- fr->adress_ex_forcecap,
- wf14);
- } else {
- nb_kernel330_adress_ex(&i1,
- &i0,
- j_index,
- &i1,
- &shift_f,
- fr->shift_vec[0],
- fshift[0],
- &gid,
- x14[0],
- f14[0],
- chargeA,
- &eps,
- &krf,
- &crf,
- egcoul,
- typeA,
- &ntype,
- nbfp,
- egnb,
- &tabscale,
- tab,
- NULL,
- NULL,
- NULL,
- NULL,
- &nthreads,
- &count,
- (void *) &mtx,
- &outeriter,
- &inneriter,
- fr->adress_ex_forcecap,
- wf14);
- }
- }
- }
-
+ energygrp_elec[gid] += velec;
+ energygrp_vdw[gid] += vvdw;
+ svmul(fscal,dx,dx);
+
/* Add the forces */
- rvec_inc(f[ai],f14[0]);
- rvec_dec(f[aj],f14[0]);
-
- if (g)
+ rvec_inc(f[ai],dx);
+ rvec_dec(f[aj],dx);
+
+ if (g)
{
/* Correct the shift forces using the graph */
- ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),dt);
- shift_vir = IVEC2IS(dt);
- rvec_inc(fshift[shift_vir],f14[0]);
- rvec_dec(fshift[CENTRAL],f14[0]);
+ ivec_sub(SHIFT_IVEC(g,ai),SHIFT_IVEC(g,aj),dt);
+ fshift_index = IVEC2IS(dt);
}
-
- /* flops: eNR_KERNEL_OUTER + eNR_KERNEL330 + 12 */
+ if(fshift_index!=CENTRAL)
+ {
+ rvec_inc(fshift[fshift_index],dx);
+ rvec_dec(fshift[CENTRAL],dx);
}
}
return 0.0;
--- /dev/null
+#!/usr/bin/env python
+# Copyright (c) 2002-2008 ActiveState Software Inc.
+# License: MIT License (http://www.opensource.org/licenses/mit-license.php)
+# Original filename preprocess.py, see http://code.google.com/p/preprocess/
+#
+# Modified by Erik Lindahl 2009-2012 <lindahl@gromacs.org>
+# to enable advanced preprocessing for Gromacs kernels, including
+# preprocessor for-loops and substitution into preprocessor directives
+# as well as program strings.
+#
+# Please feel free to redistribute under same license as original (MIT),
+# but don't blame the original authors for mistakes in this version.
+#
+
+"""
+ Preprocess a file.
+
+ Command Line Usage:
+ gmxpreprocess [<options>...] <infile>
+
+ Options:
+ -h, --help Print this help and exit.
+ -V, --version Print the version info and exit.
+ -v, --verbose Give verbose output for errors.
+
+ -o <outfile> Write output to the given file instead of to stdout.
+ -f, --force Overwrite given output file. (Otherwise an IOError
+ will be raised if <outfile> already exists.
+ -D <define> Define a variable for preprocessing. <define>
+ can simply be a variable name (in which case it
+ will be true) or it can be of the form
+ <var>=<val>. An attempt will be made to convert
+ <val> to an integer so "-D FOO=0" will create a
+ false value.
+ -I <dir> Add an directory to the include path for
+ #include directives.
+
+ -k, --keep-lines Emit empty lines for preprocessor statement
+ lines and skipped output lines. This allows line
+ numbers to stay constant.
+ -s, --no-substitute Do NOT Substitute defines into emitted lines.
+ -c, --content-types-path <path>
+ Specify a path to a content.types file to assist
+ with filetype determination. See the
+ `_gDefaultContentTypes` string in this file for
+ details on its format.
+
+ Module Usage:
+ from gmxpreprocess import gmxpreprocess
+ gmxpreprocess(infile, outfile=sys.stdout, defines={}, force=0,
+ keepLines=0, includePath=[], substitute=1,
+ contentType=None)
+
+ The <infile> can be marked up with special preprocessor statement lines
+ of the form:
+ <comment-prefix> <preprocessor-statement> <comment-suffix>
+ where the <comment-prefix/suffix> are the native comment delimiters for
+ that file type.
+
+
+ Examples
+ --------
+
+ HTML (*.htm, *.html) or XML (*.xml, *.kpf, *.xul) files:
+
+ <!-- #if FOO -->
+ ...
+ <!-- #endif -->
+
+ Python (*.py), Perl (*.pl), Tcl (*.tcl), Ruby (*.rb), Bash (*.sh),
+ or make ([Mm]akefile*) files:
+
+ # #if defined('FAV_COLOR') and FAV_COLOR == "blue"
+ ...
+ # #elif FAV_COLOR == "red"
+ ...
+ # #else
+ ...
+ # #endif
+
+ C (*.c, *.h), C++ (*.cpp, *.cxx, *.cc, *.h, *.hpp, *.hxx, *.hh),
+ Java (*.java), PHP (*.php) or C# (*.cs) files:
+
+ // #define FAV_COLOR 'blue'
+ ...
+ /* #ifndef FAV_COLOR */
+ ...
+ // #endif
+
+ Fortran 77 (*.f) or 90/95 (*.f90) files:
+
+ C #if COEFF == 'var'
+ ...
+ C #endif
+
+ And other languages.
+
+
+ Preprocessor Syntax
+ -------------------
+
+ - Valid statements:
+ #define <var> [<value>]
+ #undef <var>
+ #ifdef <var>
+ #ifndef <var>
+ #if <expr>
+ #elif <expr>
+ #else
+ #endif
+ #error <error string>
+ #include "<file>"
+ #include <var>
+ where <expr> is any valid Python expression.
+ - The expression after #if/elif may be a Python statement. It is an
+ error to refer to a variable that has not been defined by a -D
+ option or by an in-content #define.
+ - Special built-in methods for expressions:
+ defined(varName) Return true if given variable is defined.
+
+
+ Tips
+ ----
+
+ A suggested file naming convention is to let input files to
+ preprocess be of the form <basename>.p.<ext> and direct the output
+ of preprocess to <basename>.<ext>, e.g.:
+ preprocess -o foo.py foo.p.py
+ The advantage is that other tools (esp. editors) will still
+ recognize the unpreprocessed file as the original language.
+"""
+
+__version_info__ = (1, 1, 0)
+__version__ = '.'.join(map(str, __version_info__))
+
+import os
+import sys
+import getopt
+import types
+import re
+import pprint
+
+
+
+#---- exceptions
+
+class PreprocessError(Exception):
+ def __init__(self, errmsg, file=None, lineno=None, line=None):
+ self.errmsg = str(errmsg)
+ self.file = file
+ self.lineno = lineno
+ self.line = line
+ Exception.__init__(self, errmsg, file, lineno, line)
+ def __str__(self):
+ s = ""
+ if self.file is not None:
+ s += self.file + ":"
+ if self.lineno is not None:
+ s += str(self.lineno) + ":"
+ if self.file is not None or self.lineno is not None:
+ s += " "
+ s += self.errmsg
+ #if self.line is not None:
+ # s += ": " + self.line
+ return s
+
+
+
+#---- global data
+
+# Comment delimiter info.
+# A mapping of content type to a list of 2-tuples defining the line
+# prefix and suffix for a comment. Each prefix or suffix can either
+# be a string (in which case it is transformed into a pattern allowing
+# whitespace on either side) or a compiled regex.
+_commentGroups = {
+ "Python": [ ('#', '') ],
+ "Perl": [ ('#', '') ],
+ "PHP": [ ('/*', '*/'), ('//', ''), ('#', '') ],
+ "Ruby": [ ('#', '') ],
+ "Tcl": [ ('#', '') ],
+ "Shell": [ ('#', '') ],
+ # Allowing for CSS and JavaScript comments in XML/HTML.
+ "XML": [ ('<!--', '-->'), ('/*', '*/'), ('//', '') ],
+ "HTML": [ ('<!--', '-->'), ('/*', '*/'), ('//', '') ],
+ "Makefile": [ ('#', '') ],
+ "JavaScript": [ ('/*', '*/'), ('//', '') ],
+ "CSS": [ ('/*', '*/') ],
+ "C": [ ('/*', '*/') ],
+ "C++": [ ('/*', '*/'), ('//', '') ],
+ "Java": [ ('/*', '*/'), ('//', '') ],
+ "C#": [ ('/*', '*/'), ('//', '') ],
+ "IDL": [ ('/*', '*/'), ('//', '') ],
+ "Text": [ ('#', '') ],
+ "Fortran": [ (re.compile(r'^[a-zA-Z*$]\s*'), ''), ('!', '') ],
+ "TeX": [ ('%', '') ],
+}
+
+
+
+#---- internal logging facility
+
+class _Logger:
+ DEBUG, INFO, WARN, ERROR, CRITICAL = range(5)
+ def __init__(self, name, level=None, streamOrFileName=sys.stderr):
+ self._name = name
+ if level is None:
+ self.level = self.WARN
+ else:
+ self.level = level
+ if type(streamOrFileName) == types.StringType:
+ self.stream = open(streamOrFileName, 'w')
+ self._opennedStream = 1
+ else:
+ self.stream = streamOrFileName
+ self._opennedStream = 0
+ def __del__(self):
+ if self._opennedStream:
+ self.stream.close()
+ def getLevel(self):
+ return self.level
+ def setLevel(self, level):
+ self.level = level
+ def _getLevelName(self, level):
+ levelNameMap = {
+ self.DEBUG: "DEBUG",
+ self.INFO: "INFO",
+ self.WARN: "WARN",
+ self.ERROR: "ERROR",
+ self.CRITICAL: "CRITICAL",
+ }
+ return levelNameMap[level]
+ def isEnabled(self, level):
+ return level >= self.level
+ def isDebugEnabled(self): return self.isEnabled(self.DEBUG)
+ def isInfoEnabled(self): return self.isEnabled(self.INFO)
+ def isWarnEnabled(self): return self.isEnabled(self.WARN)
+ def isErrorEnabled(self): return self.isEnabled(self.ERROR)
+ def isFatalEnabled(self): return self.isEnabled(self.FATAL)
+ def log(self, level, msg, *args):
+ if level < self.level:
+ return
+ message = "%s: %s: " % (self._name, self._getLevelName(level).lower())
+ message = message + (msg % args) + "\n"
+ self.stream.write(message)
+ self.stream.flush()
+ def debug(self, msg, *args):
+ self.log(self.DEBUG, msg, *args)
+ def info(self, msg, *args):
+ self.log(self.INFO, msg, *args)
+ def warn(self, msg, *args):
+ self.log(self.WARN, msg, *args)
+ def error(self, msg, *args):
+ self.log(self.ERROR, msg, *args)
+ def fatal(self, msg, *args):
+ self.log(self.CRITICAL, msg, *args)
+
+log = _Logger("gmxpreprocess", _Logger.WARN)
+
+
+
+#---- internal support stuff
+
+def SubstituteInternal(expr, defines):
+ prevexpr = ''
+ while (expr!=prevexpr):
+ prevexpr=expr
+ for name in reversed(sorted(defines, key=len)):
+ value = defines[name]
+ expr = expr.replace(name, str(value))
+ return expr
+
+def SubstituteInCode(expr, defines):
+ prevexpr = ''
+ while (expr!=prevexpr):
+ prevexpr=expr
+ for name in reversed(sorted(defines, key=len)):
+ value = defines[name]
+ expr = expr.replace('{' + name + '}', str(value))
+ return expr
+
+
+def _evaluate(expr, defines):
+ """Evaluate the given expression string with the given context.
+
+ WARNING: This runs eval() on a user string. This is unsafe.
+ """
+ #interpolated = _interpolate(s, defines)
+
+ try:
+ rv = eval(expr, {'defined':lambda v: v in defines}, defines)
+ except Exception, ex:
+ msg = str(ex)
+ if msg.startswith("name '") and msg.endswith("' is not defined"):
+ # A common error (at least this is presumed:) is to have
+ # defined(FOO) instead of defined('FOO')
+ # We should give a little as to what might be wrong.
+ # msg == "name 'FOO' is not defined" --> varName == "FOO"
+ varName = msg[len("name '"):-len("' is not defined")]
+ if expr.find("defined(%s)" % varName) != -1:
+ # "defined(FOO)" in expr instead of "defined('FOO')"
+ msg += " (perhaps you want \"defined('%s')\" instead of "\
+ "\"defined(%s)\")" % (varName, varName)
+ elif msg.startswith("invalid syntax"):
+ msg = "invalid syntax: '%s'" % expr
+ raise PreprocessError(msg, defines['__FILE__'], defines['__LINE__'])
+ log.debug("evaluate %r -> %s (defines=%r)", expr, rv, defines)
+
+ return rv
+
+#---- module API
+
+def gmxpreprocess(infile, outfile=sys.stdout, defines={},
+ force=0, keepLines=0, includePath=[], substitute=1,
+ contentType=None, contentTypesRegistry=None,
+ __preprocessedFiles=None):
+ """Preprocess the given file.
+
+ "infile" is the input path.
+ "outfile" is the output path or stream (default is sys.stdout).
+ "defines" is a dictionary of defined variables that will be
+ understood in preprocessor statements. Keys must be strings and,
+ currently, only the truth value of any key's value matters.
+ "force" will overwrite the given outfile if it already exists. Otherwise
+ an IOError will be raise if the outfile already exists.
+ "keepLines" will cause blank lines to be emitted for preprocessor lines
+ and content lines that would otherwise be skipped.
+ "includePath" is a list of directories to search for given #include
+ directives. The directory of the file being processed is presumed.
+ "substitute", if true, will allow substitution of defines into emitted
+ lines. (NOTE: This substitution will happen within program strings
+ as well. This may not be what you expect.)
+ "contentType" can be used to specify the content type of the input
+ file. It not given, it will be guessed.
+ "contentTypesRegistry" is an instance of ContentTypesRegistry. If not specified
+ a default registry will be created.
+ "__preprocessedFiles" (for internal use only) is used to ensure files
+ are not recusively preprocessed.
+
+ Returns the modified dictionary of defines or raises PreprocessError if
+ there was some problem.
+ """
+ if __preprocessedFiles is None:
+ __preprocessedFiles = []
+ log.info("preprocess(infile=%r, outfile=%r, defines=%r, force=%r, "\
+ "keepLines=%r, includePath=%r, contentType=%r, "\
+ "__preprocessedFiles=%r)", infile, outfile, defines, force,
+ keepLines, includePath, contentType, __preprocessedFiles)
+ absInfile = os.path.normpath(os.path.abspath(infile))
+ if absInfile in __preprocessedFiles:
+ raise PreprocessError("detected recursive #include of '%s'"\
+ % infile)
+ __preprocessedFiles.append(os.path.abspath(infile))
+
+ # Determine the content type and comment info for the input file.
+ if contentType is None:
+ registry = contentTypesRegistry or getDefaultContentTypesRegistry()
+ contentType = registry.getContentType(infile)
+ if contentType is None:
+ contentType = "Text"
+ log.warn("defaulting content type for '%s' to '%s'",
+ infile, contentType)
+ try:
+ cgs = _commentGroups[contentType]
+ except KeyError:
+ raise PreprocessError("don't know comment delimiters for content "\
+ "type '%s' (file '%s')"\
+ % (contentType, infile))
+
+ # Generate statement parsing regexes. Basic format:
+ # <comment-prefix> <preprocessor-stmt> <comment-suffix>
+ # Examples:
+ # <!-- #if foo -->
+ # ...
+ # <!-- #endif -->
+ #
+ # # #if BAR
+ # ...
+ # # #else
+ # ...
+ # # #endif
+ stmts = ['##\s*(?P<op>.*?)',
+ '#\s*(?P<op>if|elif|ifdef|ifndef)\s+(?P<expr>.*?)',
+ '#\s*(?P<op>else|endif)',
+ '#\s*(?P<op>error)\s+(?P<error>.*?)',
+ '#\s*(?P<op>define)\s+(?P<var>[^\s]*?)(\s+(?P<val>.+?))?',
+ '#\s*(?P<op>undef)\s+(?P<var>[^\s]*?)',
+ '#\s*(?P<op>for)\s+(?P<var>.*?)\s+((in)|(IN))\s+(?P<valuelist>.*?)',
+ '#\s*(?P<op>endfor)',
+ '#\s*(?P<op>include)\s+"(?P<fname>.*?)"',
+ r'#\s*(?P<op>include)\s+(?P<var>[^\s]+?)',
+ ]
+ patterns = []
+ for stmt in stmts:
+ # The comment group prefix and suffix can either be just a
+ # string or a compiled regex.
+ for cprefix, csuffix in cgs:
+ if hasattr(cprefix, "pattern"):
+ pattern = cprefix.pattern
+ else:
+ pattern = r"^\s*%s\s*" % re.escape(cprefix)
+ pattern += stmt
+ if hasattr(csuffix, "pattern"):
+ pattern += csuffix.pattern
+ else:
+ pattern += r"\s*%s\s*$" % re.escape(csuffix)
+ patterns.append(pattern)
+ stmtRes = [re.compile(p) for p in patterns]
+
+ # Process the input file.
+ # (Would be helpful if I knew anything about lexing and parsing
+ # simple grammars.)
+ fin = open(infile, 'r')
+ lines = fin.readlines()
+ # Merge multi-line comments
+ for i in range(len(lines)-1,-1,-1):
+ line = lines[i].rstrip(' \r\n')
+ if len(line)>0 and line[-1]=='\\':
+ lines[i] = line[:-1] + ' ' + lines[i+1]
+ lines[i+1] = '' # keep an empty line to avoid screwing up line numbers
+
+ fin.close()
+ if type(outfile) in types.StringTypes:
+ if force and os.path.exists(outfile):
+ os.chmod(outfile, 0777)
+ os.remove(outfile)
+ fout = open(outfile, 'w')
+ else:
+ fout = outfile
+
+ defines['__FILE__'] = infile
+ SKIP, EMIT = range(2) # states
+ states = [(EMIT, # a state is (<emit-or-skip-lines-in-this-section>,
+ 0, # <have-emitted-in-this-if-block>,
+ 0)] # <have-seen-'else'-in-this-if-block>)
+ lineNum = 0
+ nlines = len(lines)
+ forlevel = 0
+ forvar = {}
+ forvaluelist = {}
+ forstartline = {}
+ foriteration = {}
+ last_emitted_was_blank = True
+
+ while lineNum<nlines:
+
+ line = lines[lineNum]
+
+ log.debug("line %d: %r", lineNum+1, line)
+ defines['__LINE__'] = lineNum+1
+
+ # Is this line a preprocessor stmt line?
+ #XXX Could probably speed this up by optimizing common case of
+ # line NOT being a preprocessor stmt line.
+ for stmtRe in stmtRes:
+ match = stmtRe.match(line)
+ if match:
+ break
+ else:
+ match = None
+
+ if match:
+
+ # Remove contents after ## (comment)
+ idx=line.find("##")
+ if(idx>0):
+ line = line[0:idx]
+
+ op = match.group("op")
+ log.debug("%r stmt (states: %r)", op, states)
+ if op == "define":
+ if not (states and states[-1][0] == SKIP):
+ var, val = match.group("var", "val")
+ val = SubstituteInternal(str(val), defines)
+
+ if val is None:
+ val = None
+ else:
+ try:
+ val = eval(val, {}, {})
+ except:
+ pass
+ defines[var] = val
+ elif op == "undef":
+ if not (states and states[-1][0] == SKIP):
+ var = match.group("var")
+ try:
+ del defines[var]
+ except KeyError:
+ pass
+ elif op == "include":
+ if not (states and states[-1][0] == SKIP):
+ if "var" in match.groupdict():
+ # This is the second include form: #include VAR
+ var = match.group("var")
+ f = defines[var]
+ else:
+ # This is the first include form: #include "path"
+ f = match.group("fname")
+
+ for d in [os.path.dirname(infile)] + includePath:
+ fname = os.path.normpath(os.path.join(d, f))
+ if os.path.exists(fname):
+ break
+ else:
+ raise PreprocessError("could not find #include'd file "\
+ "\"%s\" on include path: %r"\
+ % (f, includePath))
+ defines = gmxpreprocess(fname, fout, defines, force,
+ keepLines, includePath, substitute,
+ contentTypesRegistry=contentTypesRegistry,
+ __preprocessedFiles=__preprocessedFiles)
+ elif op in ("if", "ifdef", "ifndef"):
+ if op == "if":
+ expr = match.group("expr")
+ elif op == "ifdef":
+ expr = "defined('%s')" % match.group("expr")
+ elif op == "ifndef":
+ expr = "not defined('%s')" % match.group("expr")
+ try:
+ if states and states[-1][0] == SKIP:
+ # Were are nested in a SKIP-portion of an if-block.
+ states.append((SKIP, 0, 0))
+ elif _evaluate(expr, defines):
+ states.append((EMIT, 1, 0))
+ else:
+ states.append((SKIP, 0, 0))
+ except KeyError:
+ raise PreprocessError("use of undefined variable in "\
+ "#%s stmt" % op, defines['__FILE__'],
+ defines['__LINE__'], line)
+ elif op == "elif":
+ expr = match.group("expr")
+ try:
+ if states[-1][2]: # already had #else in this if-block
+ raise PreprocessError("illegal #elif after #else in "\
+ "same #if block", defines['__FILE__'],
+ defines['__LINE__'], line)
+ elif states[-1][1]: # if have emitted in this if-block
+ states[-1] = (SKIP, 1, 0)
+ elif states[:-1] and states[-2][0] == SKIP:
+ # Were are nested in a SKIP-portion of an if-block.
+ states[-1] = (SKIP, 0, 0)
+ elif _evaluate(expr, defines):
+ states[-1] = (EMIT, 1, 0)
+ else:
+ states[-1] = (SKIP, 0, 0)
+ except IndexError:
+ raise PreprocessError("#elif stmt without leading #if "\
+ "stmt", defines['__FILE__'],
+ defines['__LINE__'], line)
+ elif op == "else":
+ try:
+ if states[-1][2]: # already had #else in this if-block
+ raise PreprocessError("illegal #else after #else in "\
+ "same #if block", defines['__FILE__'],
+ defines['__LINE__'], line)
+ elif states[-1][1]: # if have emitted in this if-block
+ states[-1] = (SKIP, 1, 1)
+ elif states[:-1] and states[-2][0] == SKIP:
+ # Were are nested in a SKIP-portion of an if-block.
+ states[-1] = (SKIP, 0, 1)
+ else:
+ states[-1] = (EMIT, 1, 1)
+ except IndexError:
+ raise PreprocessError("#else stmt without leading #if "\
+ "stmt", defines['__FILE__'],
+ defines['__LINE__'], line)
+ elif op == "endif":
+ try:
+ states.pop()
+ except IndexError:
+ raise PreprocessError("#endif stmt without leading #if"\
+ "stmt", defines['__FILE__'],
+ defines['__LINE__'], line)
+ elif op == "for":
+
+ tmpstr = match.group("var")
+ thisforvar = tmpstr.split(",")
+ for s in thisforvar:
+ s.strip(" ")
+
+ # Thisforvar is now a _list_ if 1 or more for variables, without whitespace
+
+ # Evaluate the list-of-values just in case it refers to a list variable
+ valuelist = _evaluate(match.group("valuelist"),defines)
+ # If a string, evaluate it again
+ if(isinstance(valuelist,str)):
+ valuelist = eval(valuelist)
+
+ forlevel += 1
+
+ forvar[forlevel] = thisforvar
+ forvaluelist[forlevel] = valuelist
+ forstartline[forlevel] = lineNum + 1
+ foriteration[forlevel] = 0
+
+ if(len(valuelist)>0):
+ # set the variable for this for-loop to the first value in the list for this level
+ nvar=len(thisforvar)
+ for i in range(nvar):
+ if(nvar==1):
+ val=valuelist[0]
+ else:
+ val=valuelist[0][i]
+ defines[thisforvar[i]] = val
+
+ else:
+ # list was empty, so skip this entire section
+ states.append((SKIP, 0, 0))
+
+ elif op == "endfor":
+ foriteration[forlevel] += 1
+ # Should we do one more iteration on this level?
+ iter = foriteration[forlevel]
+ thisforvar = forvar[forlevel]
+ valuelist = forvaluelist[forlevel]
+
+ if(iter<len(valuelist)):
+
+ nvar = len(thisforvar)
+ for i in range(len(thisforvar)):
+ if(nvar==1):
+ val=valuelist[iter]
+ else:
+ val=valuelist[iter][i]
+ defines[thisforvar[i]] = val
+
+ lineNum = forstartline[forlevel]
+ continue
+ else:
+ forlevel -= 1
+ if(len(valuelist)==0):
+ states.pop()
+
+ elif op == "error":
+ if not (states and states[-1][0] == SKIP):
+ error = match.group("error")
+ raise PreprocessError("#error: "+error, defines['__FILE__'],
+ defines['__LINE__'], line)
+ log.debug("states: %r", states)
+ if keepLines:
+ fout.write("\n")
+ else:
+ try:
+ if states[-1][0] == EMIT:
+ log.debug("emit line (%s)" % states[-1][1])
+ # Substitute all defines into line.
+ # XXX Should avoid recursive substitutions. But that
+ # would be a pain right now.
+
+ sline = line
+ if substitute:
+ sline = SubstituteInCode(sline,defines)
+
+ emitted_line_is_blank = (sline.strip()=='')
+ if( not (emitted_line_is_blank and last_emitted_was_blank) and not keepLines):
+ fout.write(sline)
+ last_emitted_was_blank = emitted_line_is_blank
+
+ elif keepLines:
+ log.debug("keep blank line (%s)" % states[-1][1])
+ fout.write("\n")
+ else:
+ log.debug("skip line (%s)" % states[-1][1])
+ except IndexError:
+ raise PreprocessError("superfluous #endif before this line",
+ defines['__FILE__'],
+ defines['__LINE__'])
+ lineNum += 1
+
+ if len(states) > 1:
+ raise PreprocessError("unterminated #if block", defines['__FILE__'],
+ defines['__LINE__'])
+ elif len(states) < 1:
+ raise PreprocessError("superfluous #endif on or before this line",
+ defines['__FILE__'], defines['__LINE__'])
+
+ if fout != outfile:
+ fout.close()
+
+ return defines
+
+
+#---- content-type handling
+
+_gDefaultContentTypes = """
+ # Default file types understood by "gmxpreprocess.py".
+ #
+ # Format is an extension of 'mime.types' file syntax.
+ # - '#' indicates a comment to the end of the line.
+ # - a line is:
+ # <filetype> [<pattern>...]
+ # where,
+ # <filetype>'s are equivalent in spirit to the names used in the Windows
+ # registry in HKCR, but some of those names suck or are inconsistent;
+ # and
+ # <pattern> is a suffix (pattern starts with a '.'), a regular expression
+ # (pattern is enclosed in '/' characters), a full filename (anything
+ # else).
+ #
+ # Notes on case-sensitivity:
+ #
+ # A suffix pattern is case-insensitive on Windows and case-sensitive
+ # elsewhere. A filename pattern is case-sensitive everywhere. A regex
+ # pattern's case-sensitivity is defined by the regex. This means it is by
+ # default case-sensitive, but this can be changed using Python's inline
+ # regex option syntax. E.g.:
+ # Makefile /^(?i)makefile.*$/ # case-INsensitive regex
+
+ Python .py
+ Python .pyw
+ Perl .pl
+ Ruby .rb
+ Tcl .tcl
+ XML .xml
+ XML .kpf
+ XML .xul
+ XML .rdf
+ XML .xslt
+ XML .xsl
+ XML .wxs
+ XML .wxi
+ HTML .htm
+ HTML .html
+ XML .xhtml
+ Makefile /^[Mm]akefile.*$/
+ PHP .php
+ JavaScript .js
+ CSS .css
+ C++ .c # C++ because then we can use //-style comments
+ C++ .cpp
+ C++ .cxx
+ C++ .cc
+ C++ .h
+ C++ .hpp
+ C++ .hxx
+ C++ .hh
+ C++ .gpp # Gromacs pre-preprocessing
+ IDL .idl
+ Text .txt
+ Fortran .f
+ Fortran .f90
+ Shell .sh
+ Shell .csh
+ Shell .ksh
+ Shell .zsh
+ Java .java
+ C# .cs
+ TeX .tex
+
+ # Some Komodo-specific file extensions
+ Python .ksf # Fonts & Colors scheme files
+ Text .kkf # Keybinding schemes files
+"""
+
+class ContentTypesRegistry:
+ """A class that handles determining the filetype of a given path.
+
+ Usage:
+ >>> registry = ContentTypesRegistry()
+ >>> registry.getContentType("foo.py")
+ "Python"
+ """
+
+ def __init__(self, contentTypesPaths=None):
+ self.contentTypesPaths = contentTypesPaths
+ self._load()
+
+ def _load(self):
+ from os.path import dirname, join, exists
+
+ self.suffixMap = {}
+ self.regexMap = {}
+ self.filenameMap = {}
+
+ self._loadContentType(_gDefaultContentTypes)
+ localContentTypesPath = join(dirname(__file__), "content.types")
+ if exists(localContentTypesPath):
+ log.debug("load content types file: `%r'" % localContentTypesPath)
+ self._loadContentType(open(localContentTypesPath, 'r').read())
+ for path in (self.contentTypesPaths or []):
+ log.debug("load content types file: `%r'" % path)
+ self._loadContentType(open(path, 'r').read())
+
+ def _loadContentType(self, content, path=None):
+ """Return the registry for the given content.types file.
+
+ The registry is three mappings:
+ <suffix> -> <content type>
+ <regex> -> <content type>
+ <filename> -> <content type>
+ """
+ for line in content.splitlines(0):
+ words = line.strip().split()
+ for i in range(len(words)):
+ if words[i][0] == '#':
+ del words[i:]
+ break
+ if not words: continue
+ contentType, patterns = words[0], words[1:]
+ if not patterns:
+ if line[-1] == '\n': line = line[:-1]
+ raise PreprocessError("bogus content.types line, there must "\
+ "be one or more patterns: '%s'" % line)
+ for pattern in patterns:
+ if pattern.startswith('.'):
+ if sys.platform.startswith("win"):
+ # Suffix patterns are case-insensitive on Windows.
+ pattern = pattern.lower()
+ self.suffixMap[pattern] = contentType
+ elif pattern.startswith('/') and pattern.endswith('/'):
+ self.regexMap[re.compile(pattern[1:-1])] = contentType
+ else:
+ self.filenameMap[pattern] = contentType
+
+ def getContentType(self, path):
+ """Return a content type for the given path.
+
+ @param path {str} The path of file for which to guess the
+ content type.
+ @returns {str|None} Returns None if could not determine the
+ content type.
+ """
+ basename = os.path.basename(path)
+ contentType = None
+ # Try to determine from the path.
+ if not contentType and self.filenameMap.has_key(basename):
+ contentType = self.filenameMap[basename]
+ log.debug("Content type of '%s' is '%s' (determined from full "\
+ "path).", path, contentType)
+ # Try to determine from the suffix.
+ if not contentType and '.' in basename:
+ suffix = "." + basename.split(".")[-1]
+ if sys.platform.startswith("win"):
+ # Suffix patterns are case-insensitive on Windows.
+ suffix = suffix.lower()
+ if self.suffixMap.has_key(suffix):
+ contentType = self.suffixMap[suffix]
+ log.debug("Content type of '%s' is '%s' (determined from "\
+ "suffix '%s').", path, contentType, suffix)
+ # Try to determine from the registered set of regex patterns.
+ if not contentType:
+ for regex, ctype in self.regexMap.items():
+ if regex.search(basename):
+ contentType = ctype
+ log.debug("Content type of '%s' is '%s' (matches regex '%s')",
+ path, contentType, regex.pattern)
+ break
+ # Try to determine from the file contents.
+ content = open(path, 'rb').read()
+ if content.startswith("<?xml"): # cheap XML sniffing
+ contentType = "XML"
+ return contentType
+
+_gDefaultContentTypesRegistry = None
+def getDefaultContentTypesRegistry():
+ global _gDefaultContentTypesRegistry
+ if _gDefaultContentTypesRegistry is None:
+ _gDefaultContentTypesRegistry = ContentTypesRegistry()
+ return _gDefaultContentTypesRegistry
+
+
+#---- internal support stuff
+#TODO: move other internal stuff down to this section
+
+try:
+ reversed
+except NameError:
+ # 'reversed' added in Python 2.4 (http://www.python.org/doc/2.4/whatsnew/node7.html)
+ def reversed(seq):
+ rseq = list(seq)
+ rseq.reverse()
+ for item in rseq:
+ yield item
+try:
+ sorted
+except NameError:
+ # 'sorted' added in Python 2.4. Note that I'm only implementing enough
+ # of sorted as is used in this module.
+ def sorted(seq, key=None):
+ identity = lambda x: x
+ key_func = (key or identity)
+ sseq = list(seq)
+ sseq.sort(lambda self, other: cmp(key_func(self), key_func(other)))
+ for item in sseq:
+ yield item
+
+
+#---- mainline
+
+def main(argv):
+ try:
+ optlist, args = getopt.getopt(argv[1:], 'hVvo:D:fkI:sc:',
+ ['help', 'version', 'verbose', 'force', 'keep-lines',
+ 'no-substitute', 'content-types-path='])
+ except getopt.GetoptError, msg:
+ sys.stderr.write("gmxpreprocess: error: %s. Your invocation was: %s\n"\
+ % (msg, argv))
+ sys.stderr.write("See 'gmxpreprocess --help'.\n")
+ return 1
+ outfile = sys.stdout
+ defines = {}
+ force = 0
+ keepLines = 0
+ substitute = 1
+ includePath = []
+ contentTypesPaths = []
+ for opt, optarg in optlist:
+ if opt in ('-h', '--help'):
+ sys.stdout.write(__doc__)
+ return 0
+ elif opt in ('-V', '--version'):
+ sys.stdout.write("gmxpreprocess %s\n" % __version__)
+ return 0
+ elif opt in ('-v', '--verbose'):
+ log.setLevel(log.DEBUG)
+ elif opt == '-o':
+ outfile = optarg
+ if opt in ('-f', '--force'):
+ force = 1
+ elif opt == '-D':
+ if optarg.find('=') != -1:
+ var, val = optarg.split('=', 1)
+ try:
+ val = int(val)
+ except ValueError:
+ pass
+ else:
+ var, val = optarg, None
+ defines[var] = val
+ elif opt in ('-k', '--keep-lines'):
+ keepLines = 1
+ elif opt == '-I':
+ includePath.append(optarg)
+ elif opt in ('-s', '--no-substitute'):
+ substitute = 0
+ elif opt in ('-c', '--content-types-path'):
+ contentTypesPaths.append(optarg)
+
+ if len(args) != 1:
+ sys.stderr.write("gmxpreprocess: error: incorrect number of "\
+ "arguments: argv=%r\n" % argv)
+ return 1
+ else:
+ infile = args[0]
+
+ try:
+ contentTypesRegistry = ContentTypesRegistry(contentTypesPaths)
+ gmxpreprocess(infile, outfile, defines, force, keepLines, includePath,
+ substitute, contentTypesRegistry=contentTypesRegistry)
+ except PreprocessError, ex:
+ if log.isDebugEnabled():
+ import traceback
+ traceback.print_exc(file=sys.stderr)
+ else:
+ sys.stderr.write("gmxpreprocess: error: %s\n" % str(ex))
+ return 1
+
+if __name__ == "__main__":
+ __file__ = sys.argv[0]
+ sys.exit( main(sys.argv) )
+
#include "smalloc.h"
#include "copyrite.h"
+
+
+
+
typedef struct {
const char *name;
int flop;
static const t_nrnb_data nbdata[eNRNB] = {
- { "LJ", 33 }, /* nb_kernel010 */
- { "Buckingham", 61 }, /* nb_kernel020 */
- { "VdW(T)", 54 }, /* nb_kernel030 */
- { "Coulomb", 27 }, /* nb_kernel100 */
- { "Coulomb [W3]", 80 }, /* nb_kernel101 */
- { "Coulomb [W3-W3]", 234 }, /* nb_kernel102 */
- { "Coulomb [W4]", 80 }, /* nb_kernel103 */
- { "Coulomb [W4-W4]", 234 }, /* nb_kernel104 */
- { "Coulomb + LJ", 38 }, /* nb_kernel110 */
- { "Coulomb + LJ [W3]", 91 }, /* nb_kernel111 */
- { "Coulomb + LJ [W3-W3]", 245 }, /* nb_kernel112 */
- { "Coulomb + LJ [W4]", 113 }, /* nb_kernel113 */
- { "Coulomb + LJ [W4-W4]", 267 }, /* nb_kernel114 */
- { "Coulomb + Bham ", 64 }, /* nb_kernel120 */
- { "Coulomb + Bham [W3]", 117 }, /* nb_kernel121 */
- { "Coulomb + Bham [W3-W3]", 271 }, /* nb_kernel122 */
- { "Coulomb + Bham [W4]", 141 }, /* nb_kernel123 */
- { "Coulomb + Bham [W4-W4]", 295 }, /* nb_kernel124 */
- { "Coulomb + VdW(T) ", 59 }, /* nb_kernel130 */
- { "Coulomb + VdW(T) [W3]", 112 }, /* nb_kernel131 */
- { "Coulomb + VdW(T) [W3-W3]", 266 }, /* nb_kernel132 */
- { "Coulomb + VdW(T) [W4]", 134 }, /* nb_kernel133 */
- { "Coulomb + VdW(T) [W4-W4]", 288 }, /* nb_kernel134 */
- { "RF Coul", 33 }, /* nb_kernel200 */
- { "RF Coul [W3]", 98 }, /* nb_kernel201 */
- { "RF Coul [W3-W3]", 288 }, /* nb_kernel202 */
- { "RF Coul [W4]", 98 }, /* nb_kernel203 */
- { "RF Coul [W4-W4]", 288 }, /* nb_kernel204 */
- { "RF Coul + LJ", 44 }, /* nb_kernel210 */
- { "RF Coul + LJ [W3]", 109 }, /* nb_kernel211 */
- { "RF Coul + LJ [W3-W3]", 299 }, /* nb_kernel212 */
- { "RF Coul + LJ [W4]", 131 }, /* nb_kernel213 */
- { "RF Coul + LJ [W4-W4]", 321 }, /* nb_kernel214 */
- { "RF Coul + Bham ", 70 }, /* nb_kernel220 */
- { "RF Coul + Bham [W3]", 135 }, /* nb_kernel221 */
- { "RF Coul + Bham [W3-W3]", 325 }, /* nb_kernel222 */
- { "RF Coul + Bham [W4]", 159 }, /* nb_kernel223 */
- { "RF Coul + Bham [W4-W4]", 349 }, /* nb_kernel224 */
- { "RF Coul + VdW(T) ", 65 }, /* nb_kernel230 */
- { "RF Coul + VdW(T) [W3]", 130 }, /* nb_kernel231 */
- { "RF Coul + VdW(T) [W3-W3]", 320 }, /* nb_kernel232 */
- { "RF Coul + VdW(T) [W4]", 152 }, /* nb_kernel233 */
- { "RF Coul + VdW(T) [W4-W4]", 342 }, /* nb_kernel234 */
- { "Coul(T)", 42 }, /* nb_kernel300 */
- { "Coul(T) [W3]", 125 }, /* nb_kernel301 */
- { "Coul(T) [W3-W3]", 369 }, /* nb_kernel302 */
- { "Coul(T) [W4]", 125 }, /* nb_kernel303 */
- { "Coul(T) [W4-W4]", 369 }, /* nb_kernel304 */
- { "Coul(T) + LJ", 55 }, /* nb_kernel310 */
- { "Coul(T) + LJ [W3]", 138 }, /* nb_kernel311 */
- { "Coul(T) + LJ [W3-W3]", 382 }, /* nb_kernel312 */
- { "Coul(T) + LJ [W4]", 158 }, /* nb_kernel313 */
- { "Coul(T) + LJ [W4-W4]", 402 }, /* nb_kernel314 */
- { "Coul(T) + Bham", 81 }, /* nb_kernel320 */
- { "Coul(T) + Bham [W3]", 164 }, /* nb_kernel321 */
- { "Coul(T) + Bham [W3-W3]", 408 }, /* nb_kernel322 */
- { "Coul(T) + Bham [W4]", 186 }, /* nb_kernel323 */
- { "Coul(T) + Bham [W4-W4]", 430 }, /* nb_kernel324 */
- { "Coul(T) + VdW(T)", 68 }, /* nb_kernel330 */
- { "Coul(T) + VdW(T) [W3]", 151 }, /* nb_kernel331 */
- { "Coul(T) + VdW(T) [W3-W3]", 395 }, /* nb_kernel332 */
- { "Coul(T) + VdW(T) [W4]", 179 }, /* nb_kernel333 */
- { "Coul(T) + VdW(T) [W4-W4]", 423 }, /* nb_kernel334 */
- { "Generalized Born Coulomb", 48 }, /* nb_kernel400 */
- { "GB Coulomb + LJ", 61 }, /* nb_kernel410 */
- { "GB Coulomb + VdW(T)", 79 }, /* nb_kernel430 */
- { "LJ NF", 19 }, /* nb_kernel010nf */
- { "Buckingham NF", 48 }, /* nb_kernel020nf */
- { "VdW(T) NF", 33 }, /* nb_kernel030nf */
- { "Coulomb NF", 16 }, /* nb_kernel100nf */
- { "Coulomb [W3] NF", 47 }, /* nb_kernel101nf */
- { "Coulomb [W3-W3] NF", 135 }, /* nb_kernel102nf */
- { "Coulomb [W4] NF", 47 }, /* nb_kernel103nf */
- { "Coulomb [W4-W4] NF", 135 }, /* nb_kernel104nf */
- { "Coulomb + LJ NF", 24 }, /* nb_kernel110nf */
- { "Coulomb + LJ [W3] NF", 55 }, /* nb_kernel111nf */
- { "Coulomb + LJ [W3-W3] NF", 143 }, /* nb_kernel112nf */
- { "Coulomb + LJ [W4] NF", 66 }, /* nb_kernel113nf */
- { "Coulomb + LJ [W4-W4] NF", 154 }, /* nb_kernel114nf */
- { "Coulomb + Bham NF", 51 }, /* nb_kernel120nf */
- { "Coulomb + Bham [W3] NF", 82 }, /* nb_kernel121nf */
- { "Coulomb + Bham [W3-W3] NF", 170 }, /* nb_kernel122nf */
- { "Coulomb + Bham [W4] NF", 95 }, /* nb_kernel123nf */
- { "Coulomb + Bham [W4-W4] NF", 183 }, /* nb_kernel124nf */
- { "Coulomb + VdW(T) NF", 36 }, /* nb_kernel130nf */
- { "Coulomb + VdW(T) [W3] NF", 67 }, /* nb_kernel131nf */
- { "Coulomb + VdW(T) [W3-W3] NF", 155 }, /* nb_kernel132nf */
- { "Coulomb + VdW(T) [W4] NF", 80 }, /* nb_kernel133nf */
- { "Coulomb + VdW(T) [W4-W4] NF", 168 }, /* nb_kernel134nf */
- { "RF Coul NF", 19 }, /* nb_kernel200nf */
- { "RF Coul [W3] NF", 56 }, /* nb_kernel201nf */
- { "RF Coul [W3-W3] NF", 162 }, /* nb_kernel202nf */
- { "RF Coul [W4] NF", 56 }, /* nb_kernel203nf */
- { "RF Coul [W4-W4] NF", 162 }, /* nb_kernel204nf */
- { "RF Coul + LJ NF", 27 }, /* nb_kernel210nf */
- { "RF Coul + LJ [W3] NF", 64 }, /* nb_kernel211nf */
- { "RF Coul + LJ [W3-W3] NF", 170 }, /* nb_kernel212nf */
- { "RF Coul + LJ [W4] NF", 75 }, /* nb_kernel213nf */
- { "RF Coul + LJ [W4-W4] NF", 181 }, /* nb_kernel214nf */
- { "RF Coul + Bham NF", 54 }, /* nb_kernel220nf */
- { "RF Coul + Bham [W3] NF", 91 }, /* nb_kernel221nf */
- { "RF Coul + Bham [W3-W3] NF", 197 }, /* nb_kernel222nf */
- { "RF Coul + Bham [W4] NF", 104 }, /* nb_kernel223nf */
- { "RF Coul + Bham [W4-W4] NF", 210 }, /* nb_kernel224nf */
- { "RF Coul + VdW(T) NF", 39 }, /* nb_kernel230nf */
- { "RF Coul + VdW(T) [W3] NF", 76 }, /* nb_kernel231nf */
- { "RF Coul + VdW(T) [W3-W3] NF", 182 }, /* nb_kernel232nf */
- { "RF Coul + VdW(T) [W4] NF", 89 }, /* nb_kernel233nf */
- { "RF Coul + VdW(T) [W4-W4] NF", 195 }, /* nb_kernel234nf */
- { "Coul(T) NF", 26 }, /* nb_kernel300nf */
- { "Coul(T) [W3] NF", 77 }, /* nb_kernel301nf */
- { "Coul(T) [W3-W3] NF", 225 }, /* nb_kernel302nf */
- { "Coul(T) [W4] NF", 77 }, /* nb_kernel303nf */
- { "Coul(T) [W4-W4] NF", 225 }, /* nb_kernel304nf */
- { "Coul(T) + LJ NF", 34 }, /* nb_kernel310nf */
- { "Coul(T) + LJ [W3] NF", 85 }, /* nb_kernel311nf */
- { "Coul(T) + LJ [W3-W3] NF", 233 }, /* nb_kernel312nf */
- { "Coul(T) + LJ [W4] NF", 96 }, /* nb_kernel313nf */
- { "Coul(T) + LJ [W4-W4] NF", 244 }, /* nb_kernel314nf */
- { "Coul(T) + Bham NF", 61 }, /* nb_kernel320nf */
- { "Coul(T) + Bham [W3] NF", 112 }, /* nb_kernel321nf */
- { "Coul(T) + Bham [W3-W3] NF", 260 }, /* nb_kernel322nf */
- { "Coul(T) + Bham [W4] NF", 125 }, /* nb_kernel323nf */
- { "Coul(T) + Bham [W4-W4] NF", 273 }, /* nb_kernel324nf */
- { "Coul(T) + VdW(T) NF", 42 }, /* nb_kernel330nf */
- { "Coul(T) + VdW(T) [W3] NF", 93 }, /* nb_kernel331nf */
- { "Coul(T) + VdW(T) [W3-W3] NF", 241 }, /* nb_kernel332nf */
- { "Coul(T) + VdW(T) [W4] NF", 110 }, /* nb_kernel333nf */
- { "Coul(T) + VdW(T) [W4-W4] NF", 258 }, /* nb_kernel334nf */
- { "Generalized Born Coulomb NF", 29 }, /* nb_kernel400nf */
- { "GB Coulomb + LJ NF", 37 }, /* nb_kernel410nf */
- { "GB Coulomb + VdW(T) NF", 49 }, /* nb_kernel430nf */
- { "Free energy innerloop", 150 }, /* free energy, estimate */
- { "All-vs-All, Coul + LJ", 38 },
- { "All-vs-All, GB + LJ", 61 },
- { "Outer nonbonded loop", 10 },
+ /* These are re-used for different NB kernels, since there are so many.
+ * The actual number of flops is set dynamically.
+ */
+ { "NB VdW [V&F]", 1 },
+ { "NB VdW [F]", 1 },
+ { "NB Elec. [V&F]", 1 },
+ { "NB Elec. [F]", 1 },
+ { "NB Elec. [W3,V&F]", 1 },
+ { "NB Elec. [W3,F]", 1 },
+ { "NB Elec. [W3-W3,V&F]", 1 },
+ { "NB Elec. [W3-W3,F]", 1 },
+ { "NB Elec. [W4,V&F]", 1 },
+ { "NB Elec. [W4,F]", 1 },
+ { "NB Elec. [W4-W4,V&F]", 1 },
+ { "NB Elec. [W4-W4,F]", 1 },
+ { "NB VdW & Elec. [V&F]", 1 },
+ { "NB VdW & Elec. [F]", 1 },
+ { "NB VdW & Elec. [W3,V&F]", 1 },
+ { "NB VdW & Elec. [W3,F]", 1 },
+ { "NB VdW & Elec. [W3-W3,V&F]", 1 },
+ { "NB VdW & Elec. [W3-W3,F]", 1 },
+ { "NB VdW & Elec. [W4,V&F]", 1 },
+ { "NB VdW & Elec. [W4,F]", 1 },
+ { "NB VdW & Elec. [W4-W4,V&F]", 1 },
+ { "NB VdW & Elec. [W4-W4,F]", 1 },
+
+ { "NB Generic kernel", 1 },
+ { "NB Free energy kernel", 1 },
+ { "NB All-vs-all", 1 },
+ { "NB All-vs-all, GB", 1 },
+
{ "Pair Search distance check", 9 }, /* nbnxn pair dist. check */
/* nbnxn kernel flops are based on inner-loops without exclusion checks.
* Plain Coulomb runs through the RF kernels, except with CUDA.
* - GPU always does exclusions, which requires 2-4 flops, but as invsqrt
* is always counted as 6 flops, this roughly compensates.
*/
- { "LJ + Coulomb RF (F)", 38 }, /* nbnxn kernel LJ+RF, no ener */
- { "LJ + Coulomb RF (F+E)", 54 },
- { "LJ + Coulomb tabulated (F)", 41 }, /* nbnxn kernel LJ+tab, no en */
- { "LJ + Coulomb tabulated (F+E)", 59 },
- { "LJ (F)", 33 }, /* nbnxn kernel LJ, no ener */
- { "LJ (F+E)", 43 },
- { "Coulomb RF (F)", 31 }, /* nbnxn kernel RF, no ener */
- { "Coulomb RF (F+E)", 36 },
- { "Coulomb tabulated (F)", 34 }, /* nbnxn kernel tab, no ener */
- { "Coulomb tabulated (F+E)", 41 },
+ { "NxN RF Elec. + VdW [F]", 38 }, /* nbnxn kernel LJ+RF, no ener */
+ { "NxN RF Elec. + VdW [V&F]", 54 },
+ { "NxN CSTab Elec. + VdW [F]", 41 }, /* nbnxn kernel LJ+tab, no en */
+ { "NxN CSTab Elec. + VdW [V&F]", 59 },
+ { "NxN VdW [F]", 33 }, /* nbnxn kernel LJ, no ener */
+ { "NxN VdW [V&F]", 43 },
+ { "NxN RF Electrostatics [F]", 31 }, /* nbnxn kernel RF, no ener */
+ { "NxN RF Electrostatics [V&F]", 36 },
+ { "NxN CSTab Elec. [F]", 34 }, /* nbnxn kernel tab, no ener */
+ { "NxN CSTab Elec. [V&F]", 41 },
{ "1,4 nonbonded interactions", 90 },
{ "Born radii (Still)", 47 },
{ "Born radii (HCT/OBC)", 183 },
{ "Born force chain rule", 15 },
- { "All-vs-All Still radii", 47 },
- { "All-vs-All HCT/OBC radii", 183 },
- { "All-vs-All Born chain rule", 15 },
+ { "All-vs-All Still radii", 1 },
+ { "All-vs-All HCT/OBC radii", 1 },
+ { "All-vs-All Born chain rule", 1 },
{ "Calc Weights", 36 },
{ "Spread Q", 6 },
{ "Spread Q Bspline", 2 },
const char *myline = "-----------------------------------------------------------------------------";
*nbfs = 0.0;
- for(i=0; (i<eNR_NBKERNEL_NR); i++) {
+ for(i=0; (i<eNR_NBKERNEL_ALLVSALLGB); i++) {
if (strstr(nbdata[i].name,"W3-W3") != NULL)
*nbfs += 9e-6*nrnb->n[i];
else if (strstr(nbdata[i].name,"W3") != NULL)
fprintf(out,"\n\tM E G A - F L O P S A C C O U N T I N G\n\n");
}
- if (out) {
- fprintf(out," RF=Reaction-Field FE=Free Energy SCFE=Soft-Core/Free Energy\n");
- fprintf(out," T=Tabulated W3=SPC/TIP3p W4=TIP4p (single or pairs)\n");
- fprintf(out," NF=No Forces\n\n");
-
- fprintf(out," %-32s %16s %15s %7s\n",
- "Computing:","M-Number","M-Flops","% Flops");
- fprintf(out,"%s\n",myline);
+ if (out)
+ {
+ fprintf(out," NB=Group-cutoff nonbonded kernels NxN=N-by-N tile Verlet kernels\n");
+ fprintf(out," RF=Reaction-Field VdW=Van der Waals CSTab=Cubic-spline table\n");
+ fprintf(out," W3=SPC/TIP3p W4=TIP4p (single or pairs)\n");
+ fprintf(out," V&F=Potential and force V=Potential only F=Force only\n\n");
+
+ fprintf(out," %-32s %16s %15s %7s\n",
+ "Computing:","M-Number","M-Flops","% Flops");
+ fprintf(out,"%s\n",myline);
}
*mflop=0.0;
tfrac=0.0;
static const int force_index[]={
eNR_BONDS, eNR_ANGLES, eNR_PROPER, eNR_IMPROPER,
eNR_RB, eNR_DISRES, eNR_ORIRES, eNR_POSRES,
- eNR_NS, eNR_NBKERNEL_OUTER
+ eNR_NS,
};
#define NFORCE_INDEX asize(force_index)
for(i=0; (i<cr->nnodes); i++) {
add_nrnb(av,av,&(nrnb[i]));
/* Cost due to forces */
- for(j=0; (j<eNR_NBKERNEL_NR); j++)
+ for(j=0; (j<eNR_NBKERNEL_ALLVSALLGB); j++)
ftot[i]+=nrnb[i].n[j]*cost_nrnb(j);
for(j=0; (j<NFORCE_INDEX); j++)
ftot[i]+=nrnb[i].n[force_index[j]]*cost_nrnb(force_index[j]);
fprintf (out,"%c\n",COMMENTSIGN);
}
+
int gmx_strcasecmp_min(const char *str1, const char *str2)
{
- char ch1,ch2;
-
- do
+ char ch1,ch2;
+
+ do
{
- do
- ch1=toupper(*(str1++));
- while ((ch1=='-') || (ch1=='_'));
- do
- ch2=toupper(*(str2++));
- while ((ch2=='-') || (ch2=='_'));
- if (ch1!=ch2) return (ch1-ch2);
+ do
+ {
+ ch1=toupper(*(str1++));
+ }
+ while ((ch1=='-') || (ch1=='_'));
+ do
+ {
+ ch2=toupper(*(str2++));
+ }
+ while ((ch2=='-') || (ch2=='_'));
+
+ if (ch1!=ch2) return (ch1-ch2);
}
- while (ch1);
- return 0;
+ while (ch1);
+ return 0;
}
int gmx_strncasecmp_min(const char *str1, const char *str2, int n)
{
- char ch1,ch2;
- char *stri1, *stri2;
+ char ch1,ch2;
+ char *stri1, *stri2;
- stri1=(char *)str1;
- stri2=(char *)str2;
- do
+ stri1=(char *)str1;
+ stri2=(char *)str2;
+ do
{
- do
- ch1=toupper(*(str1++));
- while ((ch1=='-') || (ch1=='_'));
- do
- ch2=toupper(*(str2++));
- while ((ch2=='-') || (ch2=='_'));
- if (ch1!=ch2) return (ch1-ch2);
+ do
+ {
+ ch1=toupper(*(str1++));
+ }
+ while ((ch1=='-') || (ch1=='_'));
+ do
+ {
+ ch2=toupper(*(str2++));
+ }
+ while ((ch2=='-') || (ch2=='_'));
+
+ if (ch1!=ch2) return (ch1-ch2);
}
- while (ch1 && (str1-stri1<n) && (str2-stri2<n));
+ while (ch1 && (str1-stri1<n) && (str2-stri2<n));
return 0;
}
return dest;
}
+/* Magic hash init number for Dan J. Bernsteins algorithm.
+ * Do NOT use any other value unless you really know what you are doing.
+ */
+const unsigned int
+gmx_string_hash_init = 5381;
+
+
+unsigned int
+gmx_string_hash_func(const char *s, unsigned int hash_init)
+{
+ int c;
+
+ while ((c = toupper(*s++)) != '\0')
+ {
+ if(isalnum(c)) hash_init = ((hash_init << 5) + hash_init) ^ c; /* (hash * 33) xor c */
+ }
+ return hash_init;
+}
+
/*!
* \param[in] pattern Pattern to match against.
* \param[in] str String to match.
static const char *tpx_tag = TPX_TAG_RELEASE;
/* This number should be increased whenever the file format changes! */
-static const int tpx_version = 81;
+static const int tpx_version = 82;
/* This number should only be increased when you edit the TOPOLOGY section
* or the HEADER of the tpx format.
if (file_version >= 67) {
gmx_fio_do_real(fio,ir->rlistlong);
}
- gmx_fio_do_int(fio,ir->coulombtype);
+ if(file_version >= 82)
+ {
+ gmx_fio_do_int(fio,ir->nstcalclr);
+ }
+ else
+ {
+ /* Calculate at NS steps */
+ ir->nstcalclr = ir->nstlist;
+ }
+ gmx_fio_do_int(fio,ir->coulombtype);
if (file_version < 32 && ir->coulombtype == eelRF)
ir->coulombtype = eelRF_NEC;
if (file_version >= 81)
PR("verlet-buffer-drift",ir->verletbuf_drift);
PR("rlist",ir->rlist);
PR("rlistlong",ir->rlistlong);
+ PR("nstcalclr",ir->nstcalclr);
PR("rtpi",ir->rtpi);
PS("coulombtype",EELTYPE(ir->coulombtype));
PS("coulomb-modifier",INTMODIFIER(ir->coulomb_modifier));
else
sig = sqrt(sigma[n]*sigma[m]);
sig6 = pow(sig,6.0);
- C6 (nbfp,atnr,n,m) = 4*eps*sig6;
- C12(nbfp,atnr,n,m) = 4*eps*sig6*sig6;
+ /* nbfp now includes the 6.0/12.0 derivative prefactors */
+ C6 (nbfp,atnr,n,m) = 4*eps*sig6/6.0;
+ C12(nbfp,atnr,n,m) = 4*eps*sig6*sig6/12.0;
}
}
sfree(sigma);
ati = tclj->at_i;
atj = tclj->at_j;
if (atj == -1)
- atj = ati;
- tclj->c6 = C6(fr->nbfp,fr->ntype,ati,atj);
- tclj->c12 = C12(fr->nbfp,fr->ntype,ati,atj);
+ {
+ atj = ati;
+ }
+ /* nbfp now includes the 6.0/12.0 derivative prefactors */
+ tclj->c6 = C6(fr->nbfp,fr->ntype,ati,atj)/6.0;
+ tclj->c12 = C12(fr->nbfp,fr->ntype,ati,atj)/12.0;
}
}
else {
ati = tcbu->at_i;
atj = tcbu->at_j;
if (atj == -1)
- atj = ati;
+ {
+ atj = ati;
+ }
+ /* nbfp now includes the 6.0 derivative prefactors */
tcbu->a = BHAMA(fr->nbfp,fr->ntype,ati,atj);
tcbu->b = BHAMB(fr->nbfp,fr->ntype,ati,atj);
- tcbu->c = BHAMC(fr->nbfp,fr->ntype,ati,atj);
+ tcbu->c = BHAMC(fr->nbfp,fr->ntype,ati,atj)/6.0;
if (debug)
fprintf(debug,"buck (type=%d) = %e, %e, %e\n",
tcbu->at_i,tcbu->a,tcbu->b,tcbu->c);
atj = tclj->at_j;
if (atj == -1)
atj = ati;
- tclj->c6 = C6(fr->nbfp,fr->ntype,ati,atj);
- tclj->c12 = C12(fr->nbfp,fr->ntype,ati,atj);
+ /* nbfp now includes the 6.0/12.0 derivative prefactors */
+ tclj->c6 = C6(fr->nbfp,fr->ntype,ati,atj)/6.0;
+ tclj->c12 = C12(fr->nbfp,fr->ntype,ati,atj)/12.0;
}
for(i=0; (i<tcr->nBU); i++) {
atj = tcbu->at_j;
if (atj == -1)
atj = ati;
+ /* nbfp now includes the 6.0 derivative prefactor */
tcbu->a = BHAMA(fr->nbfp,fr->ntype,ati,atj);
tcbu->b = BHAMB(fr->nbfp,fr->ntype,ati,atj);
- tcbu->c = BHAMC(fr->nbfp,fr->ntype,ati,atj);
+ tcbu->c = BHAMC(fr->nbfp,fr->ntype,ati,atj)/6.0;
}
for(i=0; (i<tcr->nQ); i++) {
gmx_bool bAppend;
gmx_bool bResetCountersHalfMaxH=FALSE;
gmx_bool bVV,bIterations,bFirstIterate,bTemp,bPres,bTrotter;
+ gmx_bool bUpdateDoLR;
real mu_aver=0,dvdl;
int a0,a1,gnx=0,ii;
atom_id *grpindex=NULL;
if(MASTER(cr))
{
- fprintf(stderr,
- "\n* WARNING * WARNING * WARNING * WARNING * WARNING * WARNING *\n"
- "We have just committed the new CPU detection code in this branch,\n"
- "and will commit new SSE/AVX kernels in a few days. However, this\n"
- "means that currently only the NxN kernels are accelerated!\n"
- "In the mean time, you might want to avoid production runs in 4.6.\n\n");
+ gmx_warning("New C kernels (and force-only) kernels are now enabled,\n"
+ "but it will be another couple of days for SSE/AVX kernels.\n\n");
}
#ifdef GMX_FAHCORE
/* PME tuning is only supported with GPUs or PME nodes and not with rerun */
if ((Flags & MD_TUNEPME) &&
EEL_PME(fr->eeltype) &&
- fr->cutoff_scheme == ecutsVERLET &&
- (fr->nbv->bUseGPU || !(cr->duty & DUTY_PME)) &&
+ ( (fr->cutoff_scheme == ecutsVERLET && fr->nbv->bUseGPU) || !(cr->duty & DUTY_PME)) &&
!bRerunMD)
{
pme_loadbal_init(&pme_loadbal,ir,state->box,fr->ic,fr->pmedata);
force_flags = (GMX_FORCE_STATECHANGED |
((DYNAMIC_BOX(*ir) || bRerunMD) ? GMX_FORCE_DYNAMICBOX : 0) |
GMX_FORCE_ALLFORCES |
- (bNStList ? GMX_FORCE_DOLR : 0) |
GMX_FORCE_SEPLRF |
(bCalcVir ? GMX_FORCE_VIRIAL : 0) |
(bCalcEner ? GMX_FORCE_ENERGY : 0) |
(bDoFEP ? GMX_FORCE_DHDL : 0)
);
+
+ if(fr->bTwinRange)
+ {
+ if(do_per_step(step,ir->nstcalclr))
+ {
+ force_flags |= GMX_FORCE_DO_LR;
+ }
+ }
if (shellfc)
{
trotter_update(ir,step,ekind,enerd,state,total_vir,mdatoms,&MassQ,trotter_seq,ettTSEQ1);
}
+ /* If we are using twin-range interactions where the long-range component
+ * is only evaluated every nstcalclr>1 steps, we should do a special update
+ * step to combine the long-range forces on these steps.
+ * For nstcalclr=1 this is not done, since the forces would have been added
+ * directly to the short-range forces already.
+ */
+ bUpdateDoLR = (fr->bTwinRange && do_per_step(step,ir->nstcalclr));
+
update_coords(fplog,step,ir,mdatoms,state,fr->bMolPBC,
- f,fr->bTwinRange && bNStList,fr->f_twin,fcd,
+ f,bUpdateDoLR,fr->f_twin,fcd,
ekind,M,wcycle,upd,bInitStep,etrtVELOCITY1,
cr,nrnb,constr,&top->idef);
if (bVV)
{
+ bUpdateDoLR = (fr->bTwinRange && do_per_step(step,ir->nstcalclr));
+
/* velocity half-step update */
update_coords(fplog,step,ir,mdatoms,state,fr->bMolPBC,f,
- fr->bTwinRange && bNStList,fr->f_twin,fcd,
+ bUpdateDoLR,fr->f_twin,fcd,
ekind,M,wcycle,upd,FALSE,etrtVELOCITY2,
cr,nrnb,constr,&top->idef);
}
{
copy_rvecn(state->x,cbuf,0,state->natoms);
}
-
+ bUpdateDoLR = (fr->bTwinRange && do_per_step(step,ir->nstcalclr));
+
update_coords(fplog,step,ir,mdatoms,state,fr->bMolPBC,f,
- fr->bTwinRange && bNStList,fr->f_twin,fcd,
+ bUpdateDoLR,fr->f_twin,fcd,
ekind,M,wcycle,upd,bInitStep,etrtPOSITION,cr,nrnb,constr,&top->idef);
wallcycle_stop(wcycle,ewcUPDATE);
/* now we know the scaling, we can compute the positions again again */
copy_rvecn(cbuf,state->x,0,state->natoms);
+ bUpdateDoLR = (fr->bTwinRange && do_per_step(step,ir->nstcalclr));
+
update_coords(fplog,step,ir,mdatoms,state,fr->bMolPBC,f,
- fr->bTwinRange && bNStList,fr->f_twin,fcd,
+ bUpdateDoLR,fr->f_twin,fcd,
ekind,M,wcycle,upd,bInitStep,etrtPOSITION,cr,nrnb,constr,&top->idef);
wallcycle_stop(wcycle,ewcUPDATE);
fr->ic,fr->nbv,&fr->pmedata,
step);
+ /* Update constants in forcerec/inputrec to keep them in sync with fr->ic */
fr->ewaldcoeff = fr->ic->ewaldcoeff;
+ fr->rlist = fr->ic->rlist;
+ fr->rlistlong = fr->ic->rlistlong;
+ fr->rcoulomb = fr->ic->rcoulomb;
+ fr->rvdw = fr->ic->rvdw;
}
-
cycles_pmes = 0;
}
}
-
+
if (step_rel == wcycle_get_reset_counters(wcycle) ||
gs.set[eglsRESETCOUNTERS] != 0)
{
for (i = 0; i < natoms; i++)
{
/* i-i */
- c12 = C12(nbfp, natoms, i, i);
- c6 = C6(nbfp, natoms, i, i);
+ /* nbfp now includes the 6.0/12.0 prefactors to save flops in kernels */
+ c12 = C12(nbfp, natoms, i, i)/12.0;
+ c6 = C6(nbfp, natoms, i, i)/6.0;
convert_c_12_6(c12, c6, &sigma_ii, &eps_ii);
for (j = 0; j < i; j++)
{
/* i-j */
- c12 = C12(nbfp, natoms, i, j);
- c6 = C6(nbfp, natoms, i, j);
+ c12 = C12(nbfp, natoms, i, j)/12.0;
+ c6 = C6(nbfp, natoms, i, j)/6.0;
convert_c_12_6(c12, c6, &sigma_ij, &eps_ij);
/* j-i */
- c12 = C12(nbfp, natoms, j, i);
- c6 = C6(nbfp, natoms, j, i);
+ c12 = C12(nbfp, natoms, j, i)/12.0;
+ c6 = C6(nbfp, natoms, j, i)/6.0;
convert_c_12_6(c12, c6, &sigma_ji, &eps_ji);
/* j-j */
- c12 = C12(nbfp, natoms, j, j);
- c6 = C6(nbfp, natoms, j, j);
+ c12 = C12(nbfp, natoms, j, j)/12.0;
+ c6 = C6(nbfp, natoms, j, j)/6.0;
convert_c_12_6(c12, c6, &sigma_jj, &eps_jj);
/* OpenMM hardcoded combination rules */
sigma_comb = COMBRULE_SIGMA(sigma_ii, sigma_jj);
for (int i = 0; i < numAtoms; ++i)
{
- double c12 = nbfp[types[i]*2*ntypes+types[i]*2+1];
- double c6 = nbfp[types[i]*2*ntypes+types[i]*2];
+ /* nbfp now includes the 6.0/12.0 derivative prefactors to save flops in kernels*/
+ double c12 = nbfp[types[i]*2*ntypes+types[i]*2+1]/12.0;
+ double c6 = nbfp[types[i]*2*ntypes+types[i]*2]/6.0;
double sigma=0.0, epsilon=0.0;
convert_c_12_6(c12, c6, &sigma, &epsilon);
nonbondedForce->addParticle(charges[i], sigma, epsilon);
/* Parameters and setting for one PP-PME setup */
typedef struct {
- real rcut; /* Coulomb cut-off */
+ real rcut_coulomb; /* Coulomb cut-off */
real rlist; /* pair-list cut-off */
+ real rlistlong; /* LR pair-list cut-off */
+ int nstcalclr; /* frequency of evaluating long-range forces for group scheme */
real spacing; /* (largest) PME grid spacing */
ivec grid; /* the PME grid dimensions */
real grid_efficiency; /* ineffiency factor for non-uniform grids <= 1 */
int nstage; /* the current maximum number of stages */
real cut_spacing; /* the minimum cutoff / PME grid spacing ratio */
- real rbuf; /* the pairlist buffer size */
+ real rcut_vdw; /* Vdw cutoff (does not change) */
+ real rcut_coulomb_start; /* Initial electrostatics cutoff */
+ int nstcalclr_start; /* Initial electrostatics cutoff */
+ real rbuf_coulomb; /* the pairlist buffer size */
+ real rbuf_vdw; /* the pairlist buffer size */
matrix box_start; /* the initial simulation box */
int n; /* the count of setup as well as the allocation size */
pme_setup_t *setup; /* the PME+cutoff setups */
int start; /* start of setup range to consider in stage>0 */
int end; /* end of setup range to consider in stage>0 */
int elimited; /* was the balancing limited, uses enum above */
+ int cutoff_scheme; /* Verlet or group cut-offs */
int stage; /* the current stage */
};
/* Any number of stages >= 2 is supported */
pme_lb->nstage = 2;
- pme_lb->rbuf = ic->rlist - ic->rcoulomb;
+ pme_lb->cutoff_scheme = ir->cutoff_scheme;
+
+ if(pme_lb->cutoff_scheme == ecutsVERLET)
+ {
+ pme_lb->rbuf_coulomb = ic->rlist - ic->rcoulomb;
+ pme_lb->rbuf_vdw = pme_lb->rbuf_coulomb;
+ }
+ else
+ {
+ if(ic->rcoulomb > ic->rlist)
+ {
+ pme_lb->rbuf_coulomb = ic->rlistlong - ic->rcoulomb;
+ }
+ else
+ {
+ pme_lb->rbuf_coulomb = ic->rlist - ic->rcoulomb;
+ }
+ if(ic->rvdw > ic->rlist)
+ {
+ pme_lb->rbuf_vdw = ic->rlistlong - ic->rvdw;
+ }
+ else
+ {
+ pme_lb->rbuf_vdw = ic->rlist - ic->rvdw;
+ }
+ }
copy_mat(box,pme_lb->box_start);
if (ir->ePBC==epbcXY && ir->nwall==2)
pme_lb->n = 1;
snew(pme_lb->setup,pme_lb->n);
+ pme_lb->rcut_vdw = ic->rvdw;
+ pme_lb->rcut_coulomb_start = ir->rcoulomb;
+ pme_lb->nstcalclr_start = ir->nstcalclr;
+
pme_lb->cur = 0;
- pme_lb->setup[0].rcut = ic->rcoulomb;
- pme_lb->setup[0].rlist = ic->rlist;
- pme_lb->setup[0].grid[XX] = ir->nkx;
- pme_lb->setup[0].grid[YY] = ir->nky;
- pme_lb->setup[0].grid[ZZ] = ir->nkz;
- pme_lb->setup[0].ewaldcoeff = ic->ewaldcoeff;
+ pme_lb->setup[0].rcut_coulomb = ic->rcoulomb;
+ pme_lb->setup[0].rlist = ic->rlist;
+ pme_lb->setup[0].rlistlong = ic->rlistlong;
+ pme_lb->setup[0].nstcalclr = ir->nstcalclr;
+ pme_lb->setup[0].grid[XX] = ir->nkx;
+ pme_lb->setup[0].grid[YY] = ir->nky;
+ pme_lb->setup[0].grid[ZZ] = ir->nkz;
+ pme_lb->setup[0].ewaldcoeff = ic->ewaldcoeff;
pme_lb->setup[0].pmedata = pmedata;
{
pme_setup_t *set;
real fac,sp;
+ real tmpr_coulomb,tmpr_vdw;
int d;
/* Try to add a new setup with next larger cut-off to the list */
}
while (sp <= 1.001*pme_lb->setup[pme_lb->cur].spacing);
- set->rcut = pme_lb->cut_spacing*sp;
- set->rlist = set->rcut + pme_lb->rbuf;
- set->spacing = sp;
+ set->rcut_coulomb = pme_lb->cut_spacing*sp;
+
+ if(pme_lb->cutoff_scheme == ecutsVERLET)
+ {
+ set->rlist = set->rcut_coulomb + pme_lb->rbuf_coulomb;
+ /* We dont use LR lists with Verlet, but this avoids if-statements in further checks */
+ set->rlistlong = set->rlist;
+ }
+ else
+ {
+ tmpr_coulomb = set->rcut_coulomb + pme_lb->rbuf_coulomb;
+ tmpr_vdw = pme_lb->rcut_vdw + pme_lb->rbuf_vdw;
+ set->rlist = min(tmpr_coulomb,tmpr_vdw);
+ set->rlistlong = max(tmpr_coulomb,tmpr_vdw);
+
+ /* Set the long-range update frequency */
+ if(set->rlist == set->rlistlong)
+ {
+ /* No long-range interactions if the short-/long-range cutoffs are identical */
+ set->nstcalclr = 0;
+ }
+ else if(pme_lb->nstcalclr_start==0 || pme_lb->nstcalclr_start==1)
+ {
+ /* We were not doing long-range before, but now we are since rlist!=rlistlong */
+ set->nstcalclr = 1;
+ }
+ else
+ {
+ /* We were already doing long-range interactions from the start */
+ if(pme_lb->rcut_vdw > pme_lb->rcut_coulomb_start)
+ {
+ /* We were originally doing long-range VdW-only interactions.
+ * If rvdw is still longer than rcoulomb we keep the original nstcalclr,
+ * but if the coulomb cutoff has become longer we should update the long-range
+ * part every step.
+ */
+ set->nstcalclr = (tmpr_vdw > tmpr_coulomb) ? pme_lb->nstcalclr_start : 1;
+ }
+ else
+ {
+ /* We were not doing any long-range interaction from the start,
+ * since it is not possible to do twin-range coulomb for the PME interaction.
+ */
+ set->nstcalclr = 1;
+ }
+ }
+ }
+
+ set->spacing = sp;
/* The grid efficiency is the size wrt a grid with uniform x/y/z spacing */
set->grid_efficiency = 1;
for(d=0; d<DIM; d++)
}
/* The Ewald coefficient is inversly proportional to the cut-off */
set->ewaldcoeff =
- pme_lb->setup[0].ewaldcoeff*pme_lb->setup[0].rcut/set->rcut;
+ pme_lb->setup[0].ewaldcoeff*pme_lb->setup[0].rcut_coulomb/set->rcut_coulomb;
set->count = 0;
set->cycles = 0;
if (debug)
{
- fprintf(debug,"PME loadbal: grid %d %d %d, cutoff %f\n",
- set->grid[XX],set->grid[YY],set->grid[ZZ],set->rcut);
+ fprintf(debug,"PME loadbal: grid %d %d %d, coulomb cutoff %f\n",
+ set->grid[XX],set->grid[YY],set->grid[ZZ],set->rcut_coulomb);
}
-
return TRUE;
}
double cycles)
{
char buf[STRLEN],buft[STRLEN];
-
+
if (cycles >= 0)
{
sprintf(buft,": %.1f M-cycles",cycles*1e-6);
{
buft[0] = '\0';
}
- sprintf(buf,"%-11s%10s pme grid %d %d %d, cutoff %.3f%s",
+ sprintf(buf,"%-11s%10s pme grid %d %d %d, coulomb cutoff %.3f%s",
pre,
- desc,set->grid[XX],set->grid[YY],set->grid[ZZ],set->rcut,
+ desc,set->grid[XX],set->grid[YY],set->grid[ZZ],set->rcut_coulomb,
buft);
if (fp_err != NULL)
{
{
char buf[STRLEN],sbuf[22];
- sprintf(buf,"step %4s: the %s limited the PME load balancing to a cut-off of %.3f",
+ sprintf(buf,"step %4s: the %s limited the PME load balancing to a coulomb cut-off of %.3f",
gmx_step_str(step,sbuf),
pmelblim_str[pme_lb->elimited],
- pme_lb->setup[pme_loadbal_end(pme_lb)-1].rcut);
+ pme_lb->setup[pme_loadbal_end(pme_lb)-1].rcut_coulomb);
if (fp_err != NULL)
{
fprintf(fp_err,"\r%s\n",buf);
pme_setup_t *set;
double cycles_fast;
char buf[STRLEN],sbuf[22];
+ real rtab;
if (pme_lb->stage == pme_lb->nstage)
{
}
set = &pme_lb->setup[pme_lb->cur];
-
set->count++;
+
+ rtab = ir->rlistlong + ir->tabext;
+
if (set->count % 2 == 1)
{
/* Skip the first cycle, because the first step after a switch
/* Find the next setup */
OK = pme_loadbal_increase_cutoff(pme_lb,ir->pme_order);
}
-
+
if (OK && ir->ePBC != epbcNONE)
{
- OK = (sqr(pme_lb->setup[pme_lb->cur+1].rlist)
+ OK = (sqr(pme_lb->setup[pme_lb->cur+1].rlistlong)
<= max_cutoff2(ir->ePBC,state->box));
if (!OK)
{
if (DOMAINDECOMP(cr))
{
OK = change_dd_cutoff(cr,state,ir,
- pme_lb->setup[pme_lb->cur].rlist);
+ pme_lb->setup[pme_lb->cur].rlistlong);
if (!OK)
{
/* Failed: do not use this setup */
if (DOMAINDECOMP(cr) && pme_lb->stage > 0)
{
- OK = change_dd_cutoff(cr,state,ir,pme_lb->setup[pme_lb->cur].rlist);
+ OK = change_dd_cutoff(cr,state,ir,pme_lb->setup[pme_lb->cur].rlistlong);
if (!OK)
{
/* Failsafe solution */
set = &pme_lb->setup[pme_lb->cur];
- ic->rcoulomb = set->rcut;
+ ic->rcoulomb = set->rcut_coulomb;
ic->rlist = set->rlist;
+ ic->rlistlong = set->rlistlong;
+ ir->nstcalclr = set->nstcalclr;
ic->ewaldcoeff = set->ewaldcoeff;
- if (nbv->grp[0].kernel_type == nbk8x8x8_CUDA)
+ if (pme_lb->cutoff_scheme == ecutsVERLET && nbv->grp[0].kernel_type == nbk8x8x8_CUDA)
{
nbnxn_cuda_pme_loadbal_update_param(nbv->cu_nbv,ic);
}
else
{
- init_interaction_const_tables(NULL,ic,nbv->grp[0].kernel_type);
+ init_interaction_const_tables(NULL,ic,ir->cutoff_scheme,
+ (ir->cutoff_scheme == ecutsGROUP) ? -1 : nbv->grp[0].kernel_type,
+ rtab);
}
- if (nbv->ngrp > 1)
+ if (pme_lb->cutoff_scheme == ecutsVERLET && nbv->ngrp > 1)
{
- init_interaction_const_tables(NULL,ic,nbv->grp[1].kernel_type);
+ init_interaction_const_tables(NULL,ic,ir->cutoff_scheme,
+ (ir->cutoff_scheme == ecutsGROUP) ? -1 : nbv->grp[1].kernel_type,
+ rtab);
}
if (cr->duty & DUTY_PME)
fprintf(fplog,
" %-7s %6.3f nm %6.3f nm %3d %3d %3d %5.3f nm %5.3f nm\n",
name,
- setup->rcut,setup->rlist,
+ setup->rcut_coulomb,setup->rlist,
setup->grid[XX],setup->grid[YY],setup->grid[ZZ],
setup->spacing,1/setup->ewaldcoeff);
}
{
double pp_ratio,grid_ratio;
- pp_ratio = pow(pme_lb->setup[pme_lb->cur].rlist/pme_lb->setup[0].rlist,3.0);
+ pp_ratio = pow(pme_lb->setup[pme_lb->cur].rlist/pme_lb->setup[0].rlistlong,3.0);
grid_ratio = pme_grid_points(&pme_lb->setup[pme_lb->cur])/
(double)pme_grid_points(&pme_lb->setup[0]);
if (ir->cutoff_scheme == ecutsGROUP)
{
- if (ir->coulomb_modifier != eintmodNONE ||
- ir->vdw_modifier != eintmodNONE)
- {
- warning_error(wi,"potential modifiers are not supported (yet) with the group cut-off scheme");
- }
-
/* BASIC CUT-OFF STUFF */
if (ir->rlist == 0 ||
!((EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) && ir->rcoulomb > ir->rlist) ||
warning_error(wi,"Can not have nstlist<=0 with twin-range interactions");
}
}
-
+
+ if(ir->rlistlong == ir->rlist)
+ {
+ ir->nstcalclr = 0;
+ }
+ else if(ir->rlistlong>ir->rlist && ir->nstcalclr==0)
+ {
+ warning_error(wi,"With different cutoffs for electrostatics and VdW, nstcalclr must be -1 or a positive number");
+ }
+
if (ir->cutoff_scheme == ecutsVERLET)
{
real rc_max;
ir->rlistlong = ir->rlist;
}
+ if(ir->nstcalclr==-1)
+ {
+ /* if rlist=rlistlong, this will later be changed to nstcalclr=0 */
+ ir->nstcalclr = ir->nstlist;
+ }
+ else if(ir->nstcalclr>0)
+ {
+ if(ir->nstlist>0 && (ir->nstlist % ir->nstcalclr != 0))
+ {
+ warning_error(wi,"nstlist must be evenly divisible by nstcalclr. Use nstcalclr = -1 to automatically follow nstlist");
+ }
+ }
+ else if(ir->nstcalclr<-1)
+ {
+ warning_error(wi,"nstcalclr must be a positive number (divisor of nstcalclr), or -1 to follow nstlist.");
+ }
+
+ if(EEL_PME(ir->coulombtype) && ir->rcoulomb > ir->rvdw && ir->nstcalclr>1)
+ {
+ warning_error(wi,"When used with PME, the long-range component of twin-range interactions must be updated every step (nstcalclr)");
+ }
+
/* GENERAL INTEGRATOR STUFF */
if (!(ir->eI == eiMD || EI_VV(ir->eI)))
{
/* More checks are in triple check (grompp.c) */
if (ir->coulombtype == eelSWITCH) {
- sprintf(warn_buf,"coulombtype = %s is only for testing purposes and can lead to serious artifacts, advice: use coulombtype = %s",
+ sprintf(warn_buf,"coulombtype = %s is only for testing purposes and can lead to serious "
+ "artifacts, advice: use coulombtype = %s",
eel_names[ir->coulombtype],
eel_names[eelRF_ZERO]);
warning(wi,warn_buf);
}
if (EEL_RF(ir->coulombtype) && ir->epsilon_rf==1 && ir->epsilon_r!=1) {
- sprintf(warn_buf,"epsilon-r = %g and epsilon-rf = 1 with reaction field, assuming old format and exchanging epsilon-r and epsilon-rf",ir->epsilon_r);
+ sprintf(warn_buf,"epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old format and exchanging epsilon-r and epsilon-rf",ir->epsilon_r);
warning(wi,warn_buf);
ir->epsilon_rf = ir->epsilon_r;
ir->epsilon_r = 1.0;
/* reaction field (at the cut-off) */
if (ir->coulombtype == eelRF_ZERO) {
- sprintf(err_buf,"With coulombtype = %s, epsilon-rf must be 0",
+ sprintf(warn_buf,"With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
eel_names[ir->coulombtype]);
- CHECK(ir->epsilon_rf != 0);
+ CHECK(ir->epsilon_rf != 0);
+ ir->epsilon_rf = 0.0;
}
sprintf(err_buf,"epsilon-rf must be >= epsilon-r");
if (EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype)) {
if (EEL_SWITCHED(ir->coulombtype)) {
sprintf(err_buf,
- "With coulombtype = %s rcoulomb_switch must be < rcoulomb",
+ "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
eel_names[ir->coulombtype]);
CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
}
} else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype)) {
- if (ir->cutoff_scheme == ecutsGROUP) {
- sprintf(err_buf,"With coulombtype = %s, rcoulomb must be >= rlist",
+ if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE) {
+ sprintf(err_buf,"With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
eel_names[ir->coulombtype]);
CHECK(ir->rlist > ir->rcoulomb);
}
}
- if (EEL_FULL(ir->coulombtype)) {
- if (ir->coulombtype==eelPMESWITCH || ir->coulombtype==eelPMEUSER ||
- ir->coulombtype==eelPMEUSERSWITCH) {
- sprintf(err_buf,"With coulombtype = %s, rcoulomb must be <= rlist",
- eel_names[ir->coulombtype]);
- CHECK(ir->rcoulomb > ir->rlist);
- } else if (ir->cutoff_scheme == ecutsGROUP) {
- if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD) {
- sprintf(err_buf,
- "With coulombtype = %s, rcoulomb must be equal to rlist\n"
- "If you want optimal energy conservation or exact integration use %s",
- eel_names[ir->coulombtype],eel_names[eelPMESWITCH]);
- } else {
- sprintf(err_buf,
- "With coulombtype = %s, rcoulomb must be equal to rlist",
- eel_names[ir->coulombtype]);
+ if(ir->coulombtype==eelSWITCH || ir->coulombtype==eelSHIFT ||
+ ir->vdwtype==evdwSWITCH || ir->vdwtype==evdwSHIFT)
+ {
+ sprintf(warn_buf,
+ "The switch/shift interaction settings are just for compatibility; you will get better"
+ "performance from applying potential modifiers to your interactions!\n");
+ warning_note(wi,warn_buf);
+ }
+
+ if (EEL_FULL(ir->coulombtype))
+ {
+ if (ir->coulombtype==eelPMESWITCH || ir->coulombtype==eelPMEUSER ||
+ ir->coulombtype==eelPMEUSERSWITCH)
+ {
+ sprintf(err_buf,"With coulombtype = %s, rcoulomb must be <= rlist",
+ eel_names[ir->coulombtype]);
+ CHECK(ir->rcoulomb > ir->rlist);
+ }
+ else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
+ {
+ if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
+ {
+ sprintf(err_buf,
+ "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist.\n"
+ "If you want optimal energy conservation, consider using a potential modifier.",
+ eel_names[ir->coulombtype]);
+ CHECK(ir->rcoulomb != ir->rlist);
+ }
}
- CHECK(ir->rcoulomb != ir->rlist);
- }
}
if (EEL_PME(ir->coulombtype)) {
}
if (EVDW_SWITCHED(ir->vdwtype)) {
- sprintf(err_buf,"With vdwtype = %s rvdw-switch must be < rvdw",
+ sprintf(err_buf,"With vdwtype = %s rvdw-switch must be < rvdw. Or, better - use a potential modifier.",
evdw_names[ir->vdwtype]);
CHECK(ir->rvdw_switch >= ir->rvdw);
} else if (ir->vdwtype == evdwCUT) {
- if (ir->cutoff_scheme == ecutsGROUP) {
- sprintf(err_buf,"With vdwtype = %s, rvdw must be >= rlist",evdw_names[ir->vdwtype]);
+ if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE) {
+ sprintf(err_buf,"With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier",evdw_names[ir->vdwtype]);
CHECK(ir->rlist > ir->rvdw);
}
}
}
if (ir->nstlist == -1) {
- sprintf(err_buf,
- "nstlist=-1 only works with switched or shifted potentials,\n"
- "suggestion: use vdw-type=%s and coulomb-type=%s",
- evdw_names[evdwSHIFT],eel_names[eelPMESWITCH]);
- CHECK(!(EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) &&
- EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype)));
-
sprintf(err_buf,"With nstlist=-1 rvdw and rcoulomb should be smaller than rlist to account for diffusion and possibly charge-group radii");
CHECK(ir->rvdw >= ir->rlist || ir->rcoulomb >= ir->rlist);
}
/* ENERGY CONSERVATION */
if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
{
- if (!EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype) && ir->rvdw > 0)
+ if (!EVDW_MIGHT_BE_ZERO_AT_CUTOFF(ir->vdwtype) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
{
sprintf(warn_buf,"You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
evdw_names[evdwSHIFT]);
warning_note(wi,warn_buf);
}
- if (!EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) && ir->rcoulomb > 0)
+ if (!EEL_MIGHT_BE_ZERO_AT_CUTOFF(ir->coulombtype) && ir->rcoulomb > 0 && ir->coulomb_modifier == eintmodNONE)
{
sprintf(warn_buf,"You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
eel_names[eelPMESWITCH],eel_names[eelRF_ZERO]);
if (ir->bAdress)
{
+ warning_error(wi,"AdResS is currently disabled\n");
if (ir->cutoff_scheme != ecutsGROUP)
{
warning_error(wi,"AdresS simulation supports only cutoff-scheme=group");
RTYPE ("rlist", ir->rlist, -1);
CTYPE ("long-range cut-off for switched potentials");
RTYPE ("rlistlong", ir->rlistlong, -1);
+ ITYPE ("nstcalclr", ir->nstcalclr, -1);
/* Electrostatics */
CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
{
- warning_note(wi,"tau-t = -1 is the new value to signal that a group should not have temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
+ warning_note(wi,"tau-t = -1 is the value to signal that a group should not have temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
}
if (ir->opts.tau_t[i] >= 0)
* before the other nodes have read the tpx file and called gmx_detect_hardware.
*/
typedef struct {
- int cutoff_scheme; /* The cutoff-scheme from inputrec_t */
+ int cutoff_scheme; /* The cutoff scheme from inputrec_t */
gmx_bool bUseGPU; /* Use GPU or GPU emulation */
} master_inf_t;
cmp_real(fp,"inputrec->verletbuf_drift",-1,ir1->verletbuf_drift,ir2->verletbuf_drift,ftol,abstol);
cmp_real(fp,"inputrec->rlist",-1,ir1->rlist,ir2->rlist,ftol,abstol);
cmp_real(fp,"inputrec->rlistlong",-1,ir1->rlistlong,ir2->rlistlong,ftol,abstol);
+ cmp_int(fp,"inputrec->nstcalclr",-1,ir1->nstcalclr,ir2->nstcalclr);
cmp_real(fp,"inputrec->rtpi",-1,ir1->rtpi,ir2->rtpi,ftol,abstol);
cmp_int(fp,"inputrec->coulombtype",-1,ir1->coulombtype,ir2->coulombtype);
cmp_int(fp,"inputrec->coulomb_modifier",-1,ir1->coulomb_modifier,ir2->coulomb_modifier);
{
if (fr->n_adress_tf_grps > 0 ){
/* multi component tf is on, select the right table */
- ATFtab = fr->atf_tabs[mdatoms->tf_table_index[iatom]].tab;
+ ATFtab = fr->atf_tabs[mdatoms->tf_table_index[iatom]].data;
tabscale = fr->atf_tabs[mdatoms->tf_table_index[iatom]].scale;
}
else {
/* just on component*/
- ATFtab = fr->atf_tabs[DEFAULT_TF_TABLE].tab;
+ ATFtab = fr->atf_tabs[DEFAULT_TF_TABLE].data;
tabscale = fr->atf_tabs[DEFAULT_TF_TABLE].scale;
}
/* Cell sizes for static load balancing, first index cartesian */
real **slb_frac;
-
+
/* The width of the communicated boundaries */
real cutoff_mbody;
real cutoff;
const char *name;
sum = 0;
- for(i=eNR_NBKERNEL010; i<eNR_NBKERNEL_FREE_ENERGY; i++)
+ for(i=0; i<eNR_NBKERNEL_FREE_ENERGY; i++)
{
/* To get closer to the real timings, we half the count
* for the normal loops and again half it for water loops.
real *dvdlambda,
gmx_grppairener_t *grppener,
gmx_bool bFillGrid,
- gmx_bool bDoLongRange,
- gmx_bool bDoForces,
- rvec *f)
+ gmx_bool bDoLongRangeNS)
{
char *ptr;
int nsearch;
nsearch = search_neighbours(fp,fr,x,box,top,groups,cr,nrnb,md,
lambda,dvdlambda,grppener,
- bFillGrid,bDoLongRange,
- bDoForces,f);
+ bFillGrid,bDoLongRangeNS);
if (debug)
fprintf(debug,"nsearch = %d\n",nsearch);
t_grpopts *opts,
rvec x[], history_t *hist,
rvec f[],
+ rvec f_longrange[],
gmx_enerdata_t *enerd,
t_fcdata *fcd,
gmx_mtop_t *mtop,
if (flags & GMX_FORCE_NONBONDED)
{
donb_flags = 0;
+ /* Add short-range interactions */
+ donb_flags |= GMX_NONBONDED_DO_SR;
+
if (flags & GMX_FORCE_FORCES)
{
- donb_flags |= GMX_DONB_FORCES;
+ donb_flags |= GMX_NONBONDED_DO_FORCE;
+ }
+ if (flags & GMX_FORCE_ENERGY)
+ {
+ donb_flags |= GMX_NONBONDED_DO_POTENTIAL;
+ }
+ if (flags & GMX_FORCE_DO_LR)
+ {
+ donb_flags |= GMX_NONBONDED_DO_LR;
}
wallcycle_sub_start(wcycle, ewcsNONBONDED);
- do_nonbonded(cr,fr,x,f,md,excl,
- fr->bBHAM ?
- enerd->grpp.ener[egBHAMSR] :
- enerd->grpp.ener[egLJSR],
- enerd->grpp.ener[egCOULSR],
- enerd->grpp.ener[egGB],box_size,nrnb,
+ do_nonbonded(cr,fr,x,f,f_longrange,md,excl,
+ &enerd->grpp,box_size,nrnb,
lambda,dvdl_nb,-1,-1,donb_flags);
wallcycle_sub_stop(wcycle, ewcsNONBONDED);
}
lam_i[j] = (i==0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
}
reset_enerdata(&ir->opts,fr,TRUE,&ed_lam,FALSE);
- do_nonbonded(cr,fr,x,f,md,excl,
- fr->bBHAM ?
- ed_lam.grpp.ener[egBHAMSR] :
- ed_lam.grpp.ener[egLJSR],
- ed_lam.grpp.ener[egCOULSR],
- enerd->grpp.ener[egGB], box_size,nrnb,
+ do_nonbonded(cr,fr,x,f,f_longrange,md,excl,
+ &(ed_lam.grpp), box_size,nrnb,
lam_i,dvdl_dum,-1,-1,
- GMX_DONB_FOREIGNLAMBDA);
+ GMX_NONBONDED_DO_FOREIGNLAMBDA | GMX_NONBONDED_DO_SR);
sum_epot(&ir->opts,&ed_lam);
enerd->enerpart_lambda[i] += ed_lam.term[F_EPOT];
}
*
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
- *
+ *
* For more info, check our website at http://www.gromacs.org
*
* And Hey:
fprintf(fp,"%2d - %2d",i,j);
if (bBHAM)
fprintf(fp," a=%10g, b=%10g, c=%10g\n",BHAMA(nbfp,atnr,i,j),
- BHAMB(nbfp,atnr,i,j),BHAMC(nbfp,atnr,i,j));
+ BHAMB(nbfp,atnr,i,j),BHAMC(nbfp,atnr,i,j)/6.0);
else
- fprintf(fp," c6=%10g, c12=%10g\n",C6(nbfp,atnr,i,j),
- C12(nbfp,atnr,i,j));
+ fprintf(fp," c6=%10g, c12=%10g\n",C6(nbfp,atnr,i,j)/6.0,
+ C12(nbfp,atnr,i,j)/12.0);
}
}
}
snew(nbfp,3*atnr*atnr);
for(i=k=0; (i<atnr); i++) {
for(j=0; (j<atnr); j++,k++) {
- BHAMA(nbfp,atnr,i,j) = idef->iparams[k].bham.a;
- BHAMB(nbfp,atnr,i,j) = idef->iparams[k].bham.b;
- BHAMC(nbfp,atnr,i,j) = idef->iparams[k].bham.c;
+ BHAMA(nbfp,atnr,i,j) = idef->iparams[k].bham.a;
+ BHAMB(nbfp,atnr,i,j) = idef->iparams[k].bham.b;
+ /* nbfp now includes the 6.0 derivative prefactor */
+ BHAMC(nbfp,atnr,i,j) = idef->iparams[k].bham.c*6.0;
}
}
}
snew(nbfp,2*atnr*atnr);
for(i=k=0; (i<atnr); i++) {
for(j=0; (j<atnr); j++,k++) {
- C6(nbfp,atnr,i,j) = idef->iparams[k].lj.c6;
- C12(nbfp,atnr,i,j) = idef->iparams[k].lj.c12;
+ /* nbfp now includes the 6.0/12.0 derivative prefactors */
+ C6(nbfp,atnr,i,j) = idef->iparams[k].lj.c6*6.0;
+ C12(nbfp,atnr,i,j) = idef->iparams[k].lj.c12*12.0;
}
}
}
+
return nbfp;
}
/* So, is it an SPC?
* For this we require thatn all atoms have charge,
* the charges on atom 2 & 3 should be the same, and only
- * atom 1 should have VdW.
+ * atom 1 might have VdW.
*/
- if (has_vdw[0] == TRUE &&
- has_vdw[1] == FALSE &&
+ if (has_vdw[1] == FALSE &&
has_vdw[2] == FALSE &&
tmp_charge[0] != 0 &&
tmp_charge[1] != 0 &&
{
/* Or could it be a TIP4P?
* For this we require thatn atoms 2,3,4 have charge, but not atom 1.
- * Only atom 1 should have VdW.
+ * Only atom 1 mght have VdW.
*/
- if(has_vdw[0] == TRUE &&
- has_vdw[1] == FALSE &&
+ if(has_vdw[1] == FALSE &&
has_vdw[2] == FALSE &&
has_vdw[3] == FALSE &&
tmp_charge[0] == 0 &&
npair_ij = tmpi*(tmpi - 1)/2;
}
if (bBHAM) {
- csix += npair_ij*BHAMC(nbfp,ntp,tpi,tpj);
+ /* nbfp now includes the 6.0 derivative prefactor */
+ csix += npair_ij*BHAMC(nbfp,ntp,tpi,tpj)/6.0;
} else {
- csix += npair_ij* C6(nbfp,ntp,tpi,tpj);
- ctwelve += npair_ij* C12(nbfp,ntp,tpi,tpj);
+ /* nbfp now includes the 6.0/12.0 derivative prefactors */
+ csix += npair_ij* C6(nbfp,ntp,tpi,tpj)/6.0;
+ ctwelve += npair_ij* C12(nbfp,ntp,tpi,tpj)/12.0;
}
npair += npair_ij;
}
tpj = atoms->atom[k].typeB;
}
if (bBHAM) {
- csix -= nmol*BHAMC(nbfp,ntp,tpi,tpj);
+ /* nbfp now includes the 6.0 derivative prefactor */
+ csix -= nmol*BHAMC(nbfp,ntp,tpi,tpj)/6.0;
} else {
- csix -= nmol*C6 (nbfp,ntp,tpi,tpj);
- ctwelve -= nmol*C12(nbfp,ntp,tpi,tpj);
+ /* nbfp now includes the 6.0/12.0 derivative prefactors */
+ csix -= nmol*C6 (nbfp,ntp,tpi,tpj)/6.0;
+ ctwelve -= nmol*C12(nbfp,ntp,tpi,tpj)/12.0;
}
nexcl += nmol;
}
}
if (bBHAM)
{
- csix += nmolc*BHAMC(nbfp,ntp,tpi,tpj);
+ /* nbfp now includes the 6.0 derivative prefactor */
+ csix += nmolc*BHAMC(nbfp,ntp,tpi,tpj)/6.0;
}
else
{
- csix += nmolc*C6 (nbfp,ntp,tpi,tpj);
- ctwelve += nmolc*C12(nbfp,ntp,tpi,tpj);
+ /* nbfp now includes the 6.0/12.0 derivative prefactors */
+ csix += nmolc*C6 (nbfp,ntp,tpi,tpj)/6.0;
+ ctwelve += nmolc*C12(nbfp,ntp,tpi,tpj)/12.0;
}
npair += nmolc;
}
static void make_nbf_tables(FILE *fp,const output_env_t oenv,
t_forcerec *fr,real rtab,
- const t_commrec *cr,
- const char *tabfn,char *eg1,char *eg2,
- t_nblists *nbl)
+ const t_commrec *cr,
+ const char *tabfn,char *eg1,char *eg2,
+ t_nblists *nbl)
{
- char buf[STRLEN];
- int i,j;
+ char buf[STRLEN];
+ int i,j;
- if (tabfn == NULL) {
- if (debug)
- fprintf(debug,"No table file name passed, can not read table, can not do non-bonded interactions\n");
- return;
- }
-
- sprintf(buf,"%s",tabfn);
- if (eg1 && eg2)
+ if (tabfn == NULL) {
+ if (debug)
+ fprintf(debug,"No table file name passed, can not read table, can not do non-bonded interactions\n");
+ return;
+ }
+
+ sprintf(buf,"%s",tabfn);
+ if (eg1 && eg2)
/* Append the two energy group names */
- sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1,"_%s_%s.%s",
- eg1,eg2,ftp2ext(efXVG));
- nbl->tab = make_tables(fp,oenv,fr,MASTER(cr),buf,rtab,0);
- /* Copy the contents of the table to separate coulomb and LJ tables too,
- * to improve cache performance.
- */
-
- /* For performance reasons we want
- * the table data to be aligned to 16-byte. The pointer could be freed
- * but currently isn't.
- */
- snew_aligned(nbl->vdwtab,8*(nbl->tab.n+1),16);
- snew_aligned(nbl->coultab,4*(nbl->tab.n+1),16);
-
- for(i=0; i<=nbl->tab.n; i++) {
- for(j=0; j<4; j++)
- nbl->coultab[4*i+j] = nbl->tab.tab[12*i+j];
- for(j=0; j<8; j++)
- nbl->vdwtab [8*i+j] = nbl->tab.tab[12*i+4+j];
- }
+ sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1,"_%s_%s.%s",
+ eg1,eg2,ftp2ext(efXVG));
+ nbl->table_elec_vdw = make_tables(fp,oenv,fr,MASTER(cr),buf,rtab,0);
+ /* Copy the contents of the table to separate coulomb and LJ tables too,
+ * to improve cache performance.
+ */
+ /* For performance reasons we want
+ * the table data to be aligned to 16-byte. The pointers could be freed
+ * but currently aren't.
+ */
+ nbl->table_elec.interaction = GMX_TABLE_INTERACTION_ELEC;
+ nbl->table_elec.format = nbl->table_elec_vdw.format;
+ nbl->table_elec.r = nbl->table_elec_vdw.r;
+ nbl->table_elec.n = nbl->table_elec_vdw.n;
+ nbl->table_elec.scale = nbl->table_elec_vdw.scale;
+ nbl->table_elec.scale_exp = nbl->table_elec_vdw.scale_exp;
+ nbl->table_elec.formatsize = nbl->table_elec_vdw.formatsize;
+ nbl->table_elec.ninteractions = 1;
+ nbl->table_elec.stride = nbl->table_elec.formatsize * nbl->table_elec.ninteractions;
+ snew_aligned(nbl->table_elec.data,nbl->table_elec.stride*(nbl->table_elec.n+1),16);
+
+ nbl->table_vdw.interaction = GMX_TABLE_INTERACTION_VDWREP_VDWDISP;
+ nbl->table_vdw.format = nbl->table_elec_vdw.format;
+ nbl->table_vdw.r = nbl->table_elec_vdw.r;
+ nbl->table_vdw.n = nbl->table_elec_vdw.n;
+ nbl->table_vdw.scale = nbl->table_elec_vdw.scale;
+ nbl->table_vdw.scale_exp = nbl->table_elec_vdw.scale_exp;
+ nbl->table_vdw.formatsize = nbl->table_elec_vdw.formatsize;
+ nbl->table_vdw.ninteractions = 2;
+ nbl->table_vdw.stride = nbl->table_vdw.formatsize * nbl->table_vdw.ninteractions;
+ snew_aligned(nbl->table_vdw.data,nbl->table_vdw.stride*(nbl->table_vdw.n+1),16);
+
+ for(i=0; i<=nbl->table_elec_vdw.n; i++)
+ {
+ for(j=0; j<4; j++)
+ nbl->table_elec.data[4*i+j] = nbl->table_elec_vdw.data[12*i+j];
+ for(j=0; j<8; j++)
+ nbl->table_vdw.data[8*i+j] = nbl->table_elec_vdw.data[12*i+4+j];
+ }
}
static void count_tables(int ftype1,int ftype2,const gmx_mtop_t *mtop,
}
-static void init_verlet_ewald_f_table(interaction_const_t *ic,
- int verlet_kernel_type)
+static void init_ewald_f_table(interaction_const_t *ic,
+ int cutoff_scheme,
+ int verlet_kernel_type,
+ real rtab)
{
- if (nbnxn_kernel_pairlist_simple(verlet_kernel_type))
+ real maxr;
+
+ if (cutoff_scheme==ecutsGROUP || nbnxn_kernel_pairlist_simple(verlet_kernel_type))
{
/* With a spacing of 0.0005 we are at the force summation accuracy
* for the SSE kernels for "normal" atomistic simulations.
*/
ic->tabq_scale = ewald_spline3_table_scale(ic->ewaldcoeff,
ic->rcoulomb);
- ic->tabq_size = (int)(ic->rcoulomb*ic->tabq_scale) + 2;
-#ifndef GMX_DOUBLE
- ic->tabq_format = tableformatFDV0;
-#else
- ic->tabq_format = tableformatF;
-#endif
+
+ maxr = (rtab>ic->rcoulomb) ? rtab : ic->rcoulomb;
+ ic->tabq_size = (int)(maxr*ic->tabq_scale) + 2;
}
else
{
ic->tabq_size = GPU_EWALD_COULOMB_FORCE_TABLE_SIZE;
/* Subtract 2 iso 1 to avoid access out of range due to rounding */
ic->tabq_scale = (ic->tabq_size - 2)/ic->rcoulomb;
- if (verlet_kernel_type == nbk8x8x8_CUDA)
- {
- /* This case is handled in the nbnxn CUDA module */
- ic->tabq_format = tableformatNONE;
- }
- else
- {
- ic->tabq_format = tableformatF;
- }
- }
-
- switch (ic->tabq_format)
- {
- case tableformatNONE:
- break;
- case tableformatF:
- sfree_aligned(ic->tabq_coul_F);
- sfree_aligned(ic->tabq_coul_V);
- snew_aligned(ic->tabq_coul_F,ic->tabq_size,16);
- snew_aligned(ic->tabq_coul_V,ic->tabq_size,16);
- table_spline3_fill_ewald_lr(ic->tabq_coul_F,ic->tabq_coul_V,
- ic->tabq_size,ic->tabq_format,
- 1/ic->tabq_scale,ic->ewaldcoeff);
- break;
- case tableformatFDV0:
- sfree_aligned(ic->tabq_coul_F);
- snew_aligned(ic->tabq_coul_FDV0,ic->tabq_size*4,16);
- table_spline3_fill_ewald_lr(ic->tabq_coul_FDV0,NULL,
- ic->tabq_size,ic->tabq_format,
- 1/ic->tabq_scale,ic->ewaldcoeff);
- break;
- default:
- gmx_incons("Unknown table format");
}
+
+ sfree_aligned(ic->tabq_coul_FDV0);
+ sfree_aligned(ic->tabq_coul_F);
+ sfree_aligned(ic->tabq_coul_V);
+
+ /* Create the original table data in FDV0 */
+ snew_aligned(ic->tabq_coul_FDV0,ic->tabq_size*4,16);
+ snew_aligned(ic->tabq_coul_F,ic->tabq_size,16);
+ snew_aligned(ic->tabq_coul_V,ic->tabq_size,16);
+ table_spline3_fill_ewald_lr(ic->tabq_coul_F,ic->tabq_coul_V,ic->tabq_coul_FDV0,
+ ic->tabq_size,1/ic->tabq_scale,ic->ewaldcoeff);
}
void init_interaction_const_tables(FILE *fp,
interaction_const_t *ic,
- int verlet_kernel_type)
+ int cutoff_scheme,
+ int verlet_kernel_type,
+ real rtab)
{
real spacing;
if (ic->eeltype == eelEWALD || EEL_PME(ic->eeltype))
{
- init_verlet_ewald_f_table(ic,verlet_kernel_type);
+ init_ewald_f_table(ic,cutoff_scheme,verlet_kernel_type,rtab);
if (fp != NULL)
{
void init_interaction_const(FILE *fp,
interaction_const_t **interaction_const,
- const t_forcerec *fr)
+ const t_forcerec *fr,
+ real rtab)
{
interaction_const_t *ic;
snew(ic, 1);
- ic->rlist = fr->rlist;
+ /* Just allocate something so we can free it */
+ snew_aligned(ic->tabq_coul_FDV0,16,16);
+ snew_aligned(ic->tabq_coul_F,16,16);
+ snew_aligned(ic->tabq_coul_V,16,16);
+ ic->rlist = fr->rlist;
+ ic->rlistlong = fr->rlistlong;
+
/* Lennard-Jones */
ic->rvdw = fr->rvdw;
- if (fr->vdw_pot_shift)
+ if (fr->vdw_modifier==eintmodPOTSHIFT)
{
ic->sh_invrc6 = pow(ic->rvdw,-6.0);
}
/* Ewald */
ic->ewaldcoeff = fr->ewaldcoeff;
- if (fr->coul_pot_shift)
+ if (fr->coulomb_modifier==eintmodPOTSHIFT)
{
ic->sh_ewald = gmx_erfc(ic->ewaldcoeff*ic->rcoulomb);
}
/* For plain cut-off we might use the reaction-field kernels */
ic->epsilon_rf = ic->epsilon_r;
ic->k_rf = 0;
- if (fr->coul_pot_shift)
+ if (fr->coulomb_modifier==eintmodPOTSHIFT)
{
ic->c_rf = 1/ic->rcoulomb;
}
nbnxn_cuda_init_const(fr->nbv->cu_nbv, ic, fr->nbv);
}
- if (fr->cutoff_scheme == ecutsVERLET)
+ if(fr->cutoff_scheme == ecutsGROUP)
+ {
+ init_interaction_const_tables(fp,ic,ecutsGROUP,-1,rtab);
+ }
+ else
{
assert(fr->nbv != NULL && fr->nbv->grp != NULL);
- init_interaction_const_tables(fp,ic,fr->nbv->grp[fr->nbv->ngrp-1].kernel_type);
+ init_interaction_const_tables(fp,ic,ecutsVERLET,fr->nbv->grp[fr->nbv->ngrp-1].kernel_type,rtab);
}
}
}
bGenericKernelOnly = FALSE;
+
+ /* We now check in the NS code whether a particular combination of interactions
+ * can be used with water optimization, and disable it if that is not the case.
+ */
+
if (getenv("GMX_NB_GENERIC") != NULL)
{
if (fp != NULL)
{
fprintf(fp,
"Found environment variable GMX_NB_GENERIC.\n"
- "Disabling interaction-specific nonbonded kernels.\n\n");
+ "Disabling all interaction-specific nonbonded kernels, will only\n"
+ "use the slow generic ones in src/gmxlib/nonbonded/nb_generic.c\n\n");
}
bGenericKernelOnly = TRUE;
+ }
+
+ if (bGenericKernelOnly==TRUE)
+ {
bNoSolvOpt = TRUE;
}
}
}
+ fr->bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
+
/* Check if we can/should do all-vs-all kernels */
fr->bAllvsAll = can_use_allvsall(ir,mtop,FALSE,NULL,NULL);
fr->AllvsAll_work = NULL;
fr->bMolPBC = dd_bonded_molpbc(cr->dd,fr->ePBC);
}
}
+
fr->rc_scaling = ir->refcoord_scaling;
copy_rvec(ir->posres_com,fr->posres_com);
copy_rvec(ir->posres_comB,fr->posres_comB);
fr->eeltype = ir->coulombtype;
fr->vdwtype = ir->vdwtype;
- fr->coul_pot_shift = (ir->coulomb_modifier == eintmodPOTSHIFT);
- fr->vdw_pot_shift = (ir->vdw_modifier == eintmodPOTSHIFT);
-
+ fr->coulomb_modifier = ir->coulomb_modifier;
+ fr->vdw_modifier = ir->vdw_modifier;
+
+ /* Electrostatics: Translate from interaction-setting-in-mdp-file to kernel interaction format */
+ switch(fr->eeltype)
+ {
+ case eelCUT:
+ fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_COULOMB;
+ break;
+
+ case eelRF:
+ case eelGRF:
+ case eelRF_NEC:
+ fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD;
+ break;
+
+ case eelRF_ZERO:
+ fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD;
+ fr->coulomb_modifier = eintmodEXACTCUTOFF;
+ break;
+
+ case eelSWITCH:
+ case eelSHIFT:
+ case eelUSER:
+ case eelENCADSHIFT:
+ case eelPMESWITCH:
+ case eelPMEUSER:
+ case eelPMEUSERSWITCH:
+ fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_CUBICSPLINETABLE;
+ break;
+
+ case eelPME:
+ case eelEWALD:
+ fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_EWALD;
+ break;
+
+ default:
+ gmx_fatal(FARGS,"Unsupported electrostatic interaction: %s",eel_names[fr->eeltype]);
+ break;
+ }
+
+ /* Vdw: Translate from mdp settings to kernel format */
+ switch(fr->vdwtype)
+ {
+ case evdwCUT:
+ if(fr->bBHAM)
+ {
+ fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_BUCKINGHAM;
+ }
+ else
+ {
+ fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_LENNARDJONES;
+ }
+ break;
+
+ case evdwSWITCH:
+ case evdwSHIFT:
+ case evdwUSER:
+ case evdwENCADSHIFT:
+ fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
+ break;
+
+ default:
+ gmx_fatal(FARGS,"Unsupported vdw interaction: %s",evdw_names[fr->vdwtype]);
+ break;
+ }
+
+ /* These start out identical to ir, but might be altered if we e.g. tabulate the interaction in the kernel */
+ fr->nbkernel_elec_modifier = fr->coulomb_modifier;
+ fr->nbkernel_vdw_modifier = fr->vdw_modifier;
+
fr->bTwinRange = fr->rlistlong > fr->rlist;
fr->bEwald = (EEL_PME(fr->eeltype) || fr->eeltype==eelEWALD);
{
fr->bvdwtab = (fr->vdwtype != evdwCUT ||
!gmx_within_tol(fr->reppow,12.0,10*GMX_DOUBLE_EPS));
- fr->bcoultab = (!(fr->eeltype == eelCUT || EEL_RF(fr->eeltype)) ||
- fr->eeltype == eelRF_ZERO);
+ /* We have special kernels for standard Ewald and PME, but the pme-switch ones are tabulated above */
+ fr->bcoultab = !(fr->eeltype == eelCUT ||
+ fr->eeltype == eelEWALD ||
+ fr->eeltype == eelPME ||
+ fr->eeltype == eelRF ||
+ fr->eeltype == eelRF_ZERO);
+
+ /* If the user absolutely wants different switch/shift settings for coul/vdw, it is likely
+ * going to be faster to tabulate the interaction than calling the generic kernel.
+ */
+ if(fr->nbkernel_elec_modifier==eintmodPOTSWITCH && fr->nbkernel_vdw_modifier==eintmodPOTSWITCH)
+ {
+ if((fr->rcoulomb_switch != fr->rvdw_switch) || (fr->rcoulomb != fr->rvdw))
+ {
+ fr->bcoultab = TRUE;
+ }
+ }
+ else if((fr->nbkernel_elec_modifier==eintmodPOTSHIFT && fr->nbkernel_vdw_modifier==eintmodPOTSHIFT) ||
+ ((fr->nbkernel_elec_interaction == GMX_NBKERNEL_ELEC_REACTIONFIELD &&
+ fr->nbkernel_elec_modifier==eintmodEXACTCUTOFF &&
+ (fr->nbkernel_vdw_modifier==eintmodPOTSWITCH || fr->nbkernel_vdw_modifier==eintmodPOTSHIFT))))
+ {
+ if(fr->rcoulomb != fr->rvdw)
+ {
+ fr->bcoultab = TRUE;
+ }
+ }
if (getenv("GMX_REQUIRE_TABLES"))
{
fprintf(fp,"Table routines are used for coulomb: %s\n",bool_names[fr->bcoultab]);
fprintf(fp,"Table routines are used for vdw: %s\n",bool_names[fr->bvdwtab ]);
}
+
+ if(fr->bvdwtab==TRUE)
+ {
+ fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
+ fr->nbkernel_vdw_modifier = eintmodNONE;
+ }
+ if(fr->bcoultab==TRUE)
+ {
+ fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_CUBICSPLINETABLE;
+ fr->nbkernel_elec_modifier = eintmodNONE;
+ }
}
if (ir->cutoff_scheme == ecutsVERLET)
if (fr->nbfp == NULL) {
fr->ntype = mtop->ffparams.atnr;
- fr->bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
fr->nbfp = mk_nbfp(&mtop->ffparams,fr->bBHAM);
}
* A little unnecessary to make both vdw and coul tables sometimes,
* but what the heck... */
- bTab = fr->bcoultab || fr->bvdwtab;
+ bTab = fr->bcoultab || fr->bvdwtab || fr->bEwald;
bSep14tab = ((!bTab || fr->eeltype!=eelCUT || fr->vdwtype!=evdwCUT ||
- fr->bBHAM) &&
+ fr->bBHAM || fr->bEwald) &&
(gmx_mtop_ftype_count(mtop,F_LJ14) > 0 ||
gmx_mtop_ftype_count(mtop,F_LJC14_Q) > 0 ||
gmx_mtop_ftype_count(mtop,F_LJC_PAIRS_NB) > 0));
if (bNormalnblists) {
make_nbf_tables(fp,oenv,fr,rtab,cr,tabfn,NULL,NULL,&fr->nblists[0]);
if (!bSep14tab)
- fr->tab14 = fr->nblists[0].tab;
+ fr->tab14 = fr->nblists[0].table_elec_vdw;
m = 1;
} else {
m = 0;
/* Initialize neighbor search */
init_ns(fp,cr,&fr->ns,fr,mtop,box);
-
+
if (cr->duty & DUTY_PP)
{
- gmx_setup_kernels(fp,fr,bGenericKernelOnly);
- if (ir->bAdress)
+ gmx_nonbonded_setup(fp,fr,bGenericKernelOnly);
+ /*
+ if (ir->bAdress)
{
gmx_setup_adress_kernels(fp,bGenericKernelOnly);
}
+ */
}
/* Initialize the thread working data for bonded interactions */
}
init_nb_verlet(fp, &fr->nbv, ir, fr, cr, nbpu_opt);
-
- /* initialize interaction constants
- * TODO should be moved out during modularization.
- */
- init_interaction_const(fp, &fr->ic, fr);
}
+ /* fr->ic is used both by verlet and group kernels (to some extent) now */
+ init_interaction_const(fp, &fr->ic, fr, rtab);
if (ir->eDispCorr != edispcNO)
{
calc_enervirdiff(fp,ir->eDispCorr,fr);
/*pr_int(fp,fr->cg0);
pr_int(fp,fr->hcg);*/
for(i=0; i<fr->nnblists; i++)
- pr_int(fp,fr->nblists[i].tab.n);
+ pr_int(fp,fr->nblists[i].table_elec_vdw.n);
pr_real(fp,fr->rcoulomb_switch);
pr_real(fp,fr->rcoulomb);
#else
genborn_allvsall_calc_still_radii(fr,md,born,top,x[0],cr,&fr->AllvsAll_workgb);
#endif
- inc_nrnb(nrnb,eNR_BORN_AVA_RADII_STILL,cnt);
+ /* 13 flops in outer loop, 47 flops in inner loop */
+ inc_nrnb(nrnb,eNR_BORN_AVA_RADII_STILL,md->homenr*13+cnt*47);
}
else if(ir->gb_algorithm==egbHCT || ir->gb_algorithm==egbOBC)
{
#else
genborn_allvsall_calc_hct_obc_radii(fr,md,born,ir->gb_algorithm,top,x[0],cr,&fr->AllvsAll_workgb);
#endif
- inc_nrnb(nrnb,eNR_BORN_AVA_RADII_HCT_OBC,cnt);
+ /* 24 flops in outer loop, 183 in inner */
+ inc_nrnb(nrnb,eNR_BORN_AVA_RADII_HCT_OBC,md->homenr*24+cnt*183);
}
else
{
gmx_fatal(FARGS,"Bad gb algorithm for all-vs-all interactions");
}
- inc_nrnb(nrnb,eNR_NBKERNEL_OUTER,md->homenr);
-
return 0;
}
switch(ir->gb_algorithm)
{
case egbSTILL:
- inc_nrnb(nrnb,eNR_BORN_RADII_STILL,nl->nrj);
+ /* 17 flops per outer loop iteration, 47 flops per inner loop */
+ inc_nrnb(nrnb,eNR_BORN_RADII_STILL,nl->nri*17+nl->nrj*47);
break;
case egbHCT:
case egbOBC:
- inc_nrnb(nrnb,eNR_BORN_RADII_HCT_OBC,nl->nrj);
+ /* 61 (assuming 10 for tanh) flops for outer loop iteration, 183 flops per inner loop */
+ inc_nrnb(nrnb,eNR_BORN_RADII_HCT_OBC,nl->nri*61+nl->nrj*183);
break;
default:
break;
}
- inc_nrnb(nrnb,eNR_NBKERNEL_OUTER,nl->nri);
}
return 0;
/* Calculate the bonded GB-interactions using either table or analytical formula */
enerd->term[F_GBPOL] += gb_bonds_tab(x,f,fr->fshift, md->chargeA,&(fr->gbtabscale),
- fr->invsqrta,fr->dvda,fr->gbtab.tab,idef,born->epsilon_r,born->gb_epsilon_solvent, fr->epsfac, pbc_null, graph);
+ fr->invsqrta,fr->dvda,fr->gbtab.data,idef,born->epsilon_r,born->gb_epsilon_solvent, fr->epsfac, pbc_null, graph);
/* Calculate self corrections to the GB energies - currently only A state used! (FIXME) */
enerd->term[F_GBPOL] += calc_gb_selfcorrections(cr,born->nr,md->chargeA, born, fr->dvda, md, fr->epsfac);
genborn_allvsall_calc_chainrule(fr,md,born,x[0],f[0],gb_algorithm,fr->AllvsAll_workgb);
#endif
cnt = md->homenr*(md->nr/2+1);
- inc_nrnb(nrnb,eNR_BORN_AVA_CHAINRULE,cnt);
- inc_nrnb(nrnb,eNR_NBKERNEL_OUTER,md->homenr);
+ /* 9 flops for outer loop, 15 for inner */
+ inc_nrnb(nrnb,eNR_BORN_AVA_CHAINRULE,md->homenr*9+cnt*15);
return;
}
if(!fr->bAllvsAll)
{
- inc_nrnb(nrnb,eNR_BORN_CHAINRULE,fr->gblist.nrj);
- inc_nrnb(nrnb,eNR_NBKERNEL_OUTER,fr->gblist.nri);
-
+ /* 9 flops for outer loop, 15 for inner */
+ inc_nrnb(nrnb,eNR_BORN_CHAINRULE,fr->gblist.nri*9+fr->gblist.nrj*15);
}
}
ems->s.lambda,graph,fr,vsite,mu_tot,t,NULL,NULL,TRUE,
GMX_FORCE_STATECHANGED | GMX_FORCE_ALLFORCES |
GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY |
- (bNS ? GMX_FORCE_NS | GMX_FORCE_DOLR : 0));
+ (bNS ? GMX_FORCE_NS | GMX_FORCE_DO_LR : 0));
/* Clear the unused shake virial and pressure */
clear_mat(shake_vir);
{
if (i < ntype && j < ntype)
{
- /* We store the prefactor in the derivative of the potential
- * in the parameter to avoid multiplications in the inner loop.
+ /* fr->nbfp has been updated, so that array too now stores c6/c12 including
+ * the 6.0/12.0 prefactors to save 2 flops in the most common case (force-only).
*/
c6 = nbfp[(i*ntype+j)*2 ];
c12 = nbfp[(i*ntype+j)*2+1];
- nbat->nbfp[(i*nbat->ntype+j)*2 ] = 6.0*c6;
- nbat->nbfp[(i*nbat->ntype+j)*2+1] = 12.0*c12;
-
+ nbat->nbfp[(i*nbat->ntype+j)*2 ] = c6;
+ nbat->nbfp[(i*nbat->ntype+j)*2+1] = c12;
+ c6 /= 6.0;
+ c12 /= 12.0;
+
bCombGeom = bCombGeom &&
gmx_within_tol(c6*c6 ,nbfp[(i*ntype+i)*2 ]*nbfp[(j*ntype+j)*2 ],tol) &&
gmx_within_tol(c12*c12,nbfp[(i*ntype+i)*2+1]*nbfp[(j*ntype+j)*2+1],tol);
pmalloc((void**)&ftmp, tabsize*sizeof(*ftmp));
- table_spline3_fill_ewald_lr(ftmp, NULL, tabsize, tableformatF,
+ table_spline3_fill_ewald_lr(ftmp, NULL, NULL, tabsize,
1/tabscale, nbp->ewald_beta);
/* If the table pointer == NULL the table is generated the first time =>
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
{
if (gmx_debug_at)
{
- fprintf(debug,"reallocating neigborlist il_code=%d, maxnri=%d\n",
- nl->il_code,nl->maxnri);
+ fprintf(debug,"reallocating neigborlist (ielec=%d, ivdw=%d, igeometry=%d, free_energy=%d), maxnri=%d\n",
+ nl->ielec,nl->ivdw,nl->igeometry,nl->free_energy,nl->maxnri);
}
srenew(nl->iinr, nl->maxnri);
- if (nl->enlist == enlistCG_CG)
+ if (nl->igeometry == GMX_NBLIST_GEOMETRY_CG_CG)
{
srenew(nl->iinr_end,nl->maxnri);
}
srenew(nl->jindex, nl->maxnri+1);
}
-/* ivdw/icoul are used to determine the type of interaction, so we
- * can set an innerloop index here. The obvious choice for this would have
- * been the vdwtype/coultype values in the forcerecord, but unfortunately
- * those types are braindead - for instance both Buckingham and normal
- * Lennard-Jones use the same value (evdwCUT), and a separate gmx_boolean variable
- * to determine which interaction is used. There is further no special value
- * for 'no interaction'. For backward compatibility with old TPR files we won't
- * change this in the 3.x series, so when calling this routine you should use:
- *
- * icoul=0 no coulomb interaction
- * icoul=1 cutoff standard coulomb
- * icoul=2 reaction-field coulomb
- * icoul=3 tabulated coulomb
- *
- * ivdw=0 no vdw interaction
- * ivdw=1 standard L-J interaction
- * ivdw=2 Buckingham
- * ivdw=3 tabulated vdw.
- *
- * Kind of ugly, but it works.
- */
-static void init_nblist(t_nblist *nl_sr,t_nblist *nl_lr,
+
+static void init_nblist(FILE *log, t_nblist *nl_sr,t_nblist *nl_lr,
int maxsr,int maxlr,
- int ivdw, int icoul,
- gmx_bool bfree, int enlist)
+ int ivdw, int ivdwmod,
+ int ielec, int ielecmod,
+ gmx_bool bfree, int igeometry)
{
t_nblist *nl;
int homenr;
int i,nn;
- int inloop[20] =
- {
- eNR_NBKERNEL_NONE,
- eNR_NBKERNEL010,
- eNR_NBKERNEL020,
- eNR_NBKERNEL030,
- eNR_NBKERNEL100,
- eNR_NBKERNEL110,
- eNR_NBKERNEL120,
- eNR_NBKERNEL130,
- eNR_NBKERNEL200,
- eNR_NBKERNEL210,
- eNR_NBKERNEL220,
- eNR_NBKERNEL230,
- eNR_NBKERNEL300,
- eNR_NBKERNEL310,
- eNR_NBKERNEL320,
- eNR_NBKERNEL330,
- eNR_NBKERNEL400,
- eNR_NBKERNEL410,
- eNR_NBKERNEL_NONE,
- eNR_NBKERNEL430
- };
-
for(i=0; (i<2); i++)
{
nl = (i == 0) ? nl_sr : nl_lr;
{
continue;
}
-
+
+
/* Set coul/vdw in neighborlist, and for the normal loops we determine
* an index of which one to call.
*/
- nl->ivdw = ivdw;
- nl->icoul = icoul;
+ nl->ivdw = ivdw;
+ nl->ivdwmod = ivdwmod;
+ nl->ielec = ielec;
+ nl->ielecmod = ielecmod;
nl->free_energy = bfree;
-
+ nl->igeometry = igeometry;
+
if (bfree)
{
- nl->enlist = enlistATOM_ATOM;
- nl->il_code = eNR_NBKERNEL_FREE_ENERGY;
+ nl->igeometry = GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE;
}
- else
- {
- nl->enlist = enlist;
-
- nn = inloop[4*icoul + ivdw];
-
- /* solvent loops follow directly after the corresponding
- * ordinary loops, in the order:
- *
- * SPC, SPC-SPC, TIP4p, TIP4p-TIP4p
- *
- */
- switch (enlist) {
- case enlistATOM_ATOM:
- case enlistCG_CG:
- break;
- case enlistSPC_ATOM: nn += 1; break;
- case enlistSPC_SPC: nn += 2; break;
- case enlistTIP4P_ATOM: nn += 3; break;
- case enlistTIP4P_TIP4P: nn += 4; break;
- }
-
- nl->il_code = nn;
- }
-
- if (debug)
- fprintf(debug,"Initiating neighbourlist type %d for %s interactions,\nwith %d SR, %d LR atoms.\n",
- nl->il_code,ENLISTTYPE(enlist),maxsr,maxlr);
+
+ gmx_nonbonded_set_kernel_pointers( (i==0) ? log : NULL,nl);
/* maxnri is influenced by the number of shifts (maximum is 8)
* and the number of energy groups.
nl->jindex = NULL;
reallocate_nblist(nl);
nl->jindex[0] = 0;
+
+ if(debug)
+ {
+ fprintf(debug,"Initiating neighbourlist (ielec=%d, ivdw=%d, free=%d) for %s interactions,\nwith %d SR, %d LR atoms.\n",
+ nl->ielec,nl->ivdw,nl->free_energy,gmx_nblist_geometry_names[nl->igeometry],maxsr,maxlr);
+ }
+
#ifdef GMX_THREAD_SHM_FDECOMP
nl->counter = 0;
snew(nl->mtx,1);
* cache trashing.
*/
int maxsr,maxsr_wat,maxlr,maxlr_wat;
- int icoul,icoulf,ivdw;
+ int ielec,ielecf,ivdw,ielecmod,ielecmodf,ivdwmod;
int solvent;
- int enlist_def,enlist_w,enlist_ww;
+ int igeometry_def,igeometry_w,igeometry_ww;
int i;
t_nblists *nbl;
maxlr = maxlr_wat = 0;
}
- /* Determine the values for icoul/ivdw. */
- /* Start with GB */
- if(fr->bGB)
- {
- icoul=enbcoulGB;
- }
- else if (fr->bcoultab)
- {
- icoul = enbcoulTAB;
- }
- else if (EEL_RF(fr->eeltype))
- {
- icoul = enbcoulRF;
- }
- else
- {
- icoul = enbcoulOOR;
- }
-
- if (fr->bvdwtab)
- {
- ivdw = enbvdwTAB;
- }
- else if (fr->bBHAM)
- {
- ivdw = enbvdwBHAM;
- }
- else
- {
- ivdw = enbvdwLJ;
- }
+ /* Determine the values for ielec/ivdw. */
+ ielec = fr->nbkernel_elec_interaction;
+ ivdw = fr->nbkernel_vdw_interaction;
+ ielecmod = fr->nbkernel_elec_modifier;
+ ivdwmod = fr->nbkernel_vdw_modifier;
fr->ns.bCGlist = (getenv("GMX_NBLISTCG") != 0);
if (!fr->ns.bCGlist)
{
- enlist_def = enlistATOM_ATOM;
+ igeometry_def = GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE;
}
else
{
- enlist_def = enlistCG_CG;
+ igeometry_def = GMX_NBLIST_GEOMETRY_CG_CG;
if (log != NULL)
{
fprintf(log,"\nUsing charge-group - charge-group neighbor lists and kernels\n\n");
}
if (fr->solvent_opt == esolTIP4P) {
- enlist_w = enlistTIP4P_ATOM;
- enlist_ww = enlistTIP4P_TIP4P;
+ igeometry_w = GMX_NBLIST_GEOMETRY_WATER4_PARTICLE;
+ igeometry_ww = GMX_NBLIST_GEOMETRY_WATER4_WATER4;
} else {
- enlist_w = enlistSPC_ATOM;
- enlist_ww = enlistSPC_SPC;
+ igeometry_w = GMX_NBLIST_GEOMETRY_WATER3_PARTICLE;
+ igeometry_ww = GMX_NBLIST_GEOMETRY_WATER3_WATER3;
}
for(i=0; i<fr->nnblists; i++)
{
nbl = &(fr->nblists[i]);
- init_nblist(&nbl->nlist_sr[eNL_VDWQQ],&nbl->nlist_lr[eNL_VDWQQ],
- maxsr,maxlr,ivdw,icoul,FALSE,enlist_def);
- init_nblist(&nbl->nlist_sr[eNL_VDW],&nbl->nlist_lr[eNL_VDW],
- maxsr,maxlr,ivdw,0,FALSE,enlist_def);
- init_nblist(&nbl->nlist_sr[eNL_QQ],&nbl->nlist_lr[eNL_QQ],
- maxsr,maxlr,0,icoul,FALSE,enlist_def);
- init_nblist(&nbl->nlist_sr[eNL_VDWQQ_WATER],&nbl->nlist_lr[eNL_VDWQQ_WATER],
- maxsr_wat,maxlr_wat,ivdw,icoul, FALSE,enlist_w);
- init_nblist(&nbl->nlist_sr[eNL_QQ_WATER],&nbl->nlist_lr[eNL_QQ_WATER],
- maxsr_wat,maxlr_wat,0,icoul, FALSE,enlist_w);
- init_nblist(&nbl->nlist_sr[eNL_VDWQQ_WATERWATER],&nbl->nlist_lr[eNL_VDWQQ_WATERWATER],
- maxsr_wat,maxlr_wat,ivdw,icoul, FALSE,enlist_ww);
- init_nblist(&nbl->nlist_sr[eNL_QQ_WATERWATER],&nbl->nlist_lr[eNL_QQ_WATERWATER],
- maxsr_wat,maxlr_wat,0,icoul, FALSE,enlist_ww);
+ init_nblist(log,&nbl->nlist_sr[eNL_VDWQQ],&nbl->nlist_lr[eNL_VDWQQ],
+ maxsr,maxlr,ivdw,ivdwmod,ielec,ielecmod,FALSE,igeometry_def);
+ init_nblist(log,&nbl->nlist_sr[eNL_VDW],&nbl->nlist_lr[eNL_VDW],
+ maxsr,maxlr,ivdw,ivdwmod,GMX_NBKERNEL_ELEC_NONE,eintmodNONE,FALSE,igeometry_def);
+ init_nblist(log,&nbl->nlist_sr[eNL_QQ],&nbl->nlist_lr[eNL_QQ],
+ maxsr,maxlr,GMX_NBKERNEL_VDW_NONE,eintmodNONE,ielec,ielecmod,FALSE,igeometry_def);
+ init_nblist(log,&nbl->nlist_sr[eNL_VDWQQ_WATER],&nbl->nlist_lr[eNL_VDWQQ_WATER],
+ maxsr_wat,maxlr_wat,ivdw,ivdwmod,ielec,ielecmod, FALSE,igeometry_w);
+ init_nblist(log,&nbl->nlist_sr[eNL_QQ_WATER],&nbl->nlist_lr[eNL_QQ_WATER],
+ maxsr_wat,maxlr_wat,GMX_NBKERNEL_VDW_NONE,eintmodNONE,ielec,ielecmod, FALSE,igeometry_w);
+ init_nblist(log,&nbl->nlist_sr[eNL_VDWQQ_WATERWATER],&nbl->nlist_lr[eNL_VDWQQ_WATERWATER],
+ maxsr_wat,maxlr_wat,ivdw,ivdwmod,ielec,ielecmod, FALSE,igeometry_ww);
+ init_nblist(log,&nbl->nlist_sr[eNL_QQ_WATERWATER],&nbl->nlist_lr[eNL_QQ_WATERWATER],
+ maxsr_wat,maxlr_wat,GMX_NBKERNEL_VDW_NONE,eintmodNONE,ielec,ielecmod, FALSE,igeometry_ww);
+
+ /* Did we get the solvent loops so we can use optimized water kernels? */
+ if(nbl->nlist_sr[eNL_VDWQQ_WATER].kernelptr_vf==NULL
+ || nbl->nlist_sr[eNL_QQ_WATER].kernelptr_vf==NULL
+#ifndef DISABLE_WATERWATER_NLIST
+ || nbl->nlist_sr[eNL_VDWQQ_WATERWATER].kernelptr_vf==NULL
+ || nbl->nlist_sr[eNL_QQ_WATERWATER].kernelptr_vf==NULL
+#endif
+ )
+ {
+ fr->solvent_opt = esolNO;
+ fprintf(log,"Note: The available nonbonded kernels do not support water optimization - disabling.\n");
+ }
if (fr->efep != efepNO)
{
if ((fr->bEwald) && (fr->sc_alphacoul > 0)) /* need to handle long range differently if using softcore */
{
- icoulf = enbcoulFEWALD;
+ ielecf = GMX_NBKERNEL_ELEC_EWALD;
+ ielecmodf = eintmodNONE;
}
else
{
- icoulf = icoul;
+ ielecf = ielec;
+ ielecmodf = ielecmod;
}
- init_nblist(&nbl->nlist_sr[eNL_VDWQQ_FREE],&nbl->nlist_lr[eNL_VDWQQ_FREE],
- maxsr,maxlr,ivdw,icoulf,TRUE,enlistATOM_ATOM);
- init_nblist(&nbl->nlist_sr[eNL_VDW_FREE],&nbl->nlist_lr[eNL_VDW_FREE],
- maxsr,maxlr,ivdw,0,TRUE,enlistATOM_ATOM);
- init_nblist(&nbl->nlist_sr[eNL_QQ_FREE],&nbl->nlist_lr[eNL_QQ_FREE],
- maxsr,maxlr,0,icoulf,TRUE,enlistATOM_ATOM);
+ init_nblist(log,&nbl->nlist_sr[eNL_VDWQQ_FREE],&nbl->nlist_lr[eNL_VDWQQ_FREE],
+ maxsr,maxlr,ivdw,ivdwmod,ielecf,ielecmod,TRUE,GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE);
+ init_nblist(log,&nbl->nlist_sr[eNL_VDW_FREE],&nbl->nlist_lr[eNL_VDW_FREE],
+ maxsr,maxlr,ivdw,ivdwmod,GMX_NBKERNEL_ELEC_NONE,eintmodNONE,TRUE,GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE);
+ init_nblist(log,&nbl->nlist_sr[eNL_QQ_FREE],&nbl->nlist_lr[eNL_QQ_FREE],
+ maxsr,maxlr,GMX_NBKERNEL_VDW_NONE,eintmodNONE,ielecf,ielecmod,TRUE,GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE);
}
}
/* QMMM MM list */
if (fr->bQMMM && fr->qr->QMMMscheme != eQMMMschemeoniom)
{
- init_nblist(&fr->QMMMlist,NULL,
- maxsr,maxlr,0,icoul,FALSE,enlistATOM_ATOM);
+ init_nblist(log,&fr->QMMMlist,NULL,
+ maxsr,maxlr,0,0,ielec,ielecmod,FALSE,GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE);
+ }
+
+ if(log!=NULL)
+ {
+ fprintf(log,"\n");
}
fr->ns.nblist_initialized=TRUE;
}
}
-static void reset_neighbor_list(t_forcerec *fr,gmx_bool bLR,int nls,int eNL)
+static void reset_neighbor_lists(t_forcerec *fr,gmx_bool bResetSR, gmx_bool bResetLR)
{
int n,i;
- if (bLR)
+ if (fr->bQMMM)
{
- reset_nblist(&(fr->nblists[nls].nlist_lr[eNL]));
+ /* only reset the short-range nblist */
+ reset_nblist(&(fr->QMMMlist));
}
- else
+
+ for(n=0; n<fr->nnblists; n++)
{
- for(n=0; n<fr->nnblists; n++)
+ for(i=0; i<eNL_NR; i++)
{
- for(i=0; i<eNL_NR; i++)
+ if(bResetSR)
{
- reset_nblist(&(fr->nblists[n].nlist_sr[i]));
+ reset_nblist( &(fr->nblists[n].nlist_sr[i]) );
+ }
+ if(bResetLR)
+ {
+ reset_nblist( &(fr->nblists[n].nlist_lr[i]) );
}
- }
- if (fr->bQMMM)
- {
- /* only reset the short-range nblist */
- reset_nblist(&(fr->QMMMlist));
}
}
}
}
}
-static inline void close_neighbor_list(t_forcerec *fr,gmx_bool bLR,int nls,int eNL,
- gmx_bool bMakeQMMMnblist)
+static inline void close_neighbor_lists(t_forcerec *fr,gmx_bool bMakeQMMMnblist)
{
int n,i;
- if (bMakeQMMMnblist) {
- if (!bLR)
- {
+ if (bMakeQMMMnblist)
+ {
close_nblist(&(fr->QMMMlist));
- }
}
- else
+
+ for(n=0; n<fr->nnblists; n++)
{
- if (bLR)
+ for(i=0; (i<eNL_NR); i++)
{
- close_nblist(&(fr->nblists[nls].nlist_lr[eNL]));
- }
- else
- {
- for(n=0; n<fr->nnblists; n++)
- {
- for(i=0; (i<eNL_NR); i++)
- {
- close_nblist(&(fr->nblists[n].nlist_sr[i]));
- }
- }
+ close_nblist(&(fr->nblists[n].nlist_sr[i]));
+ close_nblist(&(fr->nblists[n].nlist_lr[i]));
}
}
}
+
static inline void add_j_to_nblist(t_nblist *nlist,atom_id j_atom,gmx_bool bLR)
{
int nrj=nlist->nrj;
{
nlist->maxnrj = over_alloc_small(nlist->nrj + 1);
if (gmx_debug_at)
- fprintf(debug,"Increasing %s nblist %s j size to %d\n",
- bLR ? "LR" : "SR",nrnb_str(nlist->il_code),nlist->maxnrj);
+ fprintf(debug,"Increasing %s nblist (ielec=%d,ivdw=%d,free=%d,igeometry=%d) j size to %d\n",
+ bLR ? "LR" : "SR",nlist->ielec,nlist->ivdw,nlist->free_energy,nlist->igeometry,nlist->maxnrj);
srenew(nlist->jjnr,nlist->maxnrj);
}
{
nlist->maxnrj = over_alloc_small(nlist->nrj + 1);
if (gmx_debug_at)
- fprintf(debug,"Increasing %s nblist %s j size to %d\n",
- bLR ? "LR" : "SR",nrnb_str(nlist->il_code),nlist->maxnrj);
+ fprintf(debug,"Increasing %s nblist (ielec=%d,ivdw=%d,free=%d,igeometry=%d) j size to %d\n",
+ bLR ? "LR" : "SR",nlist->ielec,nlist->ivdw,nlist->free_energy,nlist->igeometry,nlist->maxnrj);
srenew(nlist->jjnr ,nlist->maxnrj);
srenew(nlist->jjnr_end,nlist->maxnrj);
t_excl bExcl[],
int shift,
t_forcerec * fr,
- gmx_bool bLR,
- gmx_bool bDoVdW,
- gmx_bool bDoCoul);
+ gmx_bool bLR,
+ gmx_bool bDoVdW,
+ gmx_bool bDoCoul,
+ int solvent_opt);
static void
put_in_list_at(gmx_bool bHaveVdW[],
t_excl bExcl[],
int shift,
t_forcerec * fr,
- gmx_bool bLR,
- gmx_bool bDoVdW,
- gmx_bool bDoCoul)
+ gmx_bool bLR,
+ gmx_bool bDoVdW,
+ gmx_bool bDoCoul,
+ int solvent_opt)
{
/* The a[] index has been removed,
* to put it back in i_atom should be a[i0] and jj should be a[jj].
/* Get the i charge group info */
igid = GET_CGINFO_GID(cginfo[icg]);
- iwater = GET_CGINFO_SOLOPT(cginfo[icg]);
+
+ iwater = (solvent_opt!=esolNO) ? GET_CGINFO_SOLOPT(cginfo[icg]) : esolNO;
bFreeEnergy = FALSE;
if (md->nPerturbed)
t_excl bExcl[],
int shift,
t_forcerec * fr,
- gmx_bool bLR,
- gmx_bool bDoVdW,
- gmx_bool bDoCoul)
+ gmx_bool bLR,
+ gmx_bool bDoVdW,
+ gmx_bool bDoCoul,
+ int solvent_opt)
{
t_nblist * coul;
int i,j,jcg,igid,gid;
t_excl bExcl[],
int shift,
t_forcerec * fr,
- gmx_bool bLR,
- gmx_bool bDoVdW,
- gmx_bool bDoCoul)
+ gmx_bool bLR,
+ gmx_bool bDoVdW,
+ gmx_bool bDoCoul,
+ int solvent_opt)
{
int cginfo;
int igid,gid,nbl_ind;
if (nsbuf->nj + nrj > MAX_CG)
{
put_in_list(bHaveVdW,ngid,md,icg,jgid,nsbuf->ncg,nsbuf->jcg,
- cgs->index,bexcl,shift,fr,FALSE,TRUE,TRUE);
+ cgs->index,bexcl,shift,fr,FALSE,TRUE,TRUE,fr->solvent_opt);
/* Reset buffer contents */
nsbuf->ncg = nsbuf->nj = 0;
}
}
}
}
- }
+ }
else
{
for(j=0; (j<njcg); j++)
if (nsbuf->ncg > 0)
{
put_in_list(bHaveVdW,ngid,md,icg,nn,nsbuf->ncg,nsbuf->jcg,
- cgs->index,bexcl,k,fr,FALSE,TRUE,TRUE);
+ cgs->index,bexcl,k,fr,FALSE,TRUE,TRUE,fr->solvent_opt);
nsbuf->ncg=nsbuf->nj=0;
}
}
/* setexcl(nri,i_atoms,excl,FALSE,bexcl); */
setexcl(cgs->index[icg],cgs->index[icg+1],excl,FALSE,bexcl);
}
- close_neighbor_list(fr,FALSE,-1,-1,FALSE);
+ close_neighbor_lists(fr,FALSE);
return nsearch;
}
*
****************************************************/
-static void do_longrange(t_commrec *cr,gmx_localtop_t *top,t_forcerec *fr,
- int ngid,t_mdatoms *md,int icg,
- int jgid,int nlr,
- atom_id lr[],t_excl bexcl[],int shift,
- rvec x[],rvec box_size,t_nrnb *nrnb,
- real *lambda,real *dvdlambda,
- gmx_grppairener_t *grppener,
- gmx_bool bDoVdW,gmx_bool bDoCoul,
- gmx_bool bEvaluateNow,put_in_list_t *put_in_list,
- gmx_bool bHaveVdW[],
- gmx_bool bDoForces,rvec *f)
-{
- int n,i;
- t_nblist *nl;
-
- for(n=0; n<fr->nnblists; n++)
- {
- for(i=0; (i<eNL_NR); i++)
- {
- nl = &fr->nblists[n].nlist_lr[i];
- if ((nl->nri > nl->maxnri-32) || bEvaluateNow)
- {
- close_neighbor_list(fr,TRUE,n,i,FALSE);
- /* Evaluate the energies and forces */
- do_nonbonded(cr,fr,x,f,md,NULL,
- grppener->ener[fr->bBHAM ? egBHAMLR : egLJLR],
- grppener->ener[egCOULLR],
- grppener->ener[egGB],box_size,
- nrnb,lambda,dvdlambda,n,i,
- GMX_DONB_LR | GMX_DONB_FORCES);
-
- reset_neighbor_list(fr,TRUE,n,i);
- }
- }
- }
-
- if (!bEvaluateNow)
- {
- /* Put the long range particles in a list */
- /* do_longrange is never called for QMMM */
- put_in_list(bHaveVdW,ngid,md,icg,jgid,nlr,lr,top->cgs.index,
- bexcl,shift,fr,TRUE,bDoVdW,bDoCoul);
- }
-}
static void get_cutoff2(t_forcerec *fr,gmx_bool bDoLongRange,
real *rvdw2,real *rcoul2,
real *rs2,real *rm2,real *rl2)
{
*rs2 = sqr(fr->rlist);
+
if (bDoLongRange && fr->bTwinRange)
{
/* The VdW and elec. LR cut-off's could be different,
snew(ns->nlr_ljc,ngid);
snew(ns->nlr_one,ngid);
- if (rm2 > rs2)
- {
- /* Long range VdW and Coul buffers */
- snew(ns->nl_lr_ljc,ngid);
- }
- if (rl2 > rm2)
- {
- /* Long range VdW or Coul only buffers */
- snew(ns->nl_lr_one,ngid);
- }
+ /* Always allocate both list types, since rcoulomb might now change with PME load balancing */
+ /* Long range VdW and Coul buffers */
+ snew(ns->nl_lr_ljc,ngid);
+ /* Long range VdW or Coul only buffers */
+ snew(ns->nl_lr_one,ngid);
+
for(j=0; (j<ngid); j++) {
snew(ns->nl_sr[j],MAX_CG);
- if (rm2 > rs2)
- {
- snew(ns->nl_lr_ljc[j],MAX_CG);
- }
- if (rl2 > rm2)
- {
- snew(ns->nl_lr_one[j],MAX_CG);
- }
+ snew(ns->nl_lr_ljc[j],MAX_CG);
+ snew(ns->nl_lr_one[j],MAX_CG);
}
if (debug)
{
gmx_grppairener_t *grppener,
put_in_list_t *put_in_list,
gmx_bool bHaveVdW[],
- gmx_bool bDoLongRange,gmx_bool bDoForces,rvec *f,
- gmx_bool bMakeQMMMnblist)
+ gmx_bool bDoLongRange,gmx_bool bMakeQMMMnblist)
{
gmx_ns_t *ns;
atom_id **nl_lr_ljc,**nl_lr_one,**nl_sr;
{
if (nsr[jgid] >= MAX_CG)
{
+ /* Add to short-range list */
put_in_list(bHaveVdW,ngid,md,icg,jgid,
nsr[jgid],nl_sr[jgid],
cgs->index,/* cgsatoms, */ bexcl,
- shift,fr,FALSE,TRUE,TRUE);
+ shift,fr,FALSE,TRUE,TRUE,fr->solvent_opt);
nsr[jgid]=0;
}
nl_sr[jgid][nsr[jgid]++]=jjcg;
{
if (nlr_ljc[jgid] >= MAX_CG)
{
- do_longrange(cr,top,fr,ngid,md,icg,jgid,
- nlr_ljc[jgid],
- nl_lr_ljc[jgid],bexcl,shift,x,
- box_size,nrnb,
- lambda,dvdlambda,
- grppener,
- TRUE,TRUE,FALSE,
- put_in_list,
- bHaveVdW,
- bDoForces,f);
+ /* Add to LJ+coulomb long-range list */
+ put_in_list(bHaveVdW,ngid,md,icg,jgid,
+ nlr_ljc[jgid],nl_lr_ljc[jgid],top->cgs.index,
+ bexcl,shift,fr,TRUE,TRUE,TRUE,fr->solvent_opt);
nlr_ljc[jgid]=0;
}
nl_lr_ljc[jgid][nlr_ljc[jgid]++]=jjcg;
}
else
{
- if (nlr_one[jgid] >= MAX_CG) {
- do_longrange(cr,top,fr,ngid,md,icg,jgid,
- nlr_one[jgid],
- nl_lr_one[jgid],bexcl,shift,x,
- box_size,nrnb,
- lambda,dvdlambda,
- grppener,
- rvdw_lt_rcoul,rcoul_lt_rvdw,FALSE,
- put_in_list,
- bHaveVdW,
- bDoForces,f);
+ if (nlr_one[jgid] >= MAX_CG)
+ {
+ /* Add to long-range list with only coul, or only LJ */
+ put_in_list(bHaveVdW,ngid,md,icg,jgid,
+ nlr_one[jgid],nl_lr_one[jgid],top->cgs.index,
+ bexcl,shift,fr,TRUE,rvdw_lt_rcoul,rcoul_lt_rvdw,fr->solvent_opt);
nlr_one[jgid]=0;
}
nl_lr_one[jgid][nlr_one[jgid]++]=jjcg;
{
put_in_list(bHaveVdW,ngid,md,icg,nn,nsr[nn],nl_sr[nn],
cgs->index, /* cgsatoms, */ bexcl,
- shift,fr,FALSE,TRUE,TRUE);
+ shift,fr,FALSE,TRUE,TRUE,fr->solvent_opt);
}
if (nlr_ljc[nn] > 0)
{
- do_longrange(cr,top,fr,ngid,md,icg,nn,nlr_ljc[nn],
- nl_lr_ljc[nn],bexcl,shift,x,box_size,nrnb,
- lambda,dvdlambda,grppener,TRUE,TRUE,FALSE,
- put_in_list,bHaveVdW,bDoForces,f);
+ put_in_list(bHaveVdW,ngid,md,icg,nn,nlr_ljc[nn],
+ nl_lr_ljc[nn],top->cgs.index,
+ bexcl,shift,fr,TRUE,TRUE,TRUE,fr->solvent_opt);
}
if (nlr_one[nn] > 0)
{
- do_longrange(cr,top,fr,ngid,md,icg,nn,nlr_one[nn],
- nl_lr_one[nn],bexcl,shift,x,box_size,nrnb,
- lambda,dvdlambda,grppener,
- rvdw_lt_rcoul,rcoul_lt_rvdw,FALSE,
- put_in_list,bHaveVdW,bDoForces,f);
+ put_in_list(bHaveVdW,ngid,md,icg,nn,nlr_one[nn],
+ nl_lr_one[nn],top->cgs.index,
+ bexcl,shift,fr,TRUE,rvdw_lt_rcoul,rcoul_lt_rvdw,fr->solvent_opt);
}
}
}
/* setexcl(nri,i_atoms,&top->atoms.excl,FALSE,bexcl); */
setexcl(cgs->index[icg],cgs->index[icg+1],&top->excls,FALSE,bexcl);
}
- /* Perform any left over force calculations */
- for (nn=0; (nn<ngid); nn++)
- {
- if (rm2 > rs2)
- {
- do_longrange(cr,top,fr,0,md,icg,nn,nlr_ljc[nn],
- nl_lr_ljc[nn],bexcl,shift,x,box_size,nrnb,
- lambda,dvdlambda,grppener,
- TRUE,TRUE,TRUE,put_in_list,bHaveVdW,bDoForces,f);
- }
- if (rl2 > rm2) {
- do_longrange(cr,top,fr,0,md,icg,nn,nlr_one[nn],
- nl_lr_one[nn],bexcl,shift,x,box_size,nrnb,
- lambda,dvdlambda,grppener,
- rvdw_lt_rcoul,rcoul_lt_rvdw,
- TRUE,put_in_list,bHaveVdW,bDoForces,f);
- }
- }
+ /* No need to perform any left-over force calculations anymore (as we used to do here)
+ * since we now save the proper long-range lists for later evaluation.
+ */
+
debug_gmx();
-
- /* Close off short range neighbourlists */
- close_neighbor_list(fr,FALSE,-1,-1,bMakeQMMMnblist);
+
+ /* Close neighbourlists */
+ close_neighbor_lists(fr,bMakeQMMMnblist);
return nns;
}
real *lambda,real *dvdlambda,
gmx_grppairener_t *grppener,
gmx_bool bFillGrid,
- gmx_bool bDoLongRange,
- gmx_bool bDoForces,rvec *f)
+ gmx_bool bDoLongRangeNS)
{
t_block *cgs=&(top->cgs);
rvec box_size,grid_x0,grid_x1;
t_grid *grid;
gmx_domdec_zones_t *dd_zones;
put_in_list_t *put_in_list;
-
+
ns = &fr->ns;
/* Set some local variables */
debug_gmx();
/* Reset the neighbourlists */
- reset_neighbor_list(fr,FALSE,-1,-1);
+ reset_neighbor_lists(fr,TRUE,TRUE);
if (bGrid && bFillGrid)
{
grid,x,ns->bexcl,ns->bExcludeAlleg,
nrnb,md,lambda,dvdlambda,grppener,
put_in_list,ns->bHaveVdW,
- bDoLongRange,bDoForces,f,
- FALSE);
+ bDoLongRangeNS,FALSE);
/* neighbour searching withouth QMMM! QM atoms have zero charge in
* the classical calculation. The charge-charge interaction
grid,x,ns->bexcl,ns->bExcludeAlleg,
nrnb,md,lambda,dvdlambda,grppener,
put_in_list_qmmm,ns->bHaveVdW,
- bDoLongRange,bDoForces,f,
- TRUE);
+ bDoLongRangeNS,TRUE);
}
}
else
ngid,ns->ns_buf,put_in_list,ns->bHaveVdW);
}
debug_gmx();
-
+
#ifdef DEBUG
pr_nsblock(log);
#endif
/* we now store the LJ C6 and C12 parameters in QM rec in case
* we need to do an optimization
*/
- if(qr->qm[j]->bOPT || qr->qm[j]->bTS){
- for(i=0;i<qm_nr;i++){
- qr->qm[j]->c6[i] = C6(fr->nbfp,mtop->ffparams.atnr,
- atom->type,atom->type)/c6au;
- qr->qm[j]->c12[i] = C12(fr->nbfp,mtop->ffparams.atnr,
- atom->type,atom->type)/c12au;
- }
+ if(qr->qm[j]->bOPT || qr->qm[j]->bTS)
+ {
+ for(i=0;i<qm_nr;i++)
+ {
+ /* nbfp now includes the 6.0/12.0 derivative prefactors */
+ qr->qm[j]->c6[i] = C6(fr->nbfp,mtop->ffparams.atnr,atom->type,atom->type)/c6au/6.0;
+ qr->qm[j]->c12[i] = C12(fr->nbfp,mtop->ffparams.atnr,atom->type,atom->type)/c12au/12.0;
+ }
}
/* now we check for frontier QM atoms. These occur in pairs that
* construct the vsite
/* store QM atoms in the QMrec and initialise
*/
init_QMrec(0,qr->qm[0],qm_nr,qm_arr,mtop,ir);
- if(qr->qm[0]->bOPT || qr->qm[0]->bTS){
- for(i=0;i<qm_nr;i++){
- gmx_mtop_atomnr_to_atom(alook,qm_arr[i],&atom);
- qr->qm[0]->c6[i] = C6(fr->nbfp,mtop->ffparams.atnr,
- atom->type,atom->type)/c6au;
- qr->qm[0]->c12[i] = C12(fr->nbfp,mtop->ffparams.atnr,
- atom->type,atom->type)/c12au;
- }
-
+ if(qr->qm[0]->bOPT || qr->qm[0]->bTS)
+ {
+ for(i=0;i<qm_nr;i++)
+ {
+ gmx_mtop_atomnr_to_atom(alook,qm_arr[i],&atom);
+ /* nbfp now includes the 6.0/12.0 derivative prefactors */
+ qr->qm[0]->c6[i] = C6(fr->nbfp,mtop->ffparams.atnr,atom->type,atom->type)/c6au/6.0;
+ qr->qm[0]->c12[i] = C12(fr->nbfp,mtop->ffparams.atnr,atom->type,atom->type)/c12au/12.0;
+ }
}
-
-
/* find frontier atoms and mark them true in the frontieratoms array.
*/
*/
srenew(mm->c6,mm->nrMMatoms);
srenew(mm->c12,mm->nrMMatoms);
- for (i=0;i<mm->nrMMatoms;i++){
- mm->c6[i] = C6(fr->nbfp,top->idef.atnr,
- md->typeA[mm->indexMM[i]],
- md->typeA[mm->indexMM[i]])/c6au;
- mm->c12[i] =C12(fr->nbfp,top->idef.atnr,
- md->typeA[mm->indexMM[i]],
- md->typeA[mm->indexMM[i]])/c12au;
+ for (i=0;i<mm->nrMMatoms;i++)
+ {
+ /* nbfp now includes the 6.0/12.0 derivative prefactors */
+ mm->c6[i] = C6(fr->nbfp,top->idef.atnr,md->typeA[mm->indexMM[i]],md->typeA[mm->indexMM[i]])/c6au/6.0;
+ mm->c12[i] =C12(fr->nbfp,top->idef.atnr,md->typeA[mm->indexMM[i]],md->typeA[mm->indexMM[i]])/c12au/12.0;
}
punch_QMMM_excl(qr->qm[0],mm,&(top->excls));
}
bNS = (flags & GMX_FORCE_NS) && (fr->bAllvsAll==FALSE);
bFillGrid = (bNS && bStateChanged);
bCalcCGCM = (bFillGrid && !DOMAINDECOMP(cr));
- bDoLongRange = (fr->bTwinRange && bNS && (flags & GMX_FORCE_DOLR));
+ bDoLongRange = (fr->bTwinRange && bNS && (flags & GMX_FORCE_DO_LR));
bDoForces = (flags & GMX_FORCE_FORCES);
bSepLRF = (bDoLongRange && bDoForces && (flags & GMX_FORCE_SEPLRF));
bUseGPU = fr->nbv->bUseGPU;
}
}
- if (bSepLRF)
+ /* Clear the short- and long-range forces */
+ clear_rvecs(fr->natoms_force_constr,f);
+ if(bSepLRF && do_per_step(step,inputrec->nstcalclr))
{
- /* Add the long range forces to the short range forces */
- for(i=0; i<fr->natoms_force_constr; i++)
- {
- copy_rvec(fr->f_twin[i],f[i]);
- }
+ clear_rvecs(fr->natoms_force_constr,fr->f_twin);
}
- else if (!(fr->bTwinRange && bNS))
- {
- /* Clear the short-range forces */
- clear_rvecs(fr->natoms_force_constr,f);
- }
-
+
clear_rvec(fr->vir_diag_posres);
GMX_BARRIER(cr->mpi_comm_mygroup);
/* if we use the GPU turn off the nonbonded */
do_force_lowlevel(fplog,step,fr,inputrec,&(top->idef),
cr,nrnb,wcycle,mdatoms,&(inputrec->opts),
- x,hist,f,enerd,fcd,mtop,top,fr->born,
+ x,hist,f, bSepLRF ? fr->f_twin : f,enerd,fcd,mtop,top,fr->born,
&(top->atomtypes),bBornRadii,box,
inputrec->fepvals,lambda,graph,&(top->excls),fr->mu_tot,
((nb_kernel_type == nbk8x8x8_CUDA || nb_kernel_type == nbk8x8x8_PlainC)
? flags&~GMX_FORCE_NONBONDED : flags),
&cycles_pme);
+ if(bSepLRF)
+ {
+ if (do_per_step(step,inputrec->nstcalclr))
+ {
+ /* Add the long range forces to the short range forces */
+ for(i=0; i<fr->natoms_force_constr; i++)
+ {
+ rvec_add(fr->f_twin[i],f[i],f[i]);
+ }
+ }
+ }
+
if (!bUseOrEmulGPU)
{
/* Maybe we should move this into do_force_lowlevel */
int start,homenr;
double mu[2*DIM];
gmx_bool bSepDVDL,bStateChanged,bNS,bFillGrid,bCalcCGCM,bBS;
- gmx_bool bDoLongRange,bDoForces,bSepLRF;
+ gmx_bool bDoLongRangeNS,bDoForces,bDoPotential,bSepLRF;
gmx_bool bDoAdressWF;
matrix boxs;
rvec vzero,box_diag;
}
}
- bStateChanged = (flags & GMX_FORCE_STATECHANGED);
- bNS = (flags & GMX_FORCE_NS) && (fr->bAllvsAll==FALSE);
- bFillGrid = (bNS && bStateChanged);
- bCalcCGCM = (bFillGrid && !DOMAINDECOMP(cr));
- bDoLongRange = (fr->bTwinRange && bNS && (flags & GMX_FORCE_DOLR));
- bDoForces = (flags & GMX_FORCE_FORCES);
- bSepLRF = (bDoLongRange && bDoForces && (flags & GMX_FORCE_SEPLRF));
+ bStateChanged = (flags & GMX_FORCE_STATECHANGED);
+ bNS = (flags & GMX_FORCE_NS) && (fr->bAllvsAll==FALSE);
+ /* Should we update the long-range neighborlists at this step? */
+ bDoLongRangeNS = fr->bTwinRange && bNS;
+ /* Should we perform the long-range nonbonded evaluation inside the neighborsearching? */
+ bFillGrid = (bNS && bStateChanged);
+ bCalcCGCM = (bFillGrid && !DOMAINDECOMP(cr));
+ bDoForces = (flags & GMX_FORCE_FORCES);
+ bDoPotential = (flags & GMX_FORCE_ENERGY);
+ bSepLRF = ((inputrec->nstcalclr>1) && bDoForces &&
+ (flags & GMX_FORCE_SEPLRF) && (flags & GMX_FORCE_DO_LR));
+
/* should probably move this to the forcerec since it doesn't change */
bDoAdressWF = ((fr->adress_type!=eAdressOff));
mk_mshift(fplog,graph,fr->ePBC,box,x);
}
- /* Reset long range forces if necessary */
- if (fr->bTwinRange)
- {
- /* Reset the (long-range) forces if necessary */
- clear_rvecs(fr->natoms_force_constr,bSepLRF ? fr->f_twin : f);
- }
-
/* Do the actual neighbour searching and if twin range electrostatics
* also do the calculation of long range forces and energies.
*/
ns(fplog,fr,x,box,
groups,&(inputrec->opts),top,mdatoms,
cr,nrnb,lambda,dvdlambda,&enerd->grpp,bFillGrid,
- bDoLongRange,bDoForces,bSepLRF ? fr->f_twin : f);
+ bDoLongRangeNS);
if (bSepDVDL)
{
fprintf(fplog,sepdvdlformat,"LR non-bonded",0.0,dvdlambda);
}
}
- if (bSepLRF)
- {
- /* Add the long range forces to the short range forces */
- for(i=0; i<fr->natoms_force_constr; i++)
- {
- copy_rvec(fr->f_twin[i],f[i]);
- }
- }
- else if (!(fr->bTwinRange && bNS))
+ /* Clear the short- and long-range forces */
+ clear_rvecs(fr->natoms_force_constr,f);
+ if(bSepLRF && do_per_step(step,inputrec->nstcalclr))
{
- /* Clear the short-range forces */
- clear_rvecs(fr->natoms_force_constr,f);
+ clear_rvecs(fr->natoms_force_constr,fr->f_twin);
}
-
+
clear_rvec(fr->vir_diag_posres);
GMX_BARRIER(cr->mpi_comm_mygroup);
/* Compute the bonded and non-bonded energies and optionally forces */
do_force_lowlevel(fplog,step,fr,inputrec,&(top->idef),
cr,nrnb,wcycle,mdatoms,&(inputrec->opts),
- x,hist,f,enerd,fcd,mtop,top,fr->born,
+ x,hist,f, bSepLRF ? fr->f_twin : f,enerd,fcd,mtop,top,fr->born,
&(top->atomtypes),bBornRadii,box,
inputrec->fepvals,lambda,
graph,&(top->excls),fr->mu_tot,
flags,
&cycles_pme);
+ if(bSepLRF)
+ {
+ if (do_per_step(step,inputrec->nstcalclr))
+ {
+ /* Add the long range forces to the short range forces */
+ for(i=0; i<fr->natoms_force_constr; i++)
+ {
+ rvec_add(fr->f_twin[i],f[i],f[i]);
+ }
+ }
+ }
+
cycles_force = wallcycle_stop(wcycle,ewcFORCE);
GMX_BARRIER(cr->mpi_comm_mygroup);
double r0,r1,r,rc3,rc9,ea,eb,ec,pa,pb,pc,pd;
double invscale,invscale2,invscale3;
int ri0,ri1,ri,i,offstart,offset;
- real scale,*vdwtab;
+ real scale,*vdwtab,tabfactor,tmp;
fr->enershiftsix = 0;
fr->enershifttwelve = 0;
"With dispersion correction rvdw-switch can not be zero "
"for vdw-type = %s",evdw_names[fr->vdwtype]);
- scale = fr->nblists[0].tab.scale;
- vdwtab = fr->nblists[0].vdwtab;
+ scale = fr->nblists[0].table_elec_vdw.scale;
+ vdwtab = fr->nblists[0].table_vdw.data;
/* Round the cut-offs to exact table values for precision */
ri0 = floor(fr->rvdw_switch*scale);
rc3 = r0*r0*r0;
rc9 = rc3*rc3*rc3;
- if (fr->vdwtype == evdwSHIFT) {
- /* Determine the constant energy shift below rvdw_switch */
- fr->enershiftsix = (real)(-1.0/(rc3*rc3)) - vdwtab[8*ri0];
- fr->enershifttwelve = (real)( 1.0/(rc9*rc3)) - vdwtab[8*ri0 + 4];
+ if (fr->vdwtype == evdwSHIFT)
+ {
+ /* Determine the constant energy shift below rvdw_switch.
+ * Table has a scale factor since we have scaled it down to compensate
+ * for scaling-up c6/c12 with the derivative factors to save flops in analytical kernels.
+ */
+ fr->enershiftsix = (real)(-1.0/(rc3*rc3)) - 6.0*vdwtab[8*ri0];
+ fr->enershifttwelve = (real)( 1.0/(rc9*rc3)) - 12.0*vdwtab[8*ri0 + 4];
}
/* Add the constant part from 0 to rvdw_switch.
* This integration from 0 to rvdw_switch overcounts the number
for (i=0;i<2;i++) {
enersum = 0.0; virsum = 0.0;
if (i==0)
- offstart = 0;
- else
- offstart = 4;
+ {
+ offstart = 0;
+ /* Since the dispersion table has been scaled down a factor 6.0 and the repulsion
+ * a factor 12.0 to compensate for the c6/c12 parameters inside nbfp[] being scaled
+ * up (to save flops in kernels), we need to correct for this.
+ */
+ tabfactor = 6.0;
+ }
+ else
+ {
+ offstart = 4;
+ tabfactor = 12.0;
+ }
for (ri=ri0; ri<ri1; ri++) {
r = ri*invscale;
ea = invscale3;
pc = 3.0*invscale*r*r;
pd = r*r*r;
- /* this "8" is from the packing in the vdwtab array - perhaps
- should be #define'ed? */
+ /* this "8" is from the packing in the vdwtab array - perhaps should be #define'ed? */
offset = 8*ri + offstart;
y0 = vdwtab[offset];
- f = vdwtab[offset+1];
- g = vdwtab[offset+2];
- h = vdwtab[offset+3];
-
- enersum += y0*(ea/3 + eb/2 + ec) + f*(ea/4 + eb/3 + ec/2)+
- g*(ea/5 + eb/4 + ec/3) + h*(ea/6 + eb/5 + ec/4);
- virsum += f*(pa/4 + pb/3 + pc/2 + pd) +
- 2*g*(pa/5 + pb/4 + pc/3 + pd/2) + 3*h*(pa/6 + pb/5 + pc/4 + pd/3);
+ f = vdwtab[offset+1];
+ g = vdwtab[offset+2];
+ h = vdwtab[offset+3];
+ enersum += y0*(ea/3 + eb/2 + ec) + f*(ea/4 + eb/3 + ec/2) + g*(ea/5 + eb/4 + ec/3) + h*(ea/6 + eb/5 + ec/4);
+ virsum += f*(pa/4 + pb/3 + pc/2 + pd) + 2*g*(pa/5 + pb/4 + pc/3 + pd/2) + 3*h*(pa/6 + pb/5 + pc/4 + pd/3);
}
- enersum *= 4.0*M_PI;
- virsum *= 4.0*M_PI;
+
+ enersum *= 4.0*M_PI*tabfactor;
+ virsum *= 4.0*M_PI*tabfactor;
eners[i] -= enersum;
virs[i] -= virsum;
}
/* Contribution beyond the cut-off */
eners[0] += -4.0*M_PI/(3.0*rc3);
eners[1] += 4.0*M_PI/(9.0*rc9);
- if (fr->vdw_pot_shift) {
+ if (fr->vdw_modifier==eintmodPOTSHIFT) {
/* Contribution within the cut-off */
eners[0] += -4.0*M_PI/(3.0*rc3);
eners[1] += 4.0*M_PI/(3.0*rc9);
}
}
-void table_spline3_fill_ewald_lr(real *tabf,real *tabv,
- int ntab,int tableformat,
- real dx,real beta)
+void table_spline3_fill_ewald_lr(real *table_f,
+ real *table_v,
+ real *table_fdv0,
+ int ntab,
+ real dx,
+ real beta)
{
real tab_max;
- int stride=0;
int i,i_inrange;
double dc,dc_new;
gmx_bool bOutOfRange;
* The rms force error is the max error times 1/sqrt(5)=0.45.
*/
- switch (tableformat)
- {
- case tableformatF: stride = 1; break;
- case tableformatFDV0: stride = 4; break;
- default: gmx_incons("Unknown table format");
- }
-
bOutOfRange = FALSE;
i_inrange = ntab;
v_inrange = 0;
vi = v_inrange - dc*(i - i_inrange)*dx;
}
- switch (tableformat)
+ if(table_v!=NULL)
{
- case tableformatF:
- if (tabv != NULL)
- {
- tabv[i] = vi;
- }
- break;
- case tableformatFDV0:
- tabf[i*stride+2] = vi;
- tabf[i*stride+3] = 0;
- break;
- default:
- gmx_incons("Unknown table format");
+ table_v[i] = vi;
}
if (i == 0)
if (i == ntab - 1)
{
/* Fill the table with the force, minus the derivative of the spline */
- tabf[i*stride] = -dc;
+ table_f[i] = -dc;
}
else
{
/* tab[i] will contain the average of the splines over the two intervals */
- tabf[i*stride] += -0.5*dc;
+ table_f[i] += -0.5*dc;
}
if (!bOutOfRange)
}
}
- tabf[(i-1)*stride] = -0.5*dc;
+ table_f[(i-1)] = -0.5*dc;
}
/* Currently the last value only contains half the force: double it */
- tabf[0] *= 2;
+ table_f[0] *= 2;
- if (tableformat == tableformatFDV0)
+ if(table_v!=NULL && table_fdv0!=NULL)
{
- /* Store the force difference in the second entry */
- for(i=0; i<ntab-1; i++)
+ /* Copy to FDV0 table too. Allocation occurs in forcerec.c,
+ * init_ewald_f_table().
+ */
+ for(i=0;i<ntab-1;i++)
{
- tabf[i*stride+1] = tabf[(i+1)*stride] - tabf[i*stride];
+ table_fdv0[4*i] = table_f[i];
+ table_fdv0[4*i+1] = table_f[i+1]-table_f[i];
+ table_fdv0[4*i+2] = table_v[i];
+ table_fdv0[4*i+3] = 0.0;
}
- tabf[(ntab-1)*stride+1] = -tabf[i*stride];
+ table_fdv0[4*(ntab-1)] = table_f[(ntab-1)];
+ table_fdv0[4*(ntab-1)+1] = -table_f[(ntab-1)];
+ table_fdv0[4*(ntab-1)+2] = table_v[(ntab-1)];
+ table_fdv0[4*(ntab-1)+3] = 0.0;
}
}
}
static void copy2table(int n,int offset,int stride,
- double x[],double Vtab[],double Ftab[],
+ double x[],double Vtab[],double Ftab[],real scalefactor,
real dest[])
{
/* Use double prec. for the intermediary variables
H = 0;
}
nn0 = offset + i*stride;
- dest[nn0] = Vtab[i];
- dest[nn0+1] = F;
- dest[nn0+2] = G;
- dest[nn0+3] = H;
+ dest[nn0] = scalefactor*Vtab[i];
+ dest[nn0+1] = scalefactor*F;
+ dest[nn0+2] = scalefactor*G;
+ dest[nn0+3] = scalefactor*H;
}
}
switch (tp) {
case etabLJ6:
- /* Dispersion */
- Vtab = -r6;
- Ftab = 6.0*Vtab/r;
- break;
+ /* Dispersion */
+ Vtab = -r6;
+ Ftab = 6.0*Vtab/r;
+ break;
case etabLJ6Switch:
case etabLJ6Shift:
/* Dispersion */
if (r < rc) {
- Vtab = -r6;
- Ftab = 6.0*Vtab/r;
+ Vtab = -r6;
+ Ftab = 6.0*Vtab/r;
+ break;
}
break;
case etabLJ12:
- /* Repulsion */
- Vtab = r12;
- Ftab = reppow*Vtab/r;
+ /* Repulsion */
+ Vtab = r12;
+ Ftab = reppow*Vtab/r;
break;
case etabLJ12Switch:
case etabLJ12Shift:
/* Repulsion */
if (r < rc) {
- Vtab = r12;
- Ftab = reppow*Vtab/r;
- }
+ Vtab = r12;
+ Ftab = reppow*Vtab/r;
+ }
break;
case etabLJ6Encad:
if(r < rc) {
break;
case etabLJ12Encad:
if(r < rc) {
- Vtab = r12-12.0*(rc-r)*rc6*rc6/rc-1.0*rc6*rc6;
- Ftab = 12.0*r12/r-12.0*rc6*rc6/rc;
- } else { /* r>rc */
+ Vtab = -(r6-6.0*(rc-r)*rc6/rc-rc6);
+ Ftab = -(6.0*r6/r-6.0*rc6/rc);
+ } else { /* r>rc */
Vtab = 0;
Ftab = 0;
}
if ((r > r1) && bSwitch) {
Ftab = Ftab*swi - Vtab*swi1;
Vtab = Vtab*swi;
- }
-
+ }
+
/* Convert to single precision when we store to mem */
td->v[i] = Vtab;
td->f[i] = Ftab;
gmx_bool b14only,bReadTab,bGenTab;
real x0,y0,yp;
int i,j,k,nx,nx0,tabsel[etiNR];
-
+ real scalefactor;
+
t_forcetable table;
b14only = (flags & GMX_MAKETABLES_14ONLY);
nx0 = 10;
nx = 0;
+ table.interaction = GMX_TABLE_INTERACTION_ELEC_VDWREP_VDWDISP;
+ table.format = GMX_TABLE_FORMAT_CUBICSPLINE_YFGH;
+ table.formatsize = 4;
+ table.ninteractions = 3;
+ table.stride = table.formatsize*table.ninteractions;
+
/* Check whether we have to read or generate */
bReadTab = FALSE;
bGenTab = FALSE;
* numbers per nx+1 data points. For performance reasons we want
* the table data to be aligned to 16-byte.
*/
- snew_aligned(table.tab, 12*(nx+1)*sizeof(real),16);
+ snew_aligned(table.data, 12*(nx+1)*sizeof(real),16);
for(k=0; (k<etiNR); k++) {
if (tabsel[k] != etabUSER) {
td[k].nx,b14only?"1-4 ":"",tprops[tabsel[k]].name,
td[k].tabscale);
}
- copy2table(table.n,k*4,12,td[k].x,td[k].v,td[k].f,table.tab);
+
+ /* Set scalefactor for c6/c12 tables. This is because we save flops in the non-table kernels
+ * by including the derivative constants (6.0 or 12.0) in the parameters, since
+ * we no longer calculate force in most steps. This means the c6/c12 parameters
+ * have been scaled up, so we need to scale down the table interactions too.
+ * It comes here since we need to scale user tables too.
+ */
+ if(k==etiLJ6)
+ {
+ scalefactor = 1.0/6.0;
+ }
+ else if(k==etiLJ12 && tabsel[k]!=etabEXPMIN)
+ {
+ scalefactor = 1.0/12.0;
+ }
+ else
+ {
+ scalefactor = 1.0;
+ }
+
+ copy2table(table.n,k*4,12,td[k].x,td[k].v,td[k].f,scalefactor,table.data);
if (bDebugMode() && bVerbose) {
if (b14only)
/* plot the output 5 times denser than the table data */
for(i=5*((nx0+1)/2); i<5*table.n; i++) {
x0 = i*table.r/(5*(table.n-1));
- evaluate_table(table.tab,4*k,12,table.scale,x0,&y0,&yp);
+ evaluate_table(table.data,4*k,12,table.scale,x0,&y0,&yp);
fprintf(fp,"%15.10e %15.10e %15.10e\n",x0,y0,yp);
}
gmx_fio_fclose(fp);
* use etiNR (since we only have one table, but ...)
*/
snew(td,1);
- table.r = fr->gbtabr;
- table.scale = fr->gbtabscale;
- table.scale_exp = 0;
- table.n = table.scale*table.r;
- nx0 = 0;
- nx = table.scale*table.r;
+ table.interaction = GMX_TABLE_INTERACTION_ELEC;
+ table.format = GMX_TABLE_FORMAT_CUBICSPLINE_YFGH;
+ table.r = fr->gbtabr;
+ table.scale = fr->gbtabscale;
+ table.scale_exp = 0;
+ table.n = table.scale*table.r;
+ table.formatsize = 4;
+ table.ninteractions = 1;
+ table.stride = table.formatsize*table.ninteractions;
+ nx0 = 0;
+ nx = table.scale*table.r;
/* Check whether we have to read or generate
* We will always generate a table, so remove the read code
* to do this :-)
*/
- snew_aligned(table.tab,4*nx,16);
+ snew_aligned(table.data,4*nx,16);
init_table(out,nx,nx0,table.scale,&(td[0]),!bReadTab);
}
- copy2table(table.n,0,4,td[0].x,td[0].v,td[0].f,table.tab);
+ copy2table(table.n,0,4,td[0].x,td[0].v,td[0].f,1.0,table.data);
if(bDebugMode())
{
{
/* x0=i*table.r/(5*table.n); */
x0=i*table.r/table.n;
- evaluate_table(table.tab,0,4,table.scale,x0,&y0,&yp);
+ evaluate_table(table.data,0,4,table.scale,x0,&y0,&yp);
fprintf(fp,"%15.10e %15.10e %15.10e\n",x0,y0,yp);
}
Ftab = (r-0.25*r*expterm)/((r2+expterm)*sqrt(r2+expterm));
- evaluate_table(table.tab,0,4,table.scale,r,&y0,&yp);
+ evaluate_table(table.data,0,4,table.scale,r,&y0,&yp);
printf("gb: i=%d, x0=%g, y0=%15.15f, Vtab=%15.15f, yp=%15.15f, Ftab=%15.15f\n",i,r, y0, Vtab, yp, Ftab);
abs_error_r=fabs(y0-Vtab);
* to do this :-)
*/
- snew_aligned(table.tab,4*nx,16);
-
- copy2table(table.n,0,4,td[0].x,td[0].v,td[0].f,table.tab);
+ snew_aligned(table.data,4*nx,16);
+
+ copy2table(table.n,0,4,td[0].x,td[0].v,td[0].f,1.0,table.data);
if(bDebugMode())
{
{
/* x0=i*table.r/(5*table.n); */
x0 = i*table.r/(5*(table.n-1));
- evaluate_table(table.tab,0,4,table.scale,x0,&y0,&yp);
+ evaluate_table(table.data,0,4,table.scale,x0,&y0,&yp);
fprintf(fp,"%15.10e %15.10e %15.10e\n",x0,y0,yp);
}
done_tabledata(&(td[0]));
sfree(td);
+
+ table.interaction = GMX_TABLE_INTERACTION_ELEC_VDWREP_VDWDISP;
+ table.format = GMX_TABLE_FORMAT_CUBICSPLINE_YFGH;
+ table.formatsize = 4;
+ table.ninteractions = 3;
+ table.stride = table.formatsize*table.ninteractions;
+
return table;
}
}
tab.n = td.nx;
tab.scale = td.tabscale;
- snew(tab.tab,tab.n*4);
- copy2table(tab.n,0,4,td.x,td.v,td.f,tab.tab);
+ snew(tab.data,tab.n*4);
+ copy2table(tab.n,0,4,td.x,td.v,td.f,1.0,tab.data);
done_tabledata(&td);
return tab;
state->lambda,
NULL,fr,NULL,mu_tot,t,NULL,NULL,FALSE,
GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY |
- (bNS ? GMX_FORCE_DYNAMICBOX | GMX_FORCE_NS | GMX_FORCE_DOLR : 0) |
+ (bNS ? GMX_FORCE_DYNAMICBOX | GMX_FORCE_NS | GMX_FORCE_DO_LR : 0) |
(bStateChanged ? GMX_FORCE_STATECHANGED : 0));
cr->nnodes = nnodes;
bStateChanged = FALSE;
}
}
-static void combine_forces(int nstlist,
+static void combine_forces(int nstcalclr,
gmx_constr_t constr,
t_inputrec *ir,t_mdatoms *md,t_idef *idef,
t_commrec *cr,
NULL,NULL,nrnb,econqForce,ir->epc==epcMTTK,state->veta,state->veta);
}
- /* Add nstlist-1 times the LR force to the sum of both forces
+ /* Add nstcalclr-1 times the LR force to the sum of both forces
* and store the result in forces_lr.
*/
- nm1 = nstlist - 1;
+ nm1 = nstcalclr - 1;
for(i=start; i<nrend; i++)
{
for(d=0; d<DIM; d++)
tensor vir_con;
rvec *vcom,*xcom,*vall,*xall,*xin,*vin,*forcein,*fall,*xpall,*xprimein,*xprime;
int nth,th;
-
+
/* Running the velocity half does nothing except for velocity verlet */
if ((UpdatePart == etrtVELOCITY1 || UpdatePart == etrtVELOCITY2) &&
!EI_VV(inputrec->eI))
bNH = inputrec->etc == etcNOSEHOOVER;
bPR = ((inputrec->epc == epcPARRINELLORAHMAN) || (inputrec->epc == epcMTTK));
- if (bDoLR && inputrec->nstlist > 1 && !EI_VV(inputrec->eI)) /* get this working with VV? */
+ if (bDoLR && inputrec->nstcalclr > 1 && !EI_VV(inputrec->eI)) /* get this working with VV? */
{
- /* Store the total force + nstlist-1 times the LR force
+ /* Store the total force + nstcalclr-1 times the LR force
* in forces_lr, so it can be used in a normal update algorithm
* to produce twin time stepping.
*/
/* is this correct in the new construction? MRS */
- combine_forces(inputrec->nstlist,constr,inputrec,md,idef,cr,
+ combine_forces(inputrec->nstcalclr,constr,inputrec,md,idef,cr,
step,state,bMolPBC,
start,nrend,f,f_lr,nrnb);
force = f_lr;
/* Since wall have no charge, we can compress the table */
for(i=0; i<=tab->n; i++)
for(j=0; j<8; j++)
- tab->tab[8*i+j] = tab->tab[12*i+4+j];
+ tab->data[8*i+j] = tab->data[12*i+4+j];
}
}
}
/* The wall energy groups are always at the end of the list */
ggid = gid[i]*ngid + ngid - nwall + w;
at = type[i];
- Cd = nbfp[ntw[w]+2*at];
- Cr = nbfp[ntw[w]+2*at+1];
+ /* nbfp now includes the 6.0/12.0 derivative prefactors */
+ Cd = nbfp[ntw[w]+2*at]/6.0;
+ Cr = nbfp[ntw[w]+2*at+1]/12.0;
if (!((Cd==0 && Cr==0) || (egp_flags[ggid] & EGP_EXCL)))
{
if (w == 0)
}
tab = &(fr->wall_tab[w][gid[i]]);
tabscale = tab->scale;
- VFtab = tab->tab;
+ VFtab = tab->data;
rt = r*tabscale;
n0 = rt;
gmx_domdec_zones_t *dd_zones;
if (nblist->nri > 0) {
- fprintf(out,"il_name: %s Solvent opt: %s\n",
- nrnb_str(nblist->il_code),
- enlist_names[nblist->enlist]);
+ fprintf(out,"ielec: %d, ivdw: %d, free_energy: %d, Solvent opt: %s\n",
+ nblist->ielec,nblist->ivdw,nblist->free_energy,
+ gmx_nblist_geometry_names[nblist->igeometry]);
fprintf(out,"nri: %d npair: %d\n",nblist->nri,nblist->nrj);
if (dd) {
dd_zones = domdec_zones(dd);
if (nDNL >= 2) {
for(i=0; i<nblist->nri; i++) {
nii = 1;
- if (nDNL >= 3 && nblist->enlist != enlistATOM_ATOM)
+ if (nDNL >= 3 && nblist->igeometry != GMX_NBLIST_GEOMETRY_PARTICLE_PARTICLE)
nii = 3;
nj = nblist->jindex[i+1] - nblist->jindex[i];
fprintf(out,"i: %d shift: %d gid: %d nj: %d\n",
}
}
-int read_nblist(FILE *in,FILE *fp,int **mat,int natoms,gmx_bool bSymm)
-{
- gmx_bool bNL;
- char buf[256],b1[32],b2[32],solv[256],il_code[256];
- int i,ii,j,nnbl,full,icmp,nri,isolv;
- int iatom,nrj,nj,shift,gid,nargs,njtot=0;
-
- do {
- if (fgets2(buf,255,in) == NULL)
- gmx_fatal(FARGS,"EOF when looking for '%s' in logfile",header);
- } while (strstr(buf,header) == NULL);
-
- do {
- do {
- if (fgets2(buf,255,in) == NULL)
- return njtot;
- } while (strstr(buf,"nri:") == NULL);
-
- if (0) {
- if ((nargs = sscanf(buf,"%*s%s%*s%s",il_code,solv)) != 2) {
- fprintf(stderr,"Can not find the right il_code\n");
- return njtot;
- }
- for(isolv=0; (isolv<esolNR); isolv++)
- if (strstr(esol_names[isolv],solv) != NULL)
- break;
-
- if (isolv == esolNR) {
- fprintf(stderr,"Can not read il_code or solv (nargs=%d)\n",nargs);
- return njtot;
- }
- }
- else
- isolv = enlistATOM_ATOM;
-
- /* gmx_fatal(FARGS,"Can not read il_code or solv (nargs=%d)",nargs);*/
- if ((nargs = sscanf(buf,"%*s%d%*s%d",&nri,&nrj)) != 2)
- gmx_fatal(FARGS,"Can not read nri or nrj (nargs=%d)",nargs);
- for(ii=0; (ii<nri); ii++) {
- if ((nargs = fscanf(in,"%*s%d%*s%d%*s%d%*s%d",
- &iatom,&shift,&gid,&nj)) != 4)
- gmx_fatal(FARGS,"Can not read iatom, shift gid or nj (nargs=%d)",nargs);
- /* Number shifts from 1 to 27 iso 0 to 26 to distinguish uninitialized
- * matrix elements.
- */
- range_check(iatom,0,natoms);
- for(i=0; (i<nj); i++) {
- if ((nargs = fscanf(in,"%*s%d",&j)) != 1)
- gmx_fatal(FARGS,"Can not read j");
- range_check(j,0,natoms);
- switch (isolv) {
- case enlistATOM_ATOM:
- set_mat(fp,mat,iatom,1,j,1,bSymm,shift);
- njtot++;
- break;
- case enlistSPC_ATOM:
- set_mat(fp,mat,iatom,3,j,1,bSymm,shift);
- njtot+=3;
- break;
- case enlistSPC_SPC:
- set_mat(fp,mat,iatom,3,j,3,bSymm,shift);
- njtot+=9;
- break;
- case enlistTIP4P_ATOM:
- set_mat(fp,mat,iatom,4,j,1,bSymm,shift);
- njtot+=4;
- break;
- case enlistTIP4P_TIP4P:
- set_mat(fp,mat,iatom,4,j,4,bSymm,shift);
- njtot+=16;
- break;
- default:
- gmx_incons("non-existing solvent type");
- }
- }
- }
- fprintf(fp,"nri = %d nrj = %d\n",nri,nrj);
- } while (TRUE);
- return -1;
-}
+
void dump_nblist(FILE *out,t_commrec *cr,t_forcerec *fr,int nDNL)
{
snew(dvdl,efptNR);
init_neighbor_list(fp,fr,md->homenr);
search_neighbours(fp,fr,x,box,top,
- &mtop->groups,cr,&nrnb,md,lambda,dvdl,NULL,
- TRUE,FALSE,FALSE,NULL);
+ &mtop->groups,cr,&nrnb,md,lambda,dvdl,NULL,TRUE,FALSE);
if (debug)
dump_nblist(debug,cr,fr,0);
nlist = &fr->nblists[0].nlist_sr[nl_type];
- c_tabpot(fr->nblists[0].tab.scale,fr->nblists[0].tab.tab,
+ c_tabpot(fr->nblists[0].table_elec_vdw.scale,fr->nblists[0].table_elec_vdw.data,
nlist->nri,nlist->iinr,
nlist->shift,nlist->jindex,nlist->jjnr,
x[0],fr->epsfac,mdatoms->chargeA,pot,fr->shift_vec[0]);
* also do the calculation of long range forces and energies.
*/
ns(logf,fr,x,box,&mtop->groups,&(inputrec->opts),top,mdatoms,cr,
- &nrnb,&lam[0],&dum[0],&enerd->grpp,TRUE,FALSE,FALSE,NULL);
+ &nrnb,&lam[0],&dum[0],&enerd->grpp,TRUE,FALSE);
for(m=0; (m<DIM); m++)
box_size[m] = box[m][m];
for(i=0; (i<mdatoms->nr); i++)
if (bMicel)
rd_index(opt2fn("-nm",NFILE,fnm), 1, &nmic, &micelle, &micname);
-
- calc_h2order(ftp2fn(efTRX,NFILE,fnm), index, ngx, &slDipole, &slOrder,
+
+ calc_h2order(ftp2fn(efTRX,NFILE,fnm), index, ngx, &slDipole, &slOrder,
&slWidth, &nslices, top, ePBC, axis, bMicel, micelle, nmic,
oenv);
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff