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47 #include "gromacs/math/utilities.h"
51 #include "gmx_fatal.h"
52 #include "gmx_fatal_collective.h"
56 #include "nonbonded.h"
65 #include "md_support.h"
66 #include "md_logging.h"
70 #include "mtop_util.h"
71 #include "nbnxn_simd.h"
72 #include "nbnxn_search.h"
73 #include "nbnxn_atomdata.h"
74 #include "nbnxn_consts.h"
75 #include "gmx_omp_nthreads.h"
76 #include "gmx_detect_hardware.h"
80 /* MSVC definition for __cpuid() */
84 #include "types/nbnxn_cuda_types_ext.h"
85 #include "gpu_utils.h"
86 #include "nbnxn_cuda_data_mgmt.h"
87 #include "pmalloc_cuda.h"
89 t_forcerec *mk_forcerec(void)
99 static void pr_nbfp(FILE *fp, real *nbfp, gmx_bool bBHAM, int atnr)
103 for (i = 0; (i < atnr); i++)
105 for (j = 0; (j < atnr); j++)
107 fprintf(fp, "%2d - %2d", i, j);
110 fprintf(fp, " a=%10g, b=%10g, c=%10g\n", BHAMA(nbfp, atnr, i, j),
111 BHAMB(nbfp, atnr, i, j), BHAMC(nbfp, atnr, i, j)/6.0);
115 fprintf(fp, " c6=%10g, c12=%10g\n", C6(nbfp, atnr, i, j)/6.0,
116 C12(nbfp, atnr, i, j)/12.0);
123 static real *mk_nbfp(const gmx_ffparams_t *idef, gmx_bool bBHAM)
131 snew(nbfp, 3*atnr*atnr);
132 for (i = k = 0; (i < atnr); i++)
134 for (j = 0; (j < atnr); j++, k++)
136 BHAMA(nbfp, atnr, i, j) = idef->iparams[k].bham.a;
137 BHAMB(nbfp, atnr, i, j) = idef->iparams[k].bham.b;
138 /* nbfp now includes the 6.0 derivative prefactor */
139 BHAMC(nbfp, atnr, i, j) = idef->iparams[k].bham.c*6.0;
145 snew(nbfp, 2*atnr*atnr);
146 for (i = k = 0; (i < atnr); i++)
148 for (j = 0; (j < atnr); j++, k++)
150 /* nbfp now includes the 6.0/12.0 derivative prefactors */
151 C6(nbfp, atnr, i, j) = idef->iparams[k].lj.c6*6.0;
152 C12(nbfp, atnr, i, j) = idef->iparams[k].lj.c12*12.0;
160 static real *mk_nbfp_combination_rule(const gmx_ffparams_t *idef, int comb_rule)
164 real c6i, c6j, c12i, c12j, epsi, epsj, sigmai, sigmaj;
168 snew(nbfp, 2*atnr*atnr);
169 for (i = 0; i < atnr; ++i)
171 for (j = 0; j < atnr; ++j)
173 c6i = idef->iparams[i*(atnr+1)].lj.c6;
174 c12i = idef->iparams[i*(atnr+1)].lj.c12;
175 c6j = idef->iparams[j*(atnr+1)].lj.c6;
176 c12j = idef->iparams[j*(atnr+1)].lj.c12;
177 c6 = sqrt(c6i * c6j);
178 c12 = sqrt(c12i * c12j);
179 if (comb_rule == eCOMB_ARITHMETIC
180 && !gmx_numzero(c6) && !gmx_numzero(c12))
182 sigmai = pow(c12i / c6i, 1.0/6.0);
183 sigmaj = pow(c12j / c6j, 1.0/6.0);
184 epsi = c6i * c6i / c12i;
185 epsj = c6j * c6j / c12j;
186 c6 = epsi * epsj * pow(0.5*(sigmai+sigmaj), 6);
187 c12 = epsi * epsj * pow(0.5*(sigmai+sigmaj), 12);
189 C6(nbfp, atnr, i, j) = c6*6.0;
190 C12(nbfp, atnr, i, j) = c12*12.0;
196 /* This routine sets fr->solvent_opt to the most common solvent in the
197 * system, e.g. esolSPC or esolTIP4P. It will also mark each charge group in
198 * the fr->solvent_type array with the correct type (or esolNO).
200 * Charge groups that fulfill the conditions but are not identical to the
201 * most common one will be marked as esolNO in the solvent_type array.
203 * TIP3p is identical to SPC for these purposes, so we call it
204 * SPC in the arrays (Apologies to Bill Jorgensen ;-)
206 * NOTE: QM particle should not
207 * become an optimized solvent. Not even if there is only one charge
217 } solvent_parameters_t;
220 check_solvent_cg(const gmx_moltype_t *molt,
223 const unsigned char *qm_grpnr,
224 const t_grps *qm_grps,
226 int *n_solvent_parameters,
227 solvent_parameters_t **solvent_parameters_p,
231 const t_blocka *excl;
238 real tmp_charge[4] = { 0.0 }; /* init to zero to make gcc4.8 happy */
239 int tmp_vdwtype[4] = { 0 }; /* init to zero to make gcc4.8 happy */
242 solvent_parameters_t *solvent_parameters;
244 /* We use a list with parameters for each solvent type.
245 * Every time we discover a new molecule that fulfills the basic
246 * conditions for a solvent we compare with the previous entries
247 * in these lists. If the parameters are the same we just increment
248 * the counter for that type, and otherwise we create a new type
249 * based on the current molecule.
251 * Once we've finished going through all molecules we check which
252 * solvent is most common, and mark all those molecules while we
253 * clear the flag on all others.
256 solvent_parameters = *solvent_parameters_p;
258 /* Mark the cg first as non optimized */
261 /* Check if this cg has no exclusions with atoms in other charge groups
262 * and all atoms inside the charge group excluded.
263 * We only have 3 or 4 atom solvent loops.
265 if (GET_CGINFO_EXCL_INTER(cginfo) ||
266 !GET_CGINFO_EXCL_INTRA(cginfo))
271 /* Get the indices of the first atom in this charge group */
272 j0 = molt->cgs.index[cg0];
273 j1 = molt->cgs.index[cg0+1];
275 /* Number of atoms in our molecule */
281 "Moltype '%s': there are %d atoms in this charge group\n",
285 /* Check if it could be an SPC (3 atoms) or TIP4p (4) water,
288 if (nj < 3 || nj > 4)
293 /* Check if we are doing QM on this group */
295 if (qm_grpnr != NULL)
297 for (j = j0; j < j1 && !qm; j++)
299 qm = (qm_grpnr[j] < qm_grps->nr - 1);
302 /* Cannot use solvent optimization with QM */
308 atom = molt->atoms.atom;
310 /* Still looks like a solvent, time to check parameters */
312 /* If it is perturbed (free energy) we can't use the solvent loops,
313 * so then we just skip to the next molecule.
317 for (j = j0; j < j1 && !perturbed; j++)
319 perturbed = PERTURBED(atom[j]);
327 /* Now it's only a question if the VdW and charge parameters
328 * are OK. Before doing the check we compare and see if they are
329 * identical to a possible previous solvent type.
330 * First we assign the current types and charges.
332 for (j = 0; j < nj; j++)
334 tmp_vdwtype[j] = atom[j0+j].type;
335 tmp_charge[j] = atom[j0+j].q;
338 /* Does it match any previous solvent type? */
339 for (k = 0; k < *n_solvent_parameters; k++)
344 /* We can only match SPC with 3 atoms and TIP4p with 4 atoms */
345 if ( (solvent_parameters[k].model == esolSPC && nj != 3) ||
346 (solvent_parameters[k].model == esolTIP4P && nj != 4) )
351 /* Check that types & charges match for all atoms in molecule */
352 for (j = 0; j < nj && match == TRUE; j++)
354 if (tmp_vdwtype[j] != solvent_parameters[k].vdwtype[j])
358 if (tmp_charge[j] != solvent_parameters[k].charge[j])
365 /* Congratulations! We have a matched solvent.
366 * Flag it with this type for later processing.
369 solvent_parameters[k].count += nmol;
371 /* We are done with this charge group */
376 /* If we get here, we have a tentative new solvent type.
377 * Before we add it we must check that it fulfills the requirements
378 * of the solvent optimized loops. First determine which atoms have
381 for (j = 0; j < nj; j++)
384 tjA = tmp_vdwtype[j];
386 /* Go through all other tpes and see if any have non-zero
387 * VdW parameters when combined with this one.
389 for (k = 0; k < fr->ntype && (has_vdw[j] == FALSE); k++)
391 /* We already checked that the atoms weren't perturbed,
392 * so we only need to check state A now.
396 has_vdw[j] = (has_vdw[j] ||
397 (BHAMA(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
398 (BHAMB(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
399 (BHAMC(fr->nbfp, fr->ntype, tjA, k) != 0.0));
404 has_vdw[j] = (has_vdw[j] ||
405 (C6(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
406 (C12(fr->nbfp, fr->ntype, tjA, k) != 0.0));
411 /* Now we know all we need to make the final check and assignment. */
415 * For this we require thatn all atoms have charge,
416 * the charges on atom 2 & 3 should be the same, and only
417 * atom 1 might have VdW.
419 if (has_vdw[1] == FALSE &&
420 has_vdw[2] == FALSE &&
421 tmp_charge[0] != 0 &&
422 tmp_charge[1] != 0 &&
423 tmp_charge[2] == tmp_charge[1])
425 srenew(solvent_parameters, *n_solvent_parameters+1);
426 solvent_parameters[*n_solvent_parameters].model = esolSPC;
427 solvent_parameters[*n_solvent_parameters].count = nmol;
428 for (k = 0; k < 3; k++)
430 solvent_parameters[*n_solvent_parameters].vdwtype[k] = tmp_vdwtype[k];
431 solvent_parameters[*n_solvent_parameters].charge[k] = tmp_charge[k];
434 *cg_sp = *n_solvent_parameters;
435 (*n_solvent_parameters)++;
440 /* Or could it be a TIP4P?
441 * For this we require thatn atoms 2,3,4 have charge, but not atom 1.
442 * Only atom 1 mght have VdW.
444 if (has_vdw[1] == FALSE &&
445 has_vdw[2] == FALSE &&
446 has_vdw[3] == FALSE &&
447 tmp_charge[0] == 0 &&
448 tmp_charge[1] != 0 &&
449 tmp_charge[2] == tmp_charge[1] &&
452 srenew(solvent_parameters, *n_solvent_parameters+1);
453 solvent_parameters[*n_solvent_parameters].model = esolTIP4P;
454 solvent_parameters[*n_solvent_parameters].count = nmol;
455 for (k = 0; k < 4; k++)
457 solvent_parameters[*n_solvent_parameters].vdwtype[k] = tmp_vdwtype[k];
458 solvent_parameters[*n_solvent_parameters].charge[k] = tmp_charge[k];
461 *cg_sp = *n_solvent_parameters;
462 (*n_solvent_parameters)++;
466 *solvent_parameters_p = solvent_parameters;
470 check_solvent(FILE * fp,
471 const gmx_mtop_t * mtop,
473 cginfo_mb_t *cginfo_mb)
476 const t_block * mols;
477 const gmx_moltype_t *molt;
478 int mb, mol, cg_mol, at_offset, cg_offset, am, cgm, i, nmol_ch, nmol;
479 int n_solvent_parameters;
480 solvent_parameters_t *solvent_parameters;
486 fprintf(debug, "Going to determine what solvent types we have.\n");
491 n_solvent_parameters = 0;
492 solvent_parameters = NULL;
493 /* Allocate temporary array for solvent type */
494 snew(cg_sp, mtop->nmolblock);
498 for (mb = 0; mb < mtop->nmolblock; mb++)
500 molt = &mtop->moltype[mtop->molblock[mb].type];
502 /* Here we have to loop over all individual molecules
503 * because we need to check for QMMM particles.
505 snew(cg_sp[mb], cginfo_mb[mb].cg_mod);
506 nmol_ch = cginfo_mb[mb].cg_mod/cgs->nr;
507 nmol = mtop->molblock[mb].nmol/nmol_ch;
508 for (mol = 0; mol < nmol_ch; mol++)
511 am = mol*cgs->index[cgs->nr];
512 for (cg_mol = 0; cg_mol < cgs->nr; cg_mol++)
514 check_solvent_cg(molt, cg_mol, nmol,
515 mtop->groups.grpnr[egcQMMM] ?
516 mtop->groups.grpnr[egcQMMM]+at_offset+am : 0,
517 &mtop->groups.grps[egcQMMM],
519 &n_solvent_parameters, &solvent_parameters,
520 cginfo_mb[mb].cginfo[cgm+cg_mol],
521 &cg_sp[mb][cgm+cg_mol]);
524 cg_offset += cgs->nr;
525 at_offset += cgs->index[cgs->nr];
528 /* Puh! We finished going through all charge groups.
529 * Now find the most common solvent model.
532 /* Most common solvent this far */
534 for (i = 0; i < n_solvent_parameters; i++)
537 solvent_parameters[i].count > solvent_parameters[bestsp].count)
545 bestsol = solvent_parameters[bestsp].model;
552 #ifdef DISABLE_WATER_NLIST
557 for (mb = 0; mb < mtop->nmolblock; mb++)
559 cgs = &mtop->moltype[mtop->molblock[mb].type].cgs;
560 nmol = (mtop->molblock[mb].nmol*cgs->nr)/cginfo_mb[mb].cg_mod;
561 for (i = 0; i < cginfo_mb[mb].cg_mod; i++)
563 if (cg_sp[mb][i] == bestsp)
565 SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[i], bestsol);
570 SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[i], esolNO);
577 if (bestsol != esolNO && fp != NULL)
579 fprintf(fp, "\nEnabling %s-like water optimization for %d molecules.\n\n",
581 solvent_parameters[bestsp].count);
584 sfree(solvent_parameters);
585 fr->solvent_opt = bestsol;
589 acNONE = 0, acCONSTRAINT, acSETTLE
592 static cginfo_mb_t *init_cginfo_mb(FILE *fplog, const gmx_mtop_t *mtop,
593 t_forcerec *fr, gmx_bool bNoSolvOpt,
594 gmx_bool *bFEP_NonBonded,
595 gmx_bool *bExcl_IntraCGAll_InterCGNone)
598 const t_blocka *excl;
599 const gmx_moltype_t *molt;
600 const gmx_molblock_t *molb;
601 cginfo_mb_t *cginfo_mb;
604 int cg_offset, a_offset, cgm, am;
605 int mb, m, ncg_tot, cg, a0, a1, gid, ai, j, aj, excl_nalloc;
609 gmx_bool bId, *bExcl, bExclIntraAll, bExclInter, bHaveVDW, bHaveQ, bFEP;
611 ncg_tot = ncg_mtop(mtop);
612 snew(cginfo_mb, mtop->nmolblock);
614 snew(type_VDW, fr->ntype);
615 for (ai = 0; ai < fr->ntype; ai++)
617 type_VDW[ai] = FALSE;
618 for (j = 0; j < fr->ntype; j++)
620 type_VDW[ai] = type_VDW[ai] ||
622 C6(fr->nbfp, fr->ntype, ai, j) != 0 ||
623 C12(fr->nbfp, fr->ntype, ai, j) != 0;
627 *bFEP_NonBonded = FALSE;
628 *bExcl_IntraCGAll_InterCGNone = TRUE;
631 snew(bExcl, excl_nalloc);
634 for (mb = 0; mb < mtop->nmolblock; mb++)
636 molb = &mtop->molblock[mb];
637 molt = &mtop->moltype[molb->type];
641 /* Check if the cginfo is identical for all molecules in this block.
642 * If so, we only need an array of the size of one molecule.
643 * Otherwise we make an array of #mol times #cgs per molecule.
647 for (m = 0; m < molb->nmol; m++)
649 am = m*cgs->index[cgs->nr];
650 for (cg = 0; cg < cgs->nr; cg++)
653 a1 = cgs->index[cg+1];
654 if (ggrpnr(&mtop->groups, egcENER, a_offset+am+a0) !=
655 ggrpnr(&mtop->groups, egcENER, a_offset +a0))
659 if (mtop->groups.grpnr[egcQMMM] != NULL)
661 for (ai = a0; ai < a1; ai++)
663 if (mtop->groups.grpnr[egcQMMM][a_offset+am+ai] !=
664 mtop->groups.grpnr[egcQMMM][a_offset +ai])
673 cginfo_mb[mb].cg_start = cg_offset;
674 cginfo_mb[mb].cg_end = cg_offset + molb->nmol*cgs->nr;
675 cginfo_mb[mb].cg_mod = (bId ? 1 : molb->nmol)*cgs->nr;
676 snew(cginfo_mb[mb].cginfo, cginfo_mb[mb].cg_mod);
677 cginfo = cginfo_mb[mb].cginfo;
679 /* Set constraints flags for constrained atoms */
680 snew(a_con, molt->atoms.nr);
681 for (ftype = 0; ftype < F_NRE; ftype++)
683 if (interaction_function[ftype].flags & IF_CONSTRAINT)
688 for (ia = 0; ia < molt->ilist[ftype].nr; ia += 1+nral)
692 for (a = 0; a < nral; a++)
694 a_con[molt->ilist[ftype].iatoms[ia+1+a]] =
695 (ftype == F_SETTLE ? acSETTLE : acCONSTRAINT);
701 for (m = 0; m < (bId ? 1 : molb->nmol); m++)
704 am = m*cgs->index[cgs->nr];
705 for (cg = 0; cg < cgs->nr; cg++)
708 a1 = cgs->index[cg+1];
710 /* Store the energy group in cginfo */
711 gid = ggrpnr(&mtop->groups, egcENER, a_offset+am+a0);
712 SET_CGINFO_GID(cginfo[cgm+cg], gid);
714 /* Check the intra/inter charge group exclusions */
715 if (a1-a0 > excl_nalloc)
717 excl_nalloc = a1 - a0;
718 srenew(bExcl, excl_nalloc);
720 /* bExclIntraAll: all intra cg interactions excluded
721 * bExclInter: any inter cg interactions excluded
723 bExclIntraAll = TRUE;
728 for (ai = a0; ai < a1; ai++)
730 /* Check VDW and electrostatic interactions */
731 bHaveVDW = bHaveVDW || (type_VDW[molt->atoms.atom[ai].type] ||
732 type_VDW[molt->atoms.atom[ai].typeB]);
733 bHaveQ = bHaveQ || (molt->atoms.atom[ai].q != 0 ||
734 molt->atoms.atom[ai].qB != 0);
736 bFEP = bFEP || (PERTURBED(molt->atoms.atom[ai]) != 0);
738 /* Clear the exclusion list for atom ai */
739 for (aj = a0; aj < a1; aj++)
741 bExcl[aj-a0] = FALSE;
743 /* Loop over all the exclusions of atom ai */
744 for (j = excl->index[ai]; j < excl->index[ai+1]; j++)
747 if (aj < a0 || aj >= a1)
756 /* Check if ai excludes a0 to a1 */
757 for (aj = a0; aj < a1; aj++)
761 bExclIntraAll = FALSE;
768 SET_CGINFO_CONSTR(cginfo[cgm+cg]);
771 SET_CGINFO_SETTLE(cginfo[cgm+cg]);
779 SET_CGINFO_EXCL_INTRA(cginfo[cgm+cg]);
783 SET_CGINFO_EXCL_INTER(cginfo[cgm+cg]);
785 if (a1 - a0 > MAX_CHARGEGROUP_SIZE)
787 /* The size in cginfo is currently only read with DD */
788 gmx_fatal(FARGS, "A charge group has size %d which is larger than the limit of %d atoms", a1-a0, MAX_CHARGEGROUP_SIZE);
792 SET_CGINFO_HAS_VDW(cginfo[cgm+cg]);
796 SET_CGINFO_HAS_Q(cginfo[cgm+cg]);
800 SET_CGINFO_FEP(cginfo[cgm+cg]);
801 *bFEP_NonBonded = TRUE;
803 /* Store the charge group size */
804 SET_CGINFO_NATOMS(cginfo[cgm+cg], a1-a0);
806 if (!bExclIntraAll || bExclInter)
808 *bExcl_IntraCGAll_InterCGNone = FALSE;
815 cg_offset += molb->nmol*cgs->nr;
816 a_offset += molb->nmol*cgs->index[cgs->nr];
820 /* the solvent optimizer is called after the QM is initialized,
821 * because we don't want to have the QM subsystemto become an
825 check_solvent(fplog, mtop, fr, cginfo_mb);
827 if (getenv("GMX_NO_SOLV_OPT"))
831 fprintf(fplog, "Found environment variable GMX_NO_SOLV_OPT.\n"
832 "Disabling all solvent optimization\n");
834 fr->solvent_opt = esolNO;
838 fr->solvent_opt = esolNO;
840 if (!fr->solvent_opt)
842 for (mb = 0; mb < mtop->nmolblock; mb++)
844 for (cg = 0; cg < cginfo_mb[mb].cg_mod; cg++)
846 SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[cg], esolNO);
854 static int *cginfo_expand(int nmb, cginfo_mb_t *cgi_mb)
859 ncg = cgi_mb[nmb-1].cg_end;
862 for (cg = 0; cg < ncg; cg++)
864 while (cg >= cgi_mb[mb].cg_end)
869 cgi_mb[mb].cginfo[(cg - cgi_mb[mb].cg_start) % cgi_mb[mb].cg_mod];
875 static void set_chargesum(FILE *log, t_forcerec *fr, const gmx_mtop_t *mtop)
877 /*This now calculates sum for q and c6*/
878 double qsum, q2sum, q, c6sum, c6;
880 const t_atoms *atoms;
885 for (mb = 0; mb < mtop->nmolblock; mb++)
887 nmol = mtop->molblock[mb].nmol;
888 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
889 for (i = 0; i < atoms->nr; i++)
891 q = atoms->atom[i].q;
894 c6 = mtop->ffparams.iparams[atoms->atom[i].type*(mtop->ffparams.atnr+1)].lj.c6;
899 fr->q2sum[0] = q2sum;
900 fr->c6sum[0] = c6sum;
902 if (fr->efep != efepNO)
907 for (mb = 0; mb < mtop->nmolblock; mb++)
909 nmol = mtop->molblock[mb].nmol;
910 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
911 for (i = 0; i < atoms->nr; i++)
913 q = atoms->atom[i].qB;
916 c6 = mtop->ffparams.iparams[atoms->atom[i].typeB*(mtop->ffparams.atnr+1)].lj.c6;
920 fr->q2sum[1] = q2sum;
921 fr->c6sum[1] = c6sum;
926 fr->qsum[1] = fr->qsum[0];
927 fr->q2sum[1] = fr->q2sum[0];
928 fr->c6sum[1] = fr->c6sum[0];
932 if (fr->efep == efepNO)
934 fprintf(log, "System total charge: %.3f\n", fr->qsum[0]);
938 fprintf(log, "System total charge, top. A: %.3f top. B: %.3f\n",
939 fr->qsum[0], fr->qsum[1]);
944 void update_forcerec(t_forcerec *fr, matrix box)
946 if (fr->eeltype == eelGRF)
948 calc_rffac(NULL, fr->eeltype, fr->epsilon_r, fr->epsilon_rf,
949 fr->rcoulomb, fr->temp, fr->zsquare, box,
950 &fr->kappa, &fr->k_rf, &fr->c_rf);
954 void set_avcsixtwelve(FILE *fplog, t_forcerec *fr, const gmx_mtop_t *mtop)
956 const t_atoms *atoms, *atoms_tpi;
957 const t_blocka *excl;
958 int mb, nmol, nmolc, i, j, tpi, tpj, j1, j2, k, n, nexcl, q;
959 gmx_int64_t npair, npair_ij, tmpi, tmpj;
960 double csix, ctwelve;
964 real *nbfp_comb = NULL;
970 /* For LJ-PME, we want to correct for the difference between the
971 * actual C6 values and the C6 values used by the LJ-PME based on
972 * combination rules. */
974 if (EVDW_PME(fr->vdwtype))
976 nbfp_comb = mk_nbfp_combination_rule(&mtop->ffparams,
977 (fr->ljpme_combination_rule == eljpmeLB) ? eCOMB_ARITHMETIC : eCOMB_GEOMETRIC);
978 for (tpi = 0; tpi < ntp; ++tpi)
980 for (tpj = 0; tpj < ntp; ++tpj)
982 C6(nbfp_comb, ntp, tpi, tpj) =
983 C6(nbfp, ntp, tpi, tpj) - C6(nbfp_comb, ntp, tpi, tpj);
984 C12(nbfp_comb, ntp, tpi, tpj) = C12(nbfp, ntp, tpi, tpj);
989 for (q = 0; q < (fr->efep == efepNO ? 1 : 2); q++)
997 /* Count the types so we avoid natoms^2 operations */
998 snew(typecount, ntp);
999 gmx_mtop_count_atomtypes(mtop, q, typecount);
1001 for (tpi = 0; tpi < ntp; tpi++)
1003 for (tpj = tpi; tpj < ntp; tpj++)
1005 tmpi = typecount[tpi];
1006 tmpj = typecount[tpj];
1009 npair_ij = tmpi*tmpj;
1013 npair_ij = tmpi*(tmpi - 1)/2;
1017 /* nbfp now includes the 6.0 derivative prefactor */
1018 csix += npair_ij*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
1022 /* nbfp now includes the 6.0/12.0 derivative prefactors */
1023 csix += npair_ij* C6(nbfp, ntp, tpi, tpj)/6.0;
1024 ctwelve += npair_ij* C12(nbfp, ntp, tpi, tpj)/12.0;
1030 /* Subtract the excluded pairs.
1031 * The main reason for substracting exclusions is that in some cases
1032 * some combinations might never occur and the parameters could have
1033 * any value. These unused values should not influence the dispersion
1036 for (mb = 0; mb < mtop->nmolblock; mb++)
1038 nmol = mtop->molblock[mb].nmol;
1039 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
1040 excl = &mtop->moltype[mtop->molblock[mb].type].excls;
1041 for (i = 0; (i < atoms->nr); i++)
1045 tpi = atoms->atom[i].type;
1049 tpi = atoms->atom[i].typeB;
1051 j1 = excl->index[i];
1052 j2 = excl->index[i+1];
1053 for (j = j1; j < j2; j++)
1060 tpj = atoms->atom[k].type;
1064 tpj = atoms->atom[k].typeB;
1068 /* nbfp now includes the 6.0 derivative prefactor */
1069 csix -= nmol*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
1073 /* nbfp now includes the 6.0/12.0 derivative prefactors */
1074 csix -= nmol*C6 (nbfp, ntp, tpi, tpj)/6.0;
1075 ctwelve -= nmol*C12(nbfp, ntp, tpi, tpj)/12.0;
1085 /* Only correct for the interaction of the test particle
1086 * with the rest of the system.
1089 &mtop->moltype[mtop->molblock[mtop->nmolblock-1].type].atoms;
1092 for (mb = 0; mb < mtop->nmolblock; mb++)
1094 nmol = mtop->molblock[mb].nmol;
1095 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
1096 for (j = 0; j < atoms->nr; j++)
1099 /* Remove the interaction of the test charge group
1102 if (mb == mtop->nmolblock-1)
1106 if (mb == 0 && nmol == 1)
1108 gmx_fatal(FARGS, "Old format tpr with TPI, please generate a new tpr file");
1113 tpj = atoms->atom[j].type;
1117 tpj = atoms->atom[j].typeB;
1119 for (i = 0; i < fr->n_tpi; i++)
1123 tpi = atoms_tpi->atom[i].type;
1127 tpi = atoms_tpi->atom[i].typeB;
1131 /* nbfp now includes the 6.0 derivative prefactor */
1132 csix += nmolc*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
1136 /* nbfp now includes the 6.0/12.0 derivative prefactors */
1137 csix += nmolc*C6 (nbfp, ntp, tpi, tpj)/6.0;
1138 ctwelve += nmolc*C12(nbfp, ntp, tpi, tpj)/12.0;
1145 if (npair - nexcl <= 0 && fplog)
1147 fprintf(fplog, "\nWARNING: There are no atom pairs for dispersion correction\n\n");
1153 csix /= npair - nexcl;
1154 ctwelve /= npair - nexcl;
1158 fprintf(debug, "Counted %d exclusions\n", nexcl);
1159 fprintf(debug, "Average C6 parameter is: %10g\n", (double)csix);
1160 fprintf(debug, "Average C12 parameter is: %10g\n", (double)ctwelve);
1162 fr->avcsix[q] = csix;
1163 fr->avctwelve[q] = ctwelve;
1166 if (EVDW_PME(fr->vdwtype))
1173 if (fr->eDispCorr == edispcAllEner ||
1174 fr->eDispCorr == edispcAllEnerPres)
1176 fprintf(fplog, "Long Range LJ corr.: <C6> %10.4e, <C12> %10.4e\n",
1177 fr->avcsix[0], fr->avctwelve[0]);
1181 fprintf(fplog, "Long Range LJ corr.: <C6> %10.4e\n", fr->avcsix[0]);
1187 static void set_bham_b_max(FILE *fplog, t_forcerec *fr,
1188 const gmx_mtop_t *mtop)
1190 const t_atoms *at1, *at2;
1191 int mt1, mt2, i, j, tpi, tpj, ntypes;
1197 fprintf(fplog, "Determining largest Buckingham b parameter for table\n");
1204 for (mt1 = 0; mt1 < mtop->nmoltype; mt1++)
1206 at1 = &mtop->moltype[mt1].atoms;
1207 for (i = 0; (i < at1->nr); i++)
1209 tpi = at1->atom[i].type;
1212 gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", i, tpi, ntypes);
1215 for (mt2 = mt1; mt2 < mtop->nmoltype; mt2++)
1217 at2 = &mtop->moltype[mt2].atoms;
1218 for (j = 0; (j < at2->nr); j++)
1220 tpj = at2->atom[j].type;
1223 gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", j, tpj, ntypes);
1225 b = BHAMB(nbfp, ntypes, tpi, tpj);
1226 if (b > fr->bham_b_max)
1230 if ((b < bmin) || (bmin == -1))
1240 fprintf(fplog, "Buckingham b parameters, min: %g, max: %g\n",
1241 bmin, fr->bham_b_max);
1245 static void make_nbf_tables(FILE *fp, const output_env_t oenv,
1246 t_forcerec *fr, real rtab,
1247 const t_commrec *cr,
1248 const char *tabfn, char *eg1, char *eg2,
1258 fprintf(debug, "No table file name passed, can not read table, can not do non-bonded interactions\n");
1263 sprintf(buf, "%s", tabfn);
1266 /* Append the two energy group names */
1267 sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "_%s_%s.%s",
1268 eg1, eg2, ftp2ext(efXVG));
1270 nbl->table_elec_vdw = make_tables(fp, oenv, fr, MASTER(cr), buf, rtab, 0);
1271 /* Copy the contents of the table to separate coulomb and LJ tables too,
1272 * to improve cache performance.
1274 /* For performance reasons we want
1275 * the table data to be aligned to 16-byte. The pointers could be freed
1276 * but currently aren't.
1278 nbl->table_elec.interaction = GMX_TABLE_INTERACTION_ELEC;
1279 nbl->table_elec.format = nbl->table_elec_vdw.format;
1280 nbl->table_elec.r = nbl->table_elec_vdw.r;
1281 nbl->table_elec.n = nbl->table_elec_vdw.n;
1282 nbl->table_elec.scale = nbl->table_elec_vdw.scale;
1283 nbl->table_elec.scale_exp = nbl->table_elec_vdw.scale_exp;
1284 nbl->table_elec.formatsize = nbl->table_elec_vdw.formatsize;
1285 nbl->table_elec.ninteractions = 1;
1286 nbl->table_elec.stride = nbl->table_elec.formatsize * nbl->table_elec.ninteractions;
1287 snew_aligned(nbl->table_elec.data, nbl->table_elec.stride*(nbl->table_elec.n+1), 32);
1289 nbl->table_vdw.interaction = GMX_TABLE_INTERACTION_VDWREP_VDWDISP;
1290 nbl->table_vdw.format = nbl->table_elec_vdw.format;
1291 nbl->table_vdw.r = nbl->table_elec_vdw.r;
1292 nbl->table_vdw.n = nbl->table_elec_vdw.n;
1293 nbl->table_vdw.scale = nbl->table_elec_vdw.scale;
1294 nbl->table_vdw.scale_exp = nbl->table_elec_vdw.scale_exp;
1295 nbl->table_vdw.formatsize = nbl->table_elec_vdw.formatsize;
1296 nbl->table_vdw.ninteractions = 2;
1297 nbl->table_vdw.stride = nbl->table_vdw.formatsize * nbl->table_vdw.ninteractions;
1298 snew_aligned(nbl->table_vdw.data, nbl->table_vdw.stride*(nbl->table_vdw.n+1), 32);
1300 for (i = 0; i <= nbl->table_elec_vdw.n; i++)
1302 for (j = 0; j < 4; j++)
1304 nbl->table_elec.data[4*i+j] = nbl->table_elec_vdw.data[12*i+j];
1306 for (j = 0; j < 8; j++)
1308 nbl->table_vdw.data[8*i+j] = nbl->table_elec_vdw.data[12*i+4+j];
1313 static void count_tables(int ftype1, int ftype2, const gmx_mtop_t *mtop,
1314 int *ncount, int **count)
1316 const gmx_moltype_t *molt;
1318 int mt, ftype, stride, i, j, tabnr;
1320 for (mt = 0; mt < mtop->nmoltype; mt++)
1322 molt = &mtop->moltype[mt];
1323 for (ftype = 0; ftype < F_NRE; ftype++)
1325 if (ftype == ftype1 || ftype == ftype2)
1327 il = &molt->ilist[ftype];
1328 stride = 1 + NRAL(ftype);
1329 for (i = 0; i < il->nr; i += stride)
1331 tabnr = mtop->ffparams.iparams[il->iatoms[i]].tab.table;
1334 gmx_fatal(FARGS, "A bonded table number is smaller than 0: %d\n", tabnr);
1336 if (tabnr >= *ncount)
1338 srenew(*count, tabnr+1);
1339 for (j = *ncount; j < tabnr+1; j++)
1352 static bondedtable_t *make_bonded_tables(FILE *fplog,
1353 int ftype1, int ftype2,
1354 const gmx_mtop_t *mtop,
1355 const char *basefn, const char *tabext)
1357 int i, ncount, *count;
1365 count_tables(ftype1, ftype2, mtop, &ncount, &count);
1370 for (i = 0; i < ncount; i++)
1374 sprintf(tabfn, "%s", basefn);
1375 sprintf(tabfn + strlen(basefn) - strlen(ftp2ext(efXVG)) - 1, "_%s%d.%s",
1376 tabext, i, ftp2ext(efXVG));
1377 tab[i] = make_bonded_table(fplog, tabfn, NRAL(ftype1)-2);
1386 void forcerec_set_ranges(t_forcerec *fr,
1387 int ncg_home, int ncg_force,
1389 int natoms_force_constr, int natoms_f_novirsum)
1394 /* fr->ncg_force is unused in the standard code,
1395 * but it can be useful for modified code dealing with charge groups.
1397 fr->ncg_force = ncg_force;
1398 fr->natoms_force = natoms_force;
1399 fr->natoms_force_constr = natoms_force_constr;
1401 if (fr->natoms_force_constr > fr->nalloc_force)
1403 fr->nalloc_force = over_alloc_dd(fr->natoms_force_constr);
1407 srenew(fr->f_twin, fr->nalloc_force);
1411 if (fr->bF_NoVirSum)
1413 fr->f_novirsum_n = natoms_f_novirsum;
1414 if (fr->f_novirsum_n > fr->f_novirsum_nalloc)
1416 fr->f_novirsum_nalloc = over_alloc_dd(fr->f_novirsum_n);
1417 srenew(fr->f_novirsum_alloc, fr->f_novirsum_nalloc);
1422 fr->f_novirsum_n = 0;
1426 static real cutoff_inf(real cutoff)
1430 cutoff = GMX_CUTOFF_INF;
1436 static void make_adress_tf_tables(FILE *fp, const output_env_t oenv,
1437 t_forcerec *fr, const t_inputrec *ir,
1438 const char *tabfn, const gmx_mtop_t *mtop,
1446 gmx_fatal(FARGS, "No thermoforce table file given. Use -tabletf to specify a file\n");
1450 snew(fr->atf_tabs, ir->adress->n_tf_grps);
1452 sprintf(buf, "%s", tabfn);
1453 for (i = 0; i < ir->adress->n_tf_grps; i++)
1455 j = ir->adress->tf_table_index[i]; /* get energy group index */
1456 sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "tf_%s.%s",
1457 *(mtop->groups.grpname[mtop->groups.grps[egcENER].nm_ind[j]]), ftp2ext(efXVG));
1460 fprintf(fp, "loading tf table for energygrp index %d from %s\n", ir->adress->tf_table_index[i], buf);
1462 fr->atf_tabs[i] = make_atf_table(fp, oenv, fr, buf, box);
1467 gmx_bool can_use_allvsall(const t_inputrec *ir, gmx_bool bPrintNote, t_commrec *cr, FILE *fp)
1474 ir->rcoulomb == 0 &&
1476 ir->ePBC == epbcNONE &&
1477 ir->vdwtype == evdwCUT &&
1478 ir->coulombtype == eelCUT &&
1479 ir->efep == efepNO &&
1480 (ir->implicit_solvent == eisNO ||
1481 (ir->implicit_solvent == eisGBSA && (ir->gb_algorithm == egbSTILL ||
1482 ir->gb_algorithm == egbHCT ||
1483 ir->gb_algorithm == egbOBC))) &&
1484 getenv("GMX_NO_ALLVSALL") == NULL
1487 if (bAllvsAll && ir->opts.ngener > 1)
1489 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";
1495 fprintf(stderr, "\n%s\n", note);
1499 fprintf(fp, "\n%s\n", note);
1505 if (bAllvsAll && fp && MASTER(cr))
1507 fprintf(fp, "\nUsing SIMD all-vs-all kernels.\n\n");
1514 static void init_forcerec_f_threads(t_forcerec *fr, int nenergrp)
1518 /* These thread local data structures are used for bondeds only */
1519 fr->nthreads = gmx_omp_nthreads_get(emntBonded);
1521 if (fr->nthreads > 1)
1523 snew(fr->f_t, fr->nthreads);
1524 /* Thread 0 uses the global force and energy arrays */
1525 for (t = 1; t < fr->nthreads; t++)
1527 fr->f_t[t].f = NULL;
1528 fr->f_t[t].f_nalloc = 0;
1529 snew(fr->f_t[t].fshift, SHIFTS);
1530 fr->f_t[t].grpp.nener = nenergrp*nenergrp;
1531 for (i = 0; i < egNR; i++)
1533 snew(fr->f_t[t].grpp.ener[i], fr->f_t[t].grpp.nener);
1540 gmx_bool nbnxn_acceleration_supported(FILE *fplog,
1541 const t_commrec *cr,
1542 const t_inputrec *ir,
1545 if (!bGPU && (ir->vdwtype == evdwPME && ir->ljpme_combination_rule == eljpmeLB))
1547 md_print_warn(cr, fplog, "LJ-PME with Lorentz-Berthelot is not supported with %s, falling back to %s\n",
1548 bGPU ? "GPUs" : "SIMD kernels",
1549 bGPU ? "CPU only" : "plain-C kernels");
1557 static void pick_nbnxn_kernel_cpu(const t_inputrec gmx_unused *ir,
1561 *kernel_type = nbnxnk4x4_PlainC;
1562 *ewald_excl = ewaldexclTable;
1564 #ifdef GMX_NBNXN_SIMD
1566 #ifdef GMX_NBNXN_SIMD_4XN
1567 *kernel_type = nbnxnk4xN_SIMD_4xN;
1569 #ifdef GMX_NBNXN_SIMD_2XNN
1570 *kernel_type = nbnxnk4xN_SIMD_2xNN;
1573 #if defined GMX_NBNXN_SIMD_2XNN && defined GMX_NBNXN_SIMD_4XN
1574 /* We need to choose if we want 2x(N+N) or 4xN kernels.
1575 * Currently this is based on the SIMD acceleration choice,
1576 * but it might be better to decide this at runtime based on CPU.
1578 * 4xN calculates more (zero) interactions, but has less pair-search
1579 * work and much better kernel instruction scheduling.
1581 * Up till now we have only seen that on Intel Sandy/Ivy Bridge,
1582 * which doesn't have FMA, both the analytical and tabulated Ewald
1583 * kernels have similar pair rates for 4x8 and 2x(4+4), so we choose
1584 * 2x(4+4) because it results in significantly fewer pairs.
1585 * For RF, the raw pair rate of the 4x8 kernel is higher than 2x(4+4),
1586 * 10% with HT, 50% without HT. As we currently don't detect the actual
1587 * use of HT, use 4x8 to avoid a potential performance hit.
1588 * On Intel Haswell 4x8 is always faster.
1590 *kernel_type = nbnxnk4xN_SIMD_4xN;
1592 #ifndef GMX_SIMD_HAVE_FMA
1593 if (EEL_PME_EWALD(ir->coulombtype) ||
1594 EVDW_PME(ir->vdwtype))
1596 /* We have Ewald kernels without FMA (Intel Sandy/Ivy Bridge).
1597 * There are enough instructions to make 2x(4+4) efficient.
1599 *kernel_type = nbnxnk4xN_SIMD_2xNN;
1602 #endif /* GMX_NBNXN_SIMD_2XNN && GMX_NBNXN_SIMD_4XN */
1605 if (getenv("GMX_NBNXN_SIMD_4XN") != NULL)
1607 #ifdef GMX_NBNXN_SIMD_4XN
1608 *kernel_type = nbnxnk4xN_SIMD_4xN;
1610 gmx_fatal(FARGS, "SIMD 4xN kernels requested, but Gromacs has been compiled without support for these kernels");
1613 if (getenv("GMX_NBNXN_SIMD_2XNN") != NULL)
1615 #ifdef GMX_NBNXN_SIMD_2XNN
1616 *kernel_type = nbnxnk4xN_SIMD_2xNN;
1618 gmx_fatal(FARGS, "SIMD 2x(N+N) kernels requested, but Gromacs has been compiled without support for these kernels");
1622 /* Analytical Ewald exclusion correction is only an option in
1624 * Since table lookup's don't parallelize with SIMD, analytical
1625 * will probably always be faster for a SIMD width of 8 or more.
1626 * With FMA analytical is sometimes faster for a width if 4 as well.
1627 * On BlueGene/Q, this is faster regardless of precision.
1628 * In single precision, this is faster on Bulldozer.
1630 #if GMX_SIMD_REAL_WIDTH >= 8 || \
1631 (GMX_SIMD_REAL_WIDTH >= 4 && defined GMX_SIMD_HAVE_FMA && !defined GMX_DOUBLE) || \
1632 defined GMX_SIMD_IBM_QPX
1633 *ewald_excl = ewaldexclAnalytical;
1635 if (getenv("GMX_NBNXN_EWALD_TABLE") != NULL)
1637 *ewald_excl = ewaldexclTable;
1639 if (getenv("GMX_NBNXN_EWALD_ANALYTICAL") != NULL)
1641 *ewald_excl = ewaldexclAnalytical;
1645 #endif /* GMX_NBNXN_SIMD */
1649 const char *lookup_nbnxn_kernel_name(int kernel_type)
1651 const char *returnvalue = NULL;
1652 switch (kernel_type)
1655 returnvalue = "not set";
1657 case nbnxnk4x4_PlainC:
1658 returnvalue = "plain C";
1660 case nbnxnk4xN_SIMD_4xN:
1661 case nbnxnk4xN_SIMD_2xNN:
1662 #ifdef GMX_NBNXN_SIMD
1663 #if defined GMX_SIMD_X86_SSE2
1664 returnvalue = "SSE2";
1665 #elif defined GMX_SIMD_X86_SSE4_1
1666 returnvalue = "SSE4.1";
1667 #elif defined GMX_SIMD_X86_AVX_128_FMA
1668 returnvalue = "AVX_128_FMA";
1669 #elif defined GMX_SIMD_X86_AVX_256
1670 returnvalue = "AVX_256";
1671 #elif defined GMX_SIMD_X86_AVX2_256
1672 returnvalue = "AVX2_256";
1674 returnvalue = "SIMD";
1676 #else /* GMX_NBNXN_SIMD */
1677 returnvalue = "not available";
1678 #endif /* GMX_NBNXN_SIMD */
1680 case nbnxnk8x8x8_CUDA: returnvalue = "CUDA"; break;
1681 case nbnxnk8x8x8_PlainC: returnvalue = "plain C"; break;
1685 gmx_fatal(FARGS, "Illegal kernel type selected");
1692 static void pick_nbnxn_kernel(FILE *fp,
1693 const t_commrec *cr,
1694 gmx_bool use_simd_kernels,
1696 gmx_bool bEmulateGPU,
1697 const t_inputrec *ir,
1700 gmx_bool bDoNonbonded)
1702 assert(kernel_type);
1704 *kernel_type = nbnxnkNotSet;
1705 *ewald_excl = ewaldexclTable;
1709 *kernel_type = nbnxnk8x8x8_PlainC;
1713 md_print_warn(cr, fp, "Emulating a GPU run on the CPU (slow)");
1718 *kernel_type = nbnxnk8x8x8_CUDA;
1721 if (*kernel_type == nbnxnkNotSet)
1723 /* LJ PME with LB combination rule does 7 mesh operations.
1724 * This so slow that we don't compile SIMD non-bonded kernels for that.
1726 if (use_simd_kernels &&
1727 nbnxn_acceleration_supported(fp, cr, ir, FALSE))
1729 pick_nbnxn_kernel_cpu(ir, kernel_type, ewald_excl);
1733 *kernel_type = nbnxnk4x4_PlainC;
1737 if (bDoNonbonded && fp != NULL)
1739 fprintf(fp, "\nUsing %s %dx%d non-bonded kernels\n\n",
1740 lookup_nbnxn_kernel_name(*kernel_type),
1741 nbnxn_kernel_pairlist_simple(*kernel_type) ? NBNXN_CPU_CLUSTER_I_SIZE : NBNXN_GPU_CLUSTER_SIZE,
1742 nbnxn_kernel_to_cj_size(*kernel_type));
1746 static void pick_nbnxn_resources(const t_commrec *cr,
1747 const gmx_hw_info_t *hwinfo,
1748 gmx_bool bDoNonbonded,
1750 gmx_bool *bEmulateGPU,
1751 const gmx_gpu_opt_t *gpu_opt)
1753 gmx_bool bEmulateGPUEnvVarSet;
1754 char gpu_err_str[STRLEN];
1758 bEmulateGPUEnvVarSet = (getenv("GMX_EMULATE_GPU") != NULL);
1760 /* Run GPU emulation mode if GMX_EMULATE_GPU is defined. Because
1761 * GPUs (currently) only handle non-bonded calculations, we will
1762 * automatically switch to emulation if non-bonded calculations are
1763 * turned off via GMX_NO_NONBONDED - this is the simple and elegant
1764 * way to turn off GPU initialization, data movement, and cleanup.
1766 * GPU emulation can be useful to assess the performance one can expect by
1767 * adding GPU(s) to the machine. The conditional below allows this even
1768 * if mdrun is compiled without GPU acceleration support.
1769 * Note that you should freezing the system as otherwise it will explode.
1771 *bEmulateGPU = (bEmulateGPUEnvVarSet ||
1773 gpu_opt->ncuda_dev_use > 0));
1775 /* Enable GPU mode when GPUs are available or no GPU emulation is requested.
1777 if (gpu_opt->ncuda_dev_use > 0 && !(*bEmulateGPU))
1779 /* Each PP node will use the intra-node id-th device from the
1780 * list of detected/selected GPUs. */
1781 if (!init_gpu(cr->rank_pp_intranode, gpu_err_str,
1782 &hwinfo->gpu_info, gpu_opt))
1784 /* At this point the init should never fail as we made sure that
1785 * we have all the GPUs we need. If it still does, we'll bail. */
1786 gmx_fatal(FARGS, "On node %d failed to initialize GPU #%d: %s",
1788 get_gpu_device_id(&hwinfo->gpu_info, gpu_opt,
1789 cr->rank_pp_intranode),
1793 /* Here we actually turn on hardware GPU acceleration */
1798 gmx_bool uses_simple_tables(int cutoff_scheme,
1799 nonbonded_verlet_t *nbv,
1802 gmx_bool bUsesSimpleTables = TRUE;
1805 switch (cutoff_scheme)
1808 bUsesSimpleTables = TRUE;
1811 assert(NULL != nbv && NULL != nbv->grp);
1812 grp_index = (group < 0) ? 0 : (nbv->ngrp - 1);
1813 bUsesSimpleTables = nbnxn_kernel_pairlist_simple(nbv->grp[grp_index].kernel_type);
1816 gmx_incons("unimplemented");
1818 return bUsesSimpleTables;
1821 static void init_ewald_f_table(interaction_const_t *ic,
1822 gmx_bool bUsesSimpleTables,
1827 if (bUsesSimpleTables)
1829 /* With a spacing of 0.0005 we are at the force summation accuracy
1830 * for the SSE kernels for "normal" atomistic simulations.
1832 ic->tabq_scale = ewald_spline3_table_scale(ic->ewaldcoeff_q,
1835 maxr = (rtab > ic->rcoulomb) ? rtab : ic->rcoulomb;
1836 ic->tabq_size = (int)(maxr*ic->tabq_scale) + 2;
1840 ic->tabq_size = GPU_EWALD_COULOMB_FORCE_TABLE_SIZE;
1841 /* Subtract 2 iso 1 to avoid access out of range due to rounding */
1842 ic->tabq_scale = (ic->tabq_size - 2)/ic->rcoulomb;
1845 sfree_aligned(ic->tabq_coul_FDV0);
1846 sfree_aligned(ic->tabq_coul_F);
1847 sfree_aligned(ic->tabq_coul_V);
1849 /* Create the original table data in FDV0 */
1850 snew_aligned(ic->tabq_coul_FDV0, ic->tabq_size*4, 32);
1851 snew_aligned(ic->tabq_coul_F, ic->tabq_size, 32);
1852 snew_aligned(ic->tabq_coul_V, ic->tabq_size, 32);
1853 table_spline3_fill_ewald_lr(ic->tabq_coul_F, ic->tabq_coul_V, ic->tabq_coul_FDV0,
1854 ic->tabq_size, 1/ic->tabq_scale, ic->ewaldcoeff_q);
1857 void init_interaction_const_tables(FILE *fp,
1858 interaction_const_t *ic,
1859 gmx_bool bUsesSimpleTables,
1864 if (ic->eeltype == eelEWALD || EEL_PME(ic->eeltype))
1866 init_ewald_f_table(ic, bUsesSimpleTables, rtab);
1870 fprintf(fp, "Initialized non-bonded Ewald correction tables, spacing: %.2e size: %d\n\n",
1871 1/ic->tabq_scale, ic->tabq_size);
1876 static void clear_force_switch_constants(shift_consts_t *sc)
1883 static void force_switch_constants(real p,
1887 /* Here we determine the coefficient for shifting the force to zero
1888 * between distance rsw and the cut-off rc.
1889 * For a potential of r^-p, we have force p*r^-(p+1).
1890 * But to save flops we absorb p in the coefficient.
1892 * force/p = r^-(p+1) + c2*r^2 + c3*r^3
1893 * potential = r^-p + c2/3*r^3 + c3/4*r^4 + cpot
1895 sc->c2 = ((p + 1)*rsw - (p + 4)*rc)/(pow(rc, p + 2)*pow(rc - rsw, 2));
1896 sc->c3 = -((p + 1)*rsw - (p + 3)*rc)/(pow(rc, p + 2)*pow(rc - rsw, 3));
1897 sc->cpot = -pow(rc, -p) + p*sc->c2/3*pow(rc - rsw, 3) + p*sc->c3/4*pow(rc - rsw, 4);
1900 static void potential_switch_constants(real rsw, real rc,
1901 switch_consts_t *sc)
1903 /* The switch function is 1 at rsw and 0 at rc.
1904 * The derivative and second derivate are zero at both ends.
1905 * rsw = max(r - r_switch, 0)
1906 * sw = 1 + c3*rsw^3 + c4*rsw^4 + c5*rsw^5
1907 * dsw = 3*c3*rsw^2 + 4*c4*rsw^3 + 5*c5*rsw^4
1908 * force = force*dsw - potential*sw
1911 sc->c3 = -10*pow(rc - rsw, -3);
1912 sc->c4 = 15*pow(rc - rsw, -4);
1913 sc->c5 = -6*pow(rc - rsw, -5);
1917 init_interaction_const(FILE *fp,
1918 const t_commrec gmx_unused *cr,
1919 interaction_const_t **interaction_const,
1920 const t_forcerec *fr,
1923 interaction_const_t *ic;
1924 gmx_bool bUsesSimpleTables = TRUE;
1928 /* Just allocate something so we can free it */
1929 snew_aligned(ic->tabq_coul_FDV0, 16, 32);
1930 snew_aligned(ic->tabq_coul_F, 16, 32);
1931 snew_aligned(ic->tabq_coul_V, 16, 32);
1933 ic->rlist = fr->rlist;
1934 ic->rlistlong = fr->rlistlong;
1937 ic->vdwtype = fr->vdwtype;
1938 ic->vdw_modifier = fr->vdw_modifier;
1939 ic->rvdw = fr->rvdw;
1940 ic->rvdw_switch = fr->rvdw_switch;
1941 ic->ewaldcoeff_lj = fr->ewaldcoeff_lj;
1942 ic->ljpme_comb_rule = fr->ljpme_combination_rule;
1943 ic->sh_lj_ewald = 0;
1944 clear_force_switch_constants(&ic->dispersion_shift);
1945 clear_force_switch_constants(&ic->repulsion_shift);
1947 switch (ic->vdw_modifier)
1949 case eintmodPOTSHIFT:
1950 /* Only shift the potential, don't touch the force */
1951 ic->dispersion_shift.cpot = -pow(ic->rvdw, -6.0);
1952 ic->repulsion_shift.cpot = -pow(ic->rvdw, -12.0);
1953 if (EVDW_PME(ic->vdwtype))
1957 if (fr->cutoff_scheme == ecutsGROUP)
1959 gmx_fatal(FARGS, "Potential-shift is not (yet) implemented for LJ-PME with cutoff-scheme=group");
1961 crc2 = sqr(ic->ewaldcoeff_lj*ic->rvdw);
1962 ic->sh_lj_ewald = (exp(-crc2)*(1 + crc2 + 0.5*crc2*crc2) - 1)*pow(ic->rvdw, -6.0);
1965 case eintmodFORCESWITCH:
1966 /* Switch the force, switch and shift the potential */
1967 force_switch_constants(6.0, ic->rvdw_switch, ic->rvdw,
1968 &ic->dispersion_shift);
1969 force_switch_constants(12.0, ic->rvdw_switch, ic->rvdw,
1970 &ic->repulsion_shift);
1972 case eintmodPOTSWITCH:
1973 /* Switch the potential and force */
1974 potential_switch_constants(ic->rvdw_switch, ic->rvdw,
1978 case eintmodEXACTCUTOFF:
1979 /* Nothing to do here */
1982 gmx_incons("unimplemented potential modifier");
1985 ic->sh_invrc6 = -ic->dispersion_shift.cpot;
1987 /* Electrostatics */
1988 ic->eeltype = fr->eeltype;
1989 ic->coulomb_modifier = fr->coulomb_modifier;
1990 ic->rcoulomb = fr->rcoulomb;
1991 ic->epsilon_r = fr->epsilon_r;
1992 ic->epsfac = fr->epsfac;
1993 ic->ewaldcoeff_q = fr->ewaldcoeff_q;
1995 if (fr->coulomb_modifier == eintmodPOTSHIFT)
1997 ic->sh_ewald = gmx_erfc(ic->ewaldcoeff_q*ic->rcoulomb);
2004 /* Reaction-field */
2005 if (EEL_RF(ic->eeltype))
2007 ic->epsilon_rf = fr->epsilon_rf;
2008 ic->k_rf = fr->k_rf;
2009 ic->c_rf = fr->c_rf;
2013 /* For plain cut-off we might use the reaction-field kernels */
2014 ic->epsilon_rf = ic->epsilon_r;
2016 if (fr->coulomb_modifier == eintmodPOTSHIFT)
2018 ic->c_rf = 1/ic->rcoulomb;
2028 real dispersion_shift;
2030 dispersion_shift = ic->dispersion_shift.cpot;
2031 if (EVDW_PME(ic->vdwtype))
2033 dispersion_shift -= ic->sh_lj_ewald;
2035 fprintf(fp, "Potential shift: LJ r^-12: %.3e r^-6: %.3e",
2036 ic->repulsion_shift.cpot, dispersion_shift);
2038 if (ic->eeltype == eelCUT)
2040 fprintf(fp, ", Coulomb %.e", -ic->c_rf);
2042 else if (EEL_PME(ic->eeltype))
2044 fprintf(fp, ", Ewald %.3e", -ic->sh_ewald);
2049 *interaction_const = ic;
2051 if (fr->nbv != NULL && fr->nbv->bUseGPU)
2053 nbnxn_cuda_init_const(fr->nbv->cu_nbv, ic, fr->nbv->grp);
2055 /* With tMPI + GPUs some ranks may be sharing GPU(s) and therefore
2056 * also sharing texture references. To keep the code simple, we don't
2057 * treat texture references as shared resources, but this means that
2058 * the coulomb_tab and nbfp texture refs will get updated by multiple threads.
2059 * Hence, to ensure that the non-bonded kernels don't start before all
2060 * texture binding operations are finished, we need to wait for all ranks
2061 * to arrive here before continuing.
2063 * Note that we could omit this barrier if GPUs are not shared (or
2064 * texture objects are used), but as this is initialization code, there
2065 * is not point in complicating things.
2067 #ifdef GMX_THREAD_MPI
2072 #endif /* GMX_THREAD_MPI */
2075 bUsesSimpleTables = uses_simple_tables(fr->cutoff_scheme, fr->nbv, -1);
2076 init_interaction_const_tables(fp, ic, bUsesSimpleTables, rtab);
2079 static void init_nb_verlet(FILE *fp,
2080 nonbonded_verlet_t **nb_verlet,
2081 gmx_bool bFEP_NonBonded,
2082 const t_inputrec *ir,
2083 const t_forcerec *fr,
2084 const t_commrec *cr,
2085 const char *nbpu_opt)
2087 nonbonded_verlet_t *nbv;
2090 gmx_bool bEmulateGPU, bHybridGPURun = FALSE;
2092 nbnxn_alloc_t *nb_alloc;
2093 nbnxn_free_t *nb_free;
2097 pick_nbnxn_resources(cr, fr->hwinfo,
2105 nbv->ngrp = (DOMAINDECOMP(cr) ? 2 : 1);
2106 for (i = 0; i < nbv->ngrp; i++)
2108 nbv->grp[i].nbl_lists.nnbl = 0;
2109 nbv->grp[i].nbat = NULL;
2110 nbv->grp[i].kernel_type = nbnxnkNotSet;
2112 if (i == 0) /* local */
2114 pick_nbnxn_kernel(fp, cr, fr->use_simd_kernels,
2115 nbv->bUseGPU, bEmulateGPU, ir,
2116 &nbv->grp[i].kernel_type,
2117 &nbv->grp[i].ewald_excl,
2120 else /* non-local */
2122 if (nbpu_opt != NULL && strcmp(nbpu_opt, "gpu_cpu") == 0)
2124 /* Use GPU for local, select a CPU kernel for non-local */
2125 pick_nbnxn_kernel(fp, cr, fr->use_simd_kernels,
2127 &nbv->grp[i].kernel_type,
2128 &nbv->grp[i].ewald_excl,
2131 bHybridGPURun = TRUE;
2135 /* Use the same kernel for local and non-local interactions */
2136 nbv->grp[i].kernel_type = nbv->grp[0].kernel_type;
2137 nbv->grp[i].ewald_excl = nbv->grp[0].ewald_excl;
2144 /* init the NxN GPU data; the last argument tells whether we'll have
2145 * both local and non-local NB calculation on GPU */
2146 nbnxn_cuda_init(fp, &nbv->cu_nbv,
2147 &fr->hwinfo->gpu_info, fr->gpu_opt,
2148 cr->rank_pp_intranode,
2149 (nbv->ngrp > 1) && !bHybridGPURun);
2151 if ((env = getenv("GMX_NB_MIN_CI")) != NULL)
2155 nbv->min_ci_balanced = strtol(env, &end, 10);
2156 if (!end || (*end != 0) || nbv->min_ci_balanced <= 0)
2158 gmx_fatal(FARGS, "Invalid value passed in GMX_NB_MIN_CI=%s, positive integer required", env);
2163 fprintf(debug, "Neighbor-list balancing parameter: %d (passed as env. var.)\n",
2164 nbv->min_ci_balanced);
2169 nbv->min_ci_balanced = nbnxn_cuda_min_ci_balanced(nbv->cu_nbv);
2172 fprintf(debug, "Neighbor-list balancing parameter: %d (auto-adjusted to the number of GPU multi-processors)\n",
2173 nbv->min_ci_balanced);
2179 nbv->min_ci_balanced = 0;
2184 nbnxn_init_search(&nbv->nbs,
2185 DOMAINDECOMP(cr) ? &cr->dd->nc : NULL,
2186 DOMAINDECOMP(cr) ? domdec_zones(cr->dd) : NULL,
2188 gmx_omp_nthreads_get(emntNonbonded));
2190 for (i = 0; i < nbv->ngrp; i++)
2192 if (nbv->grp[0].kernel_type == nbnxnk8x8x8_CUDA)
2194 nb_alloc = &pmalloc;
2203 nbnxn_init_pairlist_set(&nbv->grp[i].nbl_lists,
2204 nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type),
2205 /* 8x8x8 "non-simple" lists are ATM always combined */
2206 !nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type),
2210 nbv->grp[0].kernel_type != nbv->grp[i].kernel_type)
2212 gmx_bool bSimpleList;
2213 int enbnxninitcombrule;
2215 bSimpleList = nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type);
2217 if (bSimpleList && (fr->vdwtype == evdwCUT && (fr->vdw_modifier == eintmodNONE || fr->vdw_modifier == eintmodPOTSHIFT)))
2219 /* Plain LJ cut-off: we can optimize with combination rules */
2220 enbnxninitcombrule = enbnxninitcombruleDETECT;
2222 else if (fr->vdwtype == evdwPME)
2224 /* LJ-PME: we need to use a combination rule for the grid */
2225 if (fr->ljpme_combination_rule == eljpmeGEOM)
2227 enbnxninitcombrule = enbnxninitcombruleGEOM;
2231 enbnxninitcombrule = enbnxninitcombruleLB;
2236 /* We use a full combination matrix: no rule required */
2237 enbnxninitcombrule = enbnxninitcombruleNONE;
2241 snew(nbv->grp[i].nbat, 1);
2242 nbnxn_atomdata_init(fp,
2244 nbv->grp[i].kernel_type,
2246 fr->ntype, fr->nbfp,
2248 bSimpleList ? gmx_omp_nthreads_get(emntNonbonded) : 1,
2253 nbv->grp[i].nbat = nbv->grp[0].nbat;
2258 void init_forcerec(FILE *fp,
2259 const output_env_t oenv,
2262 const t_inputrec *ir,
2263 const gmx_mtop_t *mtop,
2264 const t_commrec *cr,
2270 const char *nbpu_opt,
2271 gmx_bool bNoSolvOpt,
2274 int i, j, m, natoms, ngrp, negp_pp, negptable, egi, egj;
2279 gmx_bool bGenericKernelOnly;
2280 gmx_bool bMakeTables, bMakeSeparate14Table, bSomeNormalNbListsAreInUse;
2281 gmx_bool bFEP_NonBonded;
2283 int *nm_ind, egp_flags;
2285 if (fr->hwinfo == NULL)
2287 /* Detect hardware, gather information.
2288 * In mdrun, hwinfo has already been set before calling init_forcerec.
2289 * Here we ignore GPUs, as tools will not use them anyhow.
2291 fr->hwinfo = gmx_detect_hardware(fp, cr, FALSE);
2294 /* By default we turn SIMD kernels on, but it might be turned off further down... */
2295 fr->use_simd_kernels = TRUE;
2297 fr->bDomDec = DOMAINDECOMP(cr);
2299 natoms = mtop->natoms;
2301 if (check_box(ir->ePBC, box))
2303 gmx_fatal(FARGS, check_box(ir->ePBC, box));
2306 /* Test particle insertion ? */
2309 /* Set to the size of the molecule to be inserted (the last one) */
2310 /* Because of old style topologies, we have to use the last cg
2311 * instead of the last molecule type.
2313 cgs = &mtop->moltype[mtop->molblock[mtop->nmolblock-1].type].cgs;
2314 fr->n_tpi = cgs->index[cgs->nr] - cgs->index[cgs->nr-1];
2315 if (fr->n_tpi != mtop->mols.index[mtop->mols.nr] - mtop->mols.index[mtop->mols.nr-1])
2317 gmx_fatal(FARGS, "The molecule to insert can not consist of multiple charge groups.\nMake it a single charge group.");
2325 /* Copy AdResS parameters */
2328 fr->adress_type = ir->adress->type;
2329 fr->adress_const_wf = ir->adress->const_wf;
2330 fr->adress_ex_width = ir->adress->ex_width;
2331 fr->adress_hy_width = ir->adress->hy_width;
2332 fr->adress_icor = ir->adress->icor;
2333 fr->adress_site = ir->adress->site;
2334 fr->adress_ex_forcecap = ir->adress->ex_forcecap;
2335 fr->adress_do_hybridpairs = ir->adress->do_hybridpairs;
2338 snew(fr->adress_group_explicit, ir->adress->n_energy_grps);
2339 for (i = 0; i < ir->adress->n_energy_grps; i++)
2341 fr->adress_group_explicit[i] = ir->adress->group_explicit[i];
2344 fr->n_adress_tf_grps = ir->adress->n_tf_grps;
2345 snew(fr->adress_tf_table_index, fr->n_adress_tf_grps);
2346 for (i = 0; i < fr->n_adress_tf_grps; i++)
2348 fr->adress_tf_table_index[i] = ir->adress->tf_table_index[i];
2350 copy_rvec(ir->adress->refs, fr->adress_refs);
2354 fr->adress_type = eAdressOff;
2355 fr->adress_do_hybridpairs = FALSE;
2358 /* Copy the user determined parameters */
2359 fr->userint1 = ir->userint1;
2360 fr->userint2 = ir->userint2;
2361 fr->userint3 = ir->userint3;
2362 fr->userint4 = ir->userint4;
2363 fr->userreal1 = ir->userreal1;
2364 fr->userreal2 = ir->userreal2;
2365 fr->userreal3 = ir->userreal3;
2366 fr->userreal4 = ir->userreal4;
2369 fr->fc_stepsize = ir->fc_stepsize;
2372 fr->efep = ir->efep;
2373 fr->sc_alphavdw = ir->fepvals->sc_alpha;
2374 if (ir->fepvals->bScCoul)
2376 fr->sc_alphacoul = ir->fepvals->sc_alpha;
2377 fr->sc_sigma6_min = pow(ir->fepvals->sc_sigma_min, 6);
2381 fr->sc_alphacoul = 0;
2382 fr->sc_sigma6_min = 0; /* only needed when bScCoul is on */
2384 fr->sc_power = ir->fepvals->sc_power;
2385 fr->sc_r_power = ir->fepvals->sc_r_power;
2386 fr->sc_sigma6_def = pow(ir->fepvals->sc_sigma, 6);
2388 env = getenv("GMX_SCSIGMA_MIN");
2392 sscanf(env, "%lf", &dbl);
2393 fr->sc_sigma6_min = pow(dbl, 6);
2396 fprintf(fp, "Setting the minimum soft core sigma to %g nm\n", dbl);
2400 fr->bNonbonded = TRUE;
2401 if (getenv("GMX_NO_NONBONDED") != NULL)
2403 /* turn off non-bonded calculations */
2404 fr->bNonbonded = FALSE;
2405 md_print_warn(cr, fp,
2406 "Found environment variable GMX_NO_NONBONDED.\n"
2407 "Disabling nonbonded calculations.\n");
2410 bGenericKernelOnly = FALSE;
2412 /* We now check in the NS code whether a particular combination of interactions
2413 * can be used with water optimization, and disable it if that is not the case.
2416 if (getenv("GMX_NB_GENERIC") != NULL)
2421 "Found environment variable GMX_NB_GENERIC.\n"
2422 "Disabling all interaction-specific nonbonded kernels, will only\n"
2423 "use the slow generic ones in src/gmxlib/nonbonded/nb_generic.c\n\n");
2425 bGenericKernelOnly = TRUE;
2428 if (bGenericKernelOnly == TRUE)
2433 if ( (getenv("GMX_DISABLE_SIMD_KERNELS") != NULL) || (getenv("GMX_NOOPTIMIZEDKERNELS") != NULL) )
2435 fr->use_simd_kernels = FALSE;
2439 "\nFound environment variable GMX_DISABLE_SIMD_KERNELS.\n"
2440 "Disabling the usage of any SIMD-specific kernel routines (e.g. SSE2/SSE4.1/AVX).\n\n");
2444 fr->bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
2446 /* Check if we can/should do all-vs-all kernels */
2447 fr->bAllvsAll = can_use_allvsall(ir, FALSE, NULL, NULL);
2448 fr->AllvsAll_work = NULL;
2449 fr->AllvsAll_workgb = NULL;
2451 /* All-vs-all kernels have not been implemented in 4.6, and
2452 * the SIMD group kernels are also buggy in this case. Non-SIMD
2453 * group kernels are OK. See Redmine #1249. */
2456 fr->bAllvsAll = FALSE;
2457 fr->use_simd_kernels = FALSE;
2461 "\nYour simulation settings would have triggered the efficient all-vs-all\n"
2462 "kernels in GROMACS 4.5, but these have not been implemented in GROMACS\n"
2463 "4.6. Also, we can't use the accelerated SIMD kernels here because\n"
2464 "of an unfixed bug. The reference C kernels are correct, though, so\n"
2465 "we are proceeding by disabling all CPU architecture-specific\n"
2466 "(e.g. SSE2/SSE4/AVX) routines. If performance is important, please\n"
2467 "use GROMACS 4.5.7 or try cutoff-scheme = Verlet.\n\n");
2471 /* Neighbour searching stuff */
2472 fr->cutoff_scheme = ir->cutoff_scheme;
2473 fr->bGrid = (ir->ns_type == ensGRID);
2474 fr->ePBC = ir->ePBC;
2476 if (fr->cutoff_scheme == ecutsGROUP)
2478 const char *note = "NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be\n"
2479 "removed in a future release when 'verlet' supports all interaction forms.\n";
2483 fprintf(stderr, "\n%s\n", note);
2487 fprintf(fp, "\n%s\n", note);
2491 /* Determine if we will do PBC for distances in bonded interactions */
2492 if (fr->ePBC == epbcNONE)
2494 fr->bMolPBC = FALSE;
2498 if (!DOMAINDECOMP(cr))
2500 /* The group cut-off scheme and SHAKE assume charge groups
2501 * are whole, but not using molpbc is faster in most cases.
2503 if (fr->cutoff_scheme == ecutsGROUP ||
2504 (ir->eConstrAlg == econtSHAKE &&
2505 (gmx_mtop_ftype_count(mtop, F_CONSTR) > 0 ||
2506 gmx_mtop_ftype_count(mtop, F_CONSTRNC) > 0)))
2508 fr->bMolPBC = ir->bPeriodicMols;
2513 if (getenv("GMX_USE_GRAPH") != NULL)
2515 fr->bMolPBC = FALSE;
2518 fprintf(fp, "\nGMX_MOLPBC is set, using the graph for bonded interactions\n\n");
2525 fr->bMolPBC = dd_bonded_molpbc(cr->dd, fr->ePBC);
2528 fr->bGB = (ir->implicit_solvent == eisGBSA);
2530 fr->rc_scaling = ir->refcoord_scaling;
2531 copy_rvec(ir->posres_com, fr->posres_com);
2532 copy_rvec(ir->posres_comB, fr->posres_comB);
2533 fr->rlist = cutoff_inf(ir->rlist);
2534 fr->rlistlong = cutoff_inf(ir->rlistlong);
2535 fr->eeltype = ir->coulombtype;
2536 fr->vdwtype = ir->vdwtype;
2537 fr->ljpme_combination_rule = ir->ljpme_combination_rule;
2539 fr->coulomb_modifier = ir->coulomb_modifier;
2540 fr->vdw_modifier = ir->vdw_modifier;
2542 /* Electrostatics: Translate from interaction-setting-in-mdp-file to kernel interaction format */
2543 switch (fr->eeltype)
2546 fr->nbkernel_elec_interaction = (fr->bGB) ? GMX_NBKERNEL_ELEC_GENERALIZEDBORN : GMX_NBKERNEL_ELEC_COULOMB;
2552 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD;
2556 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD;
2557 fr->coulomb_modifier = eintmodEXACTCUTOFF;
2566 case eelPMEUSERSWITCH:
2567 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_CUBICSPLINETABLE;
2572 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_EWALD;
2576 gmx_fatal(FARGS, "Unsupported electrostatic interaction: %s", eel_names[fr->eeltype]);
2580 /* Vdw: Translate from mdp settings to kernel format */
2581 switch (fr->vdwtype)
2587 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_BUCKINGHAM;
2591 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_LENNARDJONES;
2598 case evdwENCADSHIFT:
2599 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
2603 gmx_fatal(FARGS, "Unsupported vdw interaction: %s", evdw_names[fr->vdwtype]);
2607 /* These start out identical to ir, but might be altered if we e.g. tabulate the interaction in the kernel */
2608 fr->nbkernel_elec_modifier = fr->coulomb_modifier;
2609 fr->nbkernel_vdw_modifier = fr->vdw_modifier;
2611 fr->bTwinRange = fr->rlistlong > fr->rlist;
2612 fr->bEwald = (EEL_PME(fr->eeltype) || fr->eeltype == eelEWALD);
2614 fr->reppow = mtop->ffparams.reppow;
2616 if (ir->cutoff_scheme == ecutsGROUP)
2618 fr->bvdwtab = (fr->vdwtype != evdwCUT ||
2619 !gmx_within_tol(fr->reppow, 12.0, 10*GMX_DOUBLE_EPS));
2620 /* We have special kernels for standard Ewald and PME, but the pme-switch ones are tabulated above */
2621 fr->bcoultab = !(fr->eeltype == eelCUT ||
2622 fr->eeltype == eelEWALD ||
2623 fr->eeltype == eelPME ||
2624 fr->eeltype == eelRF ||
2625 fr->eeltype == eelRF_ZERO);
2627 /* If the user absolutely wants different switch/shift settings for coul/vdw, it is likely
2628 * going to be faster to tabulate the interaction than calling the generic kernel.
2630 if (fr->nbkernel_elec_modifier == eintmodPOTSWITCH && fr->nbkernel_vdw_modifier == eintmodPOTSWITCH)
2632 if ((fr->rcoulomb_switch != fr->rvdw_switch) || (fr->rcoulomb != fr->rvdw))
2634 fr->bcoultab = TRUE;
2637 else if ((fr->nbkernel_elec_modifier == eintmodPOTSHIFT && fr->nbkernel_vdw_modifier == eintmodPOTSHIFT) ||
2638 ((fr->nbkernel_elec_interaction == GMX_NBKERNEL_ELEC_REACTIONFIELD &&
2639 fr->nbkernel_elec_modifier == eintmodEXACTCUTOFF &&
2640 (fr->nbkernel_vdw_modifier == eintmodPOTSWITCH || fr->nbkernel_vdw_modifier == eintmodPOTSHIFT))))
2642 if (fr->rcoulomb != fr->rvdw)
2644 fr->bcoultab = TRUE;
2648 if (getenv("GMX_REQUIRE_TABLES"))
2651 fr->bcoultab = TRUE;
2656 fprintf(fp, "Table routines are used for coulomb: %s\n", bool_names[fr->bcoultab]);
2657 fprintf(fp, "Table routines are used for vdw: %s\n", bool_names[fr->bvdwtab ]);
2660 if (fr->bvdwtab == TRUE)
2662 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
2663 fr->nbkernel_vdw_modifier = eintmodNONE;
2665 if (fr->bcoultab == TRUE)
2667 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_CUBICSPLINETABLE;
2668 fr->nbkernel_elec_modifier = eintmodNONE;
2672 if (ir->cutoff_scheme == ecutsVERLET)
2674 if (!gmx_within_tol(fr->reppow, 12.0, 10*GMX_DOUBLE_EPS))
2676 gmx_fatal(FARGS, "Cut-off scheme %S only supports LJ repulsion power 12", ecutscheme_names[ir->cutoff_scheme]);
2678 fr->bvdwtab = FALSE;
2679 fr->bcoultab = FALSE;
2682 /* Tables are used for direct ewald sum */
2685 if (EEL_PME(ir->coulombtype))
2689 fprintf(fp, "Will do PME sum in reciprocal space for electrostatic interactions.\n");
2691 if (ir->coulombtype == eelP3M_AD)
2693 please_cite(fp, "Hockney1988");
2694 please_cite(fp, "Ballenegger2012");
2698 please_cite(fp, "Essmann95a");
2701 if (ir->ewald_geometry == eewg3DC)
2705 fprintf(fp, "Using the Ewald3DC correction for systems with a slab geometry.\n");
2707 please_cite(fp, "In-Chul99a");
2710 fr->ewaldcoeff_q = calc_ewaldcoeff_q(ir->rcoulomb, ir->ewald_rtol);
2711 init_ewald_tab(&(fr->ewald_table), ir, fp);
2714 fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for Ewald\n",
2715 1/fr->ewaldcoeff_q);
2719 if (EVDW_PME(ir->vdwtype))
2723 fprintf(fp, "Will do PME sum in reciprocal space for LJ dispersion interactions.\n");
2725 please_cite(fp, "Essmann95a");
2726 fr->ewaldcoeff_lj = calc_ewaldcoeff_lj(ir->rvdw, ir->ewald_rtol_lj);
2729 fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for LJ Ewald\n",
2730 1/fr->ewaldcoeff_lj);
2734 /* Electrostatics */
2735 fr->epsilon_r = ir->epsilon_r;
2736 fr->epsilon_rf = ir->epsilon_rf;
2737 fr->fudgeQQ = mtop->ffparams.fudgeQQ;
2738 fr->rcoulomb_switch = ir->rcoulomb_switch;
2739 fr->rcoulomb = cutoff_inf(ir->rcoulomb);
2741 /* Parameters for generalized RF */
2745 if (fr->eeltype == eelGRF)
2747 init_generalized_rf(fp, mtop, ir, fr);
2750 fr->bF_NoVirSum = (EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype) ||
2751 gmx_mtop_ftype_count(mtop, F_POSRES) > 0 ||
2752 gmx_mtop_ftype_count(mtop, F_FBPOSRES) > 0 ||
2753 IR_ELEC_FIELD(*ir) ||
2754 (fr->adress_icor != eAdressICOff)
2757 if (fr->cutoff_scheme == ecutsGROUP &&
2758 ncg_mtop(mtop) > fr->cg_nalloc && !DOMAINDECOMP(cr))
2760 /* Count the total number of charge groups */
2761 fr->cg_nalloc = ncg_mtop(mtop);
2762 srenew(fr->cg_cm, fr->cg_nalloc);
2764 if (fr->shift_vec == NULL)
2766 snew(fr->shift_vec, SHIFTS);
2769 if (fr->fshift == NULL)
2771 snew(fr->fshift, SHIFTS);
2774 if (fr->nbfp == NULL)
2776 fr->ntype = mtop->ffparams.atnr;
2777 fr->nbfp = mk_nbfp(&mtop->ffparams, fr->bBHAM);
2780 /* Copy the energy group exclusions */
2781 fr->egp_flags = ir->opts.egp_flags;
2783 /* Van der Waals stuff */
2784 fr->rvdw = cutoff_inf(ir->rvdw);
2785 fr->rvdw_switch = ir->rvdw_switch;
2786 if ((fr->vdwtype != evdwCUT) && (fr->vdwtype != evdwUSER) && !fr->bBHAM)
2788 if (fr->rvdw_switch >= fr->rvdw)
2790 gmx_fatal(FARGS, "rvdw_switch (%f) must be < rvdw (%f)",
2791 fr->rvdw_switch, fr->rvdw);
2795 fprintf(fp, "Using %s Lennard-Jones, switch between %g and %g nm\n",
2796 (fr->eeltype == eelSWITCH) ? "switched" : "shifted",
2797 fr->rvdw_switch, fr->rvdw);
2801 if (fr->bBHAM && EVDW_PME(fr->vdwtype))
2803 gmx_fatal(FARGS, "LJ PME not supported with Buckingham");
2806 if (fr->bBHAM && (fr->vdwtype == evdwSHIFT || fr->vdwtype == evdwSWITCH))
2808 gmx_fatal(FARGS, "Switch/shift interaction not supported with Buckingham");
2813 fprintf(fp, "Cut-off's: NS: %g Coulomb: %g %s: %g\n",
2814 fr->rlist, fr->rcoulomb, fr->bBHAM ? "BHAM" : "LJ", fr->rvdw);
2817 fr->eDispCorr = ir->eDispCorr;
2818 if (ir->eDispCorr != edispcNO)
2820 set_avcsixtwelve(fp, fr, mtop);
2825 set_bham_b_max(fp, fr, mtop);
2828 fr->gb_epsilon_solvent = ir->gb_epsilon_solvent;
2830 /* Copy the GBSA data (radius, volume and surftens for each
2831 * atomtype) from the topology atomtype section to forcerec.
2833 snew(fr->atype_radius, fr->ntype);
2834 snew(fr->atype_vol, fr->ntype);
2835 snew(fr->atype_surftens, fr->ntype);
2836 snew(fr->atype_gb_radius, fr->ntype);
2837 snew(fr->atype_S_hct, fr->ntype);
2839 if (mtop->atomtypes.nr > 0)
2841 for (i = 0; i < fr->ntype; i++)
2843 fr->atype_radius[i] = mtop->atomtypes.radius[i];
2845 for (i = 0; i < fr->ntype; i++)
2847 fr->atype_vol[i] = mtop->atomtypes.vol[i];
2849 for (i = 0; i < fr->ntype; i++)
2851 fr->atype_surftens[i] = mtop->atomtypes.surftens[i];
2853 for (i = 0; i < fr->ntype; i++)
2855 fr->atype_gb_radius[i] = mtop->atomtypes.gb_radius[i];
2857 for (i = 0; i < fr->ntype; i++)
2859 fr->atype_S_hct[i] = mtop->atomtypes.S_hct[i];
2863 /* Generate the GB table if needed */
2867 fr->gbtabscale = 2000;
2869 fr->gbtabscale = 500;
2873 fr->gbtab = make_gb_table(oenv, fr);
2875 init_gb(&fr->born, fr, ir, mtop, ir->gb_algorithm);
2877 /* Copy local gb data (for dd, this is done in dd_partition_system) */
2878 if (!DOMAINDECOMP(cr))
2880 make_local_gb(cr, fr->born, ir->gb_algorithm);
2884 /* Set the charge scaling */
2885 if (fr->epsilon_r != 0)
2887 fr->epsfac = ONE_4PI_EPS0/fr->epsilon_r;
2891 /* eps = 0 is infinite dieletric: no coulomb interactions */
2895 /* Reaction field constants */
2896 if (EEL_RF(fr->eeltype))
2898 calc_rffac(fp, fr->eeltype, fr->epsilon_r, fr->epsilon_rf,
2899 fr->rcoulomb, fr->temp, fr->zsquare, box,
2900 &fr->kappa, &fr->k_rf, &fr->c_rf);
2903 /*This now calculates sum for q and c6*/
2904 set_chargesum(fp, fr, mtop);
2906 /* if we are using LR electrostatics, and they are tabulated,
2907 * the tables will contain modified coulomb interactions.
2908 * Since we want to use the non-shifted ones for 1-4
2909 * coulombic interactions, we must have an extra set of tables.
2912 /* Construct tables.
2913 * A little unnecessary to make both vdw and coul tables sometimes,
2914 * but what the heck... */
2916 bMakeTables = fr->bcoultab || fr->bvdwtab || fr->bEwald ||
2917 (ir->eDispCorr != edispcNO && ir_vdw_switched(ir));
2919 bMakeSeparate14Table = ((!bMakeTables || fr->eeltype != eelCUT || fr->vdwtype != evdwCUT ||
2920 fr->bBHAM || fr->bEwald) &&
2921 (gmx_mtop_ftype_count(mtop, F_LJ14) > 0 ||
2922 gmx_mtop_ftype_count(mtop, F_LJC14_Q) > 0 ||
2923 gmx_mtop_ftype_count(mtop, F_LJC_PAIRS_NB) > 0));
2925 negp_pp = ir->opts.ngener - ir->nwall;
2929 bSomeNormalNbListsAreInUse = TRUE;
2934 bSomeNormalNbListsAreInUse = (ir->eDispCorr != edispcNO);
2935 for (egi = 0; egi < negp_pp; egi++)
2937 for (egj = egi; egj < negp_pp; egj++)
2939 egp_flags = ir->opts.egp_flags[GID(egi, egj, ir->opts.ngener)];
2940 if (!(egp_flags & EGP_EXCL))
2942 if (egp_flags & EGP_TABLE)
2948 bSomeNormalNbListsAreInUse = TRUE;
2953 if (bSomeNormalNbListsAreInUse)
2955 fr->nnblists = negptable + 1;
2959 fr->nnblists = negptable;
2961 if (fr->nnblists > 1)
2963 snew(fr->gid2nblists, ir->opts.ngener*ir->opts.ngener);
2972 snew(fr->nblists, fr->nnblists);
2974 /* This code automatically gives table length tabext without cut-off's,
2975 * in that case grompp should already have checked that we do not need
2976 * normal tables and we only generate tables for 1-4 interactions.
2978 rtab = ir->rlistlong + ir->tabext;
2982 /* make tables for ordinary interactions */
2983 if (bSomeNormalNbListsAreInUse)
2985 make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn, NULL, NULL, &fr->nblists[0]);
2988 make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn, NULL, NULL, &fr->nblists[fr->nnblists/2]);
2990 if (!bMakeSeparate14Table)
2992 fr->tab14 = fr->nblists[0].table_elec_vdw;
3002 /* Read the special tables for certain energy group pairs */
3003 nm_ind = mtop->groups.grps[egcENER].nm_ind;
3004 for (egi = 0; egi < negp_pp; egi++)
3006 for (egj = egi; egj < negp_pp; egj++)
3008 egp_flags = ir->opts.egp_flags[GID(egi, egj, ir->opts.ngener)];
3009 if ((egp_flags & EGP_TABLE) && !(egp_flags & EGP_EXCL))
3011 nbl = &(fr->nblists[m]);
3012 if (fr->nnblists > 1)
3014 fr->gid2nblists[GID(egi, egj, ir->opts.ngener)] = m;
3016 /* Read the table file with the two energy groups names appended */
3017 make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn,
3018 *mtop->groups.grpname[nm_ind[egi]],
3019 *mtop->groups.grpname[nm_ind[egj]],
3023 make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn,
3024 *mtop->groups.grpname[nm_ind[egi]],
3025 *mtop->groups.grpname[nm_ind[egj]],
3026 &fr->nblists[fr->nnblists/2+m]);
3030 else if (fr->nnblists > 1)
3032 fr->gid2nblists[GID(egi, egj, ir->opts.ngener)] = 0;
3038 if (bMakeSeparate14Table)
3040 /* generate extra tables with plain Coulomb for 1-4 interactions only */
3041 fr->tab14 = make_tables(fp, oenv, fr, MASTER(cr), tabpfn, rtab,
3042 GMX_MAKETABLES_14ONLY);
3045 /* Read AdResS Thermo Force table if needed */
3046 if (fr->adress_icor == eAdressICThermoForce)
3048 /* old todo replace */
3050 if (ir->adress->n_tf_grps > 0)
3052 make_adress_tf_tables(fp, oenv, fr, ir, tabfn, mtop, box);
3057 /* load the default table */
3058 snew(fr->atf_tabs, 1);
3059 fr->atf_tabs[DEFAULT_TF_TABLE] = make_atf_table(fp, oenv, fr, tabafn, box);
3064 fr->nwall = ir->nwall;
3065 if (ir->nwall && ir->wall_type == ewtTABLE)
3067 make_wall_tables(fp, oenv, ir, tabfn, &mtop->groups, fr);
3072 fcd->bondtab = make_bonded_tables(fp,
3073 F_TABBONDS, F_TABBONDSNC,
3075 fcd->angletab = make_bonded_tables(fp,
3078 fcd->dihtab = make_bonded_tables(fp,
3086 fprintf(debug, "No fcdata or table file name passed, can not read table, can not do bonded interactions\n");
3090 /* QM/MM initialization if requested
3094 fprintf(stderr, "QM/MM calculation requested.\n");
3097 fr->bQMMM = ir->bQMMM;
3098 fr->qr = mk_QMMMrec();
3100 /* Set all the static charge group info */
3101 fr->cginfo_mb = init_cginfo_mb(fp, mtop, fr, bNoSolvOpt,
3103 &fr->bExcl_IntraCGAll_InterCGNone);
3104 if (DOMAINDECOMP(cr))
3110 fr->cginfo = cginfo_expand(mtop->nmolblock, fr->cginfo_mb);
3113 if (!DOMAINDECOMP(cr))
3115 forcerec_set_ranges(fr, ncg_mtop(mtop), ncg_mtop(mtop),
3116 mtop->natoms, mtop->natoms, mtop->natoms);
3119 fr->print_force = print_force;
3122 /* coarse load balancing vars */
3127 /* Initialize neighbor search */
3128 init_ns(fp, cr, &fr->ns, fr, mtop);
3130 if (cr->duty & DUTY_PP)
3132 gmx_nonbonded_setup(fr, bGenericKernelOnly);
3136 gmx_setup_adress_kernels(fp,bGenericKernelOnly);
3141 /* Initialize the thread working data for bonded interactions */
3142 init_forcerec_f_threads(fr, mtop->groups.grps[egcENER].nr);
3144 snew(fr->excl_load, fr->nthreads+1);
3146 if (fr->cutoff_scheme == ecutsVERLET)
3148 if (ir->rcoulomb != ir->rvdw)
3150 gmx_fatal(FARGS, "With Verlet lists rcoulomb and rvdw should be identical");
3153 init_nb_verlet(fp, &fr->nbv, bFEP_NonBonded, ir, fr, cr, nbpu_opt);
3156 /* fr->ic is used both by verlet and group kernels (to some extent) now */
3157 init_interaction_const(fp, cr, &fr->ic, fr, rtab);
3159 if (ir->eDispCorr != edispcNO)
3161 calc_enervirdiff(fp, ir->eDispCorr, fr);
3165 #define pr_real(fp, r) fprintf(fp, "%s: %e\n",#r, r)
3166 #define pr_int(fp, i) fprintf((fp), "%s: %d\n",#i, i)
3167 #define pr_bool(fp, b) fprintf((fp), "%s: %s\n",#b, bool_names[b])
3169 void pr_forcerec(FILE *fp, t_forcerec *fr)
3173 pr_real(fp, fr->rlist);
3174 pr_real(fp, fr->rcoulomb);
3175 pr_real(fp, fr->fudgeQQ);
3176 pr_bool(fp, fr->bGrid);
3177 pr_bool(fp, fr->bTwinRange);
3178 /*pr_int(fp,fr->cg0);
3179 pr_int(fp,fr->hcg);*/
3180 for (i = 0; i < fr->nnblists; i++)
3182 pr_int(fp, fr->nblists[i].table_elec_vdw.n);
3184 pr_real(fp, fr->rcoulomb_switch);
3185 pr_real(fp, fr->rcoulomb);
3190 void forcerec_set_excl_load(t_forcerec *fr,
3191 const gmx_localtop_t *top)
3194 int t, i, j, ntot, n, ntarget;
3196 ind = top->excls.index;
3200 for (i = 0; i < top->excls.nr; i++)
3202 for (j = ind[i]; j < ind[i+1]; j++)
3211 fr->excl_load[0] = 0;
3214 for (t = 1; t <= fr->nthreads; t++)
3216 ntarget = (ntot*t)/fr->nthreads;
3217 while (i < top->excls.nr && n < ntarget)
3219 for (j = ind[i]; j < ind[i+1]; j++)
3228 fr->excl_load[t] = i;