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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 the
1527 * x86 SIMD kernel. This is faster in single precision
1528 * on Bulldozer and slightly faster on Sandy Bridge.
1530 #if (defined GMX_X86_AVX_128_FMA || defined GMX_X86_AVX_256) && !defined GMX_DOUBLE
1531 *ewald_excl = ewaldexclAnalytical;
1533 if (getenv("GMX_NBNXN_EWALD_TABLE") != NULL)
1535 *ewald_excl = ewaldexclTable;
1537 if (getenv("GMX_NBNXN_EWALD_ANALYTICAL") != NULL)
1539 *ewald_excl = ewaldexclAnalytical;
1543 #endif /* GMX_X86_SSE2 */
1547 const char *lookup_nbnxn_kernel_name(int kernel_type)
1549 const char *returnvalue = NULL;
1550 switch (kernel_type)
1552 case nbnxnkNotSet: returnvalue = "not set"; break;
1553 case nbnxnk4x4_PlainC: returnvalue = "plain C"; break;
1554 #ifndef GMX_NBNXN_SIMD
1555 case nbnxnk4xN_SIMD_4xN: returnvalue = "not available"; break;
1556 case nbnxnk4xN_SIMD_2xNN: returnvalue = "not available"; break;
1559 #if GMX_NBNXN_SIMD_BITWIDTH == 128
1560 /* x86 SIMD intrinsics can be converted to either SSE or AVX depending
1561 * on compiler flags. As we use nearly identical intrinsics, using an AVX
1562 * compiler flag without an AVX macro effectively results in AVX kernels.
1563 * For gcc we check for __AVX__
1564 * At least a check for icc should be added (if there is a macro)
1566 #if !(defined GMX_X86_AVX_128_FMA || defined __AVX__)
1567 #ifndef GMX_X86_SSE4_1
1568 case nbnxnk4xN_SIMD_4xN: returnvalue = "SSE2"; break;
1569 case nbnxnk4xN_SIMD_2xNN: returnvalue = "SSE2"; break;
1571 case nbnxnk4xN_SIMD_4xN: returnvalue = "SSE4.1"; break;
1572 case nbnxnk4xN_SIMD_2xNN: returnvalue = "SSE4.1"; break;
1575 case nbnxnk4xN_SIMD_4xN: returnvalue = "AVX-128"; break;
1576 case nbnxnk4xN_SIMD_2xNN: returnvalue = "AVX-128"; break;
1579 #if GMX_NBNXN_SIMD_BITWIDTH == 256
1580 case nbnxnk4xN_SIMD_4xN: returnvalue = "AVX-256"; break;
1581 case nbnxnk4xN_SIMD_2xNN: returnvalue = "AVX-256"; break;
1583 #else /* not GMX_X86_SSE2 */
1584 case nbnxnk4xN_SIMD_4xN: returnvalue = "SIMD"; break;
1585 case nbnxnk4xN_SIMD_2xNN: returnvalue = "SIMD"; break;
1588 case nbnxnk8x8x8_CUDA: returnvalue = "CUDA"; break;
1589 case nbnxnk8x8x8_PlainC: returnvalue = "plain C"; break;
1593 gmx_fatal(FARGS, "Illegal kernel type selected");
1600 static void pick_nbnxn_kernel(FILE *fp,
1601 const t_commrec *cr,
1602 const gmx_hw_info_t *hwinfo,
1603 gmx_bool use_cpu_acceleration,
1605 gmx_bool bEmulateGPU,
1606 const t_inputrec *ir,
1609 gmx_bool bDoNonbonded)
1611 assert(kernel_type);
1613 *kernel_type = nbnxnkNotSet;
1614 *ewald_excl = ewaldexclTable;
1618 *kernel_type = nbnxnk8x8x8_PlainC;
1622 md_print_warn(cr, fp, "Emulating a GPU run on the CPU (slow)");
1627 *kernel_type = nbnxnk8x8x8_CUDA;
1630 if (*kernel_type == nbnxnkNotSet)
1632 if (use_cpu_acceleration)
1634 pick_nbnxn_kernel_cpu(fp, cr, hwinfo->cpuid_info, ir,
1635 kernel_type, ewald_excl);
1639 *kernel_type = nbnxnk4x4_PlainC;
1643 if (bDoNonbonded && fp != NULL)
1645 fprintf(fp, "\nUsing %s %dx%d non-bonded kernels\n\n",
1646 lookup_nbnxn_kernel_name(*kernel_type),
1647 nbnxn_kernel_pairlist_simple(*kernel_type) ? NBNXN_CPU_CLUSTER_I_SIZE : NBNXN_GPU_CLUSTER_SIZE,
1648 nbnxn_kernel_to_cj_size(*kernel_type));
1652 static void pick_nbnxn_resources(FILE *fp,
1653 const t_commrec *cr,
1654 const gmx_hw_info_t *hwinfo,
1655 gmx_bool bDoNonbonded,
1657 gmx_bool *bEmulateGPU)
1659 gmx_bool bEmulateGPUEnvVarSet;
1660 char gpu_err_str[STRLEN];
1664 bEmulateGPUEnvVarSet = (getenv("GMX_EMULATE_GPU") != NULL);
1666 /* Run GPU emulation mode if GMX_EMULATE_GPU is defined. Because
1667 * GPUs (currently) only handle non-bonded calculations, we will
1668 * automatically switch to emulation if non-bonded calculations are
1669 * turned off via GMX_NO_NONBONDED - this is the simple and elegant
1670 * way to turn off GPU initialization, data movement, and cleanup.
1672 * GPU emulation can be useful to assess the performance one can expect by
1673 * adding GPU(s) to the machine. The conditional below allows this even
1674 * if mdrun is compiled without GPU acceleration support.
1675 * Note that you should freezing the system as otherwise it will explode.
1677 *bEmulateGPU = (bEmulateGPUEnvVarSet ||
1678 (!bDoNonbonded && hwinfo->bCanUseGPU));
1680 /* Enable GPU mode when GPUs are available or no GPU emulation is requested.
1682 if (hwinfo->bCanUseGPU && !(*bEmulateGPU))
1684 /* Each PP node will use the intra-node id-th device from the
1685 * list of detected/selected GPUs. */
1686 if (!init_gpu(cr->rank_pp_intranode, gpu_err_str, &hwinfo->gpu_info))
1688 /* At this point the init should never fail as we made sure that
1689 * we have all the GPUs we need. If it still does, we'll bail. */
1690 gmx_fatal(FARGS, "On node %d failed to initialize GPU #%d: %s",
1692 get_gpu_device_id(&hwinfo->gpu_info, cr->rank_pp_intranode),
1696 /* Here we actually turn on hardware GPU acceleration */
1701 gmx_bool uses_simple_tables(int cutoff_scheme,
1702 nonbonded_verlet_t *nbv,
1705 gmx_bool bUsesSimpleTables = TRUE;
1708 switch (cutoff_scheme)
1711 bUsesSimpleTables = TRUE;
1714 assert(NULL != nbv && NULL != nbv->grp);
1715 grp_index = (group < 0) ? 0 : (nbv->ngrp - 1);
1716 bUsesSimpleTables = nbnxn_kernel_pairlist_simple(nbv->grp[grp_index].kernel_type);
1719 gmx_incons("unimplemented");
1721 return bUsesSimpleTables;
1724 static void init_ewald_f_table(interaction_const_t *ic,
1725 gmx_bool bUsesSimpleTables,
1730 if (bUsesSimpleTables)
1732 /* With a spacing of 0.0005 we are at the force summation accuracy
1733 * for the SSE kernels for "normal" atomistic simulations.
1735 ic->tabq_scale = ewald_spline3_table_scale(ic->ewaldcoeff,
1738 maxr = (rtab > ic->rcoulomb) ? rtab : ic->rcoulomb;
1739 ic->tabq_size = (int)(maxr*ic->tabq_scale) + 2;
1743 ic->tabq_size = GPU_EWALD_COULOMB_FORCE_TABLE_SIZE;
1744 /* Subtract 2 iso 1 to avoid access out of range due to rounding */
1745 ic->tabq_scale = (ic->tabq_size - 2)/ic->rcoulomb;
1748 sfree_aligned(ic->tabq_coul_FDV0);
1749 sfree_aligned(ic->tabq_coul_F);
1750 sfree_aligned(ic->tabq_coul_V);
1752 /* Create the original table data in FDV0 */
1753 snew_aligned(ic->tabq_coul_FDV0, ic->tabq_size*4, 32);
1754 snew_aligned(ic->tabq_coul_F, ic->tabq_size, 32);
1755 snew_aligned(ic->tabq_coul_V, ic->tabq_size, 32);
1756 table_spline3_fill_ewald_lr(ic->tabq_coul_F, ic->tabq_coul_V, ic->tabq_coul_FDV0,
1757 ic->tabq_size, 1/ic->tabq_scale, ic->ewaldcoeff);
1760 void init_interaction_const_tables(FILE *fp,
1761 interaction_const_t *ic,
1762 gmx_bool bUsesSimpleTables,
1767 if (ic->eeltype == eelEWALD || EEL_PME(ic->eeltype))
1769 init_ewald_f_table(ic, bUsesSimpleTables, rtab);
1773 fprintf(fp, "Initialized non-bonded Ewald correction tables, spacing: %.2e size: %d\n\n",
1774 1/ic->tabq_scale, ic->tabq_size);
1779 void init_interaction_const(FILE *fp,
1780 interaction_const_t **interaction_const,
1781 const t_forcerec *fr,
1784 interaction_const_t *ic;
1785 gmx_bool bUsesSimpleTables = TRUE;
1789 /* Just allocate something so we can free it */
1790 snew_aligned(ic->tabq_coul_FDV0, 16, 32);
1791 snew_aligned(ic->tabq_coul_F, 16, 32);
1792 snew_aligned(ic->tabq_coul_V, 16, 32);
1794 ic->rlist = fr->rlist;
1795 ic->rlistlong = fr->rlistlong;
1798 ic->rvdw = fr->rvdw;
1799 if (fr->vdw_modifier == eintmodPOTSHIFT)
1801 ic->sh_invrc6 = pow(ic->rvdw, -6.0);
1808 /* Electrostatics */
1809 ic->eeltype = fr->eeltype;
1810 ic->rcoulomb = fr->rcoulomb;
1811 ic->epsilon_r = fr->epsilon_r;
1812 ic->epsfac = fr->epsfac;
1815 ic->ewaldcoeff = fr->ewaldcoeff;
1816 if (fr->coulomb_modifier == eintmodPOTSHIFT)
1818 ic->sh_ewald = gmx_erfc(ic->ewaldcoeff*ic->rcoulomb);
1825 /* Reaction-field */
1826 if (EEL_RF(ic->eeltype))
1828 ic->epsilon_rf = fr->epsilon_rf;
1829 ic->k_rf = fr->k_rf;
1830 ic->c_rf = fr->c_rf;
1834 /* For plain cut-off we might use the reaction-field kernels */
1835 ic->epsilon_rf = ic->epsilon_r;
1837 if (fr->coulomb_modifier == eintmodPOTSHIFT)
1839 ic->c_rf = 1/ic->rcoulomb;
1849 fprintf(fp, "Potential shift: LJ r^-12: %.3f r^-6 %.3f",
1850 sqr(ic->sh_invrc6), ic->sh_invrc6);
1851 if (ic->eeltype == eelCUT)
1853 fprintf(fp, ", Coulomb %.3f", ic->c_rf);
1855 else if (EEL_PME(ic->eeltype))
1857 fprintf(fp, ", Ewald %.3e", ic->sh_ewald);
1862 *interaction_const = ic;
1864 if (fr->nbv != NULL && fr->nbv->bUseGPU)
1866 nbnxn_cuda_init_const(fr->nbv->cu_nbv, ic, fr->nbv->grp);
1869 bUsesSimpleTables = uses_simple_tables(fr->cutoff_scheme, fr->nbv, -1);
1870 init_interaction_const_tables(fp, ic, bUsesSimpleTables, rtab);
1873 static void init_nb_verlet(FILE *fp,
1874 nonbonded_verlet_t **nb_verlet,
1875 const t_inputrec *ir,
1876 const t_forcerec *fr,
1877 const t_commrec *cr,
1878 const char *nbpu_opt)
1880 nonbonded_verlet_t *nbv;
1883 gmx_bool bEmulateGPU, bHybridGPURun = FALSE;
1885 nbnxn_alloc_t *nb_alloc;
1886 nbnxn_free_t *nb_free;
1890 pick_nbnxn_resources(fp, cr, fr->hwinfo,
1897 nbv->ngrp = (DOMAINDECOMP(cr) ? 2 : 1);
1898 for (i = 0; i < nbv->ngrp; i++)
1900 nbv->grp[i].nbl_lists.nnbl = 0;
1901 nbv->grp[i].nbat = NULL;
1902 nbv->grp[i].kernel_type = nbnxnkNotSet;
1904 if (i == 0) /* local */
1906 pick_nbnxn_kernel(fp, cr, fr->hwinfo, fr->use_cpu_acceleration,
1907 nbv->bUseGPU, bEmulateGPU,
1909 &nbv->grp[i].kernel_type,
1910 &nbv->grp[i].ewald_excl,
1913 else /* non-local */
1915 if (nbpu_opt != NULL && strcmp(nbpu_opt, "gpu_cpu") == 0)
1917 /* Use GPU for local, select a CPU kernel for non-local */
1918 pick_nbnxn_kernel(fp, cr, fr->hwinfo, fr->use_cpu_acceleration,
1921 &nbv->grp[i].kernel_type,
1922 &nbv->grp[i].ewald_excl,
1925 bHybridGPURun = TRUE;
1929 /* Use the same kernel for local and non-local interactions */
1930 nbv->grp[i].kernel_type = nbv->grp[0].kernel_type;
1931 nbv->grp[i].ewald_excl = nbv->grp[0].ewald_excl;
1938 /* init the NxN GPU data; the last argument tells whether we'll have
1939 * both local and non-local NB calculation on GPU */
1940 nbnxn_cuda_init(fp, &nbv->cu_nbv,
1941 &fr->hwinfo->gpu_info, cr->rank_pp_intranode,
1942 (nbv->ngrp > 1) && !bHybridGPURun);
1944 if ((env = getenv("GMX_NB_MIN_CI")) != NULL)
1948 nbv->min_ci_balanced = strtol(env, &end, 10);
1949 if (!end || (*end != 0) || nbv->min_ci_balanced <= 0)
1951 gmx_fatal(FARGS, "Invalid value passed in GMX_NB_MIN_CI=%s, positive integer required", env);
1956 fprintf(debug, "Neighbor-list balancing parameter: %d (passed as env. var.)\n",
1957 nbv->min_ci_balanced);
1962 nbv->min_ci_balanced = nbnxn_cuda_min_ci_balanced(nbv->cu_nbv);
1965 fprintf(debug, "Neighbor-list balancing parameter: %d (auto-adjusted to the number of GPU multi-processors)\n",
1966 nbv->min_ci_balanced);
1972 nbv->min_ci_balanced = 0;
1977 nbnxn_init_search(&nbv->nbs,
1978 DOMAINDECOMP(cr) ? &cr->dd->nc : NULL,
1979 DOMAINDECOMP(cr) ? domdec_zones(cr->dd) : NULL,
1980 gmx_omp_nthreads_get(emntNonbonded));
1982 for (i = 0; i < nbv->ngrp; i++)
1984 if (nbv->grp[0].kernel_type == nbnxnk8x8x8_CUDA)
1986 nb_alloc = &pmalloc;
1995 nbnxn_init_pairlist_set(&nbv->grp[i].nbl_lists,
1996 nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type),
1997 /* 8x8x8 "non-simple" lists are ATM always combined */
1998 !nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type),
2002 nbv->grp[0].kernel_type != nbv->grp[i].kernel_type)
2004 snew(nbv->grp[i].nbat, 1);
2005 nbnxn_atomdata_init(fp,
2007 nbv->grp[i].kernel_type,
2008 fr->ntype, fr->nbfp,
2010 nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type) ? gmx_omp_nthreads_get(emntNonbonded) : 1,
2015 nbv->grp[i].nbat = nbv->grp[0].nbat;
2020 void init_forcerec(FILE *fp,
2021 const output_env_t oenv,
2024 const t_inputrec *ir,
2025 const gmx_mtop_t *mtop,
2026 const t_commrec *cr,
2033 const char *nbpu_opt,
2034 gmx_bool bNoSolvOpt,
2037 int i, j, m, natoms, ngrp, negp_pp, negptable, egi, egj;
2043 gmx_bool bGenericKernelOnly;
2044 gmx_bool bTab, bSep14tab, bNormalnblists;
2046 int *nm_ind, egp_flags;
2048 if (fr->hwinfo == NULL)
2050 /* Detect hardware, gather information.
2051 * In mdrun, hwinfo has already been set before calling init_forcerec.
2052 * Here we ignore GPUs, as tools will not use them anyhow.
2054 fr->hwinfo = gmx_detect_hardware(fp, cr, 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;
2214 /* All-vs-all kernels have not been implemented in 4.6, and
2215 * the SIMD group kernels are also buggy in this case. Non-accelerated
2216 * group kernels are OK. See Redmine #1249. */
2219 fr->bAllvsAll = FALSE;
2220 fr->use_cpu_acceleration = FALSE;
2224 "\nYour simulation settings would have triggered the efficient all-vs-all\n"
2225 "kernels in GROMACS 4.5, but these have not been implemented in GROMACS\n"
2226 "4.6. Also, we can't use the accelerated SIMD kernels here because\n"
2227 "of an unfixed bug. The reference C kernels are correct, though, so\n"
2228 "we are proceeding by disabling all CPU architecture-specific\n"
2229 "(e.g. SSE2/SSE4/AVX) routines. If performance is important, please\n"
2230 "use GROMACS 4.5.7 or try cutoff-scheme = Verlet.\n\n");
2234 /* Neighbour searching stuff */
2235 fr->cutoff_scheme = ir->cutoff_scheme;
2236 fr->bGrid = (ir->ns_type == ensGRID);
2237 fr->ePBC = ir->ePBC;
2239 /* Determine if we will do PBC for distances in bonded interactions */
2240 if (fr->ePBC == epbcNONE)
2242 fr->bMolPBC = FALSE;
2246 if (!DOMAINDECOMP(cr))
2248 /* The group cut-off scheme and SHAKE assume charge groups
2249 * are whole, but not using molpbc is faster in most cases.
2251 if (fr->cutoff_scheme == ecutsGROUP ||
2252 (ir->eConstrAlg == econtSHAKE &&
2253 (gmx_mtop_ftype_count(mtop, F_CONSTR) > 0 ||
2254 gmx_mtop_ftype_count(mtop, F_CONSTRNC) > 0)))
2256 fr->bMolPBC = ir->bPeriodicMols;
2261 if (getenv("GMX_USE_GRAPH") != NULL)
2263 fr->bMolPBC = FALSE;
2266 fprintf(fp, "\nGMX_MOLPBC is set, using the graph for bonded interactions\n\n");
2273 fr->bMolPBC = dd_bonded_molpbc(cr->dd, fr->ePBC);
2276 fr->bGB = (ir->implicit_solvent == eisGBSA);
2278 fr->rc_scaling = ir->refcoord_scaling;
2279 copy_rvec(ir->posres_com, fr->posres_com);
2280 copy_rvec(ir->posres_comB, fr->posres_comB);
2281 fr->rlist = cutoff_inf(ir->rlist);
2282 fr->rlistlong = cutoff_inf(ir->rlistlong);
2283 fr->eeltype = ir->coulombtype;
2284 fr->vdwtype = ir->vdwtype;
2286 fr->coulomb_modifier = ir->coulomb_modifier;
2287 fr->vdw_modifier = ir->vdw_modifier;
2289 /* Electrostatics: Translate from interaction-setting-in-mdp-file to kernel interaction format */
2290 switch (fr->eeltype)
2293 fr->nbkernel_elec_interaction = (fr->bGB) ? GMX_NBKERNEL_ELEC_GENERALIZEDBORN : GMX_NBKERNEL_ELEC_COULOMB;
2299 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD;
2303 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD;
2304 fr->coulomb_modifier = eintmodEXACTCUTOFF;
2313 case eelPMEUSERSWITCH:
2314 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_CUBICSPLINETABLE;
2319 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_EWALD;
2323 gmx_fatal(FARGS, "Unsupported electrostatic interaction: %s", eel_names[fr->eeltype]);
2327 /* Vdw: Translate from mdp settings to kernel format */
2328 switch (fr->vdwtype)
2333 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_BUCKINGHAM;
2337 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_LENNARDJONES;
2344 case evdwENCADSHIFT:
2345 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
2349 gmx_fatal(FARGS, "Unsupported vdw interaction: %s", evdw_names[fr->vdwtype]);
2353 /* These start out identical to ir, but might be altered if we e.g. tabulate the interaction in the kernel */
2354 fr->nbkernel_elec_modifier = fr->coulomb_modifier;
2355 fr->nbkernel_vdw_modifier = fr->vdw_modifier;
2357 fr->bTwinRange = fr->rlistlong > fr->rlist;
2358 fr->bEwald = (EEL_PME(fr->eeltype) || fr->eeltype == eelEWALD);
2360 fr->reppow = mtop->ffparams.reppow;
2362 if (ir->cutoff_scheme == ecutsGROUP)
2364 fr->bvdwtab = (fr->vdwtype != evdwCUT ||
2365 !gmx_within_tol(fr->reppow, 12.0, 10*GMX_DOUBLE_EPS));
2366 /* We have special kernels for standard Ewald and PME, but the pme-switch ones are tabulated above */
2367 fr->bcoultab = !(fr->eeltype == eelCUT ||
2368 fr->eeltype == eelEWALD ||
2369 fr->eeltype == eelPME ||
2370 fr->eeltype == eelRF ||
2371 fr->eeltype == eelRF_ZERO);
2373 /* If the user absolutely wants different switch/shift settings for coul/vdw, it is likely
2374 * going to be faster to tabulate the interaction than calling the generic kernel.
2376 if (fr->nbkernel_elec_modifier == eintmodPOTSWITCH && fr->nbkernel_vdw_modifier == eintmodPOTSWITCH)
2378 if ((fr->rcoulomb_switch != fr->rvdw_switch) || (fr->rcoulomb != fr->rvdw))
2380 fr->bcoultab = TRUE;
2383 else if ((fr->nbkernel_elec_modifier == eintmodPOTSHIFT && fr->nbkernel_vdw_modifier == eintmodPOTSHIFT) ||
2384 ((fr->nbkernel_elec_interaction == GMX_NBKERNEL_ELEC_REACTIONFIELD &&
2385 fr->nbkernel_elec_modifier == eintmodEXACTCUTOFF &&
2386 (fr->nbkernel_vdw_modifier == eintmodPOTSWITCH || fr->nbkernel_vdw_modifier == eintmodPOTSHIFT))))
2388 if (fr->rcoulomb != fr->rvdw)
2390 fr->bcoultab = TRUE;
2394 if (getenv("GMX_REQUIRE_TABLES"))
2397 fr->bcoultab = TRUE;
2402 fprintf(fp, "Table routines are used for coulomb: %s\n", bool_names[fr->bcoultab]);
2403 fprintf(fp, "Table routines are used for vdw: %s\n", bool_names[fr->bvdwtab ]);
2406 if (fr->bvdwtab == TRUE)
2408 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
2409 fr->nbkernel_vdw_modifier = eintmodNONE;
2411 if (fr->bcoultab == TRUE)
2413 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_CUBICSPLINETABLE;
2414 fr->nbkernel_elec_modifier = eintmodNONE;
2418 if (ir->cutoff_scheme == ecutsVERLET)
2420 if (!gmx_within_tol(fr->reppow, 12.0, 10*GMX_DOUBLE_EPS))
2422 gmx_fatal(FARGS, "Cut-off scheme %S only supports LJ repulsion power 12", ecutscheme_names[ir->cutoff_scheme]);
2424 fr->bvdwtab = FALSE;
2425 fr->bcoultab = FALSE;
2428 /* Tables are used for direct ewald sum */
2431 if (EEL_PME(ir->coulombtype))
2435 fprintf(fp, "Will do PME sum in reciprocal space.\n");
2437 if (ir->coulombtype == eelP3M_AD)
2439 please_cite(fp, "Hockney1988");
2440 please_cite(fp, "Ballenegger2012");
2444 please_cite(fp, "Essmann95a");
2447 if (ir->ewald_geometry == eewg3DC)
2451 fprintf(fp, "Using the Ewald3DC correction for systems with a slab geometry.\n");
2453 please_cite(fp, "In-Chul99a");
2456 fr->ewaldcoeff = calc_ewaldcoeff(ir->rcoulomb, ir->ewald_rtol);
2457 init_ewald_tab(&(fr->ewald_table), cr, ir, fp);
2460 fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for Ewald\n",
2465 /* Electrostatics */
2466 fr->epsilon_r = ir->epsilon_r;
2467 fr->epsilon_rf = ir->epsilon_rf;
2468 fr->fudgeQQ = mtop->ffparams.fudgeQQ;
2469 fr->rcoulomb_switch = ir->rcoulomb_switch;
2470 fr->rcoulomb = cutoff_inf(ir->rcoulomb);
2472 /* Parameters for generalized RF */
2476 if (fr->eeltype == eelGRF)
2478 init_generalized_rf(fp, mtop, ir, fr);
2480 else if (fr->eeltype == eelSHIFT)
2482 for (m = 0; (m < DIM); m++)
2484 box_size[m] = box[m][m];
2487 if ((fr->eeltype == eelSHIFT && fr->rcoulomb > fr->rcoulomb_switch))
2489 set_shift_consts(fp, fr->rcoulomb_switch, fr->rcoulomb, box_size, fr);
2493 fr->bF_NoVirSum = (EEL_FULL(fr->eeltype) ||
2494 gmx_mtop_ftype_count(mtop, F_POSRES) > 0 ||
2495 IR_ELEC_FIELD(*ir) ||
2496 (fr->adress_icor != eAdressICOff)
2499 if (fr->cutoff_scheme == ecutsGROUP &&
2500 ncg_mtop(mtop) > fr->cg_nalloc && !DOMAINDECOMP(cr))
2502 /* Count the total number of charge groups */
2503 fr->cg_nalloc = ncg_mtop(mtop);
2504 srenew(fr->cg_cm, fr->cg_nalloc);
2506 if (fr->shift_vec == NULL)
2508 snew(fr->shift_vec, SHIFTS);
2511 if (fr->fshift == NULL)
2513 snew(fr->fshift, SHIFTS);
2516 if (fr->nbfp == NULL)
2518 fr->ntype = mtop->ffparams.atnr;
2519 fr->nbfp = mk_nbfp(&mtop->ffparams, fr->bBHAM);
2522 /* Copy the energy group exclusions */
2523 fr->egp_flags = ir->opts.egp_flags;
2525 /* Van der Waals stuff */
2526 fr->rvdw = cutoff_inf(ir->rvdw);
2527 fr->rvdw_switch = ir->rvdw_switch;
2528 if ((fr->vdwtype != evdwCUT) && (fr->vdwtype != evdwUSER) && !fr->bBHAM)
2530 if (fr->rvdw_switch >= fr->rvdw)
2532 gmx_fatal(FARGS, "rvdw_switch (%f) must be < rvdw (%f)",
2533 fr->rvdw_switch, fr->rvdw);
2537 fprintf(fp, "Using %s Lennard-Jones, switch between %g and %g nm\n",
2538 (fr->eeltype == eelSWITCH) ? "switched" : "shifted",
2539 fr->rvdw_switch, fr->rvdw);
2543 if (fr->bBHAM && (fr->vdwtype == evdwSHIFT || fr->vdwtype == evdwSWITCH))
2545 gmx_fatal(FARGS, "Switch/shift interaction not supported with Buckingham");
2550 fprintf(fp, "Cut-off's: NS: %g Coulomb: %g %s: %g\n",
2551 fr->rlist, fr->rcoulomb, fr->bBHAM ? "BHAM" : "LJ", fr->rvdw);
2554 fr->eDispCorr = ir->eDispCorr;
2555 if (ir->eDispCorr != edispcNO)
2557 set_avcsixtwelve(fp, fr, mtop);
2562 set_bham_b_max(fp, fr, mtop);
2565 fr->gb_epsilon_solvent = ir->gb_epsilon_solvent;
2567 /* Copy the GBSA data (radius, volume and surftens for each
2568 * atomtype) from the topology atomtype section to forcerec.
2570 snew(fr->atype_radius, fr->ntype);
2571 snew(fr->atype_vol, fr->ntype);
2572 snew(fr->atype_surftens, fr->ntype);
2573 snew(fr->atype_gb_radius, fr->ntype);
2574 snew(fr->atype_S_hct, fr->ntype);
2576 if (mtop->atomtypes.nr > 0)
2578 for (i = 0; i < fr->ntype; i++)
2580 fr->atype_radius[i] = mtop->atomtypes.radius[i];
2582 for (i = 0; i < fr->ntype; i++)
2584 fr->atype_vol[i] = mtop->atomtypes.vol[i];
2586 for (i = 0; i < fr->ntype; i++)
2588 fr->atype_surftens[i] = mtop->atomtypes.surftens[i];
2590 for (i = 0; i < fr->ntype; i++)
2592 fr->atype_gb_radius[i] = mtop->atomtypes.gb_radius[i];
2594 for (i = 0; i < fr->ntype; i++)
2596 fr->atype_S_hct[i] = mtop->atomtypes.S_hct[i];
2600 /* Generate the GB table if needed */
2604 fr->gbtabscale = 2000;
2606 fr->gbtabscale = 500;
2610 fr->gbtab = make_gb_table(fp, oenv, fr, tabpfn, fr->gbtabscale);
2612 init_gb(&fr->born, cr, fr, ir, mtop, ir->rgbradii, ir->gb_algorithm);
2614 /* Copy local gb data (for dd, this is done in dd_partition_system) */
2615 if (!DOMAINDECOMP(cr))
2617 make_local_gb(cr, fr->born, ir->gb_algorithm);
2621 /* Set the charge scaling */
2622 if (fr->epsilon_r != 0)
2624 fr->epsfac = ONE_4PI_EPS0/fr->epsilon_r;
2628 /* eps = 0 is infinite dieletric: no coulomb interactions */
2632 /* Reaction field constants */
2633 if (EEL_RF(fr->eeltype))
2635 calc_rffac(fp, fr->eeltype, fr->epsilon_r, fr->epsilon_rf,
2636 fr->rcoulomb, fr->temp, fr->zsquare, box,
2637 &fr->kappa, &fr->k_rf, &fr->c_rf);
2640 set_chargesum(fp, fr, mtop);
2642 /* if we are using LR electrostatics, and they are tabulated,
2643 * the tables will contain modified coulomb interactions.
2644 * Since we want to use the non-shifted ones for 1-4
2645 * coulombic interactions, we must have an extra set of tables.
2648 /* Construct tables.
2649 * A little unnecessary to make both vdw and coul tables sometimes,
2650 * but what the heck... */
2652 bTab = fr->bcoultab || fr->bvdwtab || fr->bEwald;
2654 bSep14tab = ((!bTab || fr->eeltype != eelCUT || fr->vdwtype != evdwCUT ||
2655 fr->bBHAM || fr->bEwald) &&
2656 (gmx_mtop_ftype_count(mtop, F_LJ14) > 0 ||
2657 gmx_mtop_ftype_count(mtop, F_LJC14_Q) > 0 ||
2658 gmx_mtop_ftype_count(mtop, F_LJC_PAIRS_NB) > 0));
2660 negp_pp = ir->opts.ngener - ir->nwall;
2664 bNormalnblists = TRUE;
2669 bNormalnblists = (ir->eDispCorr != edispcNO);
2670 for (egi = 0; egi < negp_pp; egi++)
2672 for (egj = egi; egj < negp_pp; egj++)
2674 egp_flags = ir->opts.egp_flags[GID(egi, egj, ir->opts.ngener)];
2675 if (!(egp_flags & EGP_EXCL))
2677 if (egp_flags & EGP_TABLE)
2683 bNormalnblists = TRUE;
2690 fr->nnblists = negptable + 1;
2694 fr->nnblists = negptable;
2696 if (fr->nnblists > 1)
2698 snew(fr->gid2nblists, ir->opts.ngener*ir->opts.ngener);
2707 snew(fr->nblists, fr->nnblists);
2709 /* This code automatically gives table length tabext without cut-off's,
2710 * in that case grompp should already have checked that we do not need
2711 * normal tables and we only generate tables for 1-4 interactions.
2713 rtab = ir->rlistlong + ir->tabext;
2717 /* make tables for ordinary interactions */
2720 make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn, NULL, NULL, &fr->nblists[0]);
2723 make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn, NULL, NULL, &fr->nblists[fr->nnblists/2]);
2727 fr->tab14 = fr->nblists[0].table_elec_vdw;
2737 /* Read the special tables for certain energy group pairs */
2738 nm_ind = mtop->groups.grps[egcENER].nm_ind;
2739 for (egi = 0; egi < negp_pp; egi++)
2741 for (egj = egi; egj < negp_pp; egj++)
2743 egp_flags = ir->opts.egp_flags[GID(egi, egj, ir->opts.ngener)];
2744 if ((egp_flags & EGP_TABLE) && !(egp_flags & EGP_EXCL))
2746 nbl = &(fr->nblists[m]);
2747 if (fr->nnblists > 1)
2749 fr->gid2nblists[GID(egi, egj, ir->opts.ngener)] = m;
2751 /* Read the table file with the two energy groups names appended */
2752 make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn,
2753 *mtop->groups.grpname[nm_ind[egi]],
2754 *mtop->groups.grpname[nm_ind[egj]],
2758 make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn,
2759 *mtop->groups.grpname[nm_ind[egi]],
2760 *mtop->groups.grpname[nm_ind[egj]],
2761 &fr->nblists[fr->nnblists/2+m]);
2765 else if (fr->nnblists > 1)
2767 fr->gid2nblists[GID(egi, egj, ir->opts.ngener)] = 0;
2775 /* generate extra tables with plain Coulomb for 1-4 interactions only */
2776 fr->tab14 = make_tables(fp, oenv, fr, MASTER(cr), tabpfn, rtab,
2777 GMX_MAKETABLES_14ONLY);
2780 /* Read AdResS Thermo Force table if needed */
2781 if (fr->adress_icor == eAdressICThermoForce)
2783 /* old todo replace */
2785 if (ir->adress->n_tf_grps > 0)
2787 make_adress_tf_tables(fp, oenv, fr, ir, tabfn, mtop, box);
2792 /* load the default table */
2793 snew(fr->atf_tabs, 1);
2794 fr->atf_tabs[DEFAULT_TF_TABLE] = make_atf_table(fp, oenv, fr, tabafn, box);
2799 fr->nwall = ir->nwall;
2800 if (ir->nwall && ir->wall_type == ewtTABLE)
2802 make_wall_tables(fp, oenv, ir, tabfn, &mtop->groups, fr);
2807 fcd->bondtab = make_bonded_tables(fp,
2808 F_TABBONDS, F_TABBONDSNC,
2810 fcd->angletab = make_bonded_tables(fp,
2813 fcd->dihtab = make_bonded_tables(fp,
2821 fprintf(debug, "No fcdata or table file name passed, can not read table, can not do bonded interactions\n");
2825 /* QM/MM initialization if requested
2829 fprintf(stderr, "QM/MM calculation requested.\n");
2832 fr->bQMMM = ir->bQMMM;
2833 fr->qr = mk_QMMMrec();
2835 /* Set all the static charge group info */
2836 fr->cginfo_mb = init_cginfo_mb(fp, mtop, fr, bNoSolvOpt,
2837 &fr->bExcl_IntraCGAll_InterCGNone);
2838 if (DOMAINDECOMP(cr))
2844 fr->cginfo = cginfo_expand(mtop->nmolblock, fr->cginfo_mb);
2847 if (!DOMAINDECOMP(cr))
2849 /* When using particle decomposition, the effect of the second argument,
2850 * which sets fr->hcg, is corrected later in do_md and init_em.
2852 forcerec_set_ranges(fr, ncg_mtop(mtop), ncg_mtop(mtop),
2853 mtop->natoms, mtop->natoms, mtop->natoms);
2856 fr->print_force = print_force;
2859 /* coarse load balancing vars */
2864 /* Initialize neighbor search */
2865 init_ns(fp, cr, &fr->ns, fr, mtop, box);
2867 if (cr->duty & DUTY_PP)
2869 gmx_nonbonded_setup(fp, fr, bGenericKernelOnly);
2873 gmx_setup_adress_kernels(fp,bGenericKernelOnly);
2878 /* Initialize the thread working data for bonded interactions */
2879 init_forcerec_f_threads(fr, mtop->groups.grps[egcENER].nr);
2881 snew(fr->excl_load, fr->nthreads+1);
2883 if (fr->cutoff_scheme == ecutsVERLET)
2885 if (ir->rcoulomb != ir->rvdw)
2887 gmx_fatal(FARGS, "With Verlet lists rcoulomb and rvdw should be identical");
2890 init_nb_verlet(fp, &fr->nbv, ir, fr, cr, nbpu_opt);
2893 /* fr->ic is used both by verlet and group kernels (to some extent) now */
2894 init_interaction_const(fp, &fr->ic, fr, rtab);
2895 if (ir->eDispCorr != edispcNO)
2897 calc_enervirdiff(fp, ir->eDispCorr, fr);
2901 #define pr_real(fp, r) fprintf(fp, "%s: %e\n",#r, r)
2902 #define pr_int(fp, i) fprintf((fp), "%s: %d\n",#i, i)
2903 #define pr_bool(fp, b) fprintf((fp), "%s: %s\n",#b, bool_names[b])
2905 void pr_forcerec(FILE *fp, t_forcerec *fr, t_commrec *cr)
2909 pr_real(fp, fr->rlist);
2910 pr_real(fp, fr->rcoulomb);
2911 pr_real(fp, fr->fudgeQQ);
2912 pr_bool(fp, fr->bGrid);
2913 pr_bool(fp, fr->bTwinRange);
2914 /*pr_int(fp,fr->cg0);
2915 pr_int(fp,fr->hcg);*/
2916 for (i = 0; i < fr->nnblists; i++)
2918 pr_int(fp, fr->nblists[i].table_elec_vdw.n);
2920 pr_real(fp, fr->rcoulomb_switch);
2921 pr_real(fp, fr->rcoulomb);
2926 void forcerec_set_excl_load(t_forcerec *fr,
2927 const gmx_localtop_t *top, const t_commrec *cr)
2930 int t, i, j, ntot, n, ntarget;
2932 if (cr != NULL && PARTDECOMP(cr))
2934 /* No OpenMP with particle decomposition */
2942 ind = top->excls.index;
2946 for (i = 0; i < top->excls.nr; i++)
2948 for (j = ind[i]; j < ind[i+1]; j++)
2957 fr->excl_load[0] = 0;
2960 for (t = 1; t <= fr->nthreads; t++)
2962 ntarget = (ntot*t)/fr->nthreads;
2963 while (i < top->excls.nr && n < ntarget)
2965 for (j = ind[i]; j < ind[i+1]; j++)
2974 fr->excl_load[t] = i;