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48 #include "gromacs/domdec/domdec.h"
49 #include "gromacs/ewald/ewald.h"
50 #include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
51 #include "gromacs/legacyheaders/copyrite.h"
52 #include "gromacs/legacyheaders/force.h"
53 #include "gromacs/legacyheaders/gmx_detect_hardware.h"
54 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
55 #include "gromacs/legacyheaders/inputrec.h"
56 #include "gromacs/legacyheaders/macros.h"
57 #include "gromacs/legacyheaders/md_logging.h"
58 #include "gromacs/legacyheaders/md_support.h"
59 #include "gromacs/legacyheaders/names.h"
60 #include "gromacs/legacyheaders/network.h"
61 #include "gromacs/legacyheaders/nonbonded.h"
62 #include "gromacs/legacyheaders/ns.h"
63 #include "gromacs/legacyheaders/qmmm.h"
64 #include "gromacs/legacyheaders/tables.h"
65 #include "gromacs/legacyheaders/txtdump.h"
66 #include "gromacs/legacyheaders/typedefs.h"
67 #include "gromacs/legacyheaders/types/commrec.h"
68 #include "gromacs/listed-forces/manage-threading.h"
69 #include "gromacs/math/calculate-ewald-splitting-coefficient.h"
70 #include "gromacs/math/units.h"
71 #include "gromacs/math/utilities.h"
72 #include "gromacs/math/vec.h"
73 #include "gromacs/mdlib/forcerec-threading.h"
74 #include "gromacs/mdlib/nb_verlet.h"
75 #include "gromacs/mdlib/nbnxn_atomdata.h"
76 #include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
77 #include "gromacs/mdlib/nbnxn_search.h"
78 #include "gromacs/mdlib/nbnxn_simd.h"
79 #include "gromacs/pbcutil/ishift.h"
80 #include "gromacs/pbcutil/pbc.h"
81 #include "gromacs/simd/simd.h"
82 #include "gromacs/topology/mtop_util.h"
83 #include "gromacs/utility/fatalerror.h"
84 #include "gromacs/utility/smalloc.h"
86 #include "nbnxn_gpu_jit_support.h"
88 t_forcerec *mk_forcerec(void)
98 static void pr_nbfp(FILE *fp, real *nbfp, gmx_bool bBHAM, int atnr)
102 for (i = 0; (i < atnr); i++)
104 for (j = 0; (j < atnr); j++)
106 fprintf(fp, "%2d - %2d", i, j);
109 fprintf(fp, " a=%10g, b=%10g, c=%10g\n", BHAMA(nbfp, atnr, i, j),
110 BHAMB(nbfp, atnr, i, j), BHAMC(nbfp, atnr, i, j)/6.0);
114 fprintf(fp, " c6=%10g, c12=%10g\n", C6(nbfp, atnr, i, j)/6.0,
115 C12(nbfp, atnr, i, j)/12.0);
122 static real *mk_nbfp(const gmx_ffparams_t *idef, gmx_bool bBHAM)
130 snew(nbfp, 3*atnr*atnr);
131 for (i = k = 0; (i < atnr); i++)
133 for (j = 0; (j < atnr); j++, k++)
135 BHAMA(nbfp, atnr, i, j) = idef->iparams[k].bham.a;
136 BHAMB(nbfp, atnr, i, j) = idef->iparams[k].bham.b;
137 /* nbfp now includes the 6.0 derivative prefactor */
138 BHAMC(nbfp, atnr, i, j) = idef->iparams[k].bham.c*6.0;
144 snew(nbfp, 2*atnr*atnr);
145 for (i = k = 0; (i < atnr); i++)
147 for (j = 0; (j < atnr); j++, k++)
149 /* nbfp now includes the 6.0/12.0 derivative prefactors */
150 C6(nbfp, atnr, i, j) = idef->iparams[k].lj.c6*6.0;
151 C12(nbfp, atnr, i, j) = idef->iparams[k].lj.c12*12.0;
159 static real *make_ljpme_c6grid(const gmx_ffparams_t *idef, t_forcerec *fr)
162 real c6, c6i, c6j, c12i, c12j, epsi, epsj, sigmai, sigmaj;
164 const real oneOverSix = 1.0 / 6.0;
166 /* For LJ-PME simulations, we correct the energies with the reciprocal space
167 * inside of the cut-off. To do this the non-bonded kernels needs to have
168 * access to the C6-values used on the reciprocal grid in pme.c
172 snew(grid, 2*atnr*atnr);
173 for (i = k = 0; (i < atnr); i++)
175 for (j = 0; (j < atnr); j++, k++)
177 c6i = idef->iparams[i*(atnr+1)].lj.c6;
178 c12i = idef->iparams[i*(atnr+1)].lj.c12;
179 c6j = idef->iparams[j*(atnr+1)].lj.c6;
180 c12j = idef->iparams[j*(atnr+1)].lj.c12;
181 c6 = sqrt(c6i * c6j);
182 if (fr->ljpme_combination_rule == eljpmeLB
183 && !gmx_numzero(c6) && !gmx_numzero(c12i) && !gmx_numzero(c12j))
185 sigmai = pow(c12i / c6i, oneOverSix);
186 sigmaj = pow(c12j / c6j, oneOverSix);
187 epsi = c6i * c6i / c12i;
188 epsj = c6j * c6j / c12j;
189 c6 = sqrt(epsi * epsj) * pow(0.5*(sigmai+sigmaj), 6);
191 /* Store the elements at the same relative positions as C6 in nbfp in order
192 * to simplify access in the kernels
194 grid[2*(atnr*i+j)] = c6*6.0;
200 static real *mk_nbfp_combination_rule(const gmx_ffparams_t *idef, int comb_rule)
204 real c6i, c6j, c12i, c12j, epsi, epsj, sigmai, sigmaj;
206 const real oneOverSix = 1.0 / 6.0;
209 snew(nbfp, 2*atnr*atnr);
210 for (i = 0; i < atnr; ++i)
212 for (j = 0; j < atnr; ++j)
214 c6i = idef->iparams[i*(atnr+1)].lj.c6;
215 c12i = idef->iparams[i*(atnr+1)].lj.c12;
216 c6j = idef->iparams[j*(atnr+1)].lj.c6;
217 c12j = idef->iparams[j*(atnr+1)].lj.c12;
218 c6 = sqrt(c6i * c6j);
219 c12 = sqrt(c12i * c12j);
220 if (comb_rule == eCOMB_ARITHMETIC
221 && !gmx_numzero(c6) && !gmx_numzero(c12))
223 sigmai = pow(c12i / c6i, oneOverSix);
224 sigmaj = pow(c12j / c6j, oneOverSix);
225 epsi = c6i * c6i / c12i;
226 epsj = c6j * c6j / c12j;
227 c6 = sqrt(epsi * epsj) * pow(0.5*(sigmai+sigmaj), 6);
228 c12 = sqrt(epsi * epsj) * pow(0.5*(sigmai+sigmaj), 12);
230 C6(nbfp, atnr, i, j) = c6*6.0;
231 C12(nbfp, atnr, i, j) = c12*12.0;
237 /* This routine sets fr->solvent_opt to the most common solvent in the
238 * system, e.g. esolSPC or esolTIP4P. It will also mark each charge group in
239 * the fr->solvent_type array with the correct type (or esolNO).
241 * Charge groups that fulfill the conditions but are not identical to the
242 * most common one will be marked as esolNO in the solvent_type array.
244 * TIP3p is identical to SPC for these purposes, so we call it
245 * SPC in the arrays (Apologies to Bill Jorgensen ;-)
247 * NOTE: QM particle should not
248 * become an optimized solvent. Not even if there is only one charge
258 } solvent_parameters_t;
261 check_solvent_cg(const gmx_moltype_t *molt,
264 const unsigned char *qm_grpnr,
265 const t_grps *qm_grps,
267 int *n_solvent_parameters,
268 solvent_parameters_t **solvent_parameters_p,
278 real tmp_charge[4] = { 0.0 }; /* init to zero to make gcc4.8 happy */
279 int tmp_vdwtype[4] = { 0 }; /* init to zero to make gcc4.8 happy */
282 solvent_parameters_t *solvent_parameters;
284 /* We use a list with parameters for each solvent type.
285 * Every time we discover a new molecule that fulfills the basic
286 * conditions for a solvent we compare with the previous entries
287 * in these lists. If the parameters are the same we just increment
288 * the counter for that type, and otherwise we create a new type
289 * based on the current molecule.
291 * Once we've finished going through all molecules we check which
292 * solvent is most common, and mark all those molecules while we
293 * clear the flag on all others.
296 solvent_parameters = *solvent_parameters_p;
298 /* Mark the cg first as non optimized */
301 /* Check if this cg has no exclusions with atoms in other charge groups
302 * and all atoms inside the charge group excluded.
303 * We only have 3 or 4 atom solvent loops.
305 if (GET_CGINFO_EXCL_INTER(cginfo) ||
306 !GET_CGINFO_EXCL_INTRA(cginfo))
311 /* Get the indices of the first atom in this charge group */
312 j0 = molt->cgs.index[cg0];
313 j1 = molt->cgs.index[cg0+1];
315 /* Number of atoms in our molecule */
321 "Moltype '%s': there are %d atoms in this charge group\n",
325 /* Check if it could be an SPC (3 atoms) or TIP4p (4) water,
328 if (nj < 3 || nj > 4)
333 /* Check if we are doing QM on this group */
335 if (qm_grpnr != NULL)
337 for (j = j0; j < j1 && !qm; j++)
339 qm = (qm_grpnr[j] < qm_grps->nr - 1);
342 /* Cannot use solvent optimization with QM */
348 atom = molt->atoms.atom;
350 /* Still looks like a solvent, time to check parameters */
352 /* If it is perturbed (free energy) we can't use the solvent loops,
353 * so then we just skip to the next molecule.
357 for (j = j0; j < j1 && !perturbed; j++)
359 perturbed = PERTURBED(atom[j]);
367 /* Now it's only a question if the VdW and charge parameters
368 * are OK. Before doing the check we compare and see if they are
369 * identical to a possible previous solvent type.
370 * First we assign the current types and charges.
372 for (j = 0; j < nj; j++)
374 tmp_vdwtype[j] = atom[j0+j].type;
375 tmp_charge[j] = atom[j0+j].q;
378 /* Does it match any previous solvent type? */
379 for (k = 0; k < *n_solvent_parameters; k++)
384 /* We can only match SPC with 3 atoms and TIP4p with 4 atoms */
385 if ( (solvent_parameters[k].model == esolSPC && nj != 3) ||
386 (solvent_parameters[k].model == esolTIP4P && nj != 4) )
391 /* Check that types & charges match for all atoms in molecule */
392 for (j = 0; j < nj && match == TRUE; j++)
394 if (tmp_vdwtype[j] != solvent_parameters[k].vdwtype[j])
398 if (tmp_charge[j] != solvent_parameters[k].charge[j])
405 /* Congratulations! We have a matched solvent.
406 * Flag it with this type for later processing.
409 solvent_parameters[k].count += nmol;
411 /* We are done with this charge group */
416 /* If we get here, we have a tentative new solvent type.
417 * Before we add it we must check that it fulfills the requirements
418 * of the solvent optimized loops. First determine which atoms have
421 for (j = 0; j < nj; j++)
424 tjA = tmp_vdwtype[j];
426 /* Go through all other tpes and see if any have non-zero
427 * VdW parameters when combined with this one.
429 for (k = 0; k < fr->ntype && (has_vdw[j] == FALSE); k++)
431 /* We already checked that the atoms weren't perturbed,
432 * so we only need to check state A now.
436 has_vdw[j] = (has_vdw[j] ||
437 (BHAMA(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
438 (BHAMB(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
439 (BHAMC(fr->nbfp, fr->ntype, tjA, k) != 0.0));
444 has_vdw[j] = (has_vdw[j] ||
445 (C6(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
446 (C12(fr->nbfp, fr->ntype, tjA, k) != 0.0));
451 /* Now we know all we need to make the final check and assignment. */
455 * For this we require thatn all atoms have charge,
456 * the charges on atom 2 & 3 should be the same, and only
457 * atom 1 might have VdW.
459 if (has_vdw[1] == FALSE &&
460 has_vdw[2] == FALSE &&
461 tmp_charge[0] != 0 &&
462 tmp_charge[1] != 0 &&
463 tmp_charge[2] == tmp_charge[1])
465 srenew(solvent_parameters, *n_solvent_parameters+1);
466 solvent_parameters[*n_solvent_parameters].model = esolSPC;
467 solvent_parameters[*n_solvent_parameters].count = nmol;
468 for (k = 0; k < 3; k++)
470 solvent_parameters[*n_solvent_parameters].vdwtype[k] = tmp_vdwtype[k];
471 solvent_parameters[*n_solvent_parameters].charge[k] = tmp_charge[k];
474 *cg_sp = *n_solvent_parameters;
475 (*n_solvent_parameters)++;
480 /* Or could it be a TIP4P?
481 * For this we require thatn atoms 2,3,4 have charge, but not atom 1.
482 * Only atom 1 mght have VdW.
484 if (has_vdw[1] == FALSE &&
485 has_vdw[2] == FALSE &&
486 has_vdw[3] == FALSE &&
487 tmp_charge[0] == 0 &&
488 tmp_charge[1] != 0 &&
489 tmp_charge[2] == tmp_charge[1] &&
492 srenew(solvent_parameters, *n_solvent_parameters+1);
493 solvent_parameters[*n_solvent_parameters].model = esolTIP4P;
494 solvent_parameters[*n_solvent_parameters].count = nmol;
495 for (k = 0; k < 4; k++)
497 solvent_parameters[*n_solvent_parameters].vdwtype[k] = tmp_vdwtype[k];
498 solvent_parameters[*n_solvent_parameters].charge[k] = tmp_charge[k];
501 *cg_sp = *n_solvent_parameters;
502 (*n_solvent_parameters)++;
506 *solvent_parameters_p = solvent_parameters;
510 check_solvent(FILE * fp,
511 const gmx_mtop_t * mtop,
513 cginfo_mb_t *cginfo_mb)
516 const gmx_moltype_t *molt;
517 int mb, mol, cg_mol, at_offset, am, cgm, i, nmol_ch, nmol;
518 int n_solvent_parameters;
519 solvent_parameters_t *solvent_parameters;
525 fprintf(debug, "Going to determine what solvent types we have.\n");
528 n_solvent_parameters = 0;
529 solvent_parameters = NULL;
530 /* Allocate temporary array for solvent type */
531 snew(cg_sp, mtop->nmolblock);
534 for (mb = 0; mb < mtop->nmolblock; mb++)
536 molt = &mtop->moltype[mtop->molblock[mb].type];
538 /* Here we have to loop over all individual molecules
539 * because we need to check for QMMM particles.
541 snew(cg_sp[mb], cginfo_mb[mb].cg_mod);
542 nmol_ch = cginfo_mb[mb].cg_mod/cgs->nr;
543 nmol = mtop->molblock[mb].nmol/nmol_ch;
544 for (mol = 0; mol < nmol_ch; mol++)
547 am = mol*cgs->index[cgs->nr];
548 for (cg_mol = 0; cg_mol < cgs->nr; cg_mol++)
550 check_solvent_cg(molt, cg_mol, nmol,
551 mtop->groups.grpnr[egcQMMM] ?
552 mtop->groups.grpnr[egcQMMM]+at_offset+am : 0,
553 &mtop->groups.grps[egcQMMM],
555 &n_solvent_parameters, &solvent_parameters,
556 cginfo_mb[mb].cginfo[cgm+cg_mol],
557 &cg_sp[mb][cgm+cg_mol]);
560 at_offset += cgs->index[cgs->nr];
563 /* Puh! We finished going through all charge groups.
564 * Now find the most common solvent model.
567 /* Most common solvent this far */
569 for (i = 0; i < n_solvent_parameters; i++)
572 solvent_parameters[i].count > solvent_parameters[bestsp].count)
580 bestsol = solvent_parameters[bestsp].model;
588 for (mb = 0; mb < mtop->nmolblock; mb++)
590 cgs = &mtop->moltype[mtop->molblock[mb].type].cgs;
591 nmol = (mtop->molblock[mb].nmol*cgs->nr)/cginfo_mb[mb].cg_mod;
592 for (i = 0; i < cginfo_mb[mb].cg_mod; i++)
594 if (cg_sp[mb][i] == bestsp)
596 SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[i], bestsol);
601 SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[i], esolNO);
608 if (bestsol != esolNO && fp != NULL)
610 fprintf(fp, "\nEnabling %s-like water optimization for %d molecules.\n\n",
612 solvent_parameters[bestsp].count);
615 sfree(solvent_parameters);
616 fr->solvent_opt = bestsol;
620 acNONE = 0, acCONSTRAINT, acSETTLE
623 static cginfo_mb_t *init_cginfo_mb(FILE *fplog, const gmx_mtop_t *mtop,
624 t_forcerec *fr, gmx_bool bNoSolvOpt,
625 gmx_bool *bFEP_NonBonded,
626 gmx_bool *bExcl_IntraCGAll_InterCGNone)
629 const t_blocka *excl;
630 const gmx_moltype_t *molt;
631 const gmx_molblock_t *molb;
632 cginfo_mb_t *cginfo_mb;
635 int cg_offset, a_offset;
636 int mb, m, cg, a0, a1, gid, ai, j, aj, excl_nalloc;
640 gmx_bool bId, *bExcl, bExclIntraAll, bExclInter, bHaveVDW, bHaveQ, bHavePerturbedAtoms;
642 snew(cginfo_mb, mtop->nmolblock);
644 snew(type_VDW, fr->ntype);
645 for (ai = 0; ai < fr->ntype; ai++)
647 type_VDW[ai] = FALSE;
648 for (j = 0; j < fr->ntype; j++)
650 type_VDW[ai] = type_VDW[ai] ||
652 C6(fr->nbfp, fr->ntype, ai, j) != 0 ||
653 C12(fr->nbfp, fr->ntype, ai, j) != 0;
657 *bFEP_NonBonded = FALSE;
658 *bExcl_IntraCGAll_InterCGNone = TRUE;
661 snew(bExcl, excl_nalloc);
664 for (mb = 0; mb < mtop->nmolblock; mb++)
666 molb = &mtop->molblock[mb];
667 molt = &mtop->moltype[molb->type];
671 /* Check if the cginfo is identical for all molecules in this block.
672 * If so, we only need an array of the size of one molecule.
673 * Otherwise we make an array of #mol times #cgs per molecule.
676 for (m = 0; m < molb->nmol; m++)
678 int am = m*cgs->index[cgs->nr];
679 for (cg = 0; cg < cgs->nr; cg++)
682 a1 = cgs->index[cg+1];
683 if (ggrpnr(&mtop->groups, egcENER, a_offset+am+a0) !=
684 ggrpnr(&mtop->groups, egcENER, a_offset +a0))
688 if (mtop->groups.grpnr[egcQMMM] != NULL)
690 for (ai = a0; ai < a1; ai++)
692 if (mtop->groups.grpnr[egcQMMM][a_offset+am+ai] !=
693 mtop->groups.grpnr[egcQMMM][a_offset +ai])
702 cginfo_mb[mb].cg_start = cg_offset;
703 cginfo_mb[mb].cg_end = cg_offset + molb->nmol*cgs->nr;
704 cginfo_mb[mb].cg_mod = (bId ? 1 : molb->nmol)*cgs->nr;
705 snew(cginfo_mb[mb].cginfo, cginfo_mb[mb].cg_mod);
706 cginfo = cginfo_mb[mb].cginfo;
708 /* Set constraints flags for constrained atoms */
709 snew(a_con, molt->atoms.nr);
710 for (ftype = 0; ftype < F_NRE; ftype++)
712 if (interaction_function[ftype].flags & IF_CONSTRAINT)
717 for (ia = 0; ia < molt->ilist[ftype].nr; ia += 1+nral)
721 for (a = 0; a < nral; a++)
723 a_con[molt->ilist[ftype].iatoms[ia+1+a]] =
724 (ftype == F_SETTLE ? acSETTLE : acCONSTRAINT);
730 for (m = 0; m < (bId ? 1 : molb->nmol); m++)
733 int am = m*cgs->index[cgs->nr];
734 for (cg = 0; cg < cgs->nr; cg++)
737 a1 = cgs->index[cg+1];
739 /* Store the energy group in cginfo */
740 gid = ggrpnr(&mtop->groups, egcENER, a_offset+am+a0);
741 SET_CGINFO_GID(cginfo[cgm+cg], gid);
743 /* Check the intra/inter charge group exclusions */
744 if (a1-a0 > excl_nalloc)
746 excl_nalloc = a1 - a0;
747 srenew(bExcl, excl_nalloc);
749 /* bExclIntraAll: all intra cg interactions excluded
750 * bExclInter: any inter cg interactions excluded
752 bExclIntraAll = TRUE;
756 bHavePerturbedAtoms = FALSE;
757 for (ai = a0; ai < a1; ai++)
759 /* Check VDW and electrostatic interactions */
760 bHaveVDW = bHaveVDW || (type_VDW[molt->atoms.atom[ai].type] ||
761 type_VDW[molt->atoms.atom[ai].typeB]);
762 bHaveQ = bHaveQ || (molt->atoms.atom[ai].q != 0 ||
763 molt->atoms.atom[ai].qB != 0);
765 bHavePerturbedAtoms = bHavePerturbedAtoms || (PERTURBED(molt->atoms.atom[ai]) != 0);
767 /* Clear the exclusion list for atom ai */
768 for (aj = a0; aj < a1; aj++)
770 bExcl[aj-a0] = FALSE;
772 /* Loop over all the exclusions of atom ai */
773 for (j = excl->index[ai]; j < excl->index[ai+1]; j++)
776 if (aj < a0 || aj >= a1)
785 /* Check if ai excludes a0 to a1 */
786 for (aj = a0; aj < a1; aj++)
790 bExclIntraAll = FALSE;
797 SET_CGINFO_CONSTR(cginfo[cgm+cg]);
800 SET_CGINFO_SETTLE(cginfo[cgm+cg]);
808 SET_CGINFO_EXCL_INTRA(cginfo[cgm+cg]);
812 SET_CGINFO_EXCL_INTER(cginfo[cgm+cg]);
814 if (a1 - a0 > MAX_CHARGEGROUP_SIZE)
816 /* The size in cginfo is currently only read with DD */
817 gmx_fatal(FARGS, "A charge group has size %d which is larger than the limit of %d atoms", a1-a0, MAX_CHARGEGROUP_SIZE);
821 SET_CGINFO_HAS_VDW(cginfo[cgm+cg]);
825 SET_CGINFO_HAS_Q(cginfo[cgm+cg]);
827 if (bHavePerturbedAtoms && fr->efep != efepNO)
829 SET_CGINFO_FEP(cginfo[cgm+cg]);
830 *bFEP_NonBonded = TRUE;
832 /* Store the charge group size */
833 SET_CGINFO_NATOMS(cginfo[cgm+cg], a1-a0);
835 if (!bExclIntraAll || bExclInter)
837 *bExcl_IntraCGAll_InterCGNone = FALSE;
844 cg_offset += molb->nmol*cgs->nr;
845 a_offset += molb->nmol*cgs->index[cgs->nr];
849 /* the solvent optimizer is called after the QM is initialized,
850 * because we don't want to have the QM subsystemto become an
854 check_solvent(fplog, mtop, fr, cginfo_mb);
856 if (getenv("GMX_NO_SOLV_OPT"))
860 fprintf(fplog, "Found environment variable GMX_NO_SOLV_OPT.\n"
861 "Disabling all solvent optimization\n");
863 fr->solvent_opt = esolNO;
867 fr->solvent_opt = esolNO;
869 if (!fr->solvent_opt)
871 for (mb = 0; mb < mtop->nmolblock; mb++)
873 for (cg = 0; cg < cginfo_mb[mb].cg_mod; cg++)
875 SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[cg], esolNO);
883 static int *cginfo_expand(int nmb, cginfo_mb_t *cgi_mb)
888 ncg = cgi_mb[nmb-1].cg_end;
891 for (cg = 0; cg < ncg; cg++)
893 while (cg >= cgi_mb[mb].cg_end)
898 cgi_mb[mb].cginfo[(cg - cgi_mb[mb].cg_start) % cgi_mb[mb].cg_mod];
904 static void set_chargesum(FILE *log, t_forcerec *fr, const gmx_mtop_t *mtop)
906 /*This now calculates sum for q and c6*/
907 double qsum, q2sum, q, c6sum, c6;
909 const t_atoms *atoms;
914 for (mb = 0; mb < mtop->nmolblock; mb++)
916 nmol = mtop->molblock[mb].nmol;
917 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
918 for (i = 0; i < atoms->nr; i++)
920 q = atoms->atom[i].q;
923 c6 = mtop->ffparams.iparams[atoms->atom[i].type*(mtop->ffparams.atnr+1)].lj.c6;
928 fr->q2sum[0] = q2sum;
929 fr->c6sum[0] = c6sum;
931 if (fr->efep != efepNO)
936 for (mb = 0; mb < mtop->nmolblock; mb++)
938 nmol = mtop->molblock[mb].nmol;
939 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
940 for (i = 0; i < atoms->nr; i++)
942 q = atoms->atom[i].qB;
945 c6 = mtop->ffparams.iparams[atoms->atom[i].typeB*(mtop->ffparams.atnr+1)].lj.c6;
949 fr->q2sum[1] = q2sum;
950 fr->c6sum[1] = c6sum;
955 fr->qsum[1] = fr->qsum[0];
956 fr->q2sum[1] = fr->q2sum[0];
957 fr->c6sum[1] = fr->c6sum[0];
961 if (fr->efep == efepNO)
963 fprintf(log, "System total charge: %.3f\n", fr->qsum[0]);
967 fprintf(log, "System total charge, top. A: %.3f top. B: %.3f\n",
968 fr->qsum[0], fr->qsum[1]);
973 void update_forcerec(t_forcerec *fr, matrix box)
975 if (fr->eeltype == eelGRF)
977 calc_rffac(NULL, fr->eeltype, fr->epsilon_r, fr->epsilon_rf,
978 fr->rcoulomb, fr->temp, fr->zsquare, box,
979 &fr->kappa, &fr->k_rf, &fr->c_rf);
983 void set_avcsixtwelve(FILE *fplog, t_forcerec *fr, const gmx_mtop_t *mtop)
985 const t_atoms *atoms, *atoms_tpi;
986 const t_blocka *excl;
987 int mb, nmol, nmolc, i, j, tpi, tpj, j1, j2, k, nexcl, q;
988 gmx_int64_t npair, npair_ij, tmpi, tmpj;
989 double csix, ctwelve;
993 real *nbfp_comb = NULL;
999 /* For LJ-PME, we want to correct for the difference between the
1000 * actual C6 values and the C6 values used by the LJ-PME based on
1001 * combination rules. */
1003 if (EVDW_PME(fr->vdwtype))
1005 nbfp_comb = mk_nbfp_combination_rule(&mtop->ffparams,
1006 (fr->ljpme_combination_rule == eljpmeLB) ? eCOMB_ARITHMETIC : eCOMB_GEOMETRIC);
1007 for (tpi = 0; tpi < ntp; ++tpi)
1009 for (tpj = 0; tpj < ntp; ++tpj)
1011 C6(nbfp_comb, ntp, tpi, tpj) =
1012 C6(nbfp, ntp, tpi, tpj) - C6(nbfp_comb, ntp, tpi, tpj);
1013 C12(nbfp_comb, ntp, tpi, tpj) = C12(nbfp, ntp, tpi, tpj);
1018 for (q = 0; q < (fr->efep == efepNO ? 1 : 2); q++)
1026 /* Count the types so we avoid natoms^2 operations */
1027 snew(typecount, ntp);
1028 gmx_mtop_count_atomtypes(mtop, q, typecount);
1030 for (tpi = 0; tpi < ntp; tpi++)
1032 for (tpj = tpi; tpj < ntp; tpj++)
1034 tmpi = typecount[tpi];
1035 tmpj = typecount[tpj];
1038 npair_ij = tmpi*tmpj;
1042 npair_ij = tmpi*(tmpi - 1)/2;
1046 /* nbfp now includes the 6.0 derivative prefactor */
1047 csix += npair_ij*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
1051 /* nbfp now includes the 6.0/12.0 derivative prefactors */
1052 csix += npair_ij* C6(nbfp, ntp, tpi, tpj)/6.0;
1053 ctwelve += npair_ij* C12(nbfp, ntp, tpi, tpj)/12.0;
1059 /* Subtract the excluded pairs.
1060 * The main reason for substracting exclusions is that in some cases
1061 * some combinations might never occur and the parameters could have
1062 * any value. These unused values should not influence the dispersion
1065 for (mb = 0; mb < mtop->nmolblock; mb++)
1067 nmol = mtop->molblock[mb].nmol;
1068 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
1069 excl = &mtop->moltype[mtop->molblock[mb].type].excls;
1070 for (i = 0; (i < atoms->nr); i++)
1074 tpi = atoms->atom[i].type;
1078 tpi = atoms->atom[i].typeB;
1080 j1 = excl->index[i];
1081 j2 = excl->index[i+1];
1082 for (j = j1; j < j2; j++)
1089 tpj = atoms->atom[k].type;
1093 tpj = atoms->atom[k].typeB;
1097 /* nbfp now includes the 6.0 derivative prefactor */
1098 csix -= nmol*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
1102 /* nbfp now includes the 6.0/12.0 derivative prefactors */
1103 csix -= nmol*C6 (nbfp, ntp, tpi, tpj)/6.0;
1104 ctwelve -= nmol*C12(nbfp, ntp, tpi, tpj)/12.0;
1114 /* Only correct for the interaction of the test particle
1115 * with the rest of the system.
1118 &mtop->moltype[mtop->molblock[mtop->nmolblock-1].type].atoms;
1121 for (mb = 0; mb < mtop->nmolblock; mb++)
1123 nmol = mtop->molblock[mb].nmol;
1124 atoms = &mtop->moltype[mtop->molblock[mb].type].atoms;
1125 for (j = 0; j < atoms->nr; j++)
1128 /* Remove the interaction of the test charge group
1131 if (mb == mtop->nmolblock-1)
1135 if (mb == 0 && nmol == 1)
1137 gmx_fatal(FARGS, "Old format tpr with TPI, please generate a new tpr file");
1142 tpj = atoms->atom[j].type;
1146 tpj = atoms->atom[j].typeB;
1148 for (i = 0; i < fr->n_tpi; i++)
1152 tpi = atoms_tpi->atom[i].type;
1156 tpi = atoms_tpi->atom[i].typeB;
1160 /* nbfp now includes the 6.0 derivative prefactor */
1161 csix += nmolc*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
1165 /* nbfp now includes the 6.0/12.0 derivative prefactors */
1166 csix += nmolc*C6 (nbfp, ntp, tpi, tpj)/6.0;
1167 ctwelve += nmolc*C12(nbfp, ntp, tpi, tpj)/12.0;
1174 if (npair - nexcl <= 0 && fplog)
1176 fprintf(fplog, "\nWARNING: There are no atom pairs for dispersion correction\n\n");
1182 csix /= npair - nexcl;
1183 ctwelve /= npair - nexcl;
1187 fprintf(debug, "Counted %d exclusions\n", nexcl);
1188 fprintf(debug, "Average C6 parameter is: %10g\n", (double)csix);
1189 fprintf(debug, "Average C12 parameter is: %10g\n", (double)ctwelve);
1191 fr->avcsix[q] = csix;
1192 fr->avctwelve[q] = ctwelve;
1195 if (EVDW_PME(fr->vdwtype))
1202 if (fr->eDispCorr == edispcAllEner ||
1203 fr->eDispCorr == edispcAllEnerPres)
1205 fprintf(fplog, "Long Range LJ corr.: <C6> %10.4e, <C12> %10.4e\n",
1206 fr->avcsix[0], fr->avctwelve[0]);
1210 fprintf(fplog, "Long Range LJ corr.: <C6> %10.4e\n", fr->avcsix[0]);
1216 static void set_bham_b_max(FILE *fplog, t_forcerec *fr,
1217 const gmx_mtop_t *mtop)
1219 const t_atoms *at1, *at2;
1220 int mt1, mt2, i, j, tpi, tpj, ntypes;
1226 fprintf(fplog, "Determining largest Buckingham b parameter for table\n");
1233 for (mt1 = 0; mt1 < mtop->nmoltype; mt1++)
1235 at1 = &mtop->moltype[mt1].atoms;
1236 for (i = 0; (i < at1->nr); i++)
1238 tpi = at1->atom[i].type;
1241 gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", i, tpi, ntypes);
1244 for (mt2 = mt1; mt2 < mtop->nmoltype; mt2++)
1246 at2 = &mtop->moltype[mt2].atoms;
1247 for (j = 0; (j < at2->nr); j++)
1249 tpj = at2->atom[j].type;
1252 gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", j, tpj, ntypes);
1254 b = BHAMB(nbfp, ntypes, tpi, tpj);
1255 if (b > fr->bham_b_max)
1259 if ((b < bmin) || (bmin == -1))
1269 fprintf(fplog, "Buckingham b parameters, min: %g, max: %g\n",
1270 bmin, fr->bham_b_max);
1274 static void make_nbf_tables(FILE *fp, const output_env_t oenv,
1275 t_forcerec *fr, real rtab,
1276 const t_commrec *cr,
1277 const char *tabfn, char *eg1, char *eg2,
1287 fprintf(debug, "No table file name passed, can not read table, can not do non-bonded interactions\n");
1292 sprintf(buf, "%s", tabfn);
1295 /* Append the two energy group names */
1296 sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "_%s_%s.%s",
1297 eg1, eg2, ftp2ext(efXVG));
1299 nbl->table_elec_vdw = make_tables(fp, oenv, fr, MASTER(cr), buf, rtab, 0);
1300 /* Copy the contents of the table to separate coulomb and LJ tables too,
1301 * to improve cache performance.
1303 /* For performance reasons we want
1304 * the table data to be aligned to 16-byte. The pointers could be freed
1305 * but currently aren't.
1307 nbl->table_elec.interaction = GMX_TABLE_INTERACTION_ELEC;
1308 nbl->table_elec.format = nbl->table_elec_vdw.format;
1309 nbl->table_elec.r = nbl->table_elec_vdw.r;
1310 nbl->table_elec.n = nbl->table_elec_vdw.n;
1311 nbl->table_elec.scale = nbl->table_elec_vdw.scale;
1312 nbl->table_elec.scale_exp = nbl->table_elec_vdw.scale_exp;
1313 nbl->table_elec.formatsize = nbl->table_elec_vdw.formatsize;
1314 nbl->table_elec.ninteractions = 1;
1315 nbl->table_elec.stride = nbl->table_elec.formatsize * nbl->table_elec.ninteractions;
1316 snew_aligned(nbl->table_elec.data, nbl->table_elec.stride*(nbl->table_elec.n+1), 32);
1318 nbl->table_vdw.interaction = GMX_TABLE_INTERACTION_VDWREP_VDWDISP;
1319 nbl->table_vdw.format = nbl->table_elec_vdw.format;
1320 nbl->table_vdw.r = nbl->table_elec_vdw.r;
1321 nbl->table_vdw.n = nbl->table_elec_vdw.n;
1322 nbl->table_vdw.scale = nbl->table_elec_vdw.scale;
1323 nbl->table_vdw.scale_exp = nbl->table_elec_vdw.scale_exp;
1324 nbl->table_vdw.formatsize = nbl->table_elec_vdw.formatsize;
1325 nbl->table_vdw.ninteractions = 2;
1326 nbl->table_vdw.stride = nbl->table_vdw.formatsize * nbl->table_vdw.ninteractions;
1327 snew_aligned(nbl->table_vdw.data, nbl->table_vdw.stride*(nbl->table_vdw.n+1), 32);
1329 for (i = 0; i <= nbl->table_elec_vdw.n; i++)
1331 for (j = 0; j < 4; j++)
1333 nbl->table_elec.data[4*i+j] = nbl->table_elec_vdw.data[12*i+j];
1335 for (j = 0; j < 8; j++)
1337 nbl->table_vdw.data[8*i+j] = nbl->table_elec_vdw.data[12*i+4+j];
1342 static void count_tables(int ftype1, int ftype2, const gmx_mtop_t *mtop,
1343 int *ncount, int **count)
1345 const gmx_moltype_t *molt;
1347 int mt, ftype, stride, i, j, tabnr;
1349 for (mt = 0; mt < mtop->nmoltype; mt++)
1351 molt = &mtop->moltype[mt];
1352 for (ftype = 0; ftype < F_NRE; ftype++)
1354 if (ftype == ftype1 || ftype == ftype2)
1356 il = &molt->ilist[ftype];
1357 stride = 1 + NRAL(ftype);
1358 for (i = 0; i < il->nr; i += stride)
1360 tabnr = mtop->ffparams.iparams[il->iatoms[i]].tab.table;
1363 gmx_fatal(FARGS, "A bonded table number is smaller than 0: %d\n", tabnr);
1365 if (tabnr >= *ncount)
1367 srenew(*count, tabnr+1);
1368 for (j = *ncount; j < tabnr+1; j++)
1381 static bondedtable_t *make_bonded_tables(FILE *fplog,
1382 int ftype1, int ftype2,
1383 const gmx_mtop_t *mtop,
1384 const char *basefn, const char *tabext)
1386 int i, ncount, *count;
1394 count_tables(ftype1, ftype2, mtop, &ncount, &count);
1399 for (i = 0; i < ncount; i++)
1403 sprintf(tabfn, "%s", basefn);
1404 sprintf(tabfn + strlen(basefn) - strlen(ftp2ext(efXVG)) - 1, "_%s%d.%s",
1405 tabext, i, ftp2ext(efXVG));
1406 tab[i] = make_bonded_table(fplog, tabfn, NRAL(ftype1)-2);
1415 void forcerec_set_ranges(t_forcerec *fr,
1416 int ncg_home, int ncg_force,
1418 int natoms_force_constr, int natoms_f_novirsum)
1423 /* fr->ncg_force is unused in the standard code,
1424 * but it can be useful for modified code dealing with charge groups.
1426 fr->ncg_force = ncg_force;
1427 fr->natoms_force = natoms_force;
1428 fr->natoms_force_constr = natoms_force_constr;
1430 if (fr->natoms_force_constr > fr->nalloc_force)
1432 fr->nalloc_force = over_alloc_dd(fr->natoms_force_constr);
1436 srenew(fr->f_twin, fr->nalloc_force);
1440 if (fr->bF_NoVirSum)
1442 fr->f_novirsum_n = natoms_f_novirsum;
1443 if (fr->f_novirsum_n > fr->f_novirsum_nalloc)
1445 fr->f_novirsum_nalloc = over_alloc_dd(fr->f_novirsum_n);
1446 srenew(fr->f_novirsum_alloc, fr->f_novirsum_nalloc);
1451 fr->f_novirsum_n = 0;
1455 static real cutoff_inf(real cutoff)
1459 cutoff = GMX_CUTOFF_INF;
1465 static void make_adress_tf_tables(FILE *fp, const output_env_t oenv,
1466 t_forcerec *fr, const t_inputrec *ir,
1467 const char *tabfn, const gmx_mtop_t *mtop,
1475 gmx_fatal(FARGS, "No thermoforce table file given. Use -tabletf to specify a file\n");
1479 snew(fr->atf_tabs, ir->adress->n_tf_grps);
1481 sprintf(buf, "%s", tabfn);
1482 for (i = 0; i < ir->adress->n_tf_grps; i++)
1484 j = ir->adress->tf_table_index[i]; /* get energy group index */
1485 sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "tf_%s.%s",
1486 *(mtop->groups.grpname[mtop->groups.grps[egcENER].nm_ind[j]]), ftp2ext(efXVG));
1489 fprintf(fp, "loading tf table for energygrp index %d from %s\n", ir->adress->tf_table_index[i], buf);
1491 fr->atf_tabs[i] = make_atf_table(fp, oenv, fr, buf, box);
1496 gmx_bool can_use_allvsall(const t_inputrec *ir, gmx_bool bPrintNote, t_commrec *cr, FILE *fp)
1503 ir->rcoulomb == 0 &&
1505 ir->ePBC == epbcNONE &&
1506 ir->vdwtype == evdwCUT &&
1507 ir->coulombtype == eelCUT &&
1508 ir->efep == efepNO &&
1509 (ir->implicit_solvent == eisNO ||
1510 (ir->implicit_solvent == eisGBSA && (ir->gb_algorithm == egbSTILL ||
1511 ir->gb_algorithm == egbHCT ||
1512 ir->gb_algorithm == egbOBC))) &&
1513 getenv("GMX_NO_ALLVSALL") == NULL
1516 if (bAllvsAll && ir->opts.ngener > 1)
1518 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";
1524 fprintf(stderr, "\n%s\n", note);
1528 fprintf(fp, "\n%s\n", note);
1534 if (bAllvsAll && fp && MASTER(cr))
1536 fprintf(fp, "\nUsing SIMD all-vs-all kernels.\n\n");
1543 gmx_bool nbnxn_gpu_acceleration_supported(FILE *fplog,
1544 const t_commrec *cr,
1545 const t_inputrec *ir,
1548 if (bRerunMD && ir->opts.ngener > 1)
1550 /* Rerun execution time is dominated by I/O and pair search,
1551 * so GPUs are not very useful, plus they do not support more
1552 * than one energy group. If the user requested GPUs
1553 * explicitly, a fatal error is given later. With non-reruns,
1554 * we fall back to a single whole-of system energy group
1555 * (which runs much faster than a multiple-energy-groups
1556 * implementation would), and issue a note in the .log
1557 * file. Users can re-run if they want the information. */
1558 md_print_warn(cr, fplog, "Rerun with energy groups is not implemented for GPUs, falling back to the CPU\n");
1562 if (ir->vdwtype == evdwPME && ir->ljpme_combination_rule == eljpmeLB)
1564 /* LJ PME with LB combination rule does 7 mesh operations.
1565 * This so slow that we don't compile GPU non-bonded kernels for that.
1567 md_print_warn(cr, fplog, "LJ-PME with Lorentz-Berthelot is not supported with GPUs, falling back to CPU only\n");
1574 gmx_bool nbnxn_simd_supported(FILE *fplog,
1575 const t_commrec *cr,
1576 const t_inputrec *ir)
1578 if (ir->vdwtype == evdwPME && ir->ljpme_combination_rule == eljpmeLB)
1580 /* LJ PME with LB combination rule does 7 mesh operations.
1581 * This so slow that we don't compile SIMD non-bonded kernels
1583 md_print_warn(cr, fplog, "LJ-PME with Lorentz-Berthelot is not supported with SIMD kernels, falling back to plain C kernels\n");
1591 static void pick_nbnxn_kernel_cpu(const t_inputrec gmx_unused *ir,
1595 *kernel_type = nbnxnk4x4_PlainC;
1596 *ewald_excl = ewaldexclTable;
1598 #ifdef GMX_NBNXN_SIMD
1600 #ifdef GMX_NBNXN_SIMD_4XN
1601 *kernel_type = nbnxnk4xN_SIMD_4xN;
1603 #ifdef GMX_NBNXN_SIMD_2XNN
1604 *kernel_type = nbnxnk4xN_SIMD_2xNN;
1607 #if defined GMX_NBNXN_SIMD_2XNN && defined GMX_NBNXN_SIMD_4XN
1608 /* We need to choose if we want 2x(N+N) or 4xN kernels.
1609 * Currently this is based on the SIMD acceleration choice,
1610 * but it might be better to decide this at runtime based on CPU.
1612 * 4xN calculates more (zero) interactions, but has less pair-search
1613 * work and much better kernel instruction scheduling.
1615 * Up till now we have only seen that on Intel Sandy/Ivy Bridge,
1616 * which doesn't have FMA, both the analytical and tabulated Ewald
1617 * kernels have similar pair rates for 4x8 and 2x(4+4), so we choose
1618 * 2x(4+4) because it results in significantly fewer pairs.
1619 * For RF, the raw pair rate of the 4x8 kernel is higher than 2x(4+4),
1620 * 10% with HT, 50% without HT. As we currently don't detect the actual
1621 * use of HT, use 4x8 to avoid a potential performance hit.
1622 * On Intel Haswell 4x8 is always faster.
1624 *kernel_type = nbnxnk4xN_SIMD_4xN;
1626 #ifndef GMX_SIMD_HAVE_FMA
1627 if (EEL_PME_EWALD(ir->coulombtype) ||
1628 EVDW_PME(ir->vdwtype))
1630 /* We have Ewald kernels without FMA (Intel Sandy/Ivy Bridge).
1631 * There are enough instructions to make 2x(4+4) efficient.
1633 *kernel_type = nbnxnk4xN_SIMD_2xNN;
1636 #endif /* GMX_NBNXN_SIMD_2XNN && GMX_NBNXN_SIMD_4XN */
1639 if (getenv("GMX_NBNXN_SIMD_4XN") != NULL)
1641 #ifdef GMX_NBNXN_SIMD_4XN
1642 *kernel_type = nbnxnk4xN_SIMD_4xN;
1644 gmx_fatal(FARGS, "SIMD 4xN kernels requested, but GROMACS has been compiled without support for these kernels");
1647 if (getenv("GMX_NBNXN_SIMD_2XNN") != NULL)
1649 #ifdef GMX_NBNXN_SIMD_2XNN
1650 *kernel_type = nbnxnk4xN_SIMD_2xNN;
1652 gmx_fatal(FARGS, "SIMD 2x(N+N) kernels requested, but GROMACS has been compiled without support for these kernels");
1656 /* Analytical Ewald exclusion correction is only an option in
1658 * Since table lookup's don't parallelize with SIMD, analytical
1659 * will probably always be faster for a SIMD width of 8 or more.
1660 * With FMA analytical is sometimes faster for a width if 4 as well.
1661 * On BlueGene/Q, this is faster regardless of precision.
1662 * In single precision, this is faster on Bulldozer.
1664 #if GMX_SIMD_REAL_WIDTH >= 8 || \
1665 (GMX_SIMD_REAL_WIDTH >= 4 && defined GMX_SIMD_HAVE_FMA && !defined GMX_DOUBLE) || \
1666 defined GMX_SIMD_IBM_QPX
1667 *ewald_excl = ewaldexclAnalytical;
1669 if (getenv("GMX_NBNXN_EWALD_TABLE") != NULL)
1671 *ewald_excl = ewaldexclTable;
1673 if (getenv("GMX_NBNXN_EWALD_ANALYTICAL") != NULL)
1675 *ewald_excl = ewaldexclAnalytical;
1679 #endif /* GMX_NBNXN_SIMD */
1683 const char *lookup_nbnxn_kernel_name(int kernel_type)
1685 const char *returnvalue = NULL;
1686 switch (kernel_type)
1689 returnvalue = "not set";
1691 case nbnxnk4x4_PlainC:
1692 returnvalue = "plain C";
1694 case nbnxnk4xN_SIMD_4xN:
1695 case nbnxnk4xN_SIMD_2xNN:
1696 #ifdef GMX_NBNXN_SIMD
1697 #if defined GMX_SIMD_X86_SSE2
1698 returnvalue = "SSE2";
1699 #elif defined GMX_SIMD_X86_SSE4_1
1700 returnvalue = "SSE4.1";
1701 #elif defined GMX_SIMD_X86_AVX_128_FMA
1702 returnvalue = "AVX_128_FMA";
1703 #elif defined GMX_SIMD_X86_AVX_256
1704 returnvalue = "AVX_256";
1705 #elif defined GMX_SIMD_X86_AVX2_256
1706 returnvalue = "AVX2_256";
1708 returnvalue = "SIMD";
1710 #else /* GMX_NBNXN_SIMD */
1711 returnvalue = "not available";
1712 #endif /* GMX_NBNXN_SIMD */
1714 case nbnxnk8x8x8_GPU: returnvalue = "GPU"; break;
1715 case nbnxnk8x8x8_PlainC: returnvalue = "plain C"; break;
1719 gmx_fatal(FARGS, "Illegal kernel type selected");
1726 static void pick_nbnxn_kernel(FILE *fp,
1727 const t_commrec *cr,
1728 gmx_bool use_simd_kernels,
1730 gmx_bool bEmulateGPU,
1731 const t_inputrec *ir,
1734 gmx_bool bDoNonbonded)
1736 assert(kernel_type);
1738 *kernel_type = nbnxnkNotSet;
1739 *ewald_excl = ewaldexclTable;
1743 *kernel_type = nbnxnk8x8x8_PlainC;
1747 md_print_warn(cr, fp, "Emulating a GPU run on the CPU (slow)");
1752 *kernel_type = nbnxnk8x8x8_GPU;
1755 if (*kernel_type == nbnxnkNotSet)
1757 if (use_simd_kernels &&
1758 nbnxn_simd_supported(fp, cr, ir))
1760 pick_nbnxn_kernel_cpu(ir, kernel_type, ewald_excl);
1764 *kernel_type = nbnxnk4x4_PlainC;
1768 if (bDoNonbonded && fp != NULL)
1770 fprintf(fp, "\nUsing %s %dx%d non-bonded kernels\n\n",
1771 lookup_nbnxn_kernel_name(*kernel_type),
1772 nbnxn_kernel_to_ci_size(*kernel_type),
1773 nbnxn_kernel_to_cj_size(*kernel_type));
1775 if (nbnxnk4x4_PlainC == *kernel_type ||
1776 nbnxnk8x8x8_PlainC == *kernel_type)
1778 md_print_warn(cr, fp,
1779 "WARNING: Using the slow %s kernels. This should\n"
1780 "not happen during routine usage on supported platforms.\n\n",
1781 lookup_nbnxn_kernel_name(*kernel_type));
1786 static void pick_nbnxn_resources(FILE *fp,
1787 const t_commrec *cr,
1788 const gmx_hw_info_t *hwinfo,
1789 gmx_bool bDoNonbonded,
1791 gmx_bool *bEmulateGPU,
1792 const gmx_gpu_opt_t *gpu_opt)
1794 gmx_bool bEmulateGPUEnvVarSet;
1795 char gpu_err_str[STRLEN];
1799 bEmulateGPUEnvVarSet = (getenv("GMX_EMULATE_GPU") != NULL);
1801 /* Run GPU emulation mode if GMX_EMULATE_GPU is defined. Because
1802 * GPUs (currently) only handle non-bonded calculations, we will
1803 * automatically switch to emulation if non-bonded calculations are
1804 * turned off via GMX_NO_NONBONDED - this is the simple and elegant
1805 * way to turn off GPU initialization, data movement, and cleanup.
1807 * GPU emulation can be useful to assess the performance one can expect by
1808 * adding GPU(s) to the machine. The conditional below allows this even
1809 * if mdrun is compiled without GPU acceleration support.
1810 * Note that you should freezing the system as otherwise it will explode.
1812 *bEmulateGPU = (bEmulateGPUEnvVarSet ||
1813 (!bDoNonbonded && gpu_opt->n_dev_use > 0));
1815 /* Enable GPU mode when GPUs are available or no GPU emulation is requested.
1817 if (gpu_opt->n_dev_use > 0 && !(*bEmulateGPU))
1819 /* Each PP node will use the intra-node id-th device from the
1820 * list of detected/selected GPUs. */
1821 if (!init_gpu(fp, cr->rank_pp_intranode, gpu_err_str,
1822 &hwinfo->gpu_info, gpu_opt))
1824 /* At this point the init should never fail as we made sure that
1825 * we have all the GPUs we need. If it still does, we'll bail. */
1826 /* TODO the decorating of gpu_err_str is nicer if it
1827 happens inside init_gpu. Out here, the decorating with
1828 the MPI rank makes sense. */
1829 gmx_fatal(FARGS, "On rank %d failed to initialize GPU #%d: %s",
1831 get_gpu_device_id(&hwinfo->gpu_info, gpu_opt,
1832 cr->rank_pp_intranode),
1836 /* Here we actually turn on hardware GPU acceleration */
1841 gmx_bool uses_simple_tables(int cutoff_scheme,
1842 nonbonded_verlet_t *nbv,
1845 gmx_bool bUsesSimpleTables = TRUE;
1848 switch (cutoff_scheme)
1851 bUsesSimpleTables = TRUE;
1854 assert(NULL != nbv && NULL != nbv->grp);
1855 grp_index = (group < 0) ? 0 : (nbv->ngrp - 1);
1856 bUsesSimpleTables = nbnxn_kernel_pairlist_simple(nbv->grp[grp_index].kernel_type);
1859 gmx_incons("unimplemented");
1861 return bUsesSimpleTables;
1864 static void init_ewald_f_table(interaction_const_t *ic,
1869 /* Get the Ewald table spacing based on Coulomb and/or LJ
1870 * Ewald coefficients and rtol.
1872 ic->tabq_scale = ewald_spline3_table_scale(ic);
1874 if (ic->cutoff_scheme == ecutsVERLET)
1876 maxr = ic->rcoulomb;
1880 maxr = std::max(ic->rcoulomb, rtab);
1882 ic->tabq_size = static_cast<int>(maxr*ic->tabq_scale) + 2;
1884 sfree_aligned(ic->tabq_coul_FDV0);
1885 sfree_aligned(ic->tabq_coul_F);
1886 sfree_aligned(ic->tabq_coul_V);
1888 sfree_aligned(ic->tabq_vdw_FDV0);
1889 sfree_aligned(ic->tabq_vdw_F);
1890 sfree_aligned(ic->tabq_vdw_V);
1892 if (ic->eeltype == eelEWALD || EEL_PME(ic->eeltype))
1894 /* Create the original table data in FDV0 */
1895 snew_aligned(ic->tabq_coul_FDV0, ic->tabq_size*4, 32);
1896 snew_aligned(ic->tabq_coul_F, ic->tabq_size, 32);
1897 snew_aligned(ic->tabq_coul_V, ic->tabq_size, 32);
1898 table_spline3_fill_ewald_lr(ic->tabq_coul_F, ic->tabq_coul_V, ic->tabq_coul_FDV0,
1899 ic->tabq_size, 1/ic->tabq_scale, ic->ewaldcoeff_q, v_q_ewald_lr);
1902 if (EVDW_PME(ic->vdwtype))
1904 snew_aligned(ic->tabq_vdw_FDV0, ic->tabq_size*4, 32);
1905 snew_aligned(ic->tabq_vdw_F, ic->tabq_size, 32);
1906 snew_aligned(ic->tabq_vdw_V, ic->tabq_size, 32);
1907 table_spline3_fill_ewald_lr(ic->tabq_vdw_F, ic->tabq_vdw_V, ic->tabq_vdw_FDV0,
1908 ic->tabq_size, 1/ic->tabq_scale, ic->ewaldcoeff_lj, v_lj_ewald_lr);
1912 void init_interaction_const_tables(FILE *fp,
1913 interaction_const_t *ic,
1916 if (ic->eeltype == eelEWALD || EEL_PME(ic->eeltype) || EVDW_PME(ic->vdwtype))
1918 init_ewald_f_table(ic, rtab);
1922 fprintf(fp, "Initialized non-bonded Ewald correction tables, spacing: %.2e size: %d\n\n",
1923 1/ic->tabq_scale, ic->tabq_size);
1928 static void clear_force_switch_constants(shift_consts_t *sc)
1935 static void force_switch_constants(real p,
1939 /* Here we determine the coefficient for shifting the force to zero
1940 * between distance rsw and the cut-off rc.
1941 * For a potential of r^-p, we have force p*r^-(p+1).
1942 * But to save flops we absorb p in the coefficient.
1944 * force/p = r^-(p+1) + c2*r^2 + c3*r^3
1945 * potential = r^-p + c2/3*r^3 + c3/4*r^4 + cpot
1947 sc->c2 = ((p + 1)*rsw - (p + 4)*rc)/(pow(rc, p + 2)*pow(rc - rsw, 2));
1948 sc->c3 = -((p + 1)*rsw - (p + 3)*rc)/(pow(rc, p + 2)*pow(rc - rsw, 3));
1949 sc->cpot = -pow(rc, -p) + p*sc->c2/3*pow(rc - rsw, 3) + p*sc->c3/4*pow(rc - rsw, 4);
1952 static void potential_switch_constants(real rsw, real rc,
1953 switch_consts_t *sc)
1955 /* The switch function is 1 at rsw and 0 at rc.
1956 * The derivative and second derivate are zero at both ends.
1957 * rsw = max(r - r_switch, 0)
1958 * sw = 1 + c3*rsw^3 + c4*rsw^4 + c5*rsw^5
1959 * dsw = 3*c3*rsw^2 + 4*c4*rsw^3 + 5*c5*rsw^4
1960 * force = force*dsw - potential*sw
1963 sc->c3 = -10*pow(rc - rsw, -3);
1964 sc->c4 = 15*pow(rc - rsw, -4);
1965 sc->c5 = -6*pow(rc - rsw, -5);
1968 /*! \brief Construct interaction constants
1970 * This data is used (particularly) by search and force code for
1971 * short-range interactions. Many of these are constant for the whole
1972 * simulation; some are constant only after PME tuning completes.
1975 init_interaction_const(FILE *fp,
1976 interaction_const_t **interaction_const,
1977 const t_forcerec *fr)
1979 interaction_const_t *ic;
1980 const real minusSix = -6.0;
1981 const real minusTwelve = -12.0;
1985 ic->cutoff_scheme = fr->cutoff_scheme;
1987 /* Just allocate something so we can free it */
1988 snew_aligned(ic->tabq_coul_FDV0, 16, 32);
1989 snew_aligned(ic->tabq_coul_F, 16, 32);
1990 snew_aligned(ic->tabq_coul_V, 16, 32);
1992 ic->rlist = fr->rlist;
1993 ic->rlistlong = fr->rlistlong;
1996 ic->vdwtype = fr->vdwtype;
1997 ic->vdw_modifier = fr->vdw_modifier;
1998 ic->rvdw = fr->rvdw;
1999 ic->rvdw_switch = fr->rvdw_switch;
2000 ic->ewaldcoeff_lj = fr->ewaldcoeff_lj;
2001 ic->ljpme_comb_rule = fr->ljpme_combination_rule;
2002 ic->sh_lj_ewald = 0;
2003 clear_force_switch_constants(&ic->dispersion_shift);
2004 clear_force_switch_constants(&ic->repulsion_shift);
2006 switch (ic->vdw_modifier)
2008 case eintmodPOTSHIFT:
2009 /* Only shift the potential, don't touch the force */
2010 ic->dispersion_shift.cpot = -pow(ic->rvdw, minusSix);
2011 ic->repulsion_shift.cpot = -pow(ic->rvdw, minusTwelve);
2012 if (EVDW_PME(ic->vdwtype))
2016 crc2 = sqr(ic->ewaldcoeff_lj*ic->rvdw);
2017 ic->sh_lj_ewald = (exp(-crc2)*(1 + crc2 + 0.5*crc2*crc2) - 1)*pow(ic->rvdw, minusSix);
2020 case eintmodFORCESWITCH:
2021 /* Switch the force, switch and shift the potential */
2022 force_switch_constants(6.0, ic->rvdw_switch, ic->rvdw,
2023 &ic->dispersion_shift);
2024 force_switch_constants(12.0, ic->rvdw_switch, ic->rvdw,
2025 &ic->repulsion_shift);
2027 case eintmodPOTSWITCH:
2028 /* Switch the potential and force */
2029 potential_switch_constants(ic->rvdw_switch, ic->rvdw,
2033 case eintmodEXACTCUTOFF:
2034 /* Nothing to do here */
2037 gmx_incons("unimplemented potential modifier");
2040 ic->sh_invrc6 = -ic->dispersion_shift.cpot;
2042 /* Electrostatics */
2043 ic->eeltype = fr->eeltype;
2044 ic->coulomb_modifier = fr->coulomb_modifier;
2045 ic->rcoulomb = fr->rcoulomb;
2046 ic->epsilon_r = fr->epsilon_r;
2047 ic->epsfac = fr->epsfac;
2048 ic->ewaldcoeff_q = fr->ewaldcoeff_q;
2050 if (fr->coulomb_modifier == eintmodPOTSHIFT)
2052 ic->sh_ewald = gmx_erfc(ic->ewaldcoeff_q*ic->rcoulomb);
2059 /* Reaction-field */
2060 if (EEL_RF(ic->eeltype))
2062 ic->epsilon_rf = fr->epsilon_rf;
2063 ic->k_rf = fr->k_rf;
2064 ic->c_rf = fr->c_rf;
2068 /* For plain cut-off we might use the reaction-field kernels */
2069 ic->epsilon_rf = ic->epsilon_r;
2071 if (fr->coulomb_modifier == eintmodPOTSHIFT)
2073 ic->c_rf = 1/ic->rcoulomb;
2083 real dispersion_shift;
2085 dispersion_shift = ic->dispersion_shift.cpot;
2086 if (EVDW_PME(ic->vdwtype))
2088 dispersion_shift -= ic->sh_lj_ewald;
2090 fprintf(fp, "Potential shift: LJ r^-12: %.3e r^-6: %.3e",
2091 ic->repulsion_shift.cpot, dispersion_shift);
2093 if (ic->eeltype == eelCUT)
2095 fprintf(fp, ", Coulomb %.e", -ic->c_rf);
2097 else if (EEL_PME(ic->eeltype))
2099 fprintf(fp, ", Ewald %.3e", -ic->sh_ewald);
2104 *interaction_const = ic;
2107 static void init_nb_verlet(FILE *fp,
2108 nonbonded_verlet_t **nb_verlet,
2109 gmx_bool bFEP_NonBonded,
2110 const t_inputrec *ir,
2111 const t_forcerec *fr,
2112 const t_commrec *cr,
2113 const char *nbpu_opt)
2115 nonbonded_verlet_t *nbv;
2118 gmx_bool bEmulateGPU, bHybridGPURun = FALSE;
2120 nbnxn_alloc_t *nb_alloc;
2121 nbnxn_free_t *nb_free;
2125 pick_nbnxn_resources(fp, cr, fr->hwinfo,
2132 nbv->min_ci_balanced = 0;
2134 nbv->ngrp = (DOMAINDECOMP(cr) ? 2 : 1);
2135 for (i = 0; i < nbv->ngrp; i++)
2137 nbv->grp[i].nbl_lists.nnbl = 0;
2138 nbv->grp[i].nbat = NULL;
2139 nbv->grp[i].kernel_type = nbnxnkNotSet;
2141 if (i == 0) /* local */
2143 pick_nbnxn_kernel(fp, cr, fr->use_simd_kernels,
2144 nbv->bUseGPU, bEmulateGPU, ir,
2145 &nbv->grp[i].kernel_type,
2146 &nbv->grp[i].ewald_excl,
2149 else /* non-local */
2151 if (nbpu_opt != NULL && strcmp(nbpu_opt, "gpu_cpu") == 0)
2153 /* Use GPU for local, select a CPU kernel for non-local */
2154 pick_nbnxn_kernel(fp, cr, fr->use_simd_kernels,
2156 &nbv->grp[i].kernel_type,
2157 &nbv->grp[i].ewald_excl,
2160 bHybridGPURun = TRUE;
2164 /* Use the same kernel for local and non-local interactions */
2165 nbv->grp[i].kernel_type = nbv->grp[0].kernel_type;
2166 nbv->grp[i].ewald_excl = nbv->grp[0].ewald_excl;
2171 nbnxn_init_search(&nbv->nbs,
2172 DOMAINDECOMP(cr) ? &cr->dd->nc : NULL,
2173 DOMAINDECOMP(cr) ? domdec_zones(cr->dd) : NULL,
2175 gmx_omp_nthreads_get(emntPairsearch));
2177 for (i = 0; i < nbv->ngrp; i++)
2179 gpu_set_host_malloc_and_free(nbv->grp[0].kernel_type == nbnxnk8x8x8_GPU,
2180 &nb_alloc, &nb_free);
2182 nbnxn_init_pairlist_set(&nbv->grp[i].nbl_lists,
2183 nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type),
2184 /* 8x8x8 "non-simple" lists are ATM always combined */
2185 !nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type),
2189 nbv->grp[0].kernel_type != nbv->grp[i].kernel_type)
2191 gmx_bool bSimpleList;
2192 int enbnxninitcombrule;
2194 bSimpleList = nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type);
2196 if (bSimpleList && (fr->vdwtype == evdwCUT && (fr->vdw_modifier == eintmodNONE || fr->vdw_modifier == eintmodPOTSHIFT)))
2198 /* Plain LJ cut-off: we can optimize with combination rules */
2199 enbnxninitcombrule = enbnxninitcombruleDETECT;
2201 else if (fr->vdwtype == evdwPME)
2203 /* LJ-PME: we need to use a combination rule for the grid */
2204 if (fr->ljpme_combination_rule == eljpmeGEOM)
2206 enbnxninitcombrule = enbnxninitcombruleGEOM;
2210 enbnxninitcombrule = enbnxninitcombruleLB;
2215 /* We use a full combination matrix: no rule required */
2216 enbnxninitcombrule = enbnxninitcombruleNONE;
2220 snew(nbv->grp[i].nbat, 1);
2221 nbnxn_atomdata_init(fp,
2223 nbv->grp[i].kernel_type,
2225 fr->ntype, fr->nbfp,
2227 bSimpleList ? gmx_omp_nthreads_get(emntNonbonded) : 1,
2232 nbv->grp[i].nbat = nbv->grp[0].nbat;
2238 /* init the NxN GPU data; the last argument tells whether we'll have
2239 * both local and non-local NB calculation on GPU */
2240 nbnxn_gpu_init(fp, &nbv->gpu_nbv,
2241 &fr->hwinfo->gpu_info,
2245 cr->rank_pp_intranode,
2247 (nbv->ngrp > 1) && !bHybridGPURun);
2249 /* With tMPI + GPUs some ranks may be sharing GPU(s) and therefore
2250 * also sharing texture references. To keep the code simple, we don't
2251 * treat texture references as shared resources, but this means that
2252 * the coulomb_tab and nbfp texture refs will get updated by multiple threads.
2253 * Hence, to ensure that the non-bonded kernels don't start before all
2254 * texture binding operations are finished, we need to wait for all ranks
2255 * to arrive here before continuing.
2257 * Note that we could omit this barrier if GPUs are not shared (or
2258 * texture objects are used), but as this is initialization code, there
2259 * is no point in complicating things.
2261 #ifdef GMX_THREAD_MPI
2266 #endif /* GMX_THREAD_MPI */
2268 if ((env = getenv("GMX_NB_MIN_CI")) != NULL)
2272 nbv->min_ci_balanced = strtol(env, &end, 10);
2273 if (!end || (*end != 0) || nbv->min_ci_balanced <= 0)
2275 gmx_fatal(FARGS, "Invalid value passed in GMX_NB_MIN_CI=%s, positive integer required", env);
2280 fprintf(debug, "Neighbor-list balancing parameter: %d (passed as env. var.)\n",
2281 nbv->min_ci_balanced);
2286 nbv->min_ci_balanced = nbnxn_gpu_min_ci_balanced(nbv->gpu_nbv);
2289 fprintf(debug, "Neighbor-list balancing parameter: %d (auto-adjusted to the number of GPU multi-processors)\n",
2290 nbv->min_ci_balanced);
2299 gmx_bool usingGpu(nonbonded_verlet_t *nbv)
2301 return nbv != NULL && nbv->bUseGPU;
2304 void init_forcerec(FILE *fp,
2305 const output_env_t oenv,
2308 const t_inputrec *ir,
2309 const gmx_mtop_t *mtop,
2310 const t_commrec *cr,
2316 const char *nbpu_opt,
2317 gmx_bool bNoSolvOpt,
2320 int i, m, negp_pp, negptable, egi, egj;
2325 gmx_bool bGenericKernelOnly;
2326 gmx_bool bMakeTables, bMakeSeparate14Table, bSomeNormalNbListsAreInUse;
2327 gmx_bool bFEP_NonBonded;
2328 int *nm_ind, egp_flags;
2330 if (fr->hwinfo == NULL)
2332 /* Detect hardware, gather information.
2333 * In mdrun, hwinfo has already been set before calling init_forcerec.
2334 * Here we ignore GPUs, as tools will not use them anyhow.
2336 fr->hwinfo = gmx_detect_hardware(fp, cr, FALSE);
2339 /* By default we turn SIMD kernels on, but it might be turned off further down... */
2340 fr->use_simd_kernels = TRUE;
2342 fr->bDomDec = DOMAINDECOMP(cr);
2344 if (check_box(ir->ePBC, box))
2346 gmx_fatal(FARGS, check_box(ir->ePBC, box));
2349 /* Test particle insertion ? */
2352 /* Set to the size of the molecule to be inserted (the last one) */
2353 /* Because of old style topologies, we have to use the last cg
2354 * instead of the last molecule type.
2356 cgs = &mtop->moltype[mtop->molblock[mtop->nmolblock-1].type].cgs;
2357 fr->n_tpi = cgs->index[cgs->nr] - cgs->index[cgs->nr-1];
2358 if (fr->n_tpi != mtop->mols.index[mtop->mols.nr] - mtop->mols.index[mtop->mols.nr-1])
2360 gmx_fatal(FARGS, "The molecule to insert can not consist of multiple charge groups.\nMake it a single charge group.");
2368 /* Copy AdResS parameters */
2371 fr->adress_type = ir->adress->type;
2372 fr->adress_const_wf = ir->adress->const_wf;
2373 fr->adress_ex_width = ir->adress->ex_width;
2374 fr->adress_hy_width = ir->adress->hy_width;
2375 fr->adress_icor = ir->adress->icor;
2376 fr->adress_site = ir->adress->site;
2377 fr->adress_ex_forcecap = ir->adress->ex_forcecap;
2378 fr->adress_do_hybridpairs = ir->adress->do_hybridpairs;
2381 snew(fr->adress_group_explicit, ir->adress->n_energy_grps);
2382 for (i = 0; i < ir->adress->n_energy_grps; i++)
2384 fr->adress_group_explicit[i] = ir->adress->group_explicit[i];
2387 fr->n_adress_tf_grps = ir->adress->n_tf_grps;
2388 snew(fr->adress_tf_table_index, fr->n_adress_tf_grps);
2389 for (i = 0; i < fr->n_adress_tf_grps; i++)
2391 fr->adress_tf_table_index[i] = ir->adress->tf_table_index[i];
2393 copy_rvec(ir->adress->refs, fr->adress_refs);
2397 fr->adress_type = eAdressOff;
2398 fr->adress_do_hybridpairs = FALSE;
2401 /* Copy the user determined parameters */
2402 fr->userint1 = ir->userint1;
2403 fr->userint2 = ir->userint2;
2404 fr->userint3 = ir->userint3;
2405 fr->userint4 = ir->userint4;
2406 fr->userreal1 = ir->userreal1;
2407 fr->userreal2 = ir->userreal2;
2408 fr->userreal3 = ir->userreal3;
2409 fr->userreal4 = ir->userreal4;
2412 fr->fc_stepsize = ir->fc_stepsize;
2415 fr->efep = ir->efep;
2416 fr->sc_alphavdw = ir->fepvals->sc_alpha;
2417 if (ir->fepvals->bScCoul)
2419 fr->sc_alphacoul = ir->fepvals->sc_alpha;
2420 fr->sc_sigma6_min = pow(ir->fepvals->sc_sigma_min, 6);
2424 fr->sc_alphacoul = 0;
2425 fr->sc_sigma6_min = 0; /* only needed when bScCoul is on */
2427 fr->sc_power = ir->fepvals->sc_power;
2428 fr->sc_r_power = ir->fepvals->sc_r_power;
2429 fr->sc_sigma6_def = pow(ir->fepvals->sc_sigma, 6);
2431 env = getenv("GMX_SCSIGMA_MIN");
2435 sscanf(env, "%20lf", &dbl);
2436 fr->sc_sigma6_min = pow(dbl, 6);
2439 fprintf(fp, "Setting the minimum soft core sigma to %g nm\n", dbl);
2443 fr->bNonbonded = TRUE;
2444 if (getenv("GMX_NO_NONBONDED") != NULL)
2446 /* turn off non-bonded calculations */
2447 fr->bNonbonded = FALSE;
2448 md_print_warn(cr, fp,
2449 "Found environment variable GMX_NO_NONBONDED.\n"
2450 "Disabling nonbonded calculations.\n");
2453 bGenericKernelOnly = FALSE;
2455 /* We now check in the NS code whether a particular combination of interactions
2456 * can be used with water optimization, and disable it if that is not the case.
2459 if (getenv("GMX_NB_GENERIC") != NULL)
2464 "Found environment variable GMX_NB_GENERIC.\n"
2465 "Disabling all interaction-specific nonbonded kernels, will only\n"
2466 "use the slow generic ones in src/gmxlib/nonbonded/nb_generic.c\n\n");
2468 bGenericKernelOnly = TRUE;
2471 if (bGenericKernelOnly == TRUE)
2476 if ( (getenv("GMX_DISABLE_SIMD_KERNELS") != NULL) || (getenv("GMX_NOOPTIMIZEDKERNELS") != NULL) )
2478 fr->use_simd_kernels = FALSE;
2482 "\nFound environment variable GMX_DISABLE_SIMD_KERNELS.\n"
2483 "Disabling the usage of any SIMD-specific non-bonded & bonded kernel routines\n"
2484 "(e.g. SSE2/SSE4.1/AVX).\n\n");
2488 fr->bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
2490 /* Check if we can/should do all-vs-all kernels */
2491 fr->bAllvsAll = can_use_allvsall(ir, FALSE, NULL, NULL);
2492 fr->AllvsAll_work = NULL;
2493 fr->AllvsAll_workgb = NULL;
2495 /* All-vs-all kernels have not been implemented in 4.6 and later.
2496 * See Redmine #1249. */
2499 fr->bAllvsAll = FALSE;
2503 "\nYour simulation settings would have triggered the efficient all-vs-all\n"
2504 "kernels in GROMACS 4.5, but these have not been implemented in GROMACS\n"
2505 "4.6 and 5.x. If performance is important, please use GROMACS 4.5.7\n"
2506 "or try cutoff-scheme = Verlet.\n\n");
2510 /* Neighbour searching stuff */
2511 fr->cutoff_scheme = ir->cutoff_scheme;
2512 fr->bGrid = (ir->ns_type == ensGRID);
2513 fr->ePBC = ir->ePBC;
2515 if (fr->cutoff_scheme == ecutsGROUP)
2517 const char *note = "NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be\n"
2518 "removed in a future release when 'verlet' supports all interaction forms.\n";
2522 fprintf(stderr, "\n%s\n", note);
2526 fprintf(fp, "\n%s\n", note);
2530 /* Determine if we will do PBC for distances in bonded interactions */
2531 if (fr->ePBC == epbcNONE)
2533 fr->bMolPBC = FALSE;
2537 if (!DOMAINDECOMP(cr))
2541 bSHAKE = (ir->eConstrAlg == econtSHAKE &&
2542 (gmx_mtop_ftype_count(mtop, F_CONSTR) > 0 ||
2543 gmx_mtop_ftype_count(mtop, F_CONSTRNC) > 0));
2545 /* The group cut-off scheme and SHAKE assume charge groups
2546 * are whole, but not using molpbc is faster in most cases.
2547 * With intermolecular interactions we need PBC for calculating
2548 * distances between atoms in different molecules.
2550 if ((fr->cutoff_scheme == ecutsGROUP || bSHAKE) &&
2551 !mtop->bIntermolecularInteractions)
2553 fr->bMolPBC = ir->bPeriodicMols;
2555 if (bSHAKE && fr->bMolPBC)
2557 gmx_fatal(FARGS, "SHAKE is not supported with periodic molecules");
2564 if (getenv("GMX_USE_GRAPH") != NULL)
2566 fr->bMolPBC = FALSE;
2569 md_print_warn(cr, fp, "GMX_USE_GRAPH is set, using the graph for bonded interactions\n");
2572 if (mtop->bIntermolecularInteractions)
2574 md_print_warn(cr, fp, "WARNING: Molecules linked by intermolecular interactions have to reside in the same periodic image, otherwise artifacts will occur!\n");
2578 if (bSHAKE && fr->bMolPBC)
2580 gmx_fatal(FARGS, "SHAKE is not properly supported with intermolecular interactions. For short simulations where linked molecules remain in the same periodic image, the environment variable GMX_USE_GRAPH can be used to override this check.\n");
2586 fr->bMolPBC = dd_bonded_molpbc(cr->dd, fr->ePBC);
2589 fr->bGB = (ir->implicit_solvent == eisGBSA);
2591 fr->rc_scaling = ir->refcoord_scaling;
2592 copy_rvec(ir->posres_com, fr->posres_com);
2593 copy_rvec(ir->posres_comB, fr->posres_comB);
2594 fr->rlist = cutoff_inf(ir->rlist);
2595 fr->rlistlong = cutoff_inf(ir->rlistlong);
2596 fr->eeltype = ir->coulombtype;
2597 fr->vdwtype = ir->vdwtype;
2598 fr->ljpme_combination_rule = ir->ljpme_combination_rule;
2600 fr->coulomb_modifier = ir->coulomb_modifier;
2601 fr->vdw_modifier = ir->vdw_modifier;
2603 /* Electrostatics: Translate from interaction-setting-in-mdp-file to kernel interaction format */
2604 switch (fr->eeltype)
2607 fr->nbkernel_elec_interaction = (fr->bGB) ? GMX_NBKERNEL_ELEC_GENERALIZEDBORN : GMX_NBKERNEL_ELEC_COULOMB;
2613 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD;
2617 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD;
2618 fr->coulomb_modifier = eintmodEXACTCUTOFF;
2627 case eelPMEUSERSWITCH:
2628 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_CUBICSPLINETABLE;
2634 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_EWALD;
2638 gmx_fatal(FARGS, "Unsupported electrostatic interaction: %s", eel_names[fr->eeltype]);
2642 /* Vdw: Translate from mdp settings to kernel format */
2643 switch (fr->vdwtype)
2648 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_BUCKINGHAM;
2652 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_LENNARDJONES;
2656 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_LJEWALD;
2662 case evdwENCADSHIFT:
2663 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
2667 gmx_fatal(FARGS, "Unsupported vdw interaction: %s", evdw_names[fr->vdwtype]);
2671 /* These start out identical to ir, but might be altered if we e.g. tabulate the interaction in the kernel */
2672 fr->nbkernel_elec_modifier = fr->coulomb_modifier;
2673 fr->nbkernel_vdw_modifier = fr->vdw_modifier;
2675 fr->rvdw = cutoff_inf(ir->rvdw);
2676 fr->rvdw_switch = ir->rvdw_switch;
2677 fr->rcoulomb = cutoff_inf(ir->rcoulomb);
2678 fr->rcoulomb_switch = ir->rcoulomb_switch;
2680 fr->bTwinRange = fr->rlistlong > fr->rlist;
2681 fr->bEwald = (EEL_PME(fr->eeltype) || fr->eeltype == eelEWALD);
2683 fr->reppow = mtop->ffparams.reppow;
2685 if (ir->cutoff_scheme == ecutsGROUP)
2687 fr->bvdwtab = ((fr->vdwtype != evdwCUT || !gmx_within_tol(fr->reppow, 12.0, 10*GMX_DOUBLE_EPS))
2688 && !EVDW_PME(fr->vdwtype));
2689 /* We have special kernels for standard Ewald and PME, but the pme-switch ones are tabulated above */
2690 fr->bcoultab = !(fr->eeltype == eelCUT ||
2691 fr->eeltype == eelEWALD ||
2692 fr->eeltype == eelPME ||
2693 fr->eeltype == eelRF ||
2694 fr->eeltype == eelRF_ZERO);
2696 /* If the user absolutely wants different switch/shift settings for coul/vdw, it is likely
2697 * going to be faster to tabulate the interaction than calling the generic kernel.
2698 * However, if generic kernels have been requested we keep things analytically.
2700 if (fr->nbkernel_elec_modifier == eintmodPOTSWITCH &&
2701 fr->nbkernel_vdw_modifier == eintmodPOTSWITCH &&
2702 bGenericKernelOnly == FALSE)
2704 if ((fr->rcoulomb_switch != fr->rvdw_switch) || (fr->rcoulomb != fr->rvdw))
2706 fr->bcoultab = TRUE;
2707 /* Once we tabulate electrostatics, we can use the switch function for LJ,
2708 * which would otherwise need two tables.
2712 else if ((fr->nbkernel_elec_modifier == eintmodPOTSHIFT && fr->nbkernel_vdw_modifier == eintmodPOTSHIFT) ||
2713 ((fr->nbkernel_elec_interaction == GMX_NBKERNEL_ELEC_REACTIONFIELD &&
2714 fr->nbkernel_elec_modifier == eintmodEXACTCUTOFF &&
2715 (fr->nbkernel_vdw_modifier == eintmodPOTSWITCH || fr->nbkernel_vdw_modifier == eintmodPOTSHIFT))))
2717 if ((fr->rcoulomb != fr->rvdw) && (bGenericKernelOnly == FALSE))
2719 fr->bcoultab = TRUE;
2723 if (fr->nbkernel_elec_modifier == eintmodFORCESWITCH)
2725 fr->bcoultab = TRUE;
2727 if (fr->nbkernel_vdw_modifier == eintmodFORCESWITCH)
2732 if (getenv("GMX_REQUIRE_TABLES"))
2735 fr->bcoultab = TRUE;
2740 fprintf(fp, "Table routines are used for coulomb: %s\n", bool_names[fr->bcoultab]);
2741 fprintf(fp, "Table routines are used for vdw: %s\n", bool_names[fr->bvdwtab ]);
2744 if (fr->bvdwtab == TRUE)
2746 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
2747 fr->nbkernel_vdw_modifier = eintmodNONE;
2749 if (fr->bcoultab == TRUE)
2751 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_CUBICSPLINETABLE;
2752 fr->nbkernel_elec_modifier = eintmodNONE;
2756 if (ir->cutoff_scheme == ecutsVERLET)
2758 if (!gmx_within_tol(fr->reppow, 12.0, 10*GMX_DOUBLE_EPS))
2760 gmx_fatal(FARGS, "Cut-off scheme %S only supports LJ repulsion power 12", ecutscheme_names[ir->cutoff_scheme]);
2762 fr->bvdwtab = FALSE;
2763 fr->bcoultab = FALSE;
2766 /* Tables are used for direct ewald sum */
2769 if (EEL_PME(ir->coulombtype))
2773 fprintf(fp, "Will do PME sum in reciprocal space for electrostatic interactions.\n");
2775 if (ir->coulombtype == eelP3M_AD)
2777 please_cite(fp, "Hockney1988");
2778 please_cite(fp, "Ballenegger2012");
2782 please_cite(fp, "Essmann95a");
2785 if (ir->ewald_geometry == eewg3DC)
2789 fprintf(fp, "Using the Ewald3DC correction for systems with a slab geometry.\n");
2791 please_cite(fp, "In-Chul99a");
2794 fr->ewaldcoeff_q = calc_ewaldcoeff_q(ir->rcoulomb, ir->ewald_rtol);
2795 init_ewald_tab(&(fr->ewald_table), ir, fp);
2798 fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for Ewald\n",
2799 1/fr->ewaldcoeff_q);
2803 if (EVDW_PME(ir->vdwtype))
2807 fprintf(fp, "Will do PME sum in reciprocal space for LJ dispersion interactions.\n");
2809 please_cite(fp, "Essmann95a");
2810 fr->ewaldcoeff_lj = calc_ewaldcoeff_lj(ir->rvdw, ir->ewald_rtol_lj);
2813 fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for LJ Ewald\n",
2814 1/fr->ewaldcoeff_lj);
2818 /* Electrostatics */
2819 fr->epsilon_r = ir->epsilon_r;
2820 fr->epsilon_rf = ir->epsilon_rf;
2821 fr->fudgeQQ = mtop->ffparams.fudgeQQ;
2823 /* Parameters for generalized RF */
2827 if (fr->eeltype == eelGRF)
2829 init_generalized_rf(fp, mtop, ir, fr);
2832 fr->bF_NoVirSum = (EEL_FULL(fr->eeltype) || EVDW_PME(fr->vdwtype) ||
2833 gmx_mtop_ftype_count(mtop, F_POSRES) > 0 ||
2834 gmx_mtop_ftype_count(mtop, F_FBPOSRES) > 0 ||
2835 IR_ELEC_FIELD(*ir) ||
2836 (fr->adress_icor != eAdressICOff)
2839 if (fr->cutoff_scheme == ecutsGROUP &&
2840 ncg_mtop(mtop) > fr->cg_nalloc && !DOMAINDECOMP(cr))
2842 /* Count the total number of charge groups */
2843 fr->cg_nalloc = ncg_mtop(mtop);
2844 srenew(fr->cg_cm, fr->cg_nalloc);
2846 if (fr->shift_vec == NULL)
2848 snew(fr->shift_vec, SHIFTS);
2851 if (fr->fshift == NULL)
2853 snew(fr->fshift, SHIFTS);
2856 if (fr->nbfp == NULL)
2858 fr->ntype = mtop->ffparams.atnr;
2859 fr->nbfp = mk_nbfp(&mtop->ffparams, fr->bBHAM);
2860 if (EVDW_PME(fr->vdwtype))
2862 fr->ljpme_c6grid = make_ljpme_c6grid(&mtop->ffparams, fr);
2866 /* Copy the energy group exclusions */
2867 fr->egp_flags = ir->opts.egp_flags;
2869 /* Van der Waals stuff */
2870 if ((fr->vdwtype != evdwCUT) && (fr->vdwtype != evdwUSER) && !fr->bBHAM)
2872 if (fr->rvdw_switch >= fr->rvdw)
2874 gmx_fatal(FARGS, "rvdw_switch (%f) must be < rvdw (%f)",
2875 fr->rvdw_switch, fr->rvdw);
2879 fprintf(fp, "Using %s Lennard-Jones, switch between %g and %g nm\n",
2880 (fr->eeltype == eelSWITCH) ? "switched" : "shifted",
2881 fr->rvdw_switch, fr->rvdw);
2885 if (fr->bBHAM && EVDW_PME(fr->vdwtype))
2887 gmx_fatal(FARGS, "LJ PME not supported with Buckingham");
2890 if (fr->bBHAM && (fr->vdwtype == evdwSHIFT || fr->vdwtype == evdwSWITCH))
2892 gmx_fatal(FARGS, "Switch/shift interaction not supported with Buckingham");
2895 if (fr->bBHAM && fr->cutoff_scheme == ecutsVERLET)
2897 gmx_fatal(FARGS, "Verlet cutoff-scheme is not supported with Buckingham");
2902 fprintf(fp, "Cut-off's: NS: %g Coulomb: %g %s: %g\n",
2903 fr->rlist, fr->rcoulomb, fr->bBHAM ? "BHAM" : "LJ", fr->rvdw);
2906 fr->eDispCorr = ir->eDispCorr;
2907 if (ir->eDispCorr != edispcNO)
2909 set_avcsixtwelve(fp, fr, mtop);
2914 set_bham_b_max(fp, fr, mtop);
2917 fr->gb_epsilon_solvent = ir->gb_epsilon_solvent;
2919 /* Copy the GBSA data (radius, volume and surftens for each
2920 * atomtype) from the topology atomtype section to forcerec.
2922 snew(fr->atype_radius, fr->ntype);
2923 snew(fr->atype_vol, fr->ntype);
2924 snew(fr->atype_surftens, fr->ntype);
2925 snew(fr->atype_gb_radius, fr->ntype);
2926 snew(fr->atype_S_hct, fr->ntype);
2928 if (mtop->atomtypes.nr > 0)
2930 for (i = 0; i < fr->ntype; i++)
2932 fr->atype_radius[i] = mtop->atomtypes.radius[i];
2934 for (i = 0; i < fr->ntype; i++)
2936 fr->atype_vol[i] = mtop->atomtypes.vol[i];
2938 for (i = 0; i < fr->ntype; i++)
2940 fr->atype_surftens[i] = mtop->atomtypes.surftens[i];
2942 for (i = 0; i < fr->ntype; i++)
2944 fr->atype_gb_radius[i] = mtop->atomtypes.gb_radius[i];
2946 for (i = 0; i < fr->ntype; i++)
2948 fr->atype_S_hct[i] = mtop->atomtypes.S_hct[i];
2952 /* Generate the GB table if needed */
2956 fr->gbtabscale = 2000;
2958 fr->gbtabscale = 500;
2962 fr->gbtab = make_gb_table(oenv, fr);
2964 init_gb(&fr->born, fr, ir, mtop, ir->gb_algorithm);
2966 /* Copy local gb data (for dd, this is done in dd_partition_system) */
2967 if (!DOMAINDECOMP(cr))
2969 make_local_gb(cr, fr->born, ir->gb_algorithm);
2973 /* Set the charge scaling */
2974 if (fr->epsilon_r != 0)
2976 fr->epsfac = ONE_4PI_EPS0/fr->epsilon_r;
2980 /* eps = 0 is infinite dieletric: no coulomb interactions */
2984 /* Reaction field constants */
2985 if (EEL_RF(fr->eeltype))
2987 calc_rffac(fp, fr->eeltype, fr->epsilon_r, fr->epsilon_rf,
2988 fr->rcoulomb, fr->temp, fr->zsquare, box,
2989 &fr->kappa, &fr->k_rf, &fr->c_rf);
2992 /*This now calculates sum for q and c6*/
2993 set_chargesum(fp, fr, mtop);
2995 /* if we are using LR electrostatics, and they are tabulated,
2996 * the tables will contain modified coulomb interactions.
2997 * Since we want to use the non-shifted ones for 1-4
2998 * coulombic interactions, we must have an extra set of tables.
3001 /* Construct tables.
3002 * A little unnecessary to make both vdw and coul tables sometimes,
3003 * but what the heck... */
3005 bMakeTables = fr->bcoultab || fr->bvdwtab || fr->bEwald ||
3006 (ir->eDispCorr != edispcNO && ir_vdw_switched(ir));
3008 bMakeSeparate14Table = ((!bMakeTables || fr->eeltype != eelCUT || fr->vdwtype != evdwCUT ||
3009 fr->coulomb_modifier != eintmodNONE ||
3010 fr->vdw_modifier != eintmodNONE ||
3011 fr->bBHAM || fr->bEwald) &&
3012 (gmx_mtop_ftype_count(mtop, F_LJ14) > 0 ||
3013 gmx_mtop_ftype_count(mtop, F_LJC14_Q) > 0 ||
3014 gmx_mtop_ftype_count(mtop, F_LJC_PAIRS_NB) > 0));
3016 negp_pp = ir->opts.ngener - ir->nwall;
3020 bSomeNormalNbListsAreInUse = TRUE;
3025 bSomeNormalNbListsAreInUse = (ir->eDispCorr != edispcNO);
3026 for (egi = 0; egi < negp_pp; egi++)
3028 for (egj = egi; egj < negp_pp; egj++)
3030 egp_flags = ir->opts.egp_flags[GID(egi, egj, ir->opts.ngener)];
3031 if (!(egp_flags & EGP_EXCL))
3033 if (egp_flags & EGP_TABLE)
3039 bSomeNormalNbListsAreInUse = TRUE;
3044 if (bSomeNormalNbListsAreInUse)
3046 fr->nnblists = negptable + 1;
3050 fr->nnblists = negptable;
3052 if (fr->nnblists > 1)
3054 snew(fr->gid2nblists, ir->opts.ngener*ir->opts.ngener);
3063 snew(fr->nblists, fr->nnblists);
3065 /* This code automatically gives table length tabext without cut-off's,
3066 * in that case grompp should already have checked that we do not need
3067 * normal tables and we only generate tables for 1-4 interactions.
3069 rtab = ir->rlistlong + ir->tabext;
3073 /* make tables for ordinary interactions */
3074 if (bSomeNormalNbListsAreInUse)
3076 make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn, NULL, NULL, &fr->nblists[0]);
3079 make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn, NULL, NULL, &fr->nblists[fr->nnblists/2]);
3081 if (!bMakeSeparate14Table)
3083 fr->tab14 = fr->nblists[0].table_elec_vdw;
3093 /* Read the special tables for certain energy group pairs */
3094 nm_ind = mtop->groups.grps[egcENER].nm_ind;
3095 for (egi = 0; egi < negp_pp; egi++)
3097 for (egj = egi; egj < negp_pp; egj++)
3099 egp_flags = ir->opts.egp_flags[GID(egi, egj, ir->opts.ngener)];
3100 if ((egp_flags & EGP_TABLE) && !(egp_flags & EGP_EXCL))
3102 if (fr->nnblists > 1)
3104 fr->gid2nblists[GID(egi, egj, ir->opts.ngener)] = m;
3106 /* Read the table file with the two energy groups names appended */
3107 make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn,
3108 *mtop->groups.grpname[nm_ind[egi]],
3109 *mtop->groups.grpname[nm_ind[egj]],
3113 make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn,
3114 *mtop->groups.grpname[nm_ind[egi]],
3115 *mtop->groups.grpname[nm_ind[egj]],
3116 &fr->nblists[fr->nnblists/2+m]);
3120 else if (fr->nnblists > 1)
3122 fr->gid2nblists[GID(egi, egj, ir->opts.ngener)] = 0;
3128 else if ((fr->eDispCorr != edispcNO) &&
3129 ((fr->vdw_modifier == eintmodPOTSWITCH) ||
3130 (fr->vdw_modifier == eintmodFORCESWITCH) ||
3131 (fr->vdw_modifier == eintmodPOTSHIFT)))
3133 /* Tables might not be used for the potential modifier interactions per se, but
3134 * we still need them to evaluate switch/shift dispersion corrections in this case.
3136 make_nbf_tables(fp, oenv, fr, rtab, cr, tabfn, NULL, NULL, &fr->nblists[0]);
3139 if (bMakeSeparate14Table)
3141 /* generate extra tables with plain Coulomb for 1-4 interactions only */
3142 fr->tab14 = make_tables(fp, oenv, fr, MASTER(cr), tabpfn, rtab,
3143 GMX_MAKETABLES_14ONLY);
3146 /* Read AdResS Thermo Force table if needed */
3147 if (fr->adress_icor == eAdressICThermoForce)
3149 /* old todo replace */
3151 if (ir->adress->n_tf_grps > 0)
3153 make_adress_tf_tables(fp, oenv, fr, ir, tabfn, mtop, box);
3158 /* load the default table */
3159 snew(fr->atf_tabs, 1);
3160 fr->atf_tabs[DEFAULT_TF_TABLE] = make_atf_table(fp, oenv, fr, tabafn, box);
3165 fr->nwall = ir->nwall;
3166 if (ir->nwall && ir->wall_type == ewtTABLE)
3168 make_wall_tables(fp, oenv, ir, tabfn, &mtop->groups, fr);
3173 fcd->bondtab = make_bonded_tables(fp,
3174 F_TABBONDS, F_TABBONDSNC,
3176 fcd->angletab = make_bonded_tables(fp,
3179 fcd->dihtab = make_bonded_tables(fp,
3187 fprintf(debug, "No fcdata or table file name passed, can not read table, can not do bonded interactions\n");
3191 /* QM/MM initialization if requested
3195 fprintf(stderr, "QM/MM calculation requested.\n");
3198 fr->bQMMM = ir->bQMMM;
3199 fr->qr = mk_QMMMrec();
3201 /* Set all the static charge group info */
3202 fr->cginfo_mb = init_cginfo_mb(fp, mtop, fr, bNoSolvOpt,
3204 &fr->bExcl_IntraCGAll_InterCGNone);
3205 if (DOMAINDECOMP(cr))
3211 fr->cginfo = cginfo_expand(mtop->nmolblock, fr->cginfo_mb);
3214 if (!DOMAINDECOMP(cr))
3216 forcerec_set_ranges(fr, ncg_mtop(mtop), ncg_mtop(mtop),
3217 mtop->natoms, mtop->natoms, mtop->natoms);
3220 fr->print_force = print_force;
3223 /* coarse load balancing vars */
3228 /* Initialize neighbor search */
3229 init_ns(fp, cr, &fr->ns, fr, mtop);
3231 if (cr->duty & DUTY_PP)
3233 gmx_nonbonded_setup(fr, bGenericKernelOnly);
3237 gmx_setup_adress_kernels(fp,bGenericKernelOnly);
3242 /* Initialize the thread working data for bonded interactions */
3243 init_bonded_threading(fp, fr, mtop->groups.grps[egcENER].nr);
3245 snew(fr->excl_load, fr->nthreads+1);
3247 /* fr->ic is used both by verlet and group kernels (to some extent) now */
3248 init_interaction_const(fp, &fr->ic, fr);
3249 init_interaction_const_tables(fp, fr->ic, rtab);
3251 if (fr->cutoff_scheme == ecutsVERLET)
3253 if (ir->rcoulomb != ir->rvdw)
3255 gmx_fatal(FARGS, "With Verlet lists rcoulomb and rvdw should be identical");
3258 init_nb_verlet(fp, &fr->nbv, bFEP_NonBonded, ir, fr, cr, nbpu_opt);
3261 if (ir->eDispCorr != edispcNO)
3263 calc_enervirdiff(fp, ir->eDispCorr, fr);
3267 #define pr_real(fp, r) fprintf(fp, "%s: %e\n",#r, r)
3268 #define pr_int(fp, i) fprintf((fp), "%s: %d\n",#i, i)
3269 #define pr_bool(fp, b) fprintf((fp), "%s: %s\n",#b, bool_names[b])
3271 void pr_forcerec(FILE *fp, t_forcerec *fr)
3275 pr_real(fp, fr->rlist);
3276 pr_real(fp, fr->rcoulomb);
3277 pr_real(fp, fr->fudgeQQ);
3278 pr_bool(fp, fr->bGrid);
3279 pr_bool(fp, fr->bTwinRange);
3280 /*pr_int(fp,fr->cg0);
3281 pr_int(fp,fr->hcg);*/
3282 for (i = 0; i < fr->nnblists; i++)
3284 pr_int(fp, fr->nblists[i].table_elec_vdw.n);
3286 pr_real(fp, fr->rcoulomb_switch);
3287 pr_real(fp, fr->rcoulomb);
3292 void forcerec_set_excl_load(t_forcerec *fr,
3293 const gmx_localtop_t *top)
3296 int t, i, j, ntot, n, ntarget;
3298 ind = top->excls.index;
3302 for (i = 0; i < top->excls.nr; i++)
3304 for (j = ind[i]; j < ind[i+1]; j++)
3313 fr->excl_load[0] = 0;
3316 for (t = 1; t <= fr->nthreads; t++)
3318 ntarget = (ntot*t)/fr->nthreads;
3319 while (i < top->excls.nr && n < ntarget)
3321 for (j = ind[i]; j < ind[i+1]; j++)
3330 fr->excl_load[t] = i;
3334 /* Frees GPU memory and destroys the GPU context.
3336 * Note that this function needs to be called even if GPUs are not used
3337 * in this run because the PME ranks have no knowledge of whether GPUs
3338 * are used or not, but all ranks need to enter the barrier below.
3340 void free_gpu_resources(const t_forcerec *fr,
3341 const t_commrec *cr,
3342 const gmx_gpu_info_t *gpu_info,
3343 const gmx_gpu_opt_t *gpu_opt)
3345 gmx_bool bIsPPrankUsingGPU;
3346 char gpu_err_str[STRLEN];
3348 bIsPPrankUsingGPU = (cr->duty & DUTY_PP) && fr && fr->nbv && fr->nbv->bUseGPU;
3350 if (bIsPPrankUsingGPU)
3352 /* free nbnxn data in GPU memory */
3353 nbnxn_gpu_free(fr->nbv->gpu_nbv);
3355 /* With tMPI we need to wait for all ranks to finish deallocation before
3356 * destroying the context in free_gpu() as some ranks may be sharing
3358 * Note: as only PP ranks need to free GPU resources, so it is safe to
3359 * not call the barrier on PME ranks.
3361 #ifdef GMX_THREAD_MPI
3366 #endif /* GMX_THREAD_MPI */
3368 /* uninitialize GPU (by destroying the context) */
3369 if (!free_cuda_gpu(cr->rank_pp_intranode, gpu_err_str, gpu_info, gpu_opt))
3371 gmx_warning("On rank %d failed to free GPU #%d: %s",
3372 cr->nodeid, get_current_cuda_gpu_device_id(), gpu_err_str);