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52 #include "gmx_fatal.h"
53 #include "gmx_fatal_collective.h"
57 #include "nonbonded.h"
66 #include "md_support.h"
67 #include "md_logging.h"
72 #include "mtop_util.h"
73 #include "nbnxn_search.h"
74 #include "nbnxn_atomdata.h"
75 #include "nbnxn_consts.h"
77 #include "gmx_omp_nthreads.h"
78 #include "gmx_detect_hardware.h"
81 /* MSVC definition for __cpuid() */
85 #include "types/nbnxn_cuda_types_ext.h"
86 #include "gpu_utils.h"
87 #include "nbnxn_cuda_data_mgmt.h"
88 #include "pmalloc_cuda.h"
90 t_forcerec *mk_forcerec(void)
100 static void pr_nbfp(FILE *fp, real *nbfp, gmx_bool bBHAM, int atnr)
104 for (i = 0; (i < atnr); i++)
106 for (j = 0; (j < atnr); j++)
108 fprintf(fp, "%2d - %2d", i, j);
111 fprintf(fp, " a=%10g, b=%10g, c=%10g\n", BHAMA(nbfp, atnr, i, j),
112 BHAMB(nbfp, atnr, i, j), BHAMC(nbfp, atnr, i, j)/6.0);
116 fprintf(fp, " c6=%10g, c12=%10g\n", C6(nbfp, atnr, i, j)/6.0,
117 C12(nbfp, atnr, i, j)/12.0);
124 static real *mk_nbfp(const gmx_ffparams_t *idef, gmx_bool bBHAM)
132 snew(nbfp, 3*atnr*atnr);
133 for (i = k = 0; (i < atnr); i++)
135 for (j = 0; (j < atnr); j++, k++)
137 BHAMA(nbfp, atnr, i, j) = idef->iparams[k].bham.a;
138 BHAMB(nbfp, atnr, i, j) = idef->iparams[k].bham.b;
139 /* nbfp now includes the 6.0 derivative prefactor */
140 BHAMC(nbfp, atnr, i, j) = idef->iparams[k].bham.c*6.0;
146 snew(nbfp, 2*atnr*atnr);
147 for (i = k = 0; (i < atnr); i++)
149 for (j = 0; (j < atnr); j++, k++)
151 /* nbfp now includes the 6.0/12.0 derivative prefactors */
152 C6(nbfp, atnr, i, j) = idef->iparams[k].lj.c6*6.0;
153 C12(nbfp, atnr, i, j) = idef->iparams[k].lj.c12*12.0;
161 /* This routine sets fr->solvent_opt to the most common solvent in the
162 * system, e.g. esolSPC or esolTIP4P. It will also mark each charge group in
163 * the fr->solvent_type array with the correct type (or esolNO).
165 * Charge groups that fulfill the conditions but are not identical to the
166 * most common one will be marked as esolNO in the solvent_type array.
168 * TIP3p is identical to SPC for these purposes, so we call it
169 * SPC in the arrays (Apologies to Bill Jorgensen ;-)
171 * NOTE: QM particle should not
172 * become an optimized solvent. Not even if there is only one charge
182 } solvent_parameters_t;
185 check_solvent_cg(const gmx_moltype_t *molt,
188 const unsigned char *qm_grpnr,
189 const t_grps *qm_grps,
191 int *n_solvent_parameters,
192 solvent_parameters_t **solvent_parameters_p,
196 const t_blocka * excl;
207 solvent_parameters_t *solvent_parameters;
209 /* We use a list with parameters for each solvent type.
210 * Every time we discover a new molecule that fulfills the basic
211 * conditions for a solvent we compare with the previous entries
212 * in these lists. If the parameters are the same we just increment
213 * the counter for that type, and otherwise we create a new type
214 * based on the current molecule.
216 * Once we've finished going through all molecules we check which
217 * solvent is most common, and mark all those molecules while we
218 * clear the flag on all others.
221 solvent_parameters = *solvent_parameters_p;
223 /* Mark the cg first as non optimized */
226 /* Check if this cg has no exclusions with atoms in other charge groups
227 * and all atoms inside the charge group excluded.
228 * We only have 3 or 4 atom solvent loops.
230 if (GET_CGINFO_EXCL_INTER(cginfo) ||
231 !GET_CGINFO_EXCL_INTRA(cginfo))
236 /* Get the indices of the first atom in this charge group */
237 j0 = molt->cgs.index[cg0];
238 j1 = molt->cgs.index[cg0+1];
240 /* Number of atoms in our molecule */
246 "Moltype '%s': there are %d atoms in this charge group\n",
250 /* Check if it could be an SPC (3 atoms) or TIP4p (4) water,
253 if (nj < 3 || nj > 4)
258 /* Check if we are doing QM on this group */
260 if (qm_grpnr != NULL)
262 for (j = j0; j < j1 && !qm; j++)
264 qm = (qm_grpnr[j] < qm_grps->nr - 1);
267 /* Cannot use solvent optimization with QM */
273 atom = molt->atoms.atom;
275 /* Still looks like a solvent, time to check parameters */
277 /* If it is perturbed (free energy) we can't use the solvent loops,
278 * so then we just skip to the next molecule.
282 for (j = j0; j < j1 && !perturbed; j++)
284 perturbed = PERTURBED(atom[j]);
292 /* Now it's only a question if the VdW and charge parameters
293 * are OK. Before doing the check we compare and see if they are
294 * identical to a possible previous solvent type.
295 * First we assign the current types and charges.
297 for (j = 0; j < nj; j++)
299 tmp_vdwtype[j] = atom[j0+j].type;
300 tmp_charge[j] = atom[j0+j].q;
303 /* Does it match any previous solvent type? */
304 for (k = 0; k < *n_solvent_parameters; k++)
309 /* We can only match SPC with 3 atoms and TIP4p with 4 atoms */
310 if ( (solvent_parameters[k].model == esolSPC && nj != 3) ||
311 (solvent_parameters[k].model == esolTIP4P && nj != 4) )
316 /* Check that types & charges match for all atoms in molecule */
317 for (j = 0; j < nj && match == TRUE; j++)
319 if (tmp_vdwtype[j] != solvent_parameters[k].vdwtype[j])
323 if (tmp_charge[j] != solvent_parameters[k].charge[j])
330 /* Congratulations! We have a matched solvent.
331 * Flag it with this type for later processing.
334 solvent_parameters[k].count += nmol;
336 /* We are done with this charge group */
341 /* If we get here, we have a tentative new solvent type.
342 * Before we add it we must check that it fulfills the requirements
343 * of the solvent optimized loops. First determine which atoms have
346 for (j = 0; j < nj; j++)
349 tjA = tmp_vdwtype[j];
351 /* Go through all other tpes and see if any have non-zero
352 * VdW parameters when combined with this one.
354 for (k = 0; k < fr->ntype && (has_vdw[j] == FALSE); k++)
356 /* We already checked that the atoms weren't perturbed,
357 * so we only need to check state A now.
361 has_vdw[j] = (has_vdw[j] ||
362 (BHAMA(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
363 (BHAMB(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
364 (BHAMC(fr->nbfp, fr->ntype, tjA, k) != 0.0));
369 has_vdw[j] = (has_vdw[j] ||
370 (C6(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
371 (C12(fr->nbfp, fr->ntype, tjA, k) != 0.0));
376 /* Now we know all we need to make the final check and assignment. */
380 * For this we require thatn all atoms have charge,
381 * the charges on atom 2 & 3 should be the same, and only
382 * atom 1 might have VdW.
384 if (has_vdw[1] == FALSE &&
385 has_vdw[2] == FALSE &&
386 tmp_charge[0] != 0 &&
387 tmp_charge[1] != 0 &&
388 tmp_charge[2] == tmp_charge[1])
390 srenew(solvent_parameters, *n_solvent_parameters+1);
391 solvent_parameters[*n_solvent_parameters].model = esolSPC;
392 solvent_parameters[*n_solvent_parameters].count = nmol;
393 for (k = 0; k < 3; k++)
395 solvent_parameters[*n_solvent_parameters].vdwtype[k] = tmp_vdwtype[k];
396 solvent_parameters[*n_solvent_parameters].charge[k] = tmp_charge[k];
399 *cg_sp = *n_solvent_parameters;
400 (*n_solvent_parameters)++;
405 /* Or could it be a TIP4P?
406 * For this we require thatn atoms 2,3,4 have charge, but not atom 1.
407 * Only atom 1 mght have VdW.
409 if (has_vdw[1] == FALSE &&
410 has_vdw[2] == FALSE &&
411 has_vdw[3] == FALSE &&
412 tmp_charge[0] == 0 &&
413 tmp_charge[1] != 0 &&
414 tmp_charge[2] == tmp_charge[1] &&
417 srenew(solvent_parameters, *n_solvent_parameters+1);
418 solvent_parameters[*n_solvent_parameters].model = esolTIP4P;
419 solvent_parameters[*n_solvent_parameters].count = nmol;
420 for (k = 0; k < 4; k++)
422 solvent_parameters[*n_solvent_parameters].vdwtype[k] = tmp_vdwtype[k];
423 solvent_parameters[*n_solvent_parameters].charge[k] = tmp_charge[k];
426 *cg_sp = *n_solvent_parameters;
427 (*n_solvent_parameters)++;
431 *solvent_parameters_p = solvent_parameters;
435 check_solvent(FILE * fp,
436 const gmx_mtop_t * mtop,
438 cginfo_mb_t *cginfo_mb)
441 const t_block * mols;
442 const gmx_moltype_t *molt;
443 int mb, mol, cg_mol, at_offset, cg_offset, am, cgm, i, nmol_ch, nmol;
444 int n_solvent_parameters;
445 solvent_parameters_t *solvent_parameters;
451 fprintf(debug, "Going to determine what solvent types we have.\n");
456 n_solvent_parameters = 0;
457 solvent_parameters = NULL;
458 /* Allocate temporary array for solvent type */
459 snew(cg_sp, mtop->nmolblock);
463 for (mb = 0; mb < mtop->nmolblock; mb++)
465 molt = &mtop->moltype[mtop->molblock[mb].type];
467 /* Here we have to loop over all individual molecules
468 * because we need to check for QMMM particles.
470 snew(cg_sp[mb], cginfo_mb[mb].cg_mod);
471 nmol_ch = cginfo_mb[mb].cg_mod/cgs->nr;
472 nmol = mtop->molblock[mb].nmol/nmol_ch;
473 for (mol = 0; mol < nmol_ch; mol++)
476 am = mol*cgs->index[cgs->nr];
477 for (cg_mol = 0; cg_mol < cgs->nr; cg_mol++)
479 check_solvent_cg(molt, cg_mol, nmol,
480 mtop->groups.grpnr[egcQMMM] ?
481 mtop->groups.grpnr[egcQMMM]+at_offset+am : 0,
482 &mtop->groups.grps[egcQMMM],
484 &n_solvent_parameters, &solvent_parameters,
485 cginfo_mb[mb].cginfo[cgm+cg_mol],
486 &cg_sp[mb][cgm+cg_mol]);
489 cg_offset += cgs->nr;
490 at_offset += cgs->index[cgs->nr];
493 /* Puh! We finished going through all charge groups.
494 * Now find the most common solvent model.
497 /* Most common solvent this far */
499 for (i = 0; i < n_solvent_parameters; i++)
502 solvent_parameters[i].count > solvent_parameters[bestsp].count)
510 bestsol = solvent_parameters[bestsp].model;
517 #ifdef DISABLE_WATER_NLIST
522 for (mb = 0; mb < mtop->nmolblock; mb++)
524 cgs = &mtop->moltype[mtop->molblock[mb].type].cgs;
525 nmol = (mtop->molblock[mb].nmol*cgs->nr)/cginfo_mb[mb].cg_mod;
526 for (i = 0; i < cginfo_mb[mb].cg_mod; i++)
528 if (cg_sp[mb][i] == bestsp)
530 SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[i], bestsol);
535 SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[i], esolNO);
542 if (bestsol != esolNO && fp != NULL)
544 fprintf(fp, "\nEnabling %s-like water optimization for %d molecules.\n\n",
546 solvent_parameters[bestsp].count);
549 sfree(solvent_parameters);
550 fr->solvent_opt = bestsol;
554 acNONE = 0, acCONSTRAINT, acSETTLE
557 static cginfo_mb_t *init_cginfo_mb(FILE *fplog, const gmx_mtop_t *mtop,
558 t_forcerec *fr, gmx_bool bNoSolvOpt,
559 gmx_bool *bExcl_IntraCGAll_InterCGNone)
562 const t_blocka *excl;
563 const gmx_moltype_t *molt;
564 const gmx_molblock_t *molb;
565 cginfo_mb_t *cginfo_mb;
568 int cg_offset, a_offset, cgm, am;
569 int mb, m, ncg_tot, cg, a0, a1, gid, ai, j, aj, excl_nalloc;
573 gmx_bool bId, *bExcl, bExclIntraAll, bExclInter, bHaveVDW, bHaveQ;
575 ncg_tot = ncg_mtop(mtop);
576 snew(cginfo_mb, mtop->nmolblock);
578 snew(type_VDW, fr->ntype);
579 for (ai = 0; ai < fr->ntype; ai++)
581 type_VDW[ai] = FALSE;
582 for (j = 0; j < fr->ntype; j++)
584 type_VDW[ai] = type_VDW[ai] ||
586 C6(fr->nbfp, fr->ntype, ai, j) != 0 ||
587 C12(fr->nbfp, fr->ntype, ai, j) != 0;
591 *bExcl_IntraCGAll_InterCGNone = TRUE;
594 snew(bExcl, excl_nalloc);
597 for (mb = 0; mb < mtop->nmolblock; mb++)
599 molb = &mtop->molblock[mb];
600 molt = &mtop->moltype[molb->type];
604 /* Check if the cginfo is identical for all molecules in this block.
605 * If so, we only need an array of the size of one molecule.
606 * Otherwise we make an array of #mol times #cgs per molecule.
610 for (m = 0; m < molb->nmol; m++)
612 am = m*cgs->index[cgs->nr];
613 for (cg = 0; cg < cgs->nr; cg++)
616 a1 = cgs->index[cg+1];
617 if (ggrpnr(&mtop->groups, egcENER, a_offset+am+a0) !=
618 ggrpnr(&mtop->groups, egcENER, a_offset +a0))
622 if (mtop->groups.grpnr[egcQMMM] != NULL)
624 for (ai = a0; ai < a1; ai++)
626 if (mtop->groups.grpnr[egcQMMM][a_offset+am+ai] !=
627 mtop->groups.grpnr[egcQMMM][a_offset +ai])
636 cginfo_mb[mb].cg_start = cg_offset;
637 cginfo_mb[mb].cg_end = cg_offset + molb->nmol*cgs->nr;
638 cginfo_mb[mb].cg_mod = (bId ? 1 : molb->nmol)*cgs->nr;
639 snew(cginfo_mb[mb].cginfo, cginfo_mb[mb].cg_mod);
640 cginfo = cginfo_mb[mb].cginfo;
642 /* Set constraints flags for constrained atoms */
643 snew(a_con, molt->atoms.nr);
644 for (ftype = 0; ftype < F_NRE; ftype++)
646 if (interaction_function[ftype].flags & IF_CONSTRAINT)
651 for (ia = 0; ia < molt->ilist[ftype].nr; ia += 1+nral)
655 for (a = 0; a < nral; a++)
657 a_con[molt->ilist[ftype].iatoms[ia+1+a]] =
658 (ftype == F_SETTLE ? acSETTLE : acCONSTRAINT);
664 for (m = 0; m < (bId ? 1 : molb->nmol); m++)
667 am = m*cgs->index[cgs->nr];
668 for (cg = 0; cg < cgs->nr; cg++)
671 a1 = cgs->index[cg+1];
673 /* Store the energy group in cginfo */
674 gid = ggrpnr(&mtop->groups, egcENER, a_offset+am+a0);
675 SET_CGINFO_GID(cginfo[cgm+cg], gid);
677 /* Check the intra/inter charge group exclusions */
678 if (a1-a0 > excl_nalloc)
680 excl_nalloc = a1 - a0;
681 srenew(bExcl, excl_nalloc);
683 /* bExclIntraAll: all intra cg interactions excluded
684 * bExclInter: any inter cg interactions excluded
686 bExclIntraAll = TRUE;
690 for (ai = a0; ai < a1; ai++)
692 /* Check VDW and electrostatic interactions */
693 bHaveVDW = bHaveVDW || (type_VDW[molt->atoms.atom[ai].type] ||
694 type_VDW[molt->atoms.atom[ai].typeB]);
695 bHaveQ = bHaveQ || (molt->atoms.atom[ai].q != 0 ||
696 molt->atoms.atom[ai].qB != 0);
698 /* Clear the exclusion list for atom ai */
699 for (aj = a0; aj < a1; aj++)
701 bExcl[aj-a0] = FALSE;
703 /* Loop over all the exclusions of atom ai */
704 for (j = excl->index[ai]; j < excl->index[ai+1]; j++)
707 if (aj < a0 || aj >= a1)
716 /* Check if ai excludes a0 to a1 */
717 for (aj = a0; aj < a1; aj++)
721 bExclIntraAll = FALSE;
728 SET_CGINFO_CONSTR(cginfo[cgm+cg]);
731 SET_CGINFO_SETTLE(cginfo[cgm+cg]);
739 SET_CGINFO_EXCL_INTRA(cginfo[cgm+cg]);
743 SET_CGINFO_EXCL_INTER(cginfo[cgm+cg]);
745 if (a1 - a0 > MAX_CHARGEGROUP_SIZE)
747 /* The size in cginfo is currently only read with DD */
748 gmx_fatal(FARGS, "A charge group has size %d which is larger than the limit of %d atoms", a1-a0, MAX_CHARGEGROUP_SIZE);
752 SET_CGINFO_HAS_VDW(cginfo[cgm+cg]);
756 SET_CGINFO_HAS_Q(cginfo[cgm+cg]);
758 /* Store the charge group size */
759 SET_CGINFO_NATOMS(cginfo[cgm+cg], a1-a0);
761 if (!bExclIntraAll || bExclInter)
763 *bExcl_IntraCGAll_InterCGNone = FALSE;
770 cg_offset += molb->nmol*cgs->nr;
771 a_offset += molb->nmol*cgs->index[cgs->nr];
775 /* the solvent optimizer is called after the QM is initialized,
776 * because we don't want to have the QM subsystemto become an
780 check_solvent(fplog, mtop, fr, cginfo_mb);
782 if (getenv("GMX_NO_SOLV_OPT"))
786 fprintf(fplog, "Found environment variable GMX_NO_SOLV_OPT.\n"
787 "Disabling all solvent optimization\n");
789 fr->solvent_opt = esolNO;
793 fr->solvent_opt = esolNO;
795 if (!fr->solvent_opt)
797 for (mb = 0; mb < mtop->nmolblock; mb++)
799 for (cg = 0; cg < cginfo_mb[mb].cg_mod; cg++)
801 SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[cg], esolNO);
809 static int *cginfo_expand(int nmb, cginfo_mb_t *cgi_mb)
814 ncg = cgi_mb[nmb-1].cg_end;
817 for (cg = 0; cg < ncg; cg++)
819 while (cg >= cgi_mb[mb].cg_end)
824 cgi_mb[mb].cginfo[(cg - cgi_mb[mb].cg_start) % cgi_mb[mb].cg_mod];
830 static void set_chargesum(FILE *log, t_forcerec *fr, const gmx_mtop_t *mtop)
832 double qsum, q2sum, q;
834 const t_atoms *atoms;
838 for (mb = 0; mb < mtop->nmolblock; mb++)
840 nmol = mtop->molblock[mb].nmol;
841 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
842 for (i = 0; i < atoms->nr; i++)
844 q = atoms->atom[i].q;
850 fr->q2sum[0] = q2sum;
851 if (fr->efep != efepNO)
855 for (mb = 0; mb < mtop->nmolblock; mb++)
857 nmol = mtop->molblock[mb].nmol;
858 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
859 for (i = 0; i < atoms->nr; i++)
861 q = atoms->atom[i].qB;
866 fr->q2sum[1] = q2sum;
871 fr->qsum[1] = fr->qsum[0];
872 fr->q2sum[1] = fr->q2sum[0];
876 if (fr->efep == efepNO)
878 fprintf(log, "System total charge: %.3f\n", fr->qsum[0]);
882 fprintf(log, "System total charge, top. A: %.3f top. B: %.3f\n",
883 fr->qsum[0], fr->qsum[1]);
888 void update_forcerec(FILE *log, t_forcerec *fr, matrix box)
890 if (fr->eeltype == eelGRF)
892 calc_rffac(NULL, fr->eeltype, fr->epsilon_r, fr->epsilon_rf,
893 fr->rcoulomb, fr->temp, fr->zsquare, box,
894 &fr->kappa, &fr->k_rf, &fr->c_rf);
898 void set_avcsixtwelve(FILE *fplog, t_forcerec *fr, const gmx_mtop_t *mtop)
900 const t_atoms *atoms, *atoms_tpi;
901 const t_blocka *excl;
902 int mb, nmol, nmolc, i, j, tpi, tpj, j1, j2, k, n, nexcl, q;
903 #if (defined SIZEOF_LONG_LONG_INT) && (SIZEOF_LONG_LONG_INT >= 8)
904 long long int npair, npair_ij, tmpi, tmpj;
906 double npair, npair_ij, tmpi, tmpj;
908 double csix, ctwelve;
917 for (q = 0; q < (fr->efep == efepNO ? 1 : 2); q++)
925 /* Count the types so we avoid natoms^2 operations */
926 snew(typecount, ntp);
927 for (mb = 0; mb < mtop->nmolblock; mb++)
929 nmol = mtop->molblock[mb].nmol;
930 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
931 for (i = 0; i < atoms->nr; i++)
935 tpi = atoms->atom[i].type;
939 tpi = atoms->atom[i].typeB;
941 typecount[tpi] += nmol;
944 for (tpi = 0; tpi < ntp; tpi++)
946 for (tpj = tpi; tpj < ntp; tpj++)
948 tmpi = typecount[tpi];
949 tmpj = typecount[tpj];
952 npair_ij = tmpi*tmpj;
956 npair_ij = tmpi*(tmpi - 1)/2;
960 /* nbfp now includes the 6.0 derivative prefactor */
961 csix += npair_ij*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
965 /* nbfp now includes the 6.0/12.0 derivative prefactors */
966 csix += npair_ij* C6(nbfp, ntp, tpi, tpj)/6.0;
967 ctwelve += npair_ij* C12(nbfp, ntp, tpi, tpj)/12.0;
973 /* Subtract the excluded pairs.
974 * The main reason for substracting exclusions is that in some cases
975 * some combinations might never occur and the parameters could have
976 * any value. These unused values should not influence the dispersion
979 for (mb = 0; mb < mtop->nmolblock; mb++)
981 nmol = mtop->molblock[mb].nmol;
982 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
983 excl = &mtop->moltype[mtop->molblock[mb].type].excls;
984 for (i = 0; (i < atoms->nr); i++)
988 tpi = atoms->atom[i].type;
992 tpi = atoms->atom[i].typeB;
995 j2 = excl->index[i+1];
996 for (j = j1; j < j2; j++)
1003 tpj = atoms->atom[k].type;
1007 tpj = atoms->atom[k].typeB;
1011 /* nbfp now includes the 6.0 derivative prefactor */
1012 csix -= nmol*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
1016 /* nbfp now includes the 6.0/12.0 derivative prefactors */
1017 csix -= nmol*C6 (nbfp, ntp, tpi, tpj)/6.0;
1018 ctwelve -= nmol*C12(nbfp, ntp, tpi, tpj)/12.0;
1028 /* Only correct for the interaction of the test particle
1029 * with the rest of the system.
1032 &mtop->moltype[mtop->molblock[mtop->nmolblock-1].type].atoms;
1035 for (mb = 0; mb < mtop->nmolblock; mb++)
1037 nmol = mtop->molblock[mb].nmol;
1038 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
1039 for (j = 0; j < atoms->nr; j++)
1042 /* Remove the interaction of the test charge group
1045 if (mb == mtop->nmolblock-1)
1049 if (mb == 0 && nmol == 1)
1051 gmx_fatal(FARGS, "Old format tpr with TPI, please generate a new tpr file");
1056 tpj = atoms->atom[j].type;
1060 tpj = atoms->atom[j].typeB;
1062 for (i = 0; i < fr->n_tpi; i++)
1066 tpi = atoms_tpi->atom[i].type;
1070 tpi = atoms_tpi->atom[i].typeB;
1074 /* nbfp now includes the 6.0 derivative prefactor */
1075 csix += nmolc*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
1079 /* nbfp now includes the 6.0/12.0 derivative prefactors */
1080 csix += nmolc*C6 (nbfp, ntp, tpi, tpj)/6.0;
1081 ctwelve += nmolc*C12(nbfp, ntp, tpi, tpj)/12.0;
1088 if (npair - nexcl <= 0 && fplog)
1090 fprintf(fplog, "\nWARNING: There are no atom pairs for dispersion correction\n\n");
1096 csix /= npair - nexcl;
1097 ctwelve /= npair - nexcl;
1101 fprintf(debug, "Counted %d exclusions\n", nexcl);
1102 fprintf(debug, "Average C6 parameter is: %10g\n", (double)csix);
1103 fprintf(debug, "Average C12 parameter is: %10g\n", (double)ctwelve);
1105 fr->avcsix[q] = csix;
1106 fr->avctwelve[q] = ctwelve;
1110 if (fr->eDispCorr == edispcAllEner ||
1111 fr->eDispCorr == edispcAllEnerPres)
1113 fprintf(fplog, "Long Range LJ corr.: <C6> %10.4e, <C12> %10.4e\n",
1114 fr->avcsix[0], fr->avctwelve[0]);
1118 fprintf(fplog, "Long Range LJ corr.: <C6> %10.4e\n", fr->avcsix[0]);
1124 static void set_bham_b_max(FILE *fplog, t_forcerec *fr,
1125 const gmx_mtop_t *mtop)
1127 const t_atoms *at1, *at2;
1128 int mt1, mt2, i, j, tpi, tpj, ntypes;
1134 fprintf(fplog, "Determining largest Buckingham b parameter for table\n");
1141 for (mt1 = 0; mt1 < mtop->nmoltype; mt1++)
1143 at1 = &mtop->moltype[mt1].atoms;
1144 for (i = 0; (i < at1->nr); i++)
1146 tpi = at1->atom[i].type;
1149 gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", i, tpi, ntypes);
1152 for (mt2 = mt1; mt2 < mtop->nmoltype; mt2++)
1154 at2 = &mtop->moltype[mt2].atoms;
1155 for (j = 0; (j < at2->nr); j++)
1157 tpj = at2->atom[j].type;
1160 gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", j, tpj, ntypes);
1162 b = BHAMB(nbfp, ntypes, tpi, tpj);
1163 if (b > fr->bham_b_max)
1167 if ((b < bmin) || (bmin == -1))
1177 fprintf(fplog, "Buckingham b parameters, min: %g, max: %g\n",
1178 bmin, fr->bham_b_max);
1182 static void make_nbf_tables(FILE *fp, const output_env_t oenv,
1183 t_forcerec *fr, real rtab,
1184 const t_commrec *cr,
1185 const char *tabfn, char *eg1, char *eg2,
1195 fprintf(debug, "No table file name passed, can not read table, can not do non-bonded interactions\n");
1200 sprintf(buf, "%s", tabfn);
1203 /* Append the two energy group names */
1204 sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "_%s_%s.%s",
1205 eg1, eg2, ftp2ext(efXVG));
1207 nbl->table_elec_vdw = make_tables(fp, oenv, fr, MASTER(cr), buf, rtab, 0);
1208 /* Copy the contents of the table to separate coulomb and LJ tables too,
1209 * to improve cache performance.
1211 /* For performance reasons we want
1212 * the table data to be aligned to 16-byte. The pointers could be freed
1213 * but currently aren't.
1215 nbl->table_elec.interaction = GMX_TABLE_INTERACTION_ELEC;
1216 nbl->table_elec.format = nbl->table_elec_vdw.format;
1217 nbl->table_elec.r = nbl->table_elec_vdw.r;
1218 nbl->table_elec.n = nbl->table_elec_vdw.n;
1219 nbl->table_elec.scale = nbl->table_elec_vdw.scale;
1220 nbl->table_elec.scale_exp = nbl->table_elec_vdw.scale_exp;
1221 nbl->table_elec.formatsize = nbl->table_elec_vdw.formatsize;
1222 nbl->table_elec.ninteractions = 1;
1223 nbl->table_elec.stride = nbl->table_elec.formatsize * nbl->table_elec.ninteractions;
1224 snew_aligned(nbl->table_elec.data, nbl->table_elec.stride*(nbl->table_elec.n+1), 32);
1226 nbl->table_vdw.interaction = GMX_TABLE_INTERACTION_VDWREP_VDWDISP;
1227 nbl->table_vdw.format = nbl->table_elec_vdw.format;
1228 nbl->table_vdw.r = nbl->table_elec_vdw.r;
1229 nbl->table_vdw.n = nbl->table_elec_vdw.n;
1230 nbl->table_vdw.scale = nbl->table_elec_vdw.scale;
1231 nbl->table_vdw.scale_exp = nbl->table_elec_vdw.scale_exp;
1232 nbl->table_vdw.formatsize = nbl->table_elec_vdw.formatsize;
1233 nbl->table_vdw.ninteractions = 2;
1234 nbl->table_vdw.stride = nbl->table_vdw.formatsize * nbl->table_vdw.ninteractions;
1235 snew_aligned(nbl->table_vdw.data, nbl->table_vdw.stride*(nbl->table_vdw.n+1), 32);
1237 for (i = 0; i <= nbl->table_elec_vdw.n; i++)
1239 for (j = 0; j < 4; j++)
1241 nbl->table_elec.data[4*i+j] = nbl->table_elec_vdw.data[12*i+j];
1243 for (j = 0; j < 8; j++)
1245 nbl->table_vdw.data[8*i+j] = nbl->table_elec_vdw.data[12*i+4+j];
1250 static void count_tables(int ftype1, int ftype2, const gmx_mtop_t *mtop,
1251 int *ncount, int **count)
1253 const gmx_moltype_t *molt;
1255 int mt, ftype, stride, i, j, tabnr;
1257 for (mt = 0; mt < mtop->nmoltype; mt++)
1259 molt = &mtop->moltype[mt];
1260 for (ftype = 0; ftype < F_NRE; ftype++)
1262 if (ftype == ftype1 || ftype == ftype2)
1264 il = &molt->ilist[ftype];
1265 stride = 1 + NRAL(ftype);
1266 for (i = 0; i < il->nr; i += stride)
1268 tabnr = mtop->ffparams.iparams[il->iatoms[i]].tab.table;
1271 gmx_fatal(FARGS, "A bonded table number is smaller than 0: %d\n", tabnr);
1273 if (tabnr >= *ncount)
1275 srenew(*count, tabnr+1);
1276 for (j = *ncount; j < tabnr+1; j++)
1289 static bondedtable_t *make_bonded_tables(FILE *fplog,
1290 int ftype1, int ftype2,
1291 const gmx_mtop_t *mtop,
1292 const char *basefn, const char *tabext)
1294 int i, ncount, *count;
1302 count_tables(ftype1, ftype2, mtop, &ncount, &count);
1307 for (i = 0; i < ncount; i++)
1311 sprintf(tabfn, "%s", basefn);
1312 sprintf(tabfn + strlen(basefn) - strlen(ftp2ext(efXVG)) - 1, "_%s%d.%s",
1313 tabext, i, ftp2ext(efXVG));
1314 tab[i] = make_bonded_table(fplog, tabfn, NRAL(ftype1)-2);
1323 void forcerec_set_ranges(t_forcerec *fr,
1324 int ncg_home, int ncg_force,
1326 int natoms_force_constr, int natoms_f_novirsum)
1331 /* fr->ncg_force is unused in the standard code,
1332 * but it can be useful for modified code dealing with charge groups.
1334 fr->ncg_force = ncg_force;
1335 fr->natoms_force = natoms_force;
1336 fr->natoms_force_constr = natoms_force_constr;
1338 if (fr->natoms_force_constr > fr->nalloc_force)
1340 fr->nalloc_force = over_alloc_dd(fr->natoms_force_constr);
1344 srenew(fr->f_twin, fr->nalloc_force);
1348 if (fr->bF_NoVirSum)
1350 fr->f_novirsum_n = natoms_f_novirsum;
1351 if (fr->f_novirsum_n > fr->f_novirsum_nalloc)
1353 fr->f_novirsum_nalloc = over_alloc_dd(fr->f_novirsum_n);
1354 srenew(fr->f_novirsum_alloc, fr->f_novirsum_nalloc);
1359 fr->f_novirsum_n = 0;
1363 static real cutoff_inf(real cutoff)
1367 cutoff = GMX_CUTOFF_INF;
1373 static void make_adress_tf_tables(FILE *fp, const output_env_t oenv,
1374 t_forcerec *fr, const t_inputrec *ir,
1375 const char *tabfn, const gmx_mtop_t *mtop,
1383 gmx_fatal(FARGS, "No thermoforce table file given. Use -tabletf to specify a file\n");
1387 snew(fr->atf_tabs, ir->adress->n_tf_grps);
1389 sprintf(buf, "%s", tabfn);
1390 for (i = 0; i < ir->adress->n_tf_grps; i++)
1392 j = ir->adress->tf_table_index[i]; /* get energy group index */
1393 sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "tf_%s.%s",
1394 *(mtop->groups.grpname[mtop->groups.grps[egcENER].nm_ind[j]]), ftp2ext(efXVG));
1397 fprintf(fp, "loading tf table for energygrp index %d from %s\n", ir->adress->tf_table_index[i], buf);
1399 fr->atf_tabs[i] = make_atf_table(fp, oenv, fr, buf, box);
1404 gmx_bool can_use_allvsall(const t_inputrec *ir, const gmx_mtop_t *mtop,
1405 gmx_bool bPrintNote, t_commrec *cr, FILE *fp)
1412 ir->rcoulomb == 0 &&
1414 ir->ePBC == epbcNONE &&
1415 ir->vdwtype == evdwCUT &&
1416 ir->coulombtype == eelCUT &&
1417 ir->efep == efepNO &&
1418 (ir->implicit_solvent == eisNO ||
1419 (ir->implicit_solvent == eisGBSA && (ir->gb_algorithm == egbSTILL ||
1420 ir->gb_algorithm == egbHCT ||
1421 ir->gb_algorithm == egbOBC))) &&
1422 getenv("GMX_NO_ALLVSALL") == NULL
1425 if (bAllvsAll && ir->opts.ngener > 1)
1427 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";
1433 fprintf(stderr, "\n%s\n", note);
1437 fprintf(fp, "\n%s\n", note);
1443 if (bAllvsAll && fp && MASTER(cr))
1445 fprintf(fp, "\nUsing accelerated all-vs-all kernels.\n\n");
1452 static void init_forcerec_f_threads(t_forcerec *fr, int nenergrp)
1456 /* These thread local data structures are used for bondeds only */
1457 fr->nthreads = gmx_omp_nthreads_get(emntBonded);
1459 if (fr->nthreads > 1)
1461 snew(fr->f_t, fr->nthreads);
1462 /* Thread 0 uses the global force and energy arrays */
1463 for (t = 1; t < fr->nthreads; t++)
1465 fr->f_t[t].f = NULL;
1466 fr->f_t[t].f_nalloc = 0;
1467 snew(fr->f_t[t].fshift, SHIFTS);
1468 fr->f_t[t].grpp.nener = nenergrp*nenergrp;
1469 for (i = 0; i < egNR; i++)
1471 snew(fr->f_t[t].grpp.ener[i], fr->f_t[t].grpp.nener);
1478 static void pick_nbnxn_kernel_cpu(FILE *fp,
1479 const t_commrec *cr,
1480 const gmx_cpuid_t cpuid_info,
1481 const t_inputrec *ir,
1485 *kernel_type = nbnxnk4x4_PlainC;
1486 *ewald_excl = ewaldexclTable;
1488 #ifdef GMX_NBNXN_SIMD
1490 #ifdef GMX_NBNXN_SIMD_4XN
1491 *kernel_type = nbnxnk4xN_SIMD_4xN;
1493 #ifdef GMX_NBNXN_SIMD_2XNN
1494 /* We expect the 2xNN kernels to be faster in most cases */
1495 *kernel_type = nbnxnk4xN_SIMD_2xNN;
1498 #if defined GMX_NBNXN_SIMD_4XN && defined GMX_X86_AVX_256
1499 if (EEL_RF(ir->coulombtype) || ir->coulombtype == eelCUT)
1501 /* The raw pair rate of the 4x8 kernel is higher than 2x(4+4),
1502 * 10% with HT, 50% without HT, but extra zeros interactions
1503 * can compensate. As we currently don't detect the actual use
1504 * of HT, switch to 4x8 to avoid a potential performance hit.
1506 *kernel_type = nbnxnk4xN_SIMD_4xN;
1509 if (getenv("GMX_NBNXN_SIMD_4XN") != NULL)
1511 #ifdef GMX_NBNXN_SIMD_4XN
1512 *kernel_type = nbnxnk4xN_SIMD_4xN;
1514 gmx_fatal(FARGS, "SIMD 4xN kernels requested, but Gromacs has been compiled without support for these kernels");
1517 if (getenv("GMX_NBNXN_SIMD_2XNN") != NULL)
1519 #ifdef GMX_NBNXN_SIMD_2XNN
1520 *kernel_type = nbnxnk4xN_SIMD_2xNN;
1522 gmx_fatal(FARGS, "SIMD 2x(N+N) kernels requested, but Gromacs has been compiled without support for these kernels");
1526 /* Analytical Ewald exclusion correction is only an option in
1527 * the SIMD kernel. On BlueGene/Q, this is faster regardless
1528 * of precision. In single precision, this is faster on
1529 * Bulldozer, and slightly faster on Sandy Bridge.
1531 #if ((defined GMX_X86_AVX_128_FMA || defined GMX_X86_AVX_256) && !defined GMX_DOUBLE) || (defined GMX_CPU_ACCELERATION_IBM_QPX)
1532 *ewald_excl = ewaldexclAnalytical;
1534 if (getenv("GMX_NBNXN_EWALD_TABLE") != NULL)
1536 *ewald_excl = ewaldexclTable;
1538 if (getenv("GMX_NBNXN_EWALD_ANALYTICAL") != NULL)
1540 *ewald_excl = ewaldexclAnalytical;
1544 #endif /* GMX_NBNXN_SIMD */
1548 const char *lookup_nbnxn_kernel_name(int kernel_type)
1550 const char *returnvalue = NULL;
1551 switch (kernel_type)
1554 returnvalue = "not set";
1556 case nbnxnk4x4_PlainC:
1557 returnvalue = "plain C";
1559 case nbnxnk4xN_SIMD_4xN:
1560 case nbnxnk4xN_SIMD_2xNN:
1561 #ifdef GMX_NBNXN_SIMD
1563 /* We have x86 SSE2 compatible SIMD */
1564 #ifdef GMX_X86_AVX_128_FMA
1565 returnvalue = "AVX-128-FMA";
1567 #if defined GMX_X86_AVX_256 || defined __AVX__
1568 /* x86 SIMD intrinsics can be converted to SSE or AVX depending
1569 * on compiler flags. As we use nearly identical intrinsics,
1570 * compiling for AVX without an AVX macros effectively results
1572 * For gcc we check for __AVX__
1573 * At least a check for icc should be added (if there is a macro)
1575 #if defined GMX_X86_AVX_256 && !defined GMX_NBNXN_HALF_WIDTH_SIMD
1576 returnvalue = "AVX-256";
1578 returnvalue = "AVX-128";
1581 #ifdef GMX_X86_SSE4_1
1582 returnvalue = "SSE4.1";
1584 returnvalue = "SSE2";
1588 #else /* GMX_X86_SSE2 */
1589 /* not GMX_X86_SSE2, but other SIMD */
1590 returnvalue = "SIMD";
1591 #endif /* GMX_X86_SSE2 */
1592 #else /* GMX_NBNXN_SIMD */
1593 returnvalue = "not available";
1594 #endif /* GMX_NBNXN_SIMD */
1596 case nbnxnk8x8x8_CUDA: returnvalue = "CUDA"; break;
1597 case nbnxnk8x8x8_PlainC: returnvalue = "plain C"; break;
1601 gmx_fatal(FARGS, "Illegal kernel type selected");
1608 static void pick_nbnxn_kernel(FILE *fp,
1609 const t_commrec *cr,
1610 const gmx_hw_info_t *hwinfo,
1611 gmx_bool use_cpu_acceleration,
1613 gmx_bool bEmulateGPU,
1614 const t_inputrec *ir,
1617 gmx_bool bDoNonbonded)
1619 assert(kernel_type);
1621 *kernel_type = nbnxnkNotSet;
1622 *ewald_excl = ewaldexclTable;
1626 *kernel_type = nbnxnk8x8x8_PlainC;
1630 md_print_warn(cr, fp, "Emulating a GPU run on the CPU (slow)");
1635 *kernel_type = nbnxnk8x8x8_CUDA;
1638 if (*kernel_type == nbnxnkNotSet)
1640 if (use_cpu_acceleration)
1642 pick_nbnxn_kernel_cpu(fp, cr, hwinfo->cpuid_info, ir,
1643 kernel_type, ewald_excl);
1647 *kernel_type = nbnxnk4x4_PlainC;
1651 if (bDoNonbonded && fp != NULL)
1653 fprintf(fp, "\nUsing %s %dx%d non-bonded kernels\n\n",
1654 lookup_nbnxn_kernel_name(*kernel_type),
1655 nbnxn_kernel_pairlist_simple(*kernel_type) ? NBNXN_CPU_CLUSTER_I_SIZE : NBNXN_GPU_CLUSTER_SIZE,
1656 nbnxn_kernel_to_cj_size(*kernel_type));
1660 static void pick_nbnxn_resources(FILE *fp,
1661 const t_commrec *cr,
1662 const gmx_hw_info_t *hwinfo,
1663 gmx_bool bDoNonbonded,
1665 gmx_bool *bEmulateGPU)
1667 gmx_bool bEmulateGPUEnvVarSet;
1668 char gpu_err_str[STRLEN];
1672 bEmulateGPUEnvVarSet = (getenv("GMX_EMULATE_GPU") != NULL);
1674 /* Run GPU emulation mode if GMX_EMULATE_GPU is defined. Because
1675 * GPUs (currently) only handle non-bonded calculations, we will
1676 * automatically switch to emulation if non-bonded calculations are
1677 * turned off via GMX_NO_NONBONDED - this is the simple and elegant
1678 * way to turn off GPU initialization, data movement, and cleanup.
1680 * GPU emulation can be useful to assess the performance one can expect by
1681 * adding GPU(s) to the machine. The conditional below allows this even
1682 * if mdrun is compiled without GPU acceleration support.
1683 * Note that you should freezing the system as otherwise it will explode.
1685 *bEmulateGPU = (bEmulateGPUEnvVarSet ||
1686 (!bDoNonbonded && hwinfo->bCanUseGPU));
1688 /* Enable GPU mode when GPUs are available or no GPU emulation is requested.
1690 if (hwinfo->bCanUseGPU && !(*bEmulateGPU))
1692 /* Each PP node will use the intra-node id-th device from the
1693 * list of detected/selected GPUs. */
1694 if (!init_gpu(cr->rank_pp_intranode, gpu_err_str, &hwinfo->gpu_info))
1696 /* At this point the init should never fail as we made sure that
1697 * we have all the GPUs we need. If it still does, we'll bail. */
1698 gmx_fatal(FARGS, "On node %d failed to initialize GPU #%d: %s",
1700 get_gpu_device_id(&hwinfo->gpu_info, cr->rank_pp_intranode),
1704 /* Here we actually turn on hardware GPU acceleration */
1709 gmx_bool uses_simple_tables(int cutoff_scheme,
1710 nonbonded_verlet_t *nbv,
1713 gmx_bool bUsesSimpleTables = TRUE;
1716 switch (cutoff_scheme)
1719 bUsesSimpleTables = TRUE;
1722 assert(NULL != nbv && NULL != nbv->grp);
1723 grp_index = (group < 0) ? 0 : (nbv->ngrp - 1);
1724 bUsesSimpleTables = nbnxn_kernel_pairlist_simple(nbv->grp[grp_index].kernel_type);
1727 gmx_incons("unimplemented");
1729 return bUsesSimpleTables;
1732 static void init_ewald_f_table(interaction_const_t *ic,
1733 gmx_bool bUsesSimpleTables,
1738 if (bUsesSimpleTables)
1740 /* With a spacing of 0.0005 we are at the force summation accuracy
1741 * for the SSE kernels for "normal" atomistic simulations.
1743 ic->tabq_scale = ewald_spline3_table_scale(ic->ewaldcoeff,
1746 maxr = (rtab > ic->rcoulomb) ? rtab : ic->rcoulomb;
1747 ic->tabq_size = (int)(maxr*ic->tabq_scale) + 2;
1751 ic->tabq_size = GPU_EWALD_COULOMB_FORCE_TABLE_SIZE;
1752 /* Subtract 2 iso 1 to avoid access out of range due to rounding */
1753 ic->tabq_scale = (ic->tabq_size - 2)/ic->rcoulomb;
1756 sfree_aligned(ic->tabq_coul_FDV0);
1757 sfree_aligned(ic->tabq_coul_F);
1758 sfree_aligned(ic->tabq_coul_V);
1760 /* Create the original table data in FDV0 */
1761 snew_aligned(ic->tabq_coul_FDV0, ic->tabq_size*4, 32);
1762 snew_aligned(ic->tabq_coul_F, ic->tabq_size, 32);
1763 snew_aligned(ic->tabq_coul_V, ic->tabq_size, 32);
1764 table_spline3_fill_ewald_lr(ic->tabq_coul_F, ic->tabq_coul_V, ic->tabq_coul_FDV0,
1765 ic->tabq_size, 1/ic->tabq_scale, ic->ewaldcoeff);
1768 void init_interaction_const_tables(FILE *fp,
1769 interaction_const_t *ic,
1770 gmx_bool bUsesSimpleTables,
1775 if (ic->eeltype == eelEWALD || EEL_PME(ic->eeltype))
1777 init_ewald_f_table(ic, bUsesSimpleTables, rtab);
1781 fprintf(fp, "Initialized non-bonded Ewald correction tables, spacing: %.2e size: %d\n\n",
1782 1/ic->tabq_scale, ic->tabq_size);
1787 void init_interaction_const(FILE *fp,
1788 interaction_const_t **interaction_const,
1789 const t_forcerec *fr,
1792 interaction_const_t *ic;
1793 gmx_bool bUsesSimpleTables = TRUE;
1797 /* Just allocate something so we can free it */
1798 snew_aligned(ic->tabq_coul_FDV0, 16, 32);
1799 snew_aligned(ic->tabq_coul_F, 16, 32);
1800 snew_aligned(ic->tabq_coul_V, 16, 32);
1802 ic->rlist = fr->rlist;
1803 ic->rlistlong = fr->rlistlong;
1806 ic->rvdw = fr->rvdw;
1807 if (fr->vdw_modifier == eintmodPOTSHIFT)
1809 ic->sh_invrc6 = pow(ic->rvdw, -6.0);
1816 /* Electrostatics */
1817 ic->eeltype = fr->eeltype;
1818 ic->rcoulomb = fr->rcoulomb;
1819 ic->epsilon_r = fr->epsilon_r;
1820 ic->epsfac = fr->epsfac;
1823 ic->ewaldcoeff = fr->ewaldcoeff;
1824 if (fr->coulomb_modifier == eintmodPOTSHIFT)
1826 ic->sh_ewald = gmx_erfc(ic->ewaldcoeff*ic->rcoulomb);
1833 /* Reaction-field */
1834 if (EEL_RF(ic->eeltype))
1836 ic->epsilon_rf = fr->epsilon_rf;
1837 ic->k_rf = fr->k_rf;
1838 ic->c_rf = fr->c_rf;
1842 /* For plain cut-off we might use the reaction-field kernels */
1843 ic->epsilon_rf = ic->epsilon_r;
1845 if (fr->coulomb_modifier == eintmodPOTSHIFT)
1847 ic->c_rf = 1/ic->rcoulomb;
1857 fprintf(fp, "Potential shift: LJ r^-12: %.3f r^-6 %.3f",
1858 sqr(ic->sh_invrc6), ic->sh_invrc6);
1859 if (ic->eeltype == eelCUT)
1861 fprintf(fp, ", Coulomb %.3f", ic->c_rf);
1863 else if (EEL_PME(ic->eeltype))
1865 fprintf(fp, ", Ewald %.3e", ic->sh_ewald);
1870 *interaction_const = ic;
1872 if (fr->nbv != NULL && fr->nbv->bUseGPU)
1874 nbnxn_cuda_init_const(fr->nbv->cu_nbv, ic, fr->nbv->grp);
1877 bUsesSimpleTables = uses_simple_tables(fr->cutoff_scheme, fr->nbv, -1);
1878 init_interaction_const_tables(fp, ic, bUsesSimpleTables, rtab);
1881 static void init_nb_verlet(FILE *fp,
1882 nonbonded_verlet_t **nb_verlet,
1883 const t_inputrec *ir,
1884 const t_forcerec *fr,
1885 const t_commrec *cr,
1886 const char *nbpu_opt)
1888 nonbonded_verlet_t *nbv;
1891 gmx_bool bEmulateGPU, bHybridGPURun = FALSE;
1893 nbnxn_alloc_t *nb_alloc;
1894 nbnxn_free_t *nb_free;
1898 pick_nbnxn_resources(fp, cr, fr->hwinfo,
1905 nbv->ngrp = (DOMAINDECOMP(cr) ? 2 : 1);
1906 for (i = 0; i < nbv->ngrp; i++)
1908 nbv->grp[i].nbl_lists.nnbl = 0;
1909 nbv->grp[i].nbat = NULL;
1910 nbv->grp[i].kernel_type = nbnxnkNotSet;
1912 if (i == 0) /* local */
1914 pick_nbnxn_kernel(fp, cr, fr->hwinfo, fr->use_cpu_acceleration,
1915 nbv->bUseGPU, bEmulateGPU,
1917 &nbv->grp[i].kernel_type,
1918 &nbv->grp[i].ewald_excl,
1921 else /* non-local */
1923 if (nbpu_opt != NULL && strcmp(nbpu_opt, "gpu_cpu") == 0)
1925 /* Use GPU for local, select a CPU kernel for non-local */
1926 pick_nbnxn_kernel(fp, cr, fr->hwinfo, fr->use_cpu_acceleration,
1929 &nbv->grp[i].kernel_type,
1930 &nbv->grp[i].ewald_excl,
1933 bHybridGPURun = TRUE;
1937 /* Use the same kernel for local and non-local interactions */
1938 nbv->grp[i].kernel_type = nbv->grp[0].kernel_type;
1939 nbv->grp[i].ewald_excl = nbv->grp[0].ewald_excl;
1946 /* init the NxN GPU data; the last argument tells whether we'll have
1947 * both local and non-local NB calculation on GPU */
1948 nbnxn_cuda_init(fp, &nbv->cu_nbv,
1949 &fr->hwinfo->gpu_info, cr->rank_pp_intranode,
1950 (nbv->ngrp > 1) && !bHybridGPURun);
1952 if ((env = getenv("GMX_NB_MIN_CI")) != NULL)
1956 nbv->min_ci_balanced = strtol(env, &end, 10);
1957 if (!end || (*end != 0) || nbv->min_ci_balanced <= 0)
1959 gmx_fatal(FARGS, "Invalid value passed in GMX_NB_MIN_CI=%s, positive integer required", env);
1964 fprintf(debug, "Neighbor-list balancing parameter: %d (passed as env. var.)\n",
1965 nbv->min_ci_balanced);
1970 nbv->min_ci_balanced = nbnxn_cuda_min_ci_balanced(nbv->cu_nbv);
1973 fprintf(debug, "Neighbor-list balancing parameter: %d (auto-adjusted to the number of GPU multi-processors)\n",
1974 nbv->min_ci_balanced);
1980 nbv->min_ci_balanced = 0;
1985 nbnxn_init_search(&nbv->nbs,
1986 DOMAINDECOMP(cr) ? &cr->dd->nc : NULL,
1987 DOMAINDECOMP(cr) ? domdec_zones(cr->dd) : NULL,
1988 gmx_omp_nthreads_get(emntNonbonded));
1990 for (i = 0; i < nbv->ngrp; i++)
1992 if (nbv->grp[0].kernel_type == nbnxnk8x8x8_CUDA)
1994 nb_alloc = &pmalloc;
2003 nbnxn_init_pairlist_set(&nbv->grp[i].nbl_lists,
2004 nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type),
2005 /* 8x8x8 "non-simple" lists are ATM always combined */
2006 !nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type),
2010 nbv->grp[0].kernel_type != nbv->grp[i].kernel_type)
2012 snew(nbv->grp[i].nbat, 1);
2013 nbnxn_atomdata_init(fp,
2015 nbv->grp[i].kernel_type,
2016 fr->ntype, fr->nbfp,
2018 nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type) ? gmx_omp_nthreads_get(emntNonbonded) : 1,
2023 nbv->grp[i].nbat = nbv->grp[0].nbat;
2028 void init_forcerec(FILE *fp,
2029 const output_env_t oenv,
2032 const t_inputrec *ir,
2033 const gmx_mtop_t *mtop,
2034 const t_commrec *cr,
2041 const char *nbpu_opt,
2042 gmx_bool bNoSolvOpt,
2045 int i, j, m, natoms, ngrp, negp_pp, negptable, egi, egj;
2051 gmx_bool bGenericKernelOnly;
2052 gmx_bool bTab, bSep14tab, bNormalnblists;
2054 int *nm_ind, egp_flags;
2056 if (fr->hwinfo == NULL)
2058 /* Detect hardware, gather information.
2059 * In mdrun, hwinfo has already been set before calling init_forcerec.
2060 * Here we ignore GPUs, as tools will not use them anyhow.
2062 fr->hwinfo = gmx_detect_hardware(fp, cr, FALSE, FALSE, NULL);
2065 /* By default we turn acceleration on, but it might be turned off further down... */
2066 fr->use_cpu_acceleration = TRUE;
2068 fr->bDomDec = DOMAINDECOMP(cr);
2070 natoms = mtop->natoms;
2072 if (check_box(ir->ePBC, box))
2074 gmx_fatal(FARGS, check_box(ir->ePBC, box));
2077 /* Test particle insertion ? */
2080 /* Set to the size of the molecule to be inserted (the last one) */
2081 /* Because of old style topologies, we have to use the last cg
2082 * instead of the last molecule type.
2084 cgs = &mtop->moltype[mtop->molblock[mtop->nmolblock-1].type].cgs;
2085 fr->n_tpi = cgs->index[cgs->nr] - cgs->index[cgs->nr-1];
2086 if (fr->n_tpi != mtop->mols.index[mtop->mols.nr] - mtop->mols.index[mtop->mols.nr-1])
2088 gmx_fatal(FARGS, "The molecule to insert can not consist of multiple charge groups.\nMake it a single charge group.");
2096 /* Copy AdResS parameters */
2099 fr->adress_type = ir->adress->type;
2100 fr->adress_const_wf = ir->adress->const_wf;
2101 fr->adress_ex_width = ir->adress->ex_width;
2102 fr->adress_hy_width = ir->adress->hy_width;
2103 fr->adress_icor = ir->adress->icor;
2104 fr->adress_site = ir->adress->site;
2105 fr->adress_ex_forcecap = ir->adress->ex_forcecap;
2106 fr->adress_do_hybridpairs = ir->adress->do_hybridpairs;
2109 snew(fr->adress_group_explicit, ir->adress->n_energy_grps);
2110 for (i = 0; i < ir->adress->n_energy_grps; i++)
2112 fr->adress_group_explicit[i] = ir->adress->group_explicit[i];
2115 fr->n_adress_tf_grps = ir->adress->n_tf_grps;
2116 snew(fr->adress_tf_table_index, fr->n_adress_tf_grps);
2117 for (i = 0; i < fr->n_adress_tf_grps; i++)
2119 fr->adress_tf_table_index[i] = ir->adress->tf_table_index[i];
2121 copy_rvec(ir->adress->refs, fr->adress_refs);
2125 fr->adress_type = eAdressOff;
2126 fr->adress_do_hybridpairs = FALSE;
2129 /* Copy the user determined parameters */
2130 fr->userint1 = ir->userint1;
2131 fr->userint2 = ir->userint2;
2132 fr->userint3 = ir->userint3;
2133 fr->userint4 = ir->userint4;
2134 fr->userreal1 = ir->userreal1;
2135 fr->userreal2 = ir->userreal2;
2136 fr->userreal3 = ir->userreal3;
2137 fr->userreal4 = ir->userreal4;
2140 fr->fc_stepsize = ir->fc_stepsize;
2143 fr->efep = ir->efep;
2144 fr->sc_alphavdw = ir->fepvals->sc_alpha;
2145 if (ir->fepvals->bScCoul)
2147 fr->sc_alphacoul = ir->fepvals->sc_alpha;
2148 fr->sc_sigma6_min = pow(ir->fepvals->sc_sigma_min, 6);
2152 fr->sc_alphacoul = 0;
2153 fr->sc_sigma6_min = 0; /* only needed when bScCoul is on */
2155 fr->sc_power = ir->fepvals->sc_power;
2156 fr->sc_r_power = ir->fepvals->sc_r_power;
2157 fr->sc_sigma6_def = pow(ir->fepvals->sc_sigma, 6);
2159 env = getenv("GMX_SCSIGMA_MIN");
2163 sscanf(env, "%lf", &dbl);
2164 fr->sc_sigma6_min = pow(dbl, 6);
2167 fprintf(fp, "Setting the minimum soft core sigma to %g nm\n", dbl);
2171 fr->bNonbonded = TRUE;
2172 if (getenv("GMX_NO_NONBONDED") != NULL)
2174 /* turn off non-bonded calculations */
2175 fr->bNonbonded = FALSE;
2176 md_print_warn(cr, fp,
2177 "Found environment variable GMX_NO_NONBONDED.\n"
2178 "Disabling nonbonded calculations.\n");
2181 bGenericKernelOnly = FALSE;
2183 /* We now check in the NS code whether a particular combination of interactions
2184 * can be used with water optimization, and disable it if that is not the case.
2187 if (getenv("GMX_NB_GENERIC") != NULL)
2192 "Found environment variable GMX_NB_GENERIC.\n"
2193 "Disabling all interaction-specific nonbonded kernels, will only\n"
2194 "use the slow generic ones in src/gmxlib/nonbonded/nb_generic.c\n\n");
2196 bGenericKernelOnly = TRUE;
2199 if (bGenericKernelOnly == TRUE)
2204 if ( (getenv("GMX_DISABLE_CPU_ACCELERATION") != NULL) || (getenv("GMX_NOOPTIMIZEDKERNELS") != NULL) )
2206 fr->use_cpu_acceleration = FALSE;
2210 "\nFound environment variable GMX_DISABLE_CPU_ACCELERATION.\n"
2211 "Disabling all CPU architecture-specific (e.g. SSE2/SSE4/AVX) routines.\n\n");
2215 fr->bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
2217 /* Check if we can/should do all-vs-all kernels */
2218 fr->bAllvsAll = can_use_allvsall(ir, mtop, FALSE, NULL, NULL);
2219 fr->AllvsAll_work = NULL;
2220 fr->AllvsAll_workgb = NULL;
2222 /* All-vs-all kernels have not been implemented in 4.6, and
2223 * the SIMD group kernels are also buggy in this case. Non-accelerated
2224 * group kernels are OK. See Redmine #1249. */
2227 fr->bAllvsAll = FALSE;
2228 fr->use_cpu_acceleration = FALSE;
2232 "\nYour simulation settings would have triggered the efficient all-vs-all\n"
2233 "kernels in GROMACS 4.5, but these have not been implemented in GROMACS\n"
2234 "4.6. Also, we can't use the accelerated SIMD kernels here because\n"
2235 "of an unfixed bug. The reference C kernels are correct, though, so\n"
2236 "we are proceeding by disabling all CPU architecture-specific\n"
2237 "(e.g. SSE2/SSE4/AVX) routines. If performance is important, please\n"
2238 "use GROMACS 4.5.7 or try cutoff-scheme = Verlet.\n\n");
2242 /* Neighbour searching stuff */
2243 fr->cutoff_scheme = ir->cutoff_scheme;
2244 fr->bGrid = (ir->ns_type == ensGRID);
2245 fr->ePBC = ir->ePBC;
2247 /* Determine if we will do PBC for distances in bonded interactions */
2248 if (fr->ePBC == epbcNONE)
2250 fr->bMolPBC = FALSE;
2254 if (!DOMAINDECOMP(cr))
2256 /* The group cut-off scheme and SHAKE assume charge groups
2257 * are whole, but not using molpbc is faster in most cases.
2259 if (fr->cutoff_scheme == ecutsGROUP ||
2260 (ir->eConstrAlg == econtSHAKE &&
2261 (gmx_mtop_ftype_count(mtop, F_CONSTR) > 0 ||
2262 gmx_mtop_ftype_count(mtop, F_CONSTRNC) > 0)))
2264 fr->bMolPBC = ir->bPeriodicMols;
2269 if (getenv("GMX_USE_GRAPH") != NULL)
2271 fr->bMolPBC = FALSE;
2274 fprintf(fp, "\nGMX_MOLPBC is set, using the graph for bonded interactions\n\n");
2281 fr->bMolPBC = dd_bonded_molpbc(cr->dd, fr->ePBC);
2284 fr->bGB = (ir->implicit_solvent == eisGBSA);
2286 fr->rc_scaling = ir->refcoord_scaling;
2287 copy_rvec(ir->posres_com, fr->posres_com);
2288 copy_rvec(ir->posres_comB, fr->posres_comB);
2289 fr->rlist = cutoff_inf(ir->rlist);
2290 fr->rlistlong = cutoff_inf(ir->rlistlong);
2291 fr->eeltype = ir->coulombtype;
2292 fr->vdwtype = ir->vdwtype;
2294 fr->coulomb_modifier = ir->coulomb_modifier;
2295 fr->vdw_modifier = ir->vdw_modifier;
2297 /* Electrostatics: Translate from interaction-setting-in-mdp-file to kernel interaction format */
2298 switch (fr->eeltype)
2301 fr->nbkernel_elec_interaction = (fr->bGB) ? GMX_NBKERNEL_ELEC_GENERALIZEDBORN : GMX_NBKERNEL_ELEC_COULOMB;
2307 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD;
2311 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD;
2312 fr->coulomb_modifier = eintmodEXACTCUTOFF;
2321 case eelPMEUSERSWITCH:
2322 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_CUBICSPLINETABLE;
2327 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_EWALD;
2331 gmx_fatal(FARGS, "Unsupported electrostatic interaction: %s", eel_names[fr->eeltype]);
2335 /* Vdw: Translate from mdp settings to kernel format */
2336 switch (fr->vdwtype)
2341 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_BUCKINGHAM;
2345 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_LENNARDJONES;
2352 case evdwENCADSHIFT:
2353 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
2357 gmx_fatal(FARGS, "Unsupported vdw interaction: %s", evdw_names[fr->vdwtype]);
2361 /* These start out identical to ir, but might be altered if we e.g. tabulate the interaction in the kernel */
2362 fr->nbkernel_elec_modifier = fr->coulomb_modifier;
2363 fr->nbkernel_vdw_modifier = fr->vdw_modifier;
2365 fr->bTwinRange = fr->rlistlong > fr->rlist;
2366 fr->bEwald = (EEL_PME(fr->eeltype) || fr->eeltype == eelEWALD);
2368 fr->reppow = mtop->ffparams.reppow;
2370 if (ir->cutoff_scheme == ecutsGROUP)
2372 fr->bvdwtab = (fr->vdwtype != evdwCUT ||
2373 !gmx_within_tol(fr->reppow, 12.0, 10*GMX_DOUBLE_EPS));
2374 /* We have special kernels for standard Ewald and PME, but the pme-switch ones are tabulated above */
2375 fr->bcoultab = !(fr->eeltype == eelCUT ||
2376 fr->eeltype == eelEWALD ||
2377 fr->eeltype == eelPME ||
2378 fr->eeltype == eelRF ||
2379 fr->eeltype == eelRF_ZERO);
2381 /* If the user absolutely wants different switch/shift settings for coul/vdw, it is likely
2382 * going to be faster to tabulate the interaction than calling the generic kernel.
2384 if (fr->nbkernel_elec_modifier == eintmodPOTSWITCH && fr->nbkernel_vdw_modifier == eintmodPOTSWITCH)
2386 if ((fr->rcoulomb_switch != fr->rvdw_switch) || (fr->rcoulomb != fr->rvdw))
2388 fr->bcoultab = TRUE;
2391 else if ((fr->nbkernel_elec_modifier == eintmodPOTSHIFT && fr->nbkernel_vdw_modifier == eintmodPOTSHIFT) ||
2392 ((fr->nbkernel_elec_interaction == GMX_NBKERNEL_ELEC_REACTIONFIELD &&
2393 fr->nbkernel_elec_modifier == eintmodEXACTCUTOFF &&
2394 (fr->nbkernel_vdw_modifier == eintmodPOTSWITCH || fr->nbkernel_vdw_modifier == eintmodPOTSHIFT))))
2396 if (fr->rcoulomb != fr->rvdw)
2398 fr->bcoultab = TRUE;
2402 if (getenv("GMX_REQUIRE_TABLES"))
2405 fr->bcoultab = TRUE;
2410 fprintf(fp, "Table routines are used for coulomb: %s\n", bool_names[fr->bcoultab]);
2411 fprintf(fp, "Table routines are used for vdw: %s\n", bool_names[fr->bvdwtab ]);
2414 if (fr->bvdwtab == TRUE)
2416 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
2417 fr->nbkernel_vdw_modifier = eintmodNONE;
2419 if (fr->bcoultab == TRUE)
2421 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_CUBICSPLINETABLE;
2422 fr->nbkernel_elec_modifier = eintmodNONE;
2426 if (ir->cutoff_scheme == ecutsVERLET)
2428 if (!gmx_within_tol(fr->reppow, 12.0, 10*GMX_DOUBLE_EPS))
2430 gmx_fatal(FARGS, "Cut-off scheme %S only supports LJ repulsion power 12", ecutscheme_names[ir->cutoff_scheme]);
2432 fr->bvdwtab = FALSE;
2433 fr->bcoultab = FALSE;
2436 /* Tables are used for direct ewald sum */
2439 if (EEL_PME(ir->coulombtype))
2443 fprintf(fp, "Will do PME sum in reciprocal space.\n");
2445 if (ir->coulombtype == eelP3M_AD)
2447 please_cite(fp, "Hockney1988");
2448 please_cite(fp, "Ballenegger2012");
2452 please_cite(fp, "Essmann95a");
2455 if (ir->ewald_geometry == eewg3DC)
2459 fprintf(fp, "Using the Ewald3DC correction for systems with a slab geometry.\n");
2461 please_cite(fp, "In-Chul99a");
2464 fr->ewaldcoeff = calc_ewaldcoeff(ir->rcoulomb, ir->ewald_rtol);
2465 init_ewald_tab(&(fr->ewald_table), cr, ir, fp);
2468 fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for Ewald\n",
2473 /* Electrostatics */
2474 fr->epsilon_r = ir->epsilon_r;
2475 fr->epsilon_rf = ir->epsilon_rf;
2476 fr->fudgeQQ = mtop->ffparams.fudgeQQ;
2477 fr->rcoulomb_switch = ir->rcoulomb_switch;
2478 fr->rcoulomb = cutoff_inf(ir->rcoulomb);
2480 /* Parameters for generalized RF */
2484 if (fr->eeltype == eelGRF)
2486 init_generalized_rf(fp, mtop, ir, fr);
2488 else if (fr->eeltype == eelSHIFT)
2490 for (m = 0; (m < DIM); m++)
2492 box_size[m] = box[m][m];
2495 if ((fr->eeltype == eelSHIFT && fr->rcoulomb > fr->rcoulomb_switch))
2497 set_shift_consts(fp, fr->rcoulomb_switch, fr->rcoulomb, box_size, fr);
2501 fr->bF_NoVirSum = (EEL_FULL(fr->eeltype) ||
2502 gmx_mtop_ftype_count(mtop, F_POSRES) > 0 ||
2503 IR_ELEC_FIELD(*ir) ||
2504 (fr->adress_icor != eAdressICOff)
2507 if (fr->cutoff_scheme == ecutsGROUP &&
2508 ncg_mtop(mtop) > fr->cg_nalloc && !DOMAINDECOMP(cr))
2510 /* Count the total number of charge groups */
2511 fr->cg_nalloc = ncg_mtop(mtop);
2512 srenew(fr->cg_cm, fr->cg_nalloc);
2514 if (fr->shift_vec == NULL)
2516 snew(fr->shift_vec, SHIFTS);
2519 if (fr->fshift == NULL)
2521 snew(fr->fshift, SHIFTS);
2524 if (fr->nbfp == NULL)
2526 fr->ntype = mtop->ffparams.atnr;
2527 fr->nbfp = mk_nbfp(&mtop->ffparams, fr->bBHAM);
2530 /* Copy the energy group exclusions */
2531 fr->egp_flags = ir->opts.egp_flags;
2533 /* Van der Waals stuff */
2534 fr->rvdw = cutoff_inf(ir->rvdw);
2535 fr->rvdw_switch = ir->rvdw_switch;
2536 if ((fr->vdwtype != evdwCUT) && (fr->vdwtype != evdwUSER) && !fr->bBHAM)
2538 if (fr->rvdw_switch >= fr->rvdw)
2540 gmx_fatal(FARGS, "rvdw_switch (%f) must be < rvdw (%f)",
2541 fr->rvdw_switch, fr->rvdw);
2545 fprintf(fp, "Using %s Lennard-Jones, switch between %g and %g nm\n",
2546 (fr->eeltype == eelSWITCH) ? "switched" : "shifted",
2547 fr->rvdw_switch, fr->rvdw);
2551 if (fr->bBHAM && (fr->vdwtype == evdwSHIFT || fr->vdwtype == evdwSWITCH))
2553 gmx_fatal(FARGS, "Switch/shift interaction not supported with Buckingham");
2558 fprintf(fp, "Cut-off's: NS: %g Coulomb: %g %s: %g\n",
2559 fr->rlist, fr->rcoulomb, fr->bBHAM ? "BHAM" : "LJ", fr->rvdw);
2562 fr->eDispCorr = ir->eDispCorr;
2563 if (ir->eDispCorr != edispcNO)
2565 set_avcsixtwelve(fp, fr, mtop);
2570 set_bham_b_max(fp, fr, mtop);
2573 fr->gb_epsilon_solvent = ir->gb_epsilon_solvent;
2575 /* Copy the GBSA data (radius, volume and surftens for each
2576 * atomtype) from the topology atomtype section to forcerec.
2578 snew(fr->atype_radius, fr->ntype);
2579 snew(fr->atype_vol, fr->ntype);
2580 snew(fr->atype_surftens, fr->ntype);
2581 snew(fr->atype_gb_radius, fr->ntype);
2582 snew(fr->atype_S_hct, fr->ntype);
2584 if (mtop->atomtypes.nr > 0)
2586 for (i = 0; i < fr->ntype; i++)
2588 fr->atype_radius[i] = mtop->atomtypes.radius[i];
2590 for (i = 0; i < fr->ntype; i++)
2592 fr->atype_vol[i] = mtop->atomtypes.vol[i];
2594 for (i = 0; i < fr->ntype; i++)
2596 fr->atype_surftens[i] = mtop->atomtypes.surftens[i];
2598 for (i = 0; i < fr->ntype; i++)
2600 fr->atype_gb_radius[i] = mtop->atomtypes.gb_radius[i];
2602 for (i = 0; i < fr->ntype; i++)
2604 fr->atype_S_hct[i] = mtop->atomtypes.S_hct[i];
2608 /* Generate the GB table if needed */
2612 fr->gbtabscale = 2000;
2614 fr->gbtabscale = 500;
2618 fr->gbtab = make_gb_table(fp, oenv, fr, tabpfn, fr->gbtabscale);
2620 init_gb(&fr->born, cr, fr, ir, mtop, ir->rgbradii, ir->gb_algorithm);
2622 /* Copy local gb data (for dd, this is done in dd_partition_system) */
2623 if (!DOMAINDECOMP(cr))
2625 make_local_gb(cr, fr->born, ir->gb_algorithm);
2629 /* Set the charge scaling */
2630 if (fr->epsilon_r != 0)
2632 fr->epsfac = ONE_4PI_EPS0/fr->epsilon_r;
2636 /* eps = 0 is infinite dieletric: no coulomb interactions */
2640 /* Reaction field constants */
2641 if (EEL_RF(fr->eeltype))
2643 calc_rffac(fp, fr->eeltype, fr->epsilon_r, fr->epsilon_rf,
2644 fr->rcoulomb, fr->temp, fr->zsquare, box,
2645 &fr->kappa, &fr->k_rf, &fr->c_rf);
2648 set_chargesum(fp, fr, mtop);
2650 /* if we are using LR electrostatics, and they are tabulated,
2651 * the tables will contain modified coulomb interactions.
2652 * Since we want to use the non-shifted ones for 1-4
2653 * coulombic interactions, we must have an extra set of tables.
2656 /* Construct tables.
2657 * A little unnecessary to make both vdw and coul tables sometimes,
2658 * but what the heck... */
2660 bTab = fr->bcoultab || fr->bvdwtab || fr->bEwald;
2662 bSep14tab = ((!bTab || fr->eeltype != eelCUT || fr->vdwtype != evdwCUT ||
2663 fr->bBHAM || fr->bEwald) &&
2664 (gmx_mtop_ftype_count(mtop, F_LJ14) > 0 ||
2665 gmx_mtop_ftype_count(mtop, F_LJC14_Q) > 0 ||
2666 gmx_mtop_ftype_count(mtop, F_LJC_PAIRS_NB) > 0));
2668 negp_pp = ir->opts.ngener - ir->nwall;
2672 bNormalnblists = TRUE;
2677 bNormalnblists = (ir->eDispCorr != edispcNO);
2678 for (egi = 0; egi < negp_pp; egi++)
2680 for (egj = egi; egj < negp_pp; egj++)
2682 egp_flags = ir->opts.egp_flags[GID(egi, egj, ir->opts.ngener)];
2683 if (!(egp_flags & EGP_EXCL))
2685 if (egp_flags & EGP_TABLE)
2691 bNormalnblists = TRUE;
2698 fr->nnblists = negptable + 1;
2702 fr->nnblists = negptable;
2704 if (fr->nnblists > 1)
2706 snew(fr->gid2nblists, ir->opts.ngener*ir->opts.ngener);
2715 snew(fr->nblists, fr->nnblists);
2717 /* This code automatically gives table length tabext without cut-off's,
2718 * in that case grompp should already have checked that we do not need
2719 * normal tables and we only generate tables for 1-4 interactions.
2721 rtab = ir->rlistlong + ir->tabext;
2725 /* make tables for ordinary interactions */
2728 make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn, NULL, NULL, &fr->nblists[0]);
2731 make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn, NULL, NULL, &fr->nblists[fr->nnblists/2]);
2735 fr->tab14 = fr->nblists[0].table_elec_vdw;
2745 /* Read the special tables for certain energy group pairs */
2746 nm_ind = mtop->groups.grps[egcENER].nm_ind;
2747 for (egi = 0; egi < negp_pp; egi++)
2749 for (egj = egi; egj < negp_pp; egj++)
2751 egp_flags = ir->opts.egp_flags[GID(egi, egj, ir->opts.ngener)];
2752 if ((egp_flags & EGP_TABLE) && !(egp_flags & EGP_EXCL))
2754 nbl = &(fr->nblists[m]);
2755 if (fr->nnblists > 1)
2757 fr->gid2nblists[GID(egi, egj, ir->opts.ngener)] = m;
2759 /* Read the table file with the two energy groups names appended */
2760 make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn,
2761 *mtop->groups.grpname[nm_ind[egi]],
2762 *mtop->groups.grpname[nm_ind[egj]],
2766 make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn,
2767 *mtop->groups.grpname[nm_ind[egi]],
2768 *mtop->groups.grpname[nm_ind[egj]],
2769 &fr->nblists[fr->nnblists/2+m]);
2773 else if (fr->nnblists > 1)
2775 fr->gid2nblists[GID(egi, egj, ir->opts.ngener)] = 0;
2783 /* generate extra tables with plain Coulomb for 1-4 interactions only */
2784 fr->tab14 = make_tables(fp, oenv, fr, MASTER(cr), tabpfn, rtab,
2785 GMX_MAKETABLES_14ONLY);
2788 /* Read AdResS Thermo Force table if needed */
2789 if (fr->adress_icor == eAdressICThermoForce)
2791 /* old todo replace */
2793 if (ir->adress->n_tf_grps > 0)
2795 make_adress_tf_tables(fp, oenv, fr, ir, tabfn, mtop, box);
2800 /* load the default table */
2801 snew(fr->atf_tabs, 1);
2802 fr->atf_tabs[DEFAULT_TF_TABLE] = make_atf_table(fp, oenv, fr, tabafn, box);
2807 fr->nwall = ir->nwall;
2808 if (ir->nwall && ir->wall_type == ewtTABLE)
2810 make_wall_tables(fp, oenv, ir, tabfn, &mtop->groups, fr);
2815 fcd->bondtab = make_bonded_tables(fp,
2816 F_TABBONDS, F_TABBONDSNC,
2818 fcd->angletab = make_bonded_tables(fp,
2821 fcd->dihtab = make_bonded_tables(fp,
2829 fprintf(debug, "No fcdata or table file name passed, can not read table, can not do bonded interactions\n");
2833 /* QM/MM initialization if requested
2837 fprintf(stderr, "QM/MM calculation requested.\n");
2840 fr->bQMMM = ir->bQMMM;
2841 fr->qr = mk_QMMMrec();
2843 /* Set all the static charge group info */
2844 fr->cginfo_mb = init_cginfo_mb(fp, mtop, fr, bNoSolvOpt,
2845 &fr->bExcl_IntraCGAll_InterCGNone);
2846 if (DOMAINDECOMP(cr))
2852 fr->cginfo = cginfo_expand(mtop->nmolblock, fr->cginfo_mb);
2855 if (!DOMAINDECOMP(cr))
2857 /* When using particle decomposition, the effect of the second argument,
2858 * which sets fr->hcg, is corrected later in do_md and init_em.
2860 forcerec_set_ranges(fr, ncg_mtop(mtop), ncg_mtop(mtop),
2861 mtop->natoms, mtop->natoms, mtop->natoms);
2864 fr->print_force = print_force;
2867 /* coarse load balancing vars */
2872 /* Initialize neighbor search */
2873 init_ns(fp, cr, &fr->ns, fr, mtop, box);
2875 if (cr->duty & DUTY_PP)
2877 gmx_nonbonded_setup(fp, fr, bGenericKernelOnly);
2881 gmx_setup_adress_kernels(fp,bGenericKernelOnly);
2886 /* Initialize the thread working data for bonded interactions */
2887 init_forcerec_f_threads(fr, mtop->groups.grps[egcENER].nr);
2889 snew(fr->excl_load, fr->nthreads+1);
2891 if (fr->cutoff_scheme == ecutsVERLET)
2893 if (ir->rcoulomb != ir->rvdw)
2895 gmx_fatal(FARGS, "With Verlet lists rcoulomb and rvdw should be identical");
2898 init_nb_verlet(fp, &fr->nbv, ir, fr, cr, nbpu_opt);
2901 /* fr->ic is used both by verlet and group kernels (to some extent) now */
2902 init_interaction_const(fp, &fr->ic, fr, rtab);
2903 if (ir->eDispCorr != edispcNO)
2905 calc_enervirdiff(fp, ir->eDispCorr, fr);
2909 #define pr_real(fp, r) fprintf(fp, "%s: %e\n",#r, r)
2910 #define pr_int(fp, i) fprintf((fp), "%s: %d\n",#i, i)
2911 #define pr_bool(fp, b) fprintf((fp), "%s: %s\n",#b, bool_names[b])
2913 void pr_forcerec(FILE *fp, t_forcerec *fr, t_commrec *cr)
2917 pr_real(fp, fr->rlist);
2918 pr_real(fp, fr->rcoulomb);
2919 pr_real(fp, fr->fudgeQQ);
2920 pr_bool(fp, fr->bGrid);
2921 pr_bool(fp, fr->bTwinRange);
2922 /*pr_int(fp,fr->cg0);
2923 pr_int(fp,fr->hcg);*/
2924 for (i = 0; i < fr->nnblists; i++)
2926 pr_int(fp, fr->nblists[i].table_elec_vdw.n);
2928 pr_real(fp, fr->rcoulomb_switch);
2929 pr_real(fp, fr->rcoulomb);
2934 void forcerec_set_excl_load(t_forcerec *fr,
2935 const gmx_localtop_t *top, const t_commrec *cr)
2938 int t, i, j, ntot, n, ntarget;
2940 if (cr != NULL && PARTDECOMP(cr))
2942 /* No OpenMP with particle decomposition */
2950 ind = top->excls.index;
2954 for (i = 0; i < top->excls.nr; i++)
2956 for (j = ind[i]; j < ind[i+1]; j++)
2965 fr->excl_load[0] = 0;
2968 for (t = 1; t <= fr->nthreads; t++)
2970 ntarget = (ntot*t)/fr->nthreads;
2971 while (i < top->excls.nr && n < ntarget)
2973 for (j = ind[i]; j < ind[i+1]; j++)
2982 fr->excl_load[t] = i;