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41 #include "../../topology/idef.h"
42 #include "interaction_const.h"
49 } /* fixes auto-indentation problems */
52 /* Abstract type for PME that is defined only in the routine that use them. */
53 typedef struct gmx_pme *gmx_pme_t;
54 struct nonbonded_verlet_t;
56 /* Structure describing the data in a single table */
59 enum gmx_table_interaction interaction; /* Types of interactions stored in this table */
60 enum gmx_table_format format; /* Interpolation type and data format */
62 real r; /* range of the table */
63 int n; /* n+1 is the number of table points */
64 real scale; /* distance (nm) between two table points */
65 real scale_exp; /* distance for exponential part of VdW table, not always used */
66 real * data; /* the actual table data */
68 /* Some information about the table layout. This can also be derived from the interpolation
69 * type and the table interactions, but it is convenient to have here for sanity checks, and it makes it
70 * much easier to access the tables in the nonbonded kernels when we can set the data from variables.
71 * It is always true that stride = formatsize*ninteractions
73 int formatsize; /* Number of fp variables for each table point (1 for F, 2 for VF, 4 for YFGH, etc.) */
74 int ninteractions; /* Number of interactions in table, 1 for coul-only, 3 for coul+rep+disp. */
75 int stride; /* Distance to next table point (number of fp variables per table point in total) */
80 t_forcetable table_elec;
81 t_forcetable table_vdw;
82 t_forcetable table_elec_vdw;
84 /* The actual neighbor lists, short and long range, see enum above
85 * for definition of neighborlist indices.
87 t_nblist nlist_sr[eNL_NR];
88 t_nblist nlist_lr[eNL_NR];
91 /* macros for the cginfo data in forcerec
93 * Since the tpx format support max 256 energy groups, we do the same here.
94 * Note that we thus have bits 8-14 still unused.
96 * The maximum cg size in cginfo is 63
97 * because we only have space for 6 bits in cginfo,
98 * this cg size entry is actually only read with domain decomposition.
99 * But there is a smaller limit due to the t_excl data structure
100 * which is defined in nblist.h.
102 #define SET_CGINFO_GID(cgi, gid) (cgi) = (((cgi) & ~255) | (gid))
103 #define GET_CGINFO_GID(cgi) ( (cgi) & 255)
104 #define SET_CGINFO_FEP(cgi) (cgi) = ((cgi) | (1<<15))
105 #define GET_CGINFO_FEP(cgi) ( (cgi) & (1<<15))
106 #define SET_CGINFO_EXCL_INTRA(cgi) (cgi) = ((cgi) | (1<<16))
107 #define GET_CGINFO_EXCL_INTRA(cgi) ( (cgi) & (1<<16))
108 #define SET_CGINFO_EXCL_INTER(cgi) (cgi) = ((cgi) | (1<<17))
109 #define GET_CGINFO_EXCL_INTER(cgi) ( (cgi) & (1<<17))
110 #define SET_CGINFO_SOLOPT(cgi, opt) (cgi) = (((cgi) & ~(3<<18)) | ((opt)<<18))
111 #define GET_CGINFO_SOLOPT(cgi) (((cgi)>>18) & 3)
112 #define SET_CGINFO_CONSTR(cgi) (cgi) = ((cgi) | (1<<20))
113 #define GET_CGINFO_CONSTR(cgi) ( (cgi) & (1<<20))
114 #define SET_CGINFO_SETTLE(cgi) (cgi) = ((cgi) | (1<<21))
115 #define GET_CGINFO_SETTLE(cgi) ( (cgi) & (1<<21))
116 /* This bit is only used with bBondComm in the domain decomposition */
117 #define SET_CGINFO_BOND_INTER(cgi) (cgi) = ((cgi) | (1<<22))
118 #define GET_CGINFO_BOND_INTER(cgi) ( (cgi) & (1<<22))
119 #define SET_CGINFO_HAS_VDW(cgi) (cgi) = ((cgi) | (1<<23))
120 #define GET_CGINFO_HAS_VDW(cgi) ( (cgi) & (1<<23))
121 #define SET_CGINFO_HAS_Q(cgi) (cgi) = ((cgi) | (1<<24))
122 #define GET_CGINFO_HAS_Q(cgi) ( (cgi) & (1<<24))
123 #define SET_CGINFO_NATOMS(cgi, opt) (cgi) = (((cgi) & ~(63<<25)) | ((opt)<<25))
124 #define GET_CGINFO_NATOMS(cgi) (((cgi)>>25) & 63)
127 /* Value to be used in mdrun for an infinite cut-off.
128 * Since we need to compare with the cut-off squared,
129 * this value should be slighlty smaller than sqrt(GMX_FLOAT_MAX).
131 #define GMX_CUTOFF_INF 1E+18
133 /* enums for the neighborlist type */
135 enbvdwNONE, enbvdwLJ, enbvdwBHAM, enbvdwTAB, enbvdwNR
137 /* OOR is "one over r" -- standard coul */
139 enbcoulNONE, enbcoulOOR, enbcoulRF, enbcoulTAB, enbcoulGB, enbcoulFEWALD, enbcoulNR
143 egCOULSR, egLJSR, egBHAMSR, egCOULLR, egLJLR, egBHAMLR,
144 egCOUL14, egLJ14, egGB, egNR
148 int nener; /* The number of energy group pairs */
149 real *ener[egNR]; /* Energy terms for each pair of groups */
153 real term[F_NRE]; /* The energies for all different interaction types */
154 gmx_grppairener_t grpp;
155 double dvdl_lin[efptNR]; /* Contributions to dvdl with linear lam-dependence */
156 double dvdl_nonlin[efptNR]; /* Idem, but non-linear dependence */
158 int fep_state; /*current fep state -- just for printing */
159 double *enerpart_lambda; /* Partial energy for lambda and flambda[] */
160 real foreign_term[F_NRE]; /* alternate array for storing foreign lambda energies */
161 gmx_grppairener_t foreign_grpp; /* alternate array for storing foreign lambda energies */
163 /* The idea is that dvdl terms with linear lambda dependence will be added
164 * automatically to enerpart_lambda. Terms with non-linear lambda dependence
165 * should explicitly determine the energies at foreign lambda points
177 /* ewald table type */
178 typedef struct ewald_tab *ewald_tab_t;
183 unsigned red_mask; /* Mask for marking which parts of f are filled */
186 gmx_grppairener_t grpp;
195 interaction_const_t *ic;
197 /* Domain Decomposition */
207 const gmx_hw_info_t *hwinfo;
208 const gmx_gpu_opt_t *gpu_opt;
209 gmx_bool use_simd_kernels;
211 /* Interaction for calculated in kernels. In many cases this is similar to
212 * the electrostatics settings in the inputrecord, but the difference is that
213 * these variables always specify the actual interaction in the kernel - if
214 * we are tabulating reaction-field the inputrec will say reaction-field, but
215 * the kernel interaction will say cubic-spline-table. To be safe we also
216 * have a kernel-specific setting for the modifiers - if the interaction is
217 * tabulated we already included the inputrec modification there, so the kernel
218 * modification setting will say 'none' in that case.
220 int nbkernel_elec_interaction;
221 int nbkernel_vdw_interaction;
222 int nbkernel_elec_modifier;
223 int nbkernel_vdw_modifier;
225 /* Use special N*N kernels? */
227 /* Private work data */
229 void *AllvsAll_workgb;
232 * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
234 real rlist, rlistlong;
236 /* Dielectric constant resp. multiplication factor for charges */
238 real epsilon_r, epsilon_rf, epsfac;
240 /* Constants for reaction fields */
241 real kappa, k_rf, c_rf;
243 /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
249 /* Dispersion correction stuff */
252 /* The shift of the shift or user potentials */
254 real enershifttwelve;
255 /* Integrated differces for energy and virial with cut-off functions */
260 /* Constant for long range dispersion correction (average dispersion)
261 * for topology A/B ([0]/[1]) */
263 /* Constant for long range repulsion term. Relative difference of about
264 * 0.1 percent with 0.8 nm cutoffs. But hey, it's cheap anyway...
274 /* The normal tables are in the nblists struct(s) below */
275 t_forcetable tab14; /* for 1-4 interactions only */
277 /* PPPM & Shifting stuff */
278 int coulomb_modifier;
279 real rcoulomb_switch, rcoulomb;
285 real rvdw_switch, rvdw;
301 /* solvent_opt contains the enum for the most common solvent
302 * in the system, which will be optimized.
303 * It can be set to esolNO to disable all water optimization */
307 gmx_bool bExcl_IntraCGAll_InterCGNone;
308 cginfo_mb_t *cginfo_mb;
314 /* The neighborlists including tables */
319 int cutoff_scheme; /* group- or Verlet-style cutoff */
320 gmx_bool bNonbonded; /* true if nonbonded calculations are *not* turned off */
321 struct nonbonded_verlet_t *nbv;
323 /* The wall tables (if used) */
325 t_forcetable **wall_tab;
327 /* The number of charge groups participating in do_force_lowlevel */
329 /* The number of atoms participating in do_force_lowlevel */
331 /* The number of atoms participating in force and constraints */
332 int natoms_force_constr;
333 /* The allocation size of vectors of size natoms_force */
336 /* Twin Range stuff, f_twin has size natoms_force */
340 /* Constraint virial correction for multiple time stepping */
341 tensor vir_twin_constr;
343 /* Forces that should not enter into the virial summation:
344 * PPPM/PME/Ewald/posres
346 gmx_bool bF_NoVirSum;
348 int f_novirsum_nalloc;
349 rvec *f_novirsum_alloc;
350 /* Pointer that points to f_novirsum_alloc when pressure is calcaluted,
351 * points to the normal force vectors wen pressure is not requested.
355 /* Long-range forces and virial for PPPM/PME/Ewald */
357 int ljpme_combination_rule;
361 /* PME/Ewald stuff */
365 ewald_tab_t ewald_table;
369 rvec vir_diag_posres;
372 /* Non bonded Parameter lists */
373 int ntype; /* Number of atom types */
376 real *ljpme_c6grid; /* C6-values used on grid in LJPME */
378 /* Energy group pair flags */
381 /* Shell molecular dynamics flexible constraints */
384 /* Generalized born implicit solvent */
386 /* Generalized born stuff */
387 real gb_epsilon_solvent;
388 /* Table data for GB */
390 /* VdW radius for each atomtype (dim is thus ntype) */
392 /* Effective radius (derived from effective volume) for each type */
394 /* Implicit solvent - surface tension for each atomtype */
395 real *atype_surftens;
396 /* Implicit solvent - radius for GB calculation */
397 real *atype_gb_radius;
398 /* Implicit solvent - overlap for HCT model */
400 /* Generalized born interaction data */
403 /* Table scale for GB */
405 /* Table range for GB */
407 /* GB neighborlists (the sr list will contain for each atom all other atoms
408 * (for use in the SA calculation) and the lr list will contain
409 * for each atom all atoms 1-4 or greater (for use in the GB calculation)
415 /* Inverse square root of the Born radii for implicit solvent */
417 /* Derivatives of the potential with respect to the Born radii */
419 /* Derivatives of the Born radii with respect to coordinates */
422 int nalloc_dadx; /* Allocated size of dadx */
424 /* If > 0 signals Test Particle Insertion,
425 * the value is the number of atoms of the molecule to insert
426 * Only the energy difference due to the addition of the last molecule
427 * should be calculated.
431 /* Neighbor searching stuff */
438 /* QM-MM neighborlists */
441 /* Limit for printing large forces, negative is don't print */
444 /* coarse load balancing time measurement */
449 /* parameter needed for AdResS simulation */
451 gmx_bool badress_tf_full_box;
452 real adress_const_wf;
453 real adress_ex_width;
454 real adress_hy_width;
458 int n_adress_tf_grps;
459 int * adress_tf_table_index;
460 int *adress_group_explicit;
461 t_forcetable * atf_tabs;
462 real adress_ex_forcecap;
463 gmx_bool adress_do_hybridpairs;
465 /* User determined parameters, copied from the inputrec */
475 /* Thread local force and energy data */
476 /* FIXME move to bonded_thread_data_t */
482 /* Exclusion load distribution over the threads */
486 /* Important: Starting with Gromacs-4.6, the values of c6 and c12 in the nbfp array have
487 * been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere
488 * in the code, but beware if you are using these macros externally.
490 #define C6(nbfp, ntp, ai, aj) (nbfp)[2*((ntp)*(ai)+(aj))]
491 #define C12(nbfp, ntp, ai, aj) (nbfp)[2*((ntp)*(ai)+(aj))+1]
492 #define BHAMC(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))]
493 #define BHAMA(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))+1]
494 #define BHAMB(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))+2]