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42 #include "nb_verlet.h"
43 #include "interaction_const.h"
50 } /* fixes auto-indentation problems */
53 /* Abstract type for PME that is defined only in the routine that use them. */
54 typedef struct gmx_pme *gmx_pme_t;
58 /* Structure describing the data in a single table */
61 enum gmx_table_interaction interaction; /* Types of interactions stored in this table */
62 enum gmx_table_format format; /* Interpolation type and data format */
64 real r; /* range of the table */
65 int n; /* n+1 is the number of table points */
66 real scale; /* distance (nm) between two table points */
67 real scale_exp; /* distance for exponential part of VdW table, not always used */
68 real * data; /* the actual table data */
70 /* Some information about the table layout. This can also be derived from the interpolation
71 * type and the table interactions, but it is convenient to have here for sanity checks, and it makes it
72 * much easier to access the tables in the nonbonded kernels when we can set the data from variables.
73 * It is always true that stride = formatsize*ninteractions
75 int formatsize; /* Number of fp variables for each table point (1 for F, 2 for VF, 4 for YFGH, etc.) */
76 int ninteractions; /* Number of interactions in table, 1 for coul-only, 3 for coul+rep+disp. */
77 int stride; /* Distance to next table point (number of fp variables per table point in total) */
82 t_forcetable table_elec;
83 t_forcetable table_vdw;
84 t_forcetable table_elec_vdw;
86 /* The actual neighbor lists, short and long range, see enum above
87 * for definition of neighborlist indices.
89 t_nblist nlist_sr[eNL_NR];
90 t_nblist nlist_lr[eNL_NR];
93 /* macros for the cginfo data in forcerec */
94 /* The maximum cg size in cginfo is 63
95 * because we only have space for 6 bits in cginfo,
96 * this cg size entry is actually only read with domain decomposition.
97 * But there is a smaller limit due to the t_excl data structure
98 * which is defined in nblist.h.
100 #define SET_CGINFO_GID(cgi, gid) (cgi) = (((cgi) & ~65535) | (gid) )
101 #define GET_CGINFO_GID(cgi) ( (cgi) & 65535)
102 #define SET_CGINFO_EXCL_INTRA(cgi) (cgi) = ((cgi) | (1<<16))
103 #define GET_CGINFO_EXCL_INTRA(cgi) ( (cgi) & (1<<16))
104 #define SET_CGINFO_EXCL_INTER(cgi) (cgi) = ((cgi) | (1<<17))
105 #define GET_CGINFO_EXCL_INTER(cgi) ( (cgi) & (1<<17))
106 #define SET_CGINFO_SOLOPT(cgi, opt) (cgi) = (((cgi) & ~(3<<18)) | ((opt)<<18))
107 #define GET_CGINFO_SOLOPT(cgi) (((cgi)>>18) & 3)
108 #define SET_CGINFO_CONSTR(cgi) (cgi) = ((cgi) | (1<<20))
109 #define GET_CGINFO_CONSTR(cgi) ( (cgi) & (1<<20))
110 #define SET_CGINFO_SETTLE(cgi) (cgi) = ((cgi) | (1<<21))
111 #define GET_CGINFO_SETTLE(cgi) ( (cgi) & (1<<21))
112 /* This bit is only used with bBondComm in the domain decomposition */
113 #define SET_CGINFO_BOND_INTER(cgi) (cgi) = ((cgi) | (1<<22))
114 #define GET_CGINFO_BOND_INTER(cgi) ( (cgi) & (1<<22))
115 #define SET_CGINFO_HAS_VDW(cgi) (cgi) = ((cgi) | (1<<23))
116 #define GET_CGINFO_HAS_VDW(cgi) ( (cgi) & (1<<23))
117 #define SET_CGINFO_HAS_Q(cgi) (cgi) = ((cgi) | (1<<24))
118 #define GET_CGINFO_HAS_Q(cgi) ( (cgi) & (1<<24))
119 #define SET_CGINFO_NATOMS(cgi, opt) (cgi) = (((cgi) & ~(63<<25)) | ((opt)<<25))
120 #define GET_CGINFO_NATOMS(cgi) (((cgi)>>25) & 63)
123 /* Value to be used in mdrun for an infinite cut-off.
124 * Since we need to compare with the cut-off squared,
125 * this value should be slighlty smaller than sqrt(GMX_FLOAT_MAX).
127 #define GMX_CUTOFF_INF 1E+18
129 /* enums for the neighborlist type */
131 enbvdwNONE, enbvdwLJ, enbvdwBHAM, enbvdwTAB, enbvdwNR
133 /* OOR is "one over r" -- standard coul */
135 enbcoulNONE, enbcoulOOR, enbcoulRF, enbcoulTAB, enbcoulGB, enbcoulFEWALD, enbcoulNR
139 egCOULSR, egLJSR, egBHAMSR, egCOULLR, egLJLR, egBHAMLR,
140 egCOUL14, egLJ14, egGB, egNR
144 int nener; /* The number of energy group pairs */
145 real *ener[egNR]; /* Energy terms for each pair of groups */
149 real term[F_NRE]; /* The energies for all different interaction types */
150 gmx_grppairener_t grpp;
151 double dvdl_lin[efptNR]; /* Contributions to dvdl with linear lam-dependence */
152 double dvdl_nonlin[efptNR]; /* Idem, but non-linear dependence */
154 int fep_state; /*current fep state -- just for printing */
155 double *enerpart_lambda; /* Partial energy for lambda and flambda[] */
156 real foreign_term[F_NRE]; /* alternate array for storing foreign lambda energies */
157 gmx_grppairener_t foreign_grpp; /* alternate array for storing foreign lambda energies */
159 /* The idea is that dvdl terms with linear lambda dependence will be added
160 * automatically to enerpart_lambda. Terms with non-linear lambda dependence
161 * should explicitly determine the energies at foreign lambda points
173 /* ewald table type */
174 typedef struct ewald_tab *ewald_tab_t;
179 unsigned red_mask; /* Mask for marking which parts of f are filled */
182 gmx_grppairener_t grpp;
191 interaction_const_t *ic;
193 /* Domain Decomposition */
203 const gmx_hw_info_t *hwinfo;
204 const gmx_gpu_opt_t *gpu_opt;
205 gmx_bool use_simd_kernels;
207 /* Interaction for calculated in kernels. In many cases this is similar to
208 * the electrostatics settings in the inputrecord, but the difference is that
209 * these variables always specify the actual interaction in the kernel - if
210 * we are tabulating reaction-field the inputrec will say reaction-field, but
211 * the kernel interaction will say cubic-spline-table. To be safe we also
212 * have a kernel-specific setting for the modifiers - if the interaction is
213 * tabulated we already included the inputrec modification there, so the kernel
214 * modification setting will say 'none' in that case.
216 int nbkernel_elec_interaction;
217 int nbkernel_vdw_interaction;
218 int nbkernel_elec_modifier;
219 int nbkernel_vdw_modifier;
221 /* Use special N*N kernels? */
223 /* Private work data */
225 void *AllvsAll_workgb;
228 * Infinite cut-off's will be GMX_CUTOFF_INF (unlike in t_inputrec: 0).
230 real rlist, rlistlong;
232 /* Dielectric constant resp. multiplication factor for charges */
234 real epsilon_r, epsilon_rf, epsfac;
236 /* Constants for reaction fields */
237 real kappa, k_rf, c_rf;
239 /* Charge sum and dipole for topology A/B ([0]/[1]) for Ewald corrections */
245 /* Dispersion correction stuff */
248 /* The shift of the shift or user potentials */
250 real enershifttwelve;
251 /* Integrated differces for energy and virial with cut-off functions */
256 /* Constant for long range dispersion correction (average dispersion)
257 * for topology A/B ([0]/[1]) */
259 /* Constant for long range repulsion term. Relative difference of about
260 * 0.1 percent with 0.8 nm cutoffs. But hey, it's cheap anyway...
270 /* The normal tables are in the nblists struct(s) below */
271 t_forcetable tab14; /* for 1-4 interactions only */
273 /* PPPM & Shifting stuff */
274 int coulomb_modifier;
275 real rcoulomb_switch, rcoulomb;
281 real rvdw_switch, rvdw;
298 /* solvent_opt contains the enum for the most common solvent
299 * in the system, which will be optimized.
300 * It can be set to esolNO to disable all water optimization */
304 gmx_bool bExcl_IntraCGAll_InterCGNone;
305 cginfo_mb_t *cginfo_mb;
311 /* The neighborlists including tables */
316 int cutoff_scheme; /* group- or Verlet-style cutoff */
317 gmx_bool bNonbonded; /* true if nonbonded calculations are *not* turned off */
318 nonbonded_verlet_t *nbv;
320 /* The wall tables (if used) */
322 t_forcetable **wall_tab;
324 /* The number of charge groups participating in do_force_lowlevel */
326 /* The number of atoms participating in do_force_lowlevel */
328 /* The number of atoms participating in force and constraints */
329 int natoms_force_constr;
330 /* The allocation size of vectors of size natoms_force */
333 /* Twin Range stuff, f_twin has size natoms_force */
338 /* Forces that should not enter into the virial summation:
339 * PPPM/PME/Ewald/posres
341 gmx_bool bF_NoVirSum;
343 int f_novirsum_nalloc;
344 rvec *f_novirsum_alloc;
345 /* Pointer that points to f_novirsum_alloc when pressure is calcaluted,
346 * points to the normal force vectors wen pressure is not requested.
350 /* Long-range forces and virial for PPPM/PME/Ewald */
352 int ljpme_combination_rule;
356 /* PME/Ewald stuff */
360 ewald_tab_t ewald_table;
364 rvec vir_diag_posres;
367 /* Non bonded Parameter lists */
368 int ntype; /* Number of atom types */
372 /* Energy group pair flags */
375 /* Shell molecular dynamics flexible constraints */
378 /* Generalized born implicit solvent */
380 /* Generalized born stuff */
381 real gb_epsilon_solvent;
382 /* Table data for GB */
384 /* VdW radius for each atomtype (dim is thus ntype) */
386 /* Effective radius (derived from effective volume) for each type */
388 /* Implicit solvent - surface tension for each atomtype */
389 real *atype_surftens;
390 /* Implicit solvent - radius for GB calculation */
391 real *atype_gb_radius;
392 /* Implicit solvent - overlap for HCT model */
394 /* Generalized born interaction data */
397 /* Table scale for GB */
399 /* Table range for GB */
401 /* GB neighborlists (the sr list will contain for each atom all other atoms
402 * (for use in the SA calculation) and the lr list will contain
403 * for each atom all atoms 1-4 or greater (for use in the GB calculation)
409 /* Inverse square root of the Born radii for implicit solvent */
411 /* Derivatives of the potential with respect to the Born radii */
413 /* Derivatives of the Born radii with respect to coordinates */
416 int nalloc_dadx; /* Allocated size of dadx */
418 /* If > 0 signals Test Particle Insertion,
419 * the value is the number of atoms of the molecule to insert
420 * Only the energy difference due to the addition of the last molecule
421 * should be calculated.
425 /* Neighbor searching stuff */
432 /* QM-MM neighborlists */
435 /* Limit for printing large forces, negative is don't print */
438 /* coarse load balancing time measurement */
443 /* parameter needed for AdResS simulation */
445 gmx_bool badress_tf_full_box;
446 real adress_const_wf;
447 real adress_ex_width;
448 real adress_hy_width;
452 int n_adress_tf_grps;
453 int * adress_tf_table_index;
454 int *adress_group_explicit;
455 t_forcetable * atf_tabs;
456 real adress_ex_forcecap;
457 gmx_bool adress_do_hybridpairs;
459 /* User determined parameters, copied from the inputrec */
469 /* Thread local force and energy data */
470 /* FIXME move to bonded_thread_data_t */
476 /* Exclusion load distribution over the threads */
480 /* Important: Starting with Gromacs-4.6, the values of c6 and c12 in the nbfp array have
481 * been scaled by 6.0 or 12.0 to save flops in the kernels. We have corrected this everywhere
482 * in the code, but beware if you are using these macros externally.
484 #define C6(nbfp, ntp, ai, aj) (nbfp)[2*((ntp)*(ai)+(aj))]
485 #define C12(nbfp, ntp, ai, aj) (nbfp)[2*((ntp)*(ai)+(aj))+1]
486 #define BHAMC(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))]
487 #define BHAMA(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))+1]
488 #define BHAMB(nbfp, ntp, ai, aj) (nbfp)[3*((ntp)*(ai)+(aj))+2]