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50 #include "gmx_fatal.h"
51 #include "gmx_fatal_collective.h"
55 #include "nonbonded.h"
64 #include "md_support.h"
65 #include "md_logging.h"
70 #include "mtop_util.h"
71 #include "nbnxn_search.h"
72 #include "nbnxn_atomdata.h"
73 #include "nbnxn_consts.h"
75 #include "gmx_omp_nthreads.h"
76 #include "gmx_detect_hardware.h"
79 /* MSVC definition for __cpuid() */
83 #include "types/nbnxn_cuda_types_ext.h"
84 #include "gpu_utils.h"
85 #include "nbnxn_cuda_data_mgmt.h"
86 #include "pmalloc_cuda.h"
88 t_forcerec *mk_forcerec(void)
98 static void pr_nbfp(FILE *fp, real *nbfp, gmx_bool bBHAM, int atnr)
102 for (i = 0; (i < atnr); i++)
104 for (j = 0; (j < atnr); j++)
106 fprintf(fp, "%2d - %2d", i, j);
109 fprintf(fp, " a=%10g, b=%10g, c=%10g\n", BHAMA(nbfp, atnr, i, j),
110 BHAMB(nbfp, atnr, i, j), BHAMC(nbfp, atnr, i, j)/6.0);
114 fprintf(fp, " c6=%10g, c12=%10g\n", C6(nbfp, atnr, i, j)/6.0,
115 C12(nbfp, atnr, i, j)/12.0);
122 static real *mk_nbfp(const gmx_ffparams_t *idef, gmx_bool bBHAM)
130 snew(nbfp, 3*atnr*atnr);
131 for (i = k = 0; (i < atnr); i++)
133 for (j = 0; (j < atnr); j++, k++)
135 BHAMA(nbfp, atnr, i, j) = idef->iparams[k].bham.a;
136 BHAMB(nbfp, atnr, i, j) = idef->iparams[k].bham.b;
137 /* nbfp now includes the 6.0 derivative prefactor */
138 BHAMC(nbfp, atnr, i, j) = idef->iparams[k].bham.c*6.0;
144 snew(nbfp, 2*atnr*atnr);
145 for (i = k = 0; (i < atnr); i++)
147 for (j = 0; (j < atnr); j++, k++)
149 /* nbfp now includes the 6.0/12.0 derivative prefactors */
150 C6(nbfp, atnr, i, j) = idef->iparams[k].lj.c6*6.0;
151 C12(nbfp, atnr, i, j) = idef->iparams[k].lj.c12*12.0;
159 /* This routine sets fr->solvent_opt to the most common solvent in the
160 * system, e.g. esolSPC or esolTIP4P. It will also mark each charge group in
161 * the fr->solvent_type array with the correct type (or esolNO).
163 * Charge groups that fulfill the conditions but are not identical to the
164 * most common one will be marked as esolNO in the solvent_type array.
166 * TIP3p is identical to SPC for these purposes, so we call it
167 * SPC in the arrays (Apologies to Bill Jorgensen ;-)
169 * NOTE: QM particle should not
170 * become an optimized solvent. Not even if there is only one charge
180 } solvent_parameters_t;
183 check_solvent_cg(const gmx_moltype_t *molt,
186 const unsigned char *qm_grpnr,
187 const t_grps *qm_grps,
189 int *n_solvent_parameters,
190 solvent_parameters_t **solvent_parameters_p,
194 const t_blocka * excl;
205 solvent_parameters_t *solvent_parameters;
207 /* We use a list with parameters for each solvent type.
208 * Every time we discover a new molecule that fulfills the basic
209 * conditions for a solvent we compare with the previous entries
210 * in these lists. If the parameters are the same we just increment
211 * the counter for that type, and otherwise we create a new type
212 * based on the current molecule.
214 * Once we've finished going through all molecules we check which
215 * solvent is most common, and mark all those molecules while we
216 * clear the flag on all others.
219 solvent_parameters = *solvent_parameters_p;
221 /* Mark the cg first as non optimized */
224 /* Check if this cg has no exclusions with atoms in other charge groups
225 * and all atoms inside the charge group excluded.
226 * We only have 3 or 4 atom solvent loops.
228 if (GET_CGINFO_EXCL_INTER(cginfo) ||
229 !GET_CGINFO_EXCL_INTRA(cginfo))
234 /* Get the indices of the first atom in this charge group */
235 j0 = molt->cgs.index[cg0];
236 j1 = molt->cgs.index[cg0+1];
238 /* Number of atoms in our molecule */
244 "Moltype '%s': there are %d atoms in this charge group\n",
248 /* Check if it could be an SPC (3 atoms) or TIP4p (4) water,
251 if (nj < 3 || nj > 4)
256 /* Check if we are doing QM on this group */
258 if (qm_grpnr != NULL)
260 for (j = j0; j < j1 && !qm; j++)
262 qm = (qm_grpnr[j] < qm_grps->nr - 1);
265 /* Cannot use solvent optimization with QM */
271 atom = molt->atoms.atom;
273 /* Still looks like a solvent, time to check parameters */
275 /* If it is perturbed (free energy) we can't use the solvent loops,
276 * so then we just skip to the next molecule.
280 for (j = j0; j < j1 && !perturbed; j++)
282 perturbed = PERTURBED(atom[j]);
290 /* Now it's only a question if the VdW and charge parameters
291 * are OK. Before doing the check we compare and see if they are
292 * identical to a possible previous solvent type.
293 * First we assign the current types and charges.
295 for (j = 0; j < nj; j++)
297 tmp_vdwtype[j] = atom[j0+j].type;
298 tmp_charge[j] = atom[j0+j].q;
301 /* Does it match any previous solvent type? */
302 for (k = 0; k < *n_solvent_parameters; k++)
307 /* We can only match SPC with 3 atoms and TIP4p with 4 atoms */
308 if ( (solvent_parameters[k].model == esolSPC && nj != 3) ||
309 (solvent_parameters[k].model == esolTIP4P && nj != 4) )
314 /* Check that types & charges match for all atoms in molecule */
315 for (j = 0; j < nj && match == TRUE; j++)
317 if (tmp_vdwtype[j] != solvent_parameters[k].vdwtype[j])
321 if (tmp_charge[j] != solvent_parameters[k].charge[j])
328 /* Congratulations! We have a matched solvent.
329 * Flag it with this type for later processing.
332 solvent_parameters[k].count += nmol;
334 /* We are done with this charge group */
339 /* If we get here, we have a tentative new solvent type.
340 * Before we add it we must check that it fulfills the requirements
341 * of the solvent optimized loops. First determine which atoms have
344 for (j = 0; j < nj; j++)
347 tjA = tmp_vdwtype[j];
349 /* Go through all other tpes and see if any have non-zero
350 * VdW parameters when combined with this one.
352 for (k = 0; k < fr->ntype && (has_vdw[j] == FALSE); k++)
354 /* We already checked that the atoms weren't perturbed,
355 * so we only need to check state A now.
359 has_vdw[j] = (has_vdw[j] ||
360 (BHAMA(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
361 (BHAMB(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
362 (BHAMC(fr->nbfp, fr->ntype, tjA, k) != 0.0));
367 has_vdw[j] = (has_vdw[j] ||
368 (C6(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
369 (C12(fr->nbfp, fr->ntype, tjA, k) != 0.0));
374 /* Now we know all we need to make the final check and assignment. */
378 * For this we require thatn all atoms have charge,
379 * the charges on atom 2 & 3 should be the same, and only
380 * atom 1 might have VdW.
382 if (has_vdw[1] == FALSE &&
383 has_vdw[2] == FALSE &&
384 tmp_charge[0] != 0 &&
385 tmp_charge[1] != 0 &&
386 tmp_charge[2] == tmp_charge[1])
388 srenew(solvent_parameters, *n_solvent_parameters+1);
389 solvent_parameters[*n_solvent_parameters].model = esolSPC;
390 solvent_parameters[*n_solvent_parameters].count = nmol;
391 for (k = 0; k < 3; k++)
393 solvent_parameters[*n_solvent_parameters].vdwtype[k] = tmp_vdwtype[k];
394 solvent_parameters[*n_solvent_parameters].charge[k] = tmp_charge[k];
397 *cg_sp = *n_solvent_parameters;
398 (*n_solvent_parameters)++;
403 /* Or could it be a TIP4P?
404 * For this we require thatn atoms 2,3,4 have charge, but not atom 1.
405 * Only atom 1 mght have VdW.
407 if (has_vdw[1] == FALSE &&
408 has_vdw[2] == FALSE &&
409 has_vdw[3] == FALSE &&
410 tmp_charge[0] == 0 &&
411 tmp_charge[1] != 0 &&
412 tmp_charge[2] == tmp_charge[1] &&
415 srenew(solvent_parameters, *n_solvent_parameters+1);
416 solvent_parameters[*n_solvent_parameters].model = esolTIP4P;
417 solvent_parameters[*n_solvent_parameters].count = nmol;
418 for (k = 0; k < 4; k++)
420 solvent_parameters[*n_solvent_parameters].vdwtype[k] = tmp_vdwtype[k];
421 solvent_parameters[*n_solvent_parameters].charge[k] = tmp_charge[k];
424 *cg_sp = *n_solvent_parameters;
425 (*n_solvent_parameters)++;
429 *solvent_parameters_p = solvent_parameters;
433 check_solvent(FILE * fp,
434 const gmx_mtop_t * mtop,
436 cginfo_mb_t *cginfo_mb)
439 const t_block * mols;
440 const gmx_moltype_t *molt;
441 int mb, mol, cg_mol, at_offset, cg_offset, am, cgm, i, nmol_ch, nmol;
442 int n_solvent_parameters;
443 solvent_parameters_t *solvent_parameters;
449 fprintf(debug, "Going to determine what solvent types we have.\n");
454 n_solvent_parameters = 0;
455 solvent_parameters = NULL;
456 /* Allocate temporary array for solvent type */
457 snew(cg_sp, mtop->nmolblock);
461 for (mb = 0; mb < mtop->nmolblock; mb++)
463 molt = &mtop->moltype[mtop->molblock[mb].type];
465 /* Here we have to loop over all individual molecules
466 * because we need to check for QMMM particles.
468 snew(cg_sp[mb], cginfo_mb[mb].cg_mod);
469 nmol_ch = cginfo_mb[mb].cg_mod/cgs->nr;
470 nmol = mtop->molblock[mb].nmol/nmol_ch;
471 for (mol = 0; mol < nmol_ch; mol++)
474 am = mol*cgs->index[cgs->nr];
475 for (cg_mol = 0; cg_mol < cgs->nr; cg_mol++)
477 check_solvent_cg(molt, cg_mol, nmol,
478 mtop->groups.grpnr[egcQMMM] ?
479 mtop->groups.grpnr[egcQMMM]+at_offset+am : 0,
480 &mtop->groups.grps[egcQMMM],
482 &n_solvent_parameters, &solvent_parameters,
483 cginfo_mb[mb].cginfo[cgm+cg_mol],
484 &cg_sp[mb][cgm+cg_mol]);
487 cg_offset += cgs->nr;
488 at_offset += cgs->index[cgs->nr];
491 /* Puh! We finished going through all charge groups.
492 * Now find the most common solvent model.
495 /* Most common solvent this far */
497 for (i = 0; i < n_solvent_parameters; i++)
500 solvent_parameters[i].count > solvent_parameters[bestsp].count)
508 bestsol = solvent_parameters[bestsp].model;
515 #ifdef DISABLE_WATER_NLIST
520 for (mb = 0; mb < mtop->nmolblock; mb++)
522 cgs = &mtop->moltype[mtop->molblock[mb].type].cgs;
523 nmol = (mtop->molblock[mb].nmol*cgs->nr)/cginfo_mb[mb].cg_mod;
524 for (i = 0; i < cginfo_mb[mb].cg_mod; i++)
526 if (cg_sp[mb][i] == bestsp)
528 SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[i], bestsol);
533 SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[i], esolNO);
540 if (bestsol != esolNO && fp != NULL)
542 fprintf(fp, "\nEnabling %s-like water optimization for %d molecules.\n\n",
544 solvent_parameters[bestsp].count);
547 sfree(solvent_parameters);
548 fr->solvent_opt = bestsol;
552 acNONE = 0, acCONSTRAINT, acSETTLE
555 static cginfo_mb_t *init_cginfo_mb(FILE *fplog, const gmx_mtop_t *mtop,
556 t_forcerec *fr, gmx_bool bNoSolvOpt,
557 gmx_bool *bExcl_IntraCGAll_InterCGNone)
560 const t_blocka *excl;
561 const gmx_moltype_t *molt;
562 const gmx_molblock_t *molb;
563 cginfo_mb_t *cginfo_mb;
566 int cg_offset, a_offset, cgm, am;
567 int mb, m, ncg_tot, cg, a0, a1, gid, ai, j, aj, excl_nalloc;
571 gmx_bool bId, *bExcl, bExclIntraAll, bExclInter, bHaveVDW, bHaveQ;
573 ncg_tot = ncg_mtop(mtop);
574 snew(cginfo_mb, mtop->nmolblock);
576 snew(type_VDW, fr->ntype);
577 for (ai = 0; ai < fr->ntype; ai++)
579 type_VDW[ai] = FALSE;
580 for (j = 0; j < fr->ntype; j++)
582 type_VDW[ai] = type_VDW[ai] ||
584 C6(fr->nbfp, fr->ntype, ai, j) != 0 ||
585 C12(fr->nbfp, fr->ntype, ai, j) != 0;
589 *bExcl_IntraCGAll_InterCGNone = TRUE;
592 snew(bExcl, excl_nalloc);
595 for (mb = 0; mb < mtop->nmolblock; mb++)
597 molb = &mtop->molblock[mb];
598 molt = &mtop->moltype[molb->type];
602 /* Check if the cginfo is identical for all molecules in this block.
603 * If so, we only need an array of the size of one molecule.
604 * Otherwise we make an array of #mol times #cgs per molecule.
608 for (m = 0; m < molb->nmol; m++)
610 am = m*cgs->index[cgs->nr];
611 for (cg = 0; cg < cgs->nr; cg++)
614 a1 = cgs->index[cg+1];
615 if (ggrpnr(&mtop->groups, egcENER, a_offset+am+a0) !=
616 ggrpnr(&mtop->groups, egcENER, a_offset +a0))
620 if (mtop->groups.grpnr[egcQMMM] != NULL)
622 for (ai = a0; ai < a1; ai++)
624 if (mtop->groups.grpnr[egcQMMM][a_offset+am+ai] !=
625 mtop->groups.grpnr[egcQMMM][a_offset +ai])
634 cginfo_mb[mb].cg_start = cg_offset;
635 cginfo_mb[mb].cg_end = cg_offset + molb->nmol*cgs->nr;
636 cginfo_mb[mb].cg_mod = (bId ? 1 : molb->nmol)*cgs->nr;
637 snew(cginfo_mb[mb].cginfo, cginfo_mb[mb].cg_mod);
638 cginfo = cginfo_mb[mb].cginfo;
640 /* Set constraints flags for constrained atoms */
641 snew(a_con, molt->atoms.nr);
642 for (ftype = 0; ftype < F_NRE; ftype++)
644 if (interaction_function[ftype].flags & IF_CONSTRAINT)
649 for (ia = 0; ia < molt->ilist[ftype].nr; ia += 1+nral)
653 for (a = 0; a < nral; a++)
655 a_con[molt->ilist[ftype].iatoms[ia+1+a]] =
656 (ftype == F_SETTLE ? acSETTLE : acCONSTRAINT);
662 for (m = 0; m < (bId ? 1 : molb->nmol); m++)
665 am = m*cgs->index[cgs->nr];
666 for (cg = 0; cg < cgs->nr; cg++)
669 a1 = cgs->index[cg+1];
671 /* Store the energy group in cginfo */
672 gid = ggrpnr(&mtop->groups, egcENER, a_offset+am+a0);
673 SET_CGINFO_GID(cginfo[cgm+cg], gid);
675 /* Check the intra/inter charge group exclusions */
676 if (a1-a0 > excl_nalloc)
678 excl_nalloc = a1 - a0;
679 srenew(bExcl, excl_nalloc);
681 /* bExclIntraAll: all intra cg interactions excluded
682 * bExclInter: any inter cg interactions excluded
684 bExclIntraAll = TRUE;
688 for (ai = a0; ai < a1; ai++)
690 /* Check VDW and electrostatic interactions */
691 bHaveVDW = bHaveVDW || (type_VDW[molt->atoms.atom[ai].type] ||
692 type_VDW[molt->atoms.atom[ai].typeB]);
693 bHaveQ = bHaveQ || (molt->atoms.atom[ai].q != 0 ||
694 molt->atoms.atom[ai].qB != 0);
696 /* Clear the exclusion list for atom ai */
697 for (aj = a0; aj < a1; aj++)
699 bExcl[aj-a0] = FALSE;
701 /* Loop over all the exclusions of atom ai */
702 for (j = excl->index[ai]; j < excl->index[ai+1]; j++)
705 if (aj < a0 || aj >= a1)
714 /* Check if ai excludes a0 to a1 */
715 for (aj = a0; aj < a1; aj++)
719 bExclIntraAll = FALSE;
726 SET_CGINFO_CONSTR(cginfo[cgm+cg]);
729 SET_CGINFO_SETTLE(cginfo[cgm+cg]);
737 SET_CGINFO_EXCL_INTRA(cginfo[cgm+cg]);
741 SET_CGINFO_EXCL_INTER(cginfo[cgm+cg]);
743 if (a1 - a0 > MAX_CHARGEGROUP_SIZE)
745 /* The size in cginfo is currently only read with DD */
746 gmx_fatal(FARGS, "A charge group has size %d which is larger than the limit of %d atoms", a1-a0, MAX_CHARGEGROUP_SIZE);
750 SET_CGINFO_HAS_VDW(cginfo[cgm+cg]);
754 SET_CGINFO_HAS_Q(cginfo[cgm+cg]);
756 /* Store the charge group size */
757 SET_CGINFO_NATOMS(cginfo[cgm+cg], a1-a0);
759 if (!bExclIntraAll || bExclInter)
761 *bExcl_IntraCGAll_InterCGNone = FALSE;
768 cg_offset += molb->nmol*cgs->nr;
769 a_offset += molb->nmol*cgs->index[cgs->nr];
773 /* the solvent optimizer is called after the QM is initialized,
774 * because we don't want to have the QM subsystemto become an
778 check_solvent(fplog, mtop, fr, cginfo_mb);
780 if (getenv("GMX_NO_SOLV_OPT"))
784 fprintf(fplog, "Found environment variable GMX_NO_SOLV_OPT.\n"
785 "Disabling all solvent optimization\n");
787 fr->solvent_opt = esolNO;
791 fr->solvent_opt = esolNO;
793 if (!fr->solvent_opt)
795 for (mb = 0; mb < mtop->nmolblock; mb++)
797 for (cg = 0; cg < cginfo_mb[mb].cg_mod; cg++)
799 SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[cg], esolNO);
807 static int *cginfo_expand(int nmb, cginfo_mb_t *cgi_mb)
812 ncg = cgi_mb[nmb-1].cg_end;
815 for (cg = 0; cg < ncg; cg++)
817 while (cg >= cgi_mb[mb].cg_end)
822 cgi_mb[mb].cginfo[(cg - cgi_mb[mb].cg_start) % cgi_mb[mb].cg_mod];
828 static void set_chargesum(FILE *log, t_forcerec *fr, const gmx_mtop_t *mtop)
830 double qsum, q2sum, q;
832 const t_atoms *atoms;
836 for (mb = 0; mb < mtop->nmolblock; mb++)
838 nmol = mtop->molblock[mb].nmol;
839 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
840 for (i = 0; i < atoms->nr; i++)
842 q = atoms->atom[i].q;
848 fr->q2sum[0] = q2sum;
849 if (fr->efep != efepNO)
853 for (mb = 0; mb < mtop->nmolblock; mb++)
855 nmol = mtop->molblock[mb].nmol;
856 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
857 for (i = 0; i < atoms->nr; i++)
859 q = atoms->atom[i].qB;
864 fr->q2sum[1] = q2sum;
869 fr->qsum[1] = fr->qsum[0];
870 fr->q2sum[1] = fr->q2sum[0];
874 if (fr->efep == efepNO)
876 fprintf(log, "System total charge: %.3f\n", fr->qsum[0]);
880 fprintf(log, "System total charge, top. A: %.3f top. B: %.3f\n",
881 fr->qsum[0], fr->qsum[1]);
886 void update_forcerec(FILE *log, t_forcerec *fr, matrix box)
888 if (fr->eeltype == eelGRF)
890 calc_rffac(NULL, fr->eeltype, fr->epsilon_r, fr->epsilon_rf,
891 fr->rcoulomb, fr->temp, fr->zsquare, box,
892 &fr->kappa, &fr->k_rf, &fr->c_rf);
896 void set_avcsixtwelve(FILE *fplog, t_forcerec *fr, const gmx_mtop_t *mtop)
898 const t_atoms *atoms, *atoms_tpi;
899 const t_blocka *excl;
900 int mb, nmol, nmolc, i, j, tpi, tpj, j1, j2, k, n, nexcl, q;
901 #if (defined SIZEOF_LONG_LONG_INT) && (SIZEOF_LONG_LONG_INT >= 8)
902 long long int npair, npair_ij, tmpi, tmpj;
904 double npair, npair_ij, tmpi, tmpj;
906 double csix, ctwelve;
915 for (q = 0; q < (fr->efep == efepNO ? 1 : 2); q++)
923 /* Count the types so we avoid natoms^2 operations */
924 snew(typecount, ntp);
925 for (mb = 0; mb < mtop->nmolblock; mb++)
927 nmol = mtop->molblock[mb].nmol;
928 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
929 for (i = 0; i < atoms->nr; i++)
933 tpi = atoms->atom[i].type;
937 tpi = atoms->atom[i].typeB;
939 typecount[tpi] += nmol;
942 for (tpi = 0; tpi < ntp; tpi++)
944 for (tpj = tpi; tpj < ntp; tpj++)
946 tmpi = typecount[tpi];
947 tmpj = typecount[tpj];
950 npair_ij = tmpi*tmpj;
954 npair_ij = tmpi*(tmpi - 1)/2;
958 /* nbfp now includes the 6.0 derivative prefactor */
959 csix += npair_ij*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
963 /* nbfp now includes the 6.0/12.0 derivative prefactors */
964 csix += npair_ij* C6(nbfp, ntp, tpi, tpj)/6.0;
965 ctwelve += npair_ij* C12(nbfp, ntp, tpi, tpj)/12.0;
971 /* Subtract the excluded pairs.
972 * The main reason for substracting exclusions is that in some cases
973 * some combinations might never occur and the parameters could have
974 * any value. These unused values should not influence the dispersion
977 for (mb = 0; mb < mtop->nmolblock; mb++)
979 nmol = mtop->molblock[mb].nmol;
980 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
981 excl = &mtop->moltype[mtop->molblock[mb].type].excls;
982 for (i = 0; (i < atoms->nr); i++)
986 tpi = atoms->atom[i].type;
990 tpi = atoms->atom[i].typeB;
993 j2 = excl->index[i+1];
994 for (j = j1; j < j2; j++)
1001 tpj = atoms->atom[k].type;
1005 tpj = atoms->atom[k].typeB;
1009 /* nbfp now includes the 6.0 derivative prefactor */
1010 csix -= nmol*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
1014 /* nbfp now includes the 6.0/12.0 derivative prefactors */
1015 csix -= nmol*C6 (nbfp, ntp, tpi, tpj)/6.0;
1016 ctwelve -= nmol*C12(nbfp, ntp, tpi, tpj)/12.0;
1026 /* Only correct for the interaction of the test particle
1027 * with the rest of the system.
1030 &mtop->moltype[mtop->molblock[mtop->nmolblock-1].type].atoms;
1033 for (mb = 0; mb < mtop->nmolblock; mb++)
1035 nmol = mtop->molblock[mb].nmol;
1036 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
1037 for (j = 0; j < atoms->nr; j++)
1040 /* Remove the interaction of the test charge group
1043 if (mb == mtop->nmolblock-1)
1047 if (mb == 0 && nmol == 1)
1049 gmx_fatal(FARGS, "Old format tpr with TPI, please generate a new tpr file");
1054 tpj = atoms->atom[j].type;
1058 tpj = atoms->atom[j].typeB;
1060 for (i = 0; i < fr->n_tpi; i++)
1064 tpi = atoms_tpi->atom[i].type;
1068 tpi = atoms_tpi->atom[i].typeB;
1072 /* nbfp now includes the 6.0 derivative prefactor */
1073 csix += nmolc*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
1077 /* nbfp now includes the 6.0/12.0 derivative prefactors */
1078 csix += nmolc*C6 (nbfp, ntp, tpi, tpj)/6.0;
1079 ctwelve += nmolc*C12(nbfp, ntp, tpi, tpj)/12.0;
1086 if (npair - nexcl <= 0 && fplog)
1088 fprintf(fplog, "\nWARNING: There are no atom pairs for dispersion correction\n\n");
1094 csix /= npair - nexcl;
1095 ctwelve /= npair - nexcl;
1099 fprintf(debug, "Counted %d exclusions\n", nexcl);
1100 fprintf(debug, "Average C6 parameter is: %10g\n", (double)csix);
1101 fprintf(debug, "Average C12 parameter is: %10g\n", (double)ctwelve);
1103 fr->avcsix[q] = csix;
1104 fr->avctwelve[q] = ctwelve;
1108 if (fr->eDispCorr == edispcAllEner ||
1109 fr->eDispCorr == edispcAllEnerPres)
1111 fprintf(fplog, "Long Range LJ corr.: <C6> %10.4e, <C12> %10.4e\n",
1112 fr->avcsix[0], fr->avctwelve[0]);
1116 fprintf(fplog, "Long Range LJ corr.: <C6> %10.4e\n", fr->avcsix[0]);
1122 static void set_bham_b_max(FILE *fplog, t_forcerec *fr,
1123 const gmx_mtop_t *mtop)
1125 const t_atoms *at1, *at2;
1126 int mt1, mt2, i, j, tpi, tpj, ntypes;
1132 fprintf(fplog, "Determining largest Buckingham b parameter for table\n");
1139 for (mt1 = 0; mt1 < mtop->nmoltype; mt1++)
1141 at1 = &mtop->moltype[mt1].atoms;
1142 for (i = 0; (i < at1->nr); i++)
1144 tpi = at1->atom[i].type;
1147 gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", i, tpi, ntypes);
1150 for (mt2 = mt1; mt2 < mtop->nmoltype; mt2++)
1152 at2 = &mtop->moltype[mt2].atoms;
1153 for (j = 0; (j < at2->nr); j++)
1155 tpj = at2->atom[j].type;
1158 gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", j, tpj, ntypes);
1160 b = BHAMB(nbfp, ntypes, tpi, tpj);
1161 if (b > fr->bham_b_max)
1165 if ((b < bmin) || (bmin == -1))
1175 fprintf(fplog, "Buckingham b parameters, min: %g, max: %g\n",
1176 bmin, fr->bham_b_max);
1180 static void make_nbf_tables(FILE *fp, const output_env_t oenv,
1181 t_forcerec *fr, real rtab,
1182 const t_commrec *cr,
1183 const char *tabfn, char *eg1, char *eg2,
1193 fprintf(debug, "No table file name passed, can not read table, can not do non-bonded interactions\n");
1198 sprintf(buf, "%s", tabfn);
1201 /* Append the two energy group names */
1202 sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "_%s_%s.%s",
1203 eg1, eg2, ftp2ext(efXVG));
1205 nbl->table_elec_vdw = make_tables(fp, oenv, fr, MASTER(cr), buf, rtab, 0);
1206 /* Copy the contents of the table to separate coulomb and LJ tables too,
1207 * to improve cache performance.
1209 /* For performance reasons we want
1210 * the table data to be aligned to 16-byte. The pointers could be freed
1211 * but currently aren't.
1213 nbl->table_elec.interaction = GMX_TABLE_INTERACTION_ELEC;
1214 nbl->table_elec.format = nbl->table_elec_vdw.format;
1215 nbl->table_elec.r = nbl->table_elec_vdw.r;
1216 nbl->table_elec.n = nbl->table_elec_vdw.n;
1217 nbl->table_elec.scale = nbl->table_elec_vdw.scale;
1218 nbl->table_elec.scale_exp = nbl->table_elec_vdw.scale_exp;
1219 nbl->table_elec.formatsize = nbl->table_elec_vdw.formatsize;
1220 nbl->table_elec.ninteractions = 1;
1221 nbl->table_elec.stride = nbl->table_elec.formatsize * nbl->table_elec.ninteractions;
1222 snew_aligned(nbl->table_elec.data, nbl->table_elec.stride*(nbl->table_elec.n+1), 32);
1224 nbl->table_vdw.interaction = GMX_TABLE_INTERACTION_VDWREP_VDWDISP;
1225 nbl->table_vdw.format = nbl->table_elec_vdw.format;
1226 nbl->table_vdw.r = nbl->table_elec_vdw.r;
1227 nbl->table_vdw.n = nbl->table_elec_vdw.n;
1228 nbl->table_vdw.scale = nbl->table_elec_vdw.scale;
1229 nbl->table_vdw.scale_exp = nbl->table_elec_vdw.scale_exp;
1230 nbl->table_vdw.formatsize = nbl->table_elec_vdw.formatsize;
1231 nbl->table_vdw.ninteractions = 2;
1232 nbl->table_vdw.stride = nbl->table_vdw.formatsize * nbl->table_vdw.ninteractions;
1233 snew_aligned(nbl->table_vdw.data, nbl->table_vdw.stride*(nbl->table_vdw.n+1), 32);
1235 for (i = 0; i <= nbl->table_elec_vdw.n; i++)
1237 for (j = 0; j < 4; j++)
1239 nbl->table_elec.data[4*i+j] = nbl->table_elec_vdw.data[12*i+j];
1241 for (j = 0; j < 8; j++)
1243 nbl->table_vdw.data[8*i+j] = nbl->table_elec_vdw.data[12*i+4+j];
1248 static void count_tables(int ftype1, int ftype2, const gmx_mtop_t *mtop,
1249 int *ncount, int **count)
1251 const gmx_moltype_t *molt;
1253 int mt, ftype, stride, i, j, tabnr;
1255 for (mt = 0; mt < mtop->nmoltype; mt++)
1257 molt = &mtop->moltype[mt];
1258 for (ftype = 0; ftype < F_NRE; ftype++)
1260 if (ftype == ftype1 || ftype == ftype2)
1262 il = &molt->ilist[ftype];
1263 stride = 1 + NRAL(ftype);
1264 for (i = 0; i < il->nr; i += stride)
1266 tabnr = mtop->ffparams.iparams[il->iatoms[i]].tab.table;
1269 gmx_fatal(FARGS, "A bonded table number is smaller than 0: %d\n", tabnr);
1271 if (tabnr >= *ncount)
1273 srenew(*count, tabnr+1);
1274 for (j = *ncount; j < tabnr+1; j++)
1287 static bondedtable_t *make_bonded_tables(FILE *fplog,
1288 int ftype1, int ftype2,
1289 const gmx_mtop_t *mtop,
1290 const char *basefn, const char *tabext)
1292 int i, ncount, *count;
1300 count_tables(ftype1, ftype2, mtop, &ncount, &count);
1305 for (i = 0; i < ncount; i++)
1309 sprintf(tabfn, "%s", basefn);
1310 sprintf(tabfn + strlen(basefn) - strlen(ftp2ext(efXVG)) - 1, "_%s%d.%s",
1311 tabext, i, ftp2ext(efXVG));
1312 tab[i] = make_bonded_table(fplog, tabfn, NRAL(ftype1)-2);
1321 void forcerec_set_ranges(t_forcerec *fr,
1322 int ncg_home, int ncg_force,
1324 int natoms_force_constr, int natoms_f_novirsum)
1329 /* fr->ncg_force is unused in the standard code,
1330 * but it can be useful for modified code dealing with charge groups.
1332 fr->ncg_force = ncg_force;
1333 fr->natoms_force = natoms_force;
1334 fr->natoms_force_constr = natoms_force_constr;
1336 if (fr->natoms_force_constr > fr->nalloc_force)
1338 fr->nalloc_force = over_alloc_dd(fr->natoms_force_constr);
1342 srenew(fr->f_twin, fr->nalloc_force);
1346 if (fr->bF_NoVirSum)
1348 fr->f_novirsum_n = natoms_f_novirsum;
1349 if (fr->f_novirsum_n > fr->f_novirsum_nalloc)
1351 fr->f_novirsum_nalloc = over_alloc_dd(fr->f_novirsum_n);
1352 srenew(fr->f_novirsum_alloc, fr->f_novirsum_nalloc);
1357 fr->f_novirsum_n = 0;
1361 static real cutoff_inf(real cutoff)
1365 cutoff = GMX_CUTOFF_INF;
1371 static void make_adress_tf_tables(FILE *fp, const output_env_t oenv,
1372 t_forcerec *fr, const t_inputrec *ir,
1373 const char *tabfn, const gmx_mtop_t *mtop,
1381 gmx_fatal(FARGS, "No thermoforce table file given. Use -tabletf to specify a file\n");
1385 snew(fr->atf_tabs, ir->adress->n_tf_grps);
1387 sprintf(buf, "%s", tabfn);
1388 for (i = 0; i < ir->adress->n_tf_grps; i++)
1390 j = ir->adress->tf_table_index[i]; /* get energy group index */
1391 sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "tf_%s.%s",
1392 *(mtop->groups.grpname[mtop->groups.grps[egcENER].nm_ind[j]]), ftp2ext(efXVG));
1395 fprintf(fp,"loading tf table for energygrp index %d from %s\n", ir->adress->tf_table_index[i], buf);
1397 fr->atf_tabs[i] = make_atf_table(fp, oenv, fr, buf, box);
1402 gmx_bool can_use_allvsall(const t_inputrec *ir, const gmx_mtop_t *mtop,
1403 gmx_bool bPrintNote, t_commrec *cr, FILE *fp)
1410 ir->rcoulomb == 0 &&
1412 ir->ePBC == epbcNONE &&
1413 ir->vdwtype == evdwCUT &&
1414 ir->coulombtype == eelCUT &&
1415 ir->efep == efepNO &&
1416 (ir->implicit_solvent == eisNO ||
1417 (ir->implicit_solvent == eisGBSA && (ir->gb_algorithm == egbSTILL ||
1418 ir->gb_algorithm == egbHCT ||
1419 ir->gb_algorithm == egbOBC))) &&
1420 getenv("GMX_NO_ALLVSALL") == NULL
1423 if (bAllvsAll && ir->opts.ngener > 1)
1425 const char *note = "NOTE: Can not use all-vs-all force loops, because there are multiple energy monitor groups; you might get significantly higher performance when using only a single energy monitor group.\n";
1431 fprintf(stderr, "\n%s\n", note);
1435 fprintf(fp, "\n%s\n", note);
1441 if (bAllvsAll && fp && MASTER(cr))
1443 fprintf(fp, "\nUsing accelerated all-vs-all kernels.\n\n");
1450 static void init_forcerec_f_threads(t_forcerec *fr, int nenergrp)
1454 /* These thread local data structures are used for bondeds only */
1455 fr->nthreads = gmx_omp_nthreads_get(emntBonded);
1457 if (fr->nthreads > 1)
1459 snew(fr->f_t, fr->nthreads);
1460 /* Thread 0 uses the global force and energy arrays */
1461 for (t = 1; t < fr->nthreads; t++)
1463 fr->f_t[t].f = NULL;
1464 fr->f_t[t].f_nalloc = 0;
1465 snew(fr->f_t[t].fshift, SHIFTS);
1466 fr->f_t[t].grpp.nener = nenergrp*nenergrp;
1467 for (i = 0; i < egNR; i++)
1469 snew(fr->f_t[t].grpp.ener[i], fr->f_t[t].grpp.nener);
1476 static void pick_nbnxn_kernel_cpu(FILE *fp,
1477 const t_commrec *cr,
1478 const gmx_cpuid_t cpuid_info,
1479 const t_inputrec *ir,
1483 *kernel_type = nbnxnk4x4_PlainC;
1484 *ewald_excl = ewaldexclTable;
1486 #ifdef GMX_NBNXN_SIMD
1488 #ifdef GMX_NBNXN_SIMD_4XN
1489 *kernel_type = nbnxnk4xN_SIMD_4xN;
1491 #ifdef GMX_NBNXN_SIMD_2XNN
1492 /* We expect the 2xNN kernels to be faster in most cases */
1493 *kernel_type = nbnxnk4xN_SIMD_2xNN;
1496 #if defined GMX_NBNXN_SIMD_4XN && defined GMX_X86_AVX_256
1497 if (EEL_RF(ir->coulombtype) || ir->coulombtype == eelCUT)
1499 /* The raw pair rate of the 4x8 kernel is higher than 2x(4+4),
1500 * 10% with HT, 50% without HT, but extra zeros interactions
1501 * can compensate. As we currently don't detect the actual use
1502 * of HT, switch to 4x8 to avoid a potential performance hit.
1504 *kernel_type = nbnxnk4xN_SIMD_4xN;
1507 if (getenv("GMX_NBNXN_SIMD_4XN") != NULL)
1509 #ifdef GMX_NBNXN_SIMD_4XN
1510 *kernel_type = nbnxnk4xN_SIMD_4xN;
1512 gmx_fatal(FARGS, "SIMD 4xN kernels requested, but Gromacs has been compiled without support for these kernels");
1515 if (getenv("GMX_NBNXN_SIMD_2XNN") != NULL)
1517 #ifdef GMX_NBNXN_SIMD_2XNN
1518 *kernel_type = nbnxnk4xN_SIMD_2xNN;
1520 gmx_fatal(FARGS, "SIMD 2x(N+N) kernels requested, but Gromacs has been compiled without support for these kernels");
1524 /* Analytical Ewald exclusion correction is only an option in the
1525 * x86 SIMD kernel. This is faster in single precision
1526 * on Bulldozer and slightly faster on Sandy Bridge.
1528 #if (defined GMX_X86_AVX_128_FMA || defined GMX_X86_AVX_256) && !defined GMX_DOUBLE
1529 *ewald_excl = ewaldexclAnalytical;
1531 if (getenv("GMX_NBNXN_EWALD_TABLE") != NULL)
1533 *ewald_excl = ewaldexclTable;
1535 if (getenv("GMX_NBNXN_EWALD_ANALYTICAL") != NULL)
1537 *ewald_excl = ewaldexclAnalytical;
1541 #endif /* GMX_X86_SSE2 */
1545 const char *lookup_nbnxn_kernel_name(int kernel_type)
1547 const char *returnvalue = NULL;
1548 switch (kernel_type)
1550 case nbnxnkNotSet: returnvalue = "not set"; break;
1551 case nbnxnk4x4_PlainC: returnvalue = "plain C"; break;
1552 #ifndef GMX_NBNXN_SIMD
1553 case nbnxnk4xN_SIMD_4xN: returnvalue = "not available"; break;
1554 case nbnxnk4xN_SIMD_2xNN: returnvalue = "not available"; break;
1557 #if GMX_NBNXN_SIMD_BITWIDTH == 128
1558 /* x86 SIMD intrinsics can be converted to either SSE or AVX depending
1559 * on compiler flags. As we use nearly identical intrinsics, using an AVX
1560 * compiler flag without an AVX macro effectively results in AVX kernels.
1561 * For gcc we check for __AVX__
1562 * At least a check for icc should be added (if there is a macro)
1564 #if !(defined GMX_X86_AVX_128_FMA || defined __AVX__)
1565 #ifndef GMX_X86_SSE4_1
1566 case nbnxnk4xN_SIMD_4xN: returnvalue = "SSE2"; break;
1567 case nbnxnk4xN_SIMD_2xNN: returnvalue = "SSE2"; break;
1569 case nbnxnk4xN_SIMD_4xN: returnvalue = "SSE4.1"; break;
1570 case nbnxnk4xN_SIMD_2xNN: returnvalue = "SSE4.1"; break;
1573 case nbnxnk4xN_SIMD_4xN: returnvalue = "AVX-128"; break;
1574 case nbnxnk4xN_SIMD_2xNN: returnvalue = "AVX-128"; break;
1577 #if GMX_NBNXN_SIMD_BITWIDTH == 256
1578 case nbnxnk4xN_SIMD_4xN: returnvalue = "AVX-256"; break;
1579 case nbnxnk4xN_SIMD_2xNN: returnvalue = "AVX-256"; break;
1581 #else /* not GMX_X86_SSE2 */
1582 case nbnxnk4xN_SIMD_4xN: returnvalue = "SIMD"; break;
1583 case nbnxnk4xN_SIMD_2xNN: returnvalue = "SIMD"; break;
1586 case nbnxnk8x8x8_CUDA: returnvalue = "CUDA"; break;
1587 case nbnxnk8x8x8_PlainC: returnvalue = "plain C"; break;
1591 gmx_fatal(FARGS, "Illegal kernel type selected");
1598 static void pick_nbnxn_kernel(FILE *fp,
1599 const t_commrec *cr,
1600 const gmx_hw_info_t *hwinfo,
1601 gmx_bool use_cpu_acceleration,
1603 gmx_bool bEmulateGPU,
1604 const t_inputrec *ir,
1607 gmx_bool bDoNonbonded)
1609 assert(kernel_type);
1611 *kernel_type = nbnxnkNotSet;
1612 *ewald_excl = ewaldexclTable;
1616 *kernel_type = nbnxnk8x8x8_PlainC;
1620 md_print_warn(cr, fp, "Emulating a GPU run on the CPU (slow)");
1625 *kernel_type = nbnxnk8x8x8_CUDA;
1628 if (*kernel_type == nbnxnkNotSet)
1630 if (use_cpu_acceleration)
1632 pick_nbnxn_kernel_cpu(fp, cr, hwinfo->cpuid_info, ir,
1633 kernel_type, ewald_excl);
1637 *kernel_type = nbnxnk4x4_PlainC;
1641 if (bDoNonbonded && fp != NULL)
1643 fprintf(fp, "\nUsing %s %dx%d non-bonded kernels\n\n",
1644 lookup_nbnxn_kernel_name(*kernel_type),
1645 nbnxn_kernel_pairlist_simple(*kernel_type) ? NBNXN_CPU_CLUSTER_I_SIZE : NBNXN_GPU_CLUSTER_SIZE,
1646 nbnxn_kernel_to_cj_size(*kernel_type));
1650 static void pick_nbnxn_resources(FILE *fp,
1651 const t_commrec *cr,
1652 const gmx_hw_info_t *hwinfo,
1653 gmx_bool bDoNonbonded,
1655 gmx_bool *bEmulateGPU)
1657 gmx_bool bEmulateGPUEnvVarSet;
1658 char gpu_err_str[STRLEN];
1662 bEmulateGPUEnvVarSet = (getenv("GMX_EMULATE_GPU") != NULL);
1664 /* Run GPU emulation mode if GMX_EMULATE_GPU is defined. Because
1665 * GPUs (currently) only handle non-bonded calculations, we will
1666 * automatically switch to emulation if non-bonded calculations are
1667 * turned off via GMX_NO_NONBONDED - this is the simple and elegant
1668 * way to turn off GPU initialization, data movement, and cleanup.
1670 * GPU emulation can be useful to assess the performance one can expect by
1671 * adding GPU(s) to the machine. The conditional below allows this even
1672 * if mdrun is compiled without GPU acceleration support.
1673 * Note that you should freezing the system as otherwise it will explode.
1675 *bEmulateGPU = (bEmulateGPUEnvVarSet ||
1676 (!bDoNonbonded && hwinfo->bCanUseGPU));
1678 /* Enable GPU mode when GPUs are available or no GPU emulation is requested.
1680 if (hwinfo->bCanUseGPU && !(*bEmulateGPU))
1682 /* Each PP node will use the intra-node id-th device from the
1683 * list of detected/selected GPUs. */
1684 if (!init_gpu(cr->rank_pp_intranode, gpu_err_str, &hwinfo->gpu_info))
1686 /* At this point the init should never fail as we made sure that
1687 * we have all the GPUs we need. If it still does, we'll bail. */
1688 gmx_fatal(FARGS, "On node %d failed to initialize GPU #%d: %s",
1690 get_gpu_device_id(&hwinfo->gpu_info, cr->rank_pp_intranode),
1694 /* Here we actually turn on hardware GPU acceleration */
1699 gmx_bool uses_simple_tables(int cutoff_scheme,
1700 nonbonded_verlet_t *nbv,
1703 gmx_bool bUsesSimpleTables = TRUE;
1706 switch (cutoff_scheme)
1709 bUsesSimpleTables = TRUE;
1712 assert(NULL != nbv && NULL != nbv->grp);
1713 grp_index = (group < 0) ? 0 : (nbv->ngrp - 1);
1714 bUsesSimpleTables = nbnxn_kernel_pairlist_simple(nbv->grp[grp_index].kernel_type);
1717 gmx_incons("unimplemented");
1719 return bUsesSimpleTables;
1722 static void init_ewald_f_table(interaction_const_t *ic,
1723 gmx_bool bUsesSimpleTables,
1728 if (bUsesSimpleTables)
1730 /* With a spacing of 0.0005 we are at the force summation accuracy
1731 * for the SSE kernels for "normal" atomistic simulations.
1733 ic->tabq_scale = ewald_spline3_table_scale(ic->ewaldcoeff,
1736 maxr = (rtab > ic->rcoulomb) ? rtab : ic->rcoulomb;
1737 ic->tabq_size = (int)(maxr*ic->tabq_scale) + 2;
1741 ic->tabq_size = GPU_EWALD_COULOMB_FORCE_TABLE_SIZE;
1742 /* Subtract 2 iso 1 to avoid access out of range due to rounding */
1743 ic->tabq_scale = (ic->tabq_size - 2)/ic->rcoulomb;
1746 sfree_aligned(ic->tabq_coul_FDV0);
1747 sfree_aligned(ic->tabq_coul_F);
1748 sfree_aligned(ic->tabq_coul_V);
1750 /* Create the original table data in FDV0 */
1751 snew_aligned(ic->tabq_coul_FDV0, ic->tabq_size*4, 32);
1752 snew_aligned(ic->tabq_coul_F, ic->tabq_size, 32);
1753 snew_aligned(ic->tabq_coul_V, ic->tabq_size, 32);
1754 table_spline3_fill_ewald_lr(ic->tabq_coul_F, ic->tabq_coul_V, ic->tabq_coul_FDV0,
1755 ic->tabq_size, 1/ic->tabq_scale, ic->ewaldcoeff);
1758 void init_interaction_const_tables(FILE *fp,
1759 interaction_const_t *ic,
1760 gmx_bool bUsesSimpleTables,
1765 if (ic->eeltype == eelEWALD || EEL_PME(ic->eeltype))
1767 init_ewald_f_table(ic, bUsesSimpleTables, rtab);
1771 fprintf(fp, "Initialized non-bonded Ewald correction tables, spacing: %.2e size: %d\n\n",
1772 1/ic->tabq_scale, ic->tabq_size);
1777 void init_interaction_const(FILE *fp,
1778 interaction_const_t **interaction_const,
1779 const t_forcerec *fr,
1782 interaction_const_t *ic;
1783 gmx_bool bUsesSimpleTables = TRUE;
1787 /* Just allocate something so we can free it */
1788 snew_aligned(ic->tabq_coul_FDV0, 16, 32);
1789 snew_aligned(ic->tabq_coul_F, 16, 32);
1790 snew_aligned(ic->tabq_coul_V, 16, 32);
1792 ic->rlist = fr->rlist;
1793 ic->rlistlong = fr->rlistlong;
1796 ic->rvdw = fr->rvdw;
1797 if (fr->vdw_modifier == eintmodPOTSHIFT)
1799 ic->sh_invrc6 = pow(ic->rvdw, -6.0);
1806 /* Electrostatics */
1807 ic->eeltype = fr->eeltype;
1808 ic->rcoulomb = fr->rcoulomb;
1809 ic->epsilon_r = fr->epsilon_r;
1810 ic->epsfac = fr->epsfac;
1813 ic->ewaldcoeff = fr->ewaldcoeff;
1814 if (fr->coulomb_modifier == eintmodPOTSHIFT)
1816 ic->sh_ewald = gmx_erfc(ic->ewaldcoeff*ic->rcoulomb);
1823 /* Reaction-field */
1824 if (EEL_RF(ic->eeltype))
1826 ic->epsilon_rf = fr->epsilon_rf;
1827 ic->k_rf = fr->k_rf;
1828 ic->c_rf = fr->c_rf;
1832 /* For plain cut-off we might use the reaction-field kernels */
1833 ic->epsilon_rf = ic->epsilon_r;
1835 if (fr->coulomb_modifier == eintmodPOTSHIFT)
1837 ic->c_rf = 1/ic->rcoulomb;
1847 fprintf(fp, "Potential shift: LJ r^-12: %.3f r^-6 %.3f",
1848 sqr(ic->sh_invrc6), ic->sh_invrc6);
1849 if (ic->eeltype == eelCUT)
1851 fprintf(fp, ", Coulomb %.3f", ic->c_rf);
1853 else if (EEL_PME(ic->eeltype))
1855 fprintf(fp, ", Ewald %.3e", ic->sh_ewald);
1860 *interaction_const = ic;
1862 if (fr->nbv != NULL && fr->nbv->bUseGPU)
1864 nbnxn_cuda_init_const(fr->nbv->cu_nbv, ic, fr->nbv);
1867 bUsesSimpleTables = uses_simple_tables(fr->cutoff_scheme, fr->nbv, -1);
1868 init_interaction_const_tables(fp, ic, bUsesSimpleTables, rtab);
1871 static void init_nb_verlet(FILE *fp,
1872 nonbonded_verlet_t **nb_verlet,
1873 const t_inputrec *ir,
1874 const t_forcerec *fr,
1875 const t_commrec *cr,
1876 const char *nbpu_opt)
1878 nonbonded_verlet_t *nbv;
1881 gmx_bool bEmulateGPU, bHybridGPURun = FALSE;
1883 nbnxn_alloc_t *nb_alloc;
1884 nbnxn_free_t *nb_free;
1888 pick_nbnxn_resources(fp, cr, fr->hwinfo,
1895 nbv->ngrp = (DOMAINDECOMP(cr) ? 2 : 1);
1896 for (i = 0; i < nbv->ngrp; i++)
1898 nbv->grp[i].nbl_lists.nnbl = 0;
1899 nbv->grp[i].nbat = NULL;
1900 nbv->grp[i].kernel_type = nbnxnkNotSet;
1902 if (i == 0) /* local */
1904 pick_nbnxn_kernel(fp, cr, fr->hwinfo, fr->use_cpu_acceleration,
1905 nbv->bUseGPU, bEmulateGPU,
1907 &nbv->grp[i].kernel_type,
1908 &nbv->grp[i].ewald_excl,
1911 else /* non-local */
1913 if (nbpu_opt != NULL && strcmp(nbpu_opt, "gpu_cpu") == 0)
1915 /* Use GPU for local, select a CPU kernel for non-local */
1916 pick_nbnxn_kernel(fp, cr, fr->hwinfo, fr->use_cpu_acceleration,
1919 &nbv->grp[i].kernel_type,
1920 &nbv->grp[i].ewald_excl,
1923 bHybridGPURun = TRUE;
1927 /* Use the same kernel for local and non-local interactions */
1928 nbv->grp[i].kernel_type = nbv->grp[0].kernel_type;
1929 nbv->grp[i].ewald_excl = nbv->grp[0].ewald_excl;
1936 /* init the NxN GPU data; the last argument tells whether we'll have
1937 * both local and non-local NB calculation on GPU */
1938 nbnxn_cuda_init(fp, &nbv->cu_nbv,
1939 &fr->hwinfo->gpu_info, cr->rank_pp_intranode,
1940 (nbv->ngrp > 1) && !bHybridGPURun);
1942 if ((env = getenv("GMX_NB_MIN_CI")) != NULL)
1946 nbv->min_ci_balanced = strtol(env, &end, 10);
1947 if (!end || (*end != 0) || nbv->min_ci_balanced <= 0)
1949 gmx_fatal(FARGS, "Invalid value passed in GMX_NB_MIN_CI=%s, positive integer required", env);
1954 fprintf(debug, "Neighbor-list balancing parameter: %d (passed as env. var.)\n",
1955 nbv->min_ci_balanced);
1960 nbv->min_ci_balanced = nbnxn_cuda_min_ci_balanced(nbv->cu_nbv);
1963 fprintf(debug, "Neighbor-list balancing parameter: %d (auto-adjusted to the number of GPU multi-processors)\n",
1964 nbv->min_ci_balanced);
1970 nbv->min_ci_balanced = 0;
1975 nbnxn_init_search(&nbv->nbs,
1976 DOMAINDECOMP(cr) ? &cr->dd->nc : NULL,
1977 DOMAINDECOMP(cr) ? domdec_zones(cr->dd) : NULL,
1978 gmx_omp_nthreads_get(emntNonbonded));
1980 for (i = 0; i < nbv->ngrp; i++)
1982 if (nbv->grp[0].kernel_type == nbnxnk8x8x8_CUDA)
1984 nb_alloc = &pmalloc;
1993 nbnxn_init_pairlist_set(&nbv->grp[i].nbl_lists,
1994 nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type),
1995 /* 8x8x8 "non-simple" lists are ATM always combined */
1996 !nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type),
2000 nbv->grp[0].kernel_type != nbv->grp[i].kernel_type)
2002 snew(nbv->grp[i].nbat, 1);
2003 nbnxn_atomdata_init(fp,
2005 nbv->grp[i].kernel_type,
2006 fr->ntype, fr->nbfp,
2008 nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type) ? gmx_omp_nthreads_get(emntNonbonded) : 1,
2013 nbv->grp[i].nbat = nbv->grp[0].nbat;
2018 void init_forcerec(FILE *fp,
2019 const output_env_t oenv,
2022 const t_inputrec *ir,
2023 const gmx_mtop_t *mtop,
2024 const t_commrec *cr,
2031 const char *nbpu_opt,
2032 gmx_bool bNoSolvOpt,
2035 int i, j, m, natoms, ngrp, negp_pp, negptable, egi, egj;
2041 gmx_bool bGenericKernelOnly;
2042 gmx_bool bTab, bSep14tab, bNormalnblists;
2044 int *nm_ind, egp_flags;
2046 if (fr->hwinfo == NULL)
2048 /* Detect hardware, gather information.
2049 * In mdrun, hwinfo has already been set before calling init_forcerec.
2050 * Here we ignore GPUs, as tools will not use them anyhow.
2052 snew(fr->hwinfo, 1);
2053 gmx_detect_hardware(fp, fr->hwinfo, cr,
2054 FALSE, FALSE, NULL);
2057 /* By default we turn acceleration on, but it might be turned off further down... */
2058 fr->use_cpu_acceleration = TRUE;
2060 fr->bDomDec = DOMAINDECOMP(cr);
2062 natoms = mtop->natoms;
2064 if (check_box(ir->ePBC, box))
2066 gmx_fatal(FARGS, check_box(ir->ePBC, box));
2069 /* Test particle insertion ? */
2072 /* Set to the size of the molecule to be inserted (the last one) */
2073 /* Because of old style topologies, we have to use the last cg
2074 * instead of the last molecule type.
2076 cgs = &mtop->moltype[mtop->molblock[mtop->nmolblock-1].type].cgs;
2077 fr->n_tpi = cgs->index[cgs->nr] - cgs->index[cgs->nr-1];
2078 if (fr->n_tpi != mtop->mols.index[mtop->mols.nr] - mtop->mols.index[mtop->mols.nr-1])
2080 gmx_fatal(FARGS, "The molecule to insert can not consist of multiple charge groups.\nMake it a single charge group.");
2088 /* Copy AdResS parameters */
2091 fr->adress_type = ir->adress->type;
2092 fr->adress_const_wf = ir->adress->const_wf;
2093 fr->adress_ex_width = ir->adress->ex_width;
2094 fr->adress_hy_width = ir->adress->hy_width;
2095 fr->adress_icor = ir->adress->icor;
2096 fr->adress_site = ir->adress->site;
2097 fr->adress_ex_forcecap = ir->adress->ex_forcecap;
2098 fr->adress_do_hybridpairs = ir->adress->do_hybridpairs;
2101 snew(fr->adress_group_explicit, ir->adress->n_energy_grps);
2102 for (i = 0; i < ir->adress->n_energy_grps; i++)
2104 fr->adress_group_explicit[i] = ir->adress->group_explicit[i];
2107 fr->n_adress_tf_grps = ir->adress->n_tf_grps;
2108 snew(fr->adress_tf_table_index, fr->n_adress_tf_grps);
2109 for (i = 0; i < fr->n_adress_tf_grps; i++)
2111 fr->adress_tf_table_index[i] = ir->adress->tf_table_index[i];
2113 copy_rvec(ir->adress->refs, fr->adress_refs);
2117 fr->adress_type = eAdressOff;
2118 fr->adress_do_hybridpairs = FALSE;
2121 /* Copy the user determined parameters */
2122 fr->userint1 = ir->userint1;
2123 fr->userint2 = ir->userint2;
2124 fr->userint3 = ir->userint3;
2125 fr->userint4 = ir->userint4;
2126 fr->userreal1 = ir->userreal1;
2127 fr->userreal2 = ir->userreal2;
2128 fr->userreal3 = ir->userreal3;
2129 fr->userreal4 = ir->userreal4;
2132 fr->fc_stepsize = ir->fc_stepsize;
2135 fr->efep = ir->efep;
2136 fr->sc_alphavdw = ir->fepvals->sc_alpha;
2137 if (ir->fepvals->bScCoul)
2139 fr->sc_alphacoul = ir->fepvals->sc_alpha;
2140 fr->sc_sigma6_min = pow(ir->fepvals->sc_sigma_min, 6);
2144 fr->sc_alphacoul = 0;
2145 fr->sc_sigma6_min = 0; /* only needed when bScCoul is on */
2147 fr->sc_power = ir->fepvals->sc_power;
2148 fr->sc_r_power = ir->fepvals->sc_r_power;
2149 fr->sc_sigma6_def = pow(ir->fepvals->sc_sigma, 6);
2151 env = getenv("GMX_SCSIGMA_MIN");
2155 sscanf(env, "%lf", &dbl);
2156 fr->sc_sigma6_min = pow(dbl, 6);
2159 fprintf(fp, "Setting the minimum soft core sigma to %g nm\n", dbl);
2163 fr->bNonbonded = TRUE;
2164 if (getenv("GMX_NO_NONBONDED") != NULL)
2166 /* turn off non-bonded calculations */
2167 fr->bNonbonded = FALSE;
2168 md_print_warn(cr, fp,
2169 "Found environment variable GMX_NO_NONBONDED.\n"
2170 "Disabling nonbonded calculations.\n");
2173 bGenericKernelOnly = FALSE;
2175 /* We now check in the NS code whether a particular combination of interactions
2176 * can be used with water optimization, and disable it if that is not the case.
2179 if (getenv("GMX_NB_GENERIC") != NULL)
2184 "Found environment variable GMX_NB_GENERIC.\n"
2185 "Disabling all interaction-specific nonbonded kernels, will only\n"
2186 "use the slow generic ones in src/gmxlib/nonbonded/nb_generic.c\n\n");
2188 bGenericKernelOnly = TRUE;
2191 if (bGenericKernelOnly == TRUE)
2196 if ( (getenv("GMX_DISABLE_CPU_ACCELERATION") != NULL) || (getenv("GMX_NOOPTIMIZEDKERNELS") != NULL) )
2198 fr->use_cpu_acceleration = FALSE;
2202 "\nFound environment variable GMX_DISABLE_CPU_ACCELERATION.\n"
2203 "Disabling all CPU architecture-specific (e.g. SSE2/SSE4/AVX) routines.\n\n");
2207 fr->bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
2209 /* Check if we can/should do all-vs-all kernels */
2210 fr->bAllvsAll = can_use_allvsall(ir, mtop, FALSE, NULL, NULL);
2211 fr->AllvsAll_work = NULL;
2212 fr->AllvsAll_workgb = NULL;
2215 /* Neighbour searching stuff */
2216 fr->cutoff_scheme = ir->cutoff_scheme;
2217 fr->bGrid = (ir->ns_type == ensGRID);
2218 fr->ePBC = ir->ePBC;
2220 /* Determine if we will do PBC for distances in bonded interactions */
2221 if (fr->ePBC == epbcNONE)
2223 fr->bMolPBC = FALSE;
2227 if (!DOMAINDECOMP(cr))
2229 /* The group cut-off scheme and SHAKE assume charge groups
2230 * are whole, but not using molpbc is faster in most cases.
2232 if (fr->cutoff_scheme == ecutsGROUP ||
2233 (ir->eConstrAlg == econtSHAKE &&
2234 (gmx_mtop_ftype_count(mtop, F_CONSTR) > 0 ||
2235 gmx_mtop_ftype_count(mtop, F_CONSTRNC) > 0)))
2237 fr->bMolPBC = ir->bPeriodicMols;
2242 if (getenv("GMX_USE_GRAPH") != NULL)
2244 fr->bMolPBC = FALSE;
2247 fprintf(fp, "\nGMX_MOLPBC is set, using the graph for bonded interactions\n\n");
2254 fr->bMolPBC = dd_bonded_molpbc(cr->dd, fr->ePBC);
2257 fr->bGB = (ir->implicit_solvent == eisGBSA);
2259 fr->rc_scaling = ir->refcoord_scaling;
2260 copy_rvec(ir->posres_com, fr->posres_com);
2261 copy_rvec(ir->posres_comB, fr->posres_comB);
2262 fr->rlist = cutoff_inf(ir->rlist);
2263 fr->rlistlong = cutoff_inf(ir->rlistlong);
2264 fr->eeltype = ir->coulombtype;
2265 fr->vdwtype = ir->vdwtype;
2267 fr->coulomb_modifier = ir->coulomb_modifier;
2268 fr->vdw_modifier = ir->vdw_modifier;
2270 /* Electrostatics: Translate from interaction-setting-in-mdp-file to kernel interaction format */
2271 switch (fr->eeltype)
2274 fr->nbkernel_elec_interaction = (fr->bGB) ? GMX_NBKERNEL_ELEC_GENERALIZEDBORN : GMX_NBKERNEL_ELEC_COULOMB;
2280 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD;
2284 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD;
2285 fr->coulomb_modifier = eintmodEXACTCUTOFF;
2294 case eelPMEUSERSWITCH:
2295 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_CUBICSPLINETABLE;
2300 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_EWALD;
2304 gmx_fatal(FARGS, "Unsupported electrostatic interaction: %s", eel_names[fr->eeltype]);
2308 /* Vdw: Translate from mdp settings to kernel format */
2309 switch (fr->vdwtype)
2314 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_BUCKINGHAM;
2318 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_LENNARDJONES;
2325 case evdwENCADSHIFT:
2326 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
2330 gmx_fatal(FARGS, "Unsupported vdw interaction: %s", evdw_names[fr->vdwtype]);
2334 /* These start out identical to ir, but might be altered if we e.g. tabulate the interaction in the kernel */
2335 fr->nbkernel_elec_modifier = fr->coulomb_modifier;
2336 fr->nbkernel_vdw_modifier = fr->vdw_modifier;
2338 fr->bTwinRange = fr->rlistlong > fr->rlist;
2339 fr->bEwald = (EEL_PME(fr->eeltype) || fr->eeltype == eelEWALD);
2341 fr->reppow = mtop->ffparams.reppow;
2343 if (ir->cutoff_scheme == ecutsGROUP)
2345 fr->bvdwtab = (fr->vdwtype != evdwCUT ||
2346 !gmx_within_tol(fr->reppow, 12.0, 10*GMX_DOUBLE_EPS));
2347 /* We have special kernels for standard Ewald and PME, but the pme-switch ones are tabulated above */
2348 fr->bcoultab = !(fr->eeltype == eelCUT ||
2349 fr->eeltype == eelEWALD ||
2350 fr->eeltype == eelPME ||
2351 fr->eeltype == eelRF ||
2352 fr->eeltype == eelRF_ZERO);
2354 /* If the user absolutely wants different switch/shift settings for coul/vdw, it is likely
2355 * going to be faster to tabulate the interaction than calling the generic kernel.
2357 if (fr->nbkernel_elec_modifier == eintmodPOTSWITCH && fr->nbkernel_vdw_modifier == eintmodPOTSWITCH)
2359 if ((fr->rcoulomb_switch != fr->rvdw_switch) || (fr->rcoulomb != fr->rvdw))
2361 fr->bcoultab = TRUE;
2364 else if ((fr->nbkernel_elec_modifier == eintmodPOTSHIFT && fr->nbkernel_vdw_modifier == eintmodPOTSHIFT) ||
2365 ((fr->nbkernel_elec_interaction == GMX_NBKERNEL_ELEC_REACTIONFIELD &&
2366 fr->nbkernel_elec_modifier == eintmodEXACTCUTOFF &&
2367 (fr->nbkernel_vdw_modifier == eintmodPOTSWITCH || fr->nbkernel_vdw_modifier == eintmodPOTSHIFT))))
2369 if (fr->rcoulomb != fr->rvdw)
2371 fr->bcoultab = TRUE;
2375 if (getenv("GMX_REQUIRE_TABLES"))
2378 fr->bcoultab = TRUE;
2383 fprintf(fp, "Table routines are used for coulomb: %s\n", bool_names[fr->bcoultab]);
2384 fprintf(fp, "Table routines are used for vdw: %s\n", bool_names[fr->bvdwtab ]);
2387 if (fr->bvdwtab == TRUE)
2389 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
2390 fr->nbkernel_vdw_modifier = eintmodNONE;
2392 if (fr->bcoultab == TRUE)
2394 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_CUBICSPLINETABLE;
2395 fr->nbkernel_elec_modifier = eintmodNONE;
2399 if (ir->cutoff_scheme == ecutsVERLET)
2401 if (!gmx_within_tol(fr->reppow, 12.0, 10*GMX_DOUBLE_EPS))
2403 gmx_fatal(FARGS, "Cut-off scheme %S only supports LJ repulsion power 12", ecutscheme_names[ir->cutoff_scheme]);
2405 fr->bvdwtab = FALSE;
2406 fr->bcoultab = FALSE;
2409 /* Tables are used for direct ewald sum */
2412 if (EEL_PME(ir->coulombtype))
2416 fprintf(fp, "Will do PME sum in reciprocal space.\n");
2418 if (ir->coulombtype == eelP3M_AD)
2420 please_cite(fp, "Hockney1988");
2421 please_cite(fp, "Ballenegger2012");
2425 please_cite(fp, "Essmann95a");
2428 if (ir->ewald_geometry == eewg3DC)
2432 fprintf(fp, "Using the Ewald3DC correction for systems with a slab geometry.\n");
2434 please_cite(fp, "In-Chul99a");
2437 fr->ewaldcoeff = calc_ewaldcoeff(ir->rcoulomb, ir->ewald_rtol);
2438 init_ewald_tab(&(fr->ewald_table), cr, ir, fp);
2441 fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for Ewald\n",
2446 /* Electrostatics */
2447 fr->epsilon_r = ir->epsilon_r;
2448 fr->epsilon_rf = ir->epsilon_rf;
2449 fr->fudgeQQ = mtop->ffparams.fudgeQQ;
2450 fr->rcoulomb_switch = ir->rcoulomb_switch;
2451 fr->rcoulomb = cutoff_inf(ir->rcoulomb);
2453 /* Parameters for generalized RF */
2457 if (fr->eeltype == eelGRF)
2459 init_generalized_rf(fp, mtop, ir, fr);
2461 else if (fr->eeltype == eelSHIFT)
2463 for (m = 0; (m < DIM); m++)
2465 box_size[m] = box[m][m];
2468 if ((fr->eeltype == eelSHIFT && fr->rcoulomb > fr->rcoulomb_switch))
2470 set_shift_consts(fp, fr->rcoulomb_switch, fr->rcoulomb, box_size, fr);
2474 fr->bF_NoVirSum = (EEL_FULL(fr->eeltype) ||
2475 gmx_mtop_ftype_count(mtop, F_POSRES) > 0 ||
2476 gmx_mtop_ftype_count(mtop, F_FBPOSRES) > 0 ||
2477 IR_ELEC_FIELD(*ir) ||
2478 (fr->adress_icor != eAdressICOff)
2481 if (fr->cutoff_scheme == ecutsGROUP &&
2482 ncg_mtop(mtop) > fr->cg_nalloc && !DOMAINDECOMP(cr))
2484 /* Count the total number of charge groups */
2485 fr->cg_nalloc = ncg_mtop(mtop);
2486 srenew(fr->cg_cm, fr->cg_nalloc);
2488 if (fr->shift_vec == NULL)
2490 snew(fr->shift_vec, SHIFTS);
2493 if (fr->fshift == NULL)
2495 snew(fr->fshift, SHIFTS);
2498 if (fr->nbfp == NULL)
2500 fr->ntype = mtop->ffparams.atnr;
2501 fr->nbfp = mk_nbfp(&mtop->ffparams, fr->bBHAM);
2504 /* Copy the energy group exclusions */
2505 fr->egp_flags = ir->opts.egp_flags;
2507 /* Van der Waals stuff */
2508 fr->rvdw = cutoff_inf(ir->rvdw);
2509 fr->rvdw_switch = ir->rvdw_switch;
2510 if ((fr->vdwtype != evdwCUT) && (fr->vdwtype != evdwUSER) && !fr->bBHAM)
2512 if (fr->rvdw_switch >= fr->rvdw)
2514 gmx_fatal(FARGS, "rvdw_switch (%f) must be < rvdw (%f)",
2515 fr->rvdw_switch, fr->rvdw);
2519 fprintf(fp, "Using %s Lennard-Jones, switch between %g and %g nm\n",
2520 (fr->eeltype == eelSWITCH) ? "switched" : "shifted",
2521 fr->rvdw_switch, fr->rvdw);
2525 if (fr->bBHAM && (fr->vdwtype == evdwSHIFT || fr->vdwtype == evdwSWITCH))
2527 gmx_fatal(FARGS, "Switch/shift interaction not supported with Buckingham");
2532 fprintf(fp, "Cut-off's: NS: %g Coulomb: %g %s: %g\n",
2533 fr->rlist, fr->rcoulomb, fr->bBHAM ? "BHAM" : "LJ", fr->rvdw);
2536 fr->eDispCorr = ir->eDispCorr;
2537 if (ir->eDispCorr != edispcNO)
2539 set_avcsixtwelve(fp, fr, mtop);
2544 set_bham_b_max(fp, fr, mtop);
2547 fr->gb_epsilon_solvent = ir->gb_epsilon_solvent;
2549 /* Copy the GBSA data (radius, volume and surftens for each
2550 * atomtype) from the topology atomtype section to forcerec.
2552 snew(fr->atype_radius, fr->ntype);
2553 snew(fr->atype_vol, fr->ntype);
2554 snew(fr->atype_surftens, fr->ntype);
2555 snew(fr->atype_gb_radius, fr->ntype);
2556 snew(fr->atype_S_hct, fr->ntype);
2558 if (mtop->atomtypes.nr > 0)
2560 for (i = 0; i < fr->ntype; i++)
2562 fr->atype_radius[i] = mtop->atomtypes.radius[i];
2564 for (i = 0; i < fr->ntype; i++)
2566 fr->atype_vol[i] = mtop->atomtypes.vol[i];
2568 for (i = 0; i < fr->ntype; i++)
2570 fr->atype_surftens[i] = mtop->atomtypes.surftens[i];
2572 for (i = 0; i < fr->ntype; i++)
2574 fr->atype_gb_radius[i] = mtop->atomtypes.gb_radius[i];
2576 for (i = 0; i < fr->ntype; i++)
2578 fr->atype_S_hct[i] = mtop->atomtypes.S_hct[i];
2582 /* Generate the GB table if needed */
2586 fr->gbtabscale = 2000;
2588 fr->gbtabscale = 500;
2592 fr->gbtab = make_gb_table(fp, oenv, fr, tabpfn, fr->gbtabscale);
2594 init_gb(&fr->born, cr, fr, ir, mtop, ir->rgbradii, ir->gb_algorithm);
2596 /* Copy local gb data (for dd, this is done in dd_partition_system) */
2597 if (!DOMAINDECOMP(cr))
2599 make_local_gb(cr, fr->born, ir->gb_algorithm);
2603 /* Set the charge scaling */
2604 if (fr->epsilon_r != 0)
2606 fr->epsfac = ONE_4PI_EPS0/fr->epsilon_r;
2610 /* eps = 0 is infinite dieletric: no coulomb interactions */
2614 /* Reaction field constants */
2615 if (EEL_RF(fr->eeltype))
2617 calc_rffac(fp, fr->eeltype, fr->epsilon_r, fr->epsilon_rf,
2618 fr->rcoulomb, fr->temp, fr->zsquare, box,
2619 &fr->kappa, &fr->k_rf, &fr->c_rf);
2622 set_chargesum(fp, fr, mtop);
2624 /* if we are using LR electrostatics, and they are tabulated,
2625 * the tables will contain modified coulomb interactions.
2626 * Since we want to use the non-shifted ones for 1-4
2627 * coulombic interactions, we must have an extra set of tables.
2630 /* Construct tables.
2631 * A little unnecessary to make both vdw and coul tables sometimes,
2632 * but what the heck... */
2634 bTab = fr->bcoultab || fr->bvdwtab || fr->bEwald;
2636 bSep14tab = ((!bTab || fr->eeltype != eelCUT || fr->vdwtype != evdwCUT ||
2637 fr->bBHAM || fr->bEwald) &&
2638 (gmx_mtop_ftype_count(mtop, F_LJ14) > 0 ||
2639 gmx_mtop_ftype_count(mtop, F_LJC14_Q) > 0 ||
2640 gmx_mtop_ftype_count(mtop, F_LJC_PAIRS_NB) > 0));
2642 negp_pp = ir->opts.ngener - ir->nwall;
2646 bNormalnblists = TRUE;
2651 bNormalnblists = (ir->eDispCorr != edispcNO);
2652 for (egi = 0; egi < negp_pp; egi++)
2654 for (egj = egi; egj < negp_pp; egj++)
2656 egp_flags = ir->opts.egp_flags[GID(egi, egj, ir->opts.ngener)];
2657 if (!(egp_flags & EGP_EXCL))
2659 if (egp_flags & EGP_TABLE)
2665 bNormalnblists = TRUE;
2672 fr->nnblists = negptable + 1;
2676 fr->nnblists = negptable;
2678 if (fr->nnblists > 1)
2680 snew(fr->gid2nblists, ir->opts.ngener*ir->opts.ngener);
2689 snew(fr->nblists, fr->nnblists);
2691 /* This code automatically gives table length tabext without cut-off's,
2692 * in that case grompp should already have checked that we do not need
2693 * normal tables and we only generate tables for 1-4 interactions.
2695 rtab = ir->rlistlong + ir->tabext;
2699 /* make tables for ordinary interactions */
2702 make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn, NULL, NULL, &fr->nblists[0]);
2705 make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn, NULL, NULL, &fr->nblists[fr->nnblists/2]);
2709 fr->tab14 = fr->nblists[0].table_elec_vdw;
2719 /* Read the special tables for certain energy group pairs */
2720 nm_ind = mtop->groups.grps[egcENER].nm_ind;
2721 for (egi = 0; egi < negp_pp; egi++)
2723 for (egj = egi; egj < negp_pp; egj++)
2725 egp_flags = ir->opts.egp_flags[GID(egi, egj, ir->opts.ngener)];
2726 if ((egp_flags & EGP_TABLE) && !(egp_flags & EGP_EXCL))
2728 nbl = &(fr->nblists[m]);
2729 if (fr->nnblists > 1)
2731 fr->gid2nblists[GID(egi, egj, ir->opts.ngener)] = m;
2733 /* Read the table file with the two energy groups names appended */
2734 make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn,
2735 *mtop->groups.grpname[nm_ind[egi]],
2736 *mtop->groups.grpname[nm_ind[egj]],
2740 make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn,
2741 *mtop->groups.grpname[nm_ind[egi]],
2742 *mtop->groups.grpname[nm_ind[egj]],
2743 &fr->nblists[fr->nnblists/2+m]);
2747 else if (fr->nnblists > 1)
2749 fr->gid2nblists[GID(egi, egj, ir->opts.ngener)] = 0;
2757 /* generate extra tables with plain Coulomb for 1-4 interactions only */
2758 fr->tab14 = make_tables(fp, oenv, fr, MASTER(cr), tabpfn, rtab,
2759 GMX_MAKETABLES_14ONLY);
2762 /* Read AdResS Thermo Force table if needed */
2763 if (fr->adress_icor == eAdressICThermoForce)
2765 /* old todo replace */
2767 if (ir->adress->n_tf_grps > 0)
2769 make_adress_tf_tables(fp, oenv, fr, ir, tabfn, mtop, box);
2774 /* load the default table */
2775 snew(fr->atf_tabs, 1);
2776 fr->atf_tabs[DEFAULT_TF_TABLE] = make_atf_table(fp, oenv, fr, tabafn, box);
2781 fr->nwall = ir->nwall;
2782 if (ir->nwall && ir->wall_type == ewtTABLE)
2784 make_wall_tables(fp, oenv, ir, tabfn, &mtop->groups, fr);
2789 fcd->bondtab = make_bonded_tables(fp,
2790 F_TABBONDS, F_TABBONDSNC,
2792 fcd->angletab = make_bonded_tables(fp,
2795 fcd->dihtab = make_bonded_tables(fp,
2803 fprintf(debug, "No fcdata or table file name passed, can not read table, can not do bonded interactions\n");
2807 /* QM/MM initialization if requested
2811 fprintf(stderr, "QM/MM calculation requested.\n");
2814 fr->bQMMM = ir->bQMMM;
2815 fr->qr = mk_QMMMrec();
2817 /* Set all the static charge group info */
2818 fr->cginfo_mb = init_cginfo_mb(fp, mtop, fr, bNoSolvOpt,
2819 &fr->bExcl_IntraCGAll_InterCGNone);
2820 if (DOMAINDECOMP(cr))
2826 fr->cginfo = cginfo_expand(mtop->nmolblock, fr->cginfo_mb);
2829 if (!DOMAINDECOMP(cr))
2831 /* When using particle decomposition, the effect of the second argument,
2832 * which sets fr->hcg, is corrected later in do_md and init_em.
2834 forcerec_set_ranges(fr, ncg_mtop(mtop), ncg_mtop(mtop),
2835 mtop->natoms, mtop->natoms, mtop->natoms);
2838 fr->print_force = print_force;
2841 /* coarse load balancing vars */
2846 /* Initialize neighbor search */
2847 init_ns(fp, cr, &fr->ns, fr, mtop, box);
2849 if (cr->duty & DUTY_PP)
2851 gmx_nonbonded_setup(fp, fr, bGenericKernelOnly);
2855 gmx_setup_adress_kernels(fp,bGenericKernelOnly);
2860 /* Initialize the thread working data for bonded interactions */
2861 init_forcerec_f_threads(fr, mtop->groups.grps[egcENER].nr);
2863 snew(fr->excl_load, fr->nthreads+1);
2865 if (fr->cutoff_scheme == ecutsVERLET)
2867 if (ir->rcoulomb != ir->rvdw)
2869 gmx_fatal(FARGS, "With Verlet lists rcoulomb and rvdw should be identical");
2872 init_nb_verlet(fp, &fr->nbv, ir, fr, cr, nbpu_opt);
2875 /* fr->ic is used both by verlet and group kernels (to some extent) now */
2876 init_interaction_const(fp, &fr->ic, fr, rtab);
2877 if (ir->eDispCorr != edispcNO)
2879 calc_enervirdiff(fp, ir->eDispCorr, fr);
2883 #define pr_real(fp, r) fprintf(fp, "%s: %e\n",#r, r)
2884 #define pr_int(fp, i) fprintf((fp), "%s: %d\n",#i, i)
2885 #define pr_bool(fp, b) fprintf((fp), "%s: %s\n",#b, bool_names[b])
2887 void pr_forcerec(FILE *fp, t_forcerec *fr, t_commrec *cr)
2891 pr_real(fp, fr->rlist);
2892 pr_real(fp, fr->rcoulomb);
2893 pr_real(fp, fr->fudgeQQ);
2894 pr_bool(fp, fr->bGrid);
2895 pr_bool(fp, fr->bTwinRange);
2896 /*pr_int(fp,fr->cg0);
2897 pr_int(fp,fr->hcg);*/
2898 for (i = 0; i < fr->nnblists; i++)
2900 pr_int(fp, fr->nblists[i].table_elec_vdw.n);
2902 pr_real(fp, fr->rcoulomb_switch);
2903 pr_real(fp, fr->rcoulomb);
2908 void forcerec_set_excl_load(t_forcerec *fr,
2909 const gmx_localtop_t *top, const t_commrec *cr)
2912 int t, i, j, ntot, n, ntarget;
2914 if (cr != NULL && PARTDECOMP(cr))
2916 /* No OpenMP with particle decomposition */
2924 ind = top->excls.index;
2928 for (i = 0; i < top->excls.nr; i++)
2930 for (j = ind[i]; j < ind[i+1]; j++)
2939 fr->excl_load[0] = 0;
2942 for (t = 1; t <= fr->nthreads; t++)
2944 ntarget = (ntot*t)/fr->nthreads;
2945 while (i < top->excls.nr && n < ntarget)
2947 for (j = ind[i]; j < ind[i+1]; j++)
2956 fr->excl_load[t] = i;