2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
51 #include "gromacs/commandline/filenm.h"
52 #include "gromacs/domdec/domdec.h"
53 #include "gromacs/domdec/domdec_struct.h"
54 #include "gromacs/ewald/ewald.h"
55 #include "gromacs/ewald/ewald_utils.h"
56 #include "gromacs/fileio/filetypes.h"
57 #include "gromacs/gmxlib/network.h"
58 #include "gromacs/gmxlib/nonbonded/nonbonded.h"
59 #include "gromacs/gpu_utils/gpu_utils.h"
60 #include "gromacs/hardware/hw_info.h"
61 #include "gromacs/listed_forces/gpubonded.h"
62 #include "gromacs/listed_forces/manage_threading.h"
63 #include "gromacs/listed_forces/pairs.h"
64 #include "gromacs/math/functions.h"
65 #include "gromacs/math/units.h"
66 #include "gromacs/math/utilities.h"
67 #include "gromacs/math/vec.h"
68 #include "gromacs/mdlib/dispersioncorrection.h"
69 #include "gromacs/mdlib/force.h"
70 #include "gromacs/mdlib/forcerec_threading.h"
71 #include "gromacs/mdlib/gmx_omp_nthreads.h"
72 #include "gromacs/mdlib/md_support.h"
73 #include "gromacs/mdlib/ns.h"
74 #include "gromacs/mdlib/qmmm.h"
75 #include "gromacs/mdlib/rf_util.h"
76 #include "gromacs/mdlib/wall.h"
77 #include "gromacs/mdtypes/commrec.h"
78 #include "gromacs/mdtypes/fcdata.h"
79 #include "gromacs/mdtypes/group.h"
80 #include "gromacs/mdtypes/iforceprovider.h"
81 #include "gromacs/mdtypes/inputrec.h"
82 #include "gromacs/mdtypes/md_enums.h"
83 #include "gromacs/nbnxm/gpu_data_mgmt.h"
84 #include "gromacs/nbnxm/nbnxm.h"
85 #include "gromacs/nbnxm/nbnxm_geometry.h"
86 #include "gromacs/pbcutil/ishift.h"
87 #include "gromacs/pbcutil/pbc.h"
88 #include "gromacs/tables/forcetable.h"
89 #include "gromacs/topology/mtop_util.h"
90 #include "gromacs/trajectory/trajectoryframe.h"
91 #include "gromacs/utility/cstringutil.h"
92 #include "gromacs/utility/exceptions.h"
93 #include "gromacs/utility/fatalerror.h"
94 #include "gromacs/utility/gmxassert.h"
95 #include "gromacs/utility/logger.h"
96 #include "gromacs/utility/physicalnodecommunicator.h"
97 #include "gromacs/utility/pleasecite.h"
98 #include "gromacs/utility/smalloc.h"
99 #include "gromacs/utility/strconvert.h"
101 static real *mk_nbfp(const gmx_ffparams_t *idef, gmx_bool bBHAM)
109 snew(nbfp, 3*atnr*atnr);
110 for (i = k = 0; (i < atnr); i++)
112 for (j = 0; (j < atnr); j++, k++)
114 BHAMA(nbfp, atnr, i, j) = idef->iparams[k].bham.a;
115 BHAMB(nbfp, atnr, i, j) = idef->iparams[k].bham.b;
116 /* nbfp now includes the 6.0 derivative prefactor */
117 BHAMC(nbfp, atnr, i, j) = idef->iparams[k].bham.c*6.0;
123 snew(nbfp, 2*atnr*atnr);
124 for (i = k = 0; (i < atnr); i++)
126 for (j = 0; (j < atnr); j++, k++)
128 /* nbfp now includes the 6.0/12.0 derivative prefactors */
129 C6(nbfp, atnr, i, j) = idef->iparams[k].lj.c6*6.0;
130 C12(nbfp, atnr, i, j) = idef->iparams[k].lj.c12*12.0;
138 static real *make_ljpme_c6grid(const gmx_ffparams_t *idef, t_forcerec *fr)
141 real c6, c6i, c6j, c12i, c12j, epsi, epsj, sigmai, sigmaj;
144 /* For LJ-PME simulations, we correct the energies with the reciprocal space
145 * inside of the cut-off. To do this the non-bonded kernels needs to have
146 * access to the C6-values used on the reciprocal grid in pme.c
150 snew(grid, 2*atnr*atnr);
151 for (i = k = 0; (i < atnr); i++)
153 for (j = 0; (j < atnr); j++, k++)
155 c6i = idef->iparams[i*(atnr+1)].lj.c6;
156 c12i = idef->iparams[i*(atnr+1)].lj.c12;
157 c6j = idef->iparams[j*(atnr+1)].lj.c6;
158 c12j = idef->iparams[j*(atnr+1)].lj.c12;
159 c6 = std::sqrt(c6i * c6j);
160 if (fr->ljpme_combination_rule == eljpmeLB
161 && !gmx_numzero(c6) && !gmx_numzero(c12i) && !gmx_numzero(c12j))
163 sigmai = gmx::sixthroot(c12i / c6i);
164 sigmaj = gmx::sixthroot(c12j / c6j);
165 epsi = c6i * c6i / c12i;
166 epsj = c6j * c6j / c12j;
167 c6 = std::sqrt(epsi * epsj) * gmx::power6(0.5*(sigmai+sigmaj));
169 /* Store the elements at the same relative positions as C6 in nbfp in order
170 * to simplify access in the kernels
172 grid[2*(atnr*i+j)] = c6*6.0;
178 /* This routine sets fr->solvent_opt to the most common solvent in the
179 * system, e.g. esolSPC or esolTIP4P. It will also mark each charge group in
180 * the fr->solvent_type array with the correct type (or esolNO).
182 * Charge groups that fulfill the conditions but are not identical to the
183 * most common one will be marked as esolNO in the solvent_type array.
185 * TIP3p is identical to SPC for these purposes, so we call it
186 * SPC in the arrays (Apologies to Bill Jorgensen ;-)
188 * NOTE: QM particle should not
189 * become an optimized solvent. Not even if there is only one charge
199 } solvent_parameters_t;
202 check_solvent_cg(const gmx_moltype_t *molt,
205 const unsigned char *qm_grpnr,
206 const t_grps *qm_grps,
208 int *n_solvent_parameters,
209 solvent_parameters_t **solvent_parameters_p,
219 real tmp_charge[4] = { 0.0 }; /* init to zero to make gcc 7 happy */
220 int tmp_vdwtype[4] = { 0 }; /* init to zero to make gcc 7 happy */
223 solvent_parameters_t *solvent_parameters;
225 /* We use a list with parameters for each solvent type.
226 * Every time we discover a new molecule that fulfills the basic
227 * conditions for a solvent we compare with the previous entries
228 * in these lists. If the parameters are the same we just increment
229 * the counter for that type, and otherwise we create a new type
230 * based on the current molecule.
232 * Once we've finished going through all molecules we check which
233 * solvent is most common, and mark all those molecules while we
234 * clear the flag on all others.
237 solvent_parameters = *solvent_parameters_p;
239 /* Mark the cg first as non optimized */
242 /* Check if this cg has no exclusions with atoms in other charge groups
243 * and all atoms inside the charge group excluded.
244 * We only have 3 or 4 atom solvent loops.
246 if (GET_CGINFO_EXCL_INTER(cginfo) ||
247 !GET_CGINFO_EXCL_INTRA(cginfo))
252 /* Get the indices of the first atom in this charge group */
253 j0 = molt->cgs.index[cg0];
254 j1 = molt->cgs.index[cg0+1];
256 /* Number of atoms in our molecule */
262 "Moltype '%s': there are %d atoms in this charge group\n",
266 /* Check if it could be an SPC (3 atoms) or TIP4p (4) water,
269 if (nj < 3 || nj > 4)
274 /* Check if we are doing QM on this group */
276 if (qm_grpnr != nullptr)
278 for (j = j0; j < j1 && !qm; j++)
280 qm = (qm_grpnr[j] < qm_grps->nr - 1);
283 /* Cannot use solvent optimization with QM */
289 atom = molt->atoms.atom;
291 /* Still looks like a solvent, time to check parameters */
293 /* If it is perturbed (free energy) we can't use the solvent loops,
294 * so then we just skip to the next molecule.
298 for (j = j0; j < j1 && !perturbed; j++)
300 perturbed = PERTURBED(atom[j]);
308 /* Now it's only a question if the VdW and charge parameters
309 * are OK. Before doing the check we compare and see if they are
310 * identical to a possible previous solvent type.
311 * First we assign the current types and charges.
313 for (j = 0; j < nj; j++)
315 tmp_vdwtype[j] = atom[j0+j].type;
316 tmp_charge[j] = atom[j0+j].q;
319 /* Does it match any previous solvent type? */
320 for (k = 0; k < *n_solvent_parameters; k++)
325 /* We can only match SPC with 3 atoms and TIP4p with 4 atoms */
326 if ( (solvent_parameters[k].model == esolSPC && nj != 3) ||
327 (solvent_parameters[k].model == esolTIP4P && nj != 4) )
332 /* Check that types & charges match for all atoms in molecule */
333 for (j = 0; j < nj && match; j++)
335 if (tmp_vdwtype[j] != solvent_parameters[k].vdwtype[j])
339 if (tmp_charge[j] != solvent_parameters[k].charge[j])
346 /* Congratulations! We have a matched solvent.
347 * Flag it with this type for later processing.
350 solvent_parameters[k].count += nmol;
352 /* We are done with this charge group */
357 /* If we get here, we have a tentative new solvent type.
358 * Before we add it we must check that it fulfills the requirements
359 * of the solvent optimized loops. First determine which atoms have
362 for (j = 0; j < nj; j++)
365 tjA = tmp_vdwtype[j];
367 /* Go through all other tpes and see if any have non-zero
368 * VdW parameters when combined with this one.
370 for (k = 0; k < fr->ntype && (!has_vdw[j]); k++)
372 /* We already checked that the atoms weren't perturbed,
373 * so we only need to check state A now.
377 has_vdw[j] = (has_vdw[j] ||
378 (BHAMA(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
379 (BHAMB(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
380 (BHAMC(fr->nbfp, fr->ntype, tjA, k) != 0.0));
385 has_vdw[j] = (has_vdw[j] ||
386 (C6(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
387 (C12(fr->nbfp, fr->ntype, tjA, k) != 0.0));
392 /* Now we know all we need to make the final check and assignment. */
396 * For this we require thatn all atoms have charge,
397 * the charges on atom 2 & 3 should be the same, and only
398 * atom 1 might have VdW.
402 tmp_charge[0] != 0 &&
403 tmp_charge[1] != 0 &&
404 tmp_charge[2] == tmp_charge[1])
406 srenew(solvent_parameters, *n_solvent_parameters+1);
407 solvent_parameters[*n_solvent_parameters].model = esolSPC;
408 solvent_parameters[*n_solvent_parameters].count = nmol;
409 for (k = 0; k < 3; k++)
411 solvent_parameters[*n_solvent_parameters].vdwtype[k] = tmp_vdwtype[k];
412 solvent_parameters[*n_solvent_parameters].charge[k] = tmp_charge[k];
415 *cg_sp = *n_solvent_parameters;
416 (*n_solvent_parameters)++;
421 /* Or could it be a TIP4P?
422 * For this we require thatn atoms 2,3,4 have charge, but not atom 1.
423 * Only atom 1 mght have VdW.
428 tmp_charge[0] == 0 &&
429 tmp_charge[1] != 0 &&
430 tmp_charge[2] == tmp_charge[1] &&
433 srenew(solvent_parameters, *n_solvent_parameters+1);
434 solvent_parameters[*n_solvent_parameters].model = esolTIP4P;
435 solvent_parameters[*n_solvent_parameters].count = nmol;
436 for (k = 0; k < 4; k++)
438 solvent_parameters[*n_solvent_parameters].vdwtype[k] = tmp_vdwtype[k];
439 solvent_parameters[*n_solvent_parameters].charge[k] = tmp_charge[k];
442 *cg_sp = *n_solvent_parameters;
443 (*n_solvent_parameters)++;
447 *solvent_parameters_p = solvent_parameters;
451 check_solvent(FILE * fp,
452 const gmx_mtop_t * mtop,
454 cginfo_mb_t *cginfo_mb)
457 const gmx_moltype_t *molt;
458 int mol, cg_mol, at_offset, am, cgm, i, nmol_ch, nmol;
459 int n_solvent_parameters;
460 solvent_parameters_t *solvent_parameters;
466 fprintf(debug, "Going to determine what solvent types we have.\n");
469 n_solvent_parameters = 0;
470 solvent_parameters = nullptr;
471 /* Allocate temporary array for solvent type */
472 snew(cg_sp, mtop->molblock.size());
475 for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
477 molt = &mtop->moltype[mtop->molblock[mb].type];
479 /* Here we have to loop over all individual molecules
480 * because we need to check for QMMM particles.
482 snew(cg_sp[mb], cginfo_mb[mb].cg_mod);
483 nmol_ch = cginfo_mb[mb].cg_mod/cgs->nr;
484 nmol = mtop->molblock[mb].nmol/nmol_ch;
485 for (mol = 0; mol < nmol_ch; mol++)
488 am = mol*cgs->index[cgs->nr];
489 for (cg_mol = 0; cg_mol < cgs->nr; cg_mol++)
491 check_solvent_cg(molt, cg_mol, nmol,
492 mtop->groups.grpnr[egcQMMM] ?
493 mtop->groups.grpnr[egcQMMM]+at_offset+am : nullptr,
494 &mtop->groups.grps[egcQMMM],
496 &n_solvent_parameters, &solvent_parameters,
497 cginfo_mb[mb].cginfo[cgm+cg_mol],
498 &cg_sp[mb][cgm+cg_mol]);
501 at_offset += cgs->index[cgs->nr];
504 /* Puh! We finished going through all charge groups.
505 * Now find the most common solvent model.
508 /* Most common solvent this far */
510 for (i = 0; i < n_solvent_parameters; i++)
513 solvent_parameters[i].count > solvent_parameters[bestsp].count)
521 bestsol = solvent_parameters[bestsp].model;
529 for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
531 cgs = &mtop->moltype[mtop->molblock[mb].type].cgs;
532 nmol = (mtop->molblock[mb].nmol*cgs->nr)/cginfo_mb[mb].cg_mod;
533 for (i = 0; i < cginfo_mb[mb].cg_mod; i++)
535 if (cg_sp[mb][i] == bestsp)
537 SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[i], bestsol);
542 SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[i], esolNO);
549 if (bestsol != esolNO && fp != nullptr)
551 fprintf(fp, "\nEnabling %s-like water optimization for %d molecules.\n\n",
553 solvent_parameters[bestsp].count);
556 sfree(solvent_parameters);
557 fr->solvent_opt = bestsol;
561 acNONE = 0, acCONSTRAINT, acSETTLE
564 static cginfo_mb_t *init_cginfo_mb(FILE *fplog, const gmx_mtop_t *mtop,
565 t_forcerec *fr, gmx_bool bNoSolvOpt,
566 gmx_bool *bFEP_NonBonded,
567 gmx_bool *bExcl_IntraCGAll_InterCGNone)
570 const t_blocka *excl;
571 const gmx_moltype_t *molt;
572 const gmx_molblock_t *molb;
573 cginfo_mb_t *cginfo_mb;
576 int cg_offset, a_offset;
577 int m, cg, a0, a1, gid, ai, j, aj, excl_nalloc;
581 gmx_bool bId, *bExcl, bExclIntraAll, bExclInter, bHaveVDW, bHaveQ, bHavePerturbedAtoms;
583 snew(cginfo_mb, mtop->molblock.size());
585 snew(type_VDW, fr->ntype);
586 for (ai = 0; ai < fr->ntype; ai++)
588 type_VDW[ai] = FALSE;
589 for (j = 0; j < fr->ntype; j++)
591 type_VDW[ai] = type_VDW[ai] ||
593 C6(fr->nbfp, fr->ntype, ai, j) != 0 ||
594 C12(fr->nbfp, fr->ntype, ai, j) != 0;
598 *bFEP_NonBonded = FALSE;
599 *bExcl_IntraCGAll_InterCGNone = TRUE;
602 snew(bExcl, excl_nalloc);
605 for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
607 molb = &mtop->molblock[mb];
608 molt = &mtop->moltype[molb->type];
612 /* Check if the cginfo is identical for all molecules in this block.
613 * If so, we only need an array of the size of one molecule.
614 * Otherwise we make an array of #mol times #cgs per molecule.
617 for (m = 0; m < molb->nmol; m++)
619 int am = m*cgs->index[cgs->nr];
620 for (cg = 0; cg < cgs->nr; cg++)
623 a1 = cgs->index[cg+1];
624 if (getGroupType(mtop->groups, egcENER, a_offset+am+a0) !=
625 getGroupType(mtop->groups, egcENER, a_offset +a0))
629 if (mtop->groups.grpnr[egcQMMM] != nullptr)
631 for (ai = a0; ai < a1; ai++)
633 if (mtop->groups.grpnr[egcQMMM][a_offset+am+ai] !=
634 mtop->groups.grpnr[egcQMMM][a_offset +ai])
643 cginfo_mb[mb].cg_start = cg_offset;
644 cginfo_mb[mb].cg_end = cg_offset + molb->nmol*cgs->nr;
645 cginfo_mb[mb].cg_mod = (bId ? 1 : molb->nmol)*cgs->nr;
646 snew(cginfo_mb[mb].cginfo, cginfo_mb[mb].cg_mod);
647 cginfo = cginfo_mb[mb].cginfo;
649 /* Set constraints flags for constrained atoms */
650 snew(a_con, molt->atoms.nr);
651 for (ftype = 0; ftype < F_NRE; ftype++)
653 if (interaction_function[ftype].flags & IF_CONSTRAINT)
658 for (ia = 0; ia < molt->ilist[ftype].size(); ia += 1+nral)
662 for (a = 0; a < nral; a++)
664 a_con[molt->ilist[ftype].iatoms[ia+1+a]] =
665 (ftype == F_SETTLE ? acSETTLE : acCONSTRAINT);
671 for (m = 0; m < (bId ? 1 : molb->nmol); m++)
674 int am = m*cgs->index[cgs->nr];
675 for (cg = 0; cg < cgs->nr; cg++)
678 a1 = cgs->index[cg+1];
680 /* Store the energy group in cginfo */
681 gid = getGroupType(mtop->groups, egcENER, a_offset+am+a0);
682 SET_CGINFO_GID(cginfo[cgm+cg], gid);
684 /* Check the intra/inter charge group exclusions */
685 if (a1-a0 > excl_nalloc)
687 excl_nalloc = a1 - a0;
688 srenew(bExcl, excl_nalloc);
690 /* bExclIntraAll: all intra cg interactions excluded
691 * bExclInter: any inter cg interactions excluded
693 bExclIntraAll = TRUE;
697 bHavePerturbedAtoms = FALSE;
698 for (ai = a0; ai < a1; ai++)
700 /* Check VDW and electrostatic interactions */
701 bHaveVDW = bHaveVDW || (type_VDW[molt->atoms.atom[ai].type] ||
702 type_VDW[molt->atoms.atom[ai].typeB]);
703 bHaveQ = bHaveQ || (molt->atoms.atom[ai].q != 0 ||
704 molt->atoms.atom[ai].qB != 0);
706 bHavePerturbedAtoms = bHavePerturbedAtoms || (PERTURBED(molt->atoms.atom[ai]) != 0);
708 /* Clear the exclusion list for atom ai */
709 for (aj = a0; aj < a1; aj++)
711 bExcl[aj-a0] = FALSE;
713 /* Loop over all the exclusions of atom ai */
714 for (j = excl->index[ai]; j < excl->index[ai+1]; j++)
717 if (aj < a0 || aj >= a1)
726 /* Check if ai excludes a0 to a1 */
727 for (aj = a0; aj < a1; aj++)
731 bExclIntraAll = FALSE;
738 SET_CGINFO_CONSTR(cginfo[cgm+cg]);
741 SET_CGINFO_SETTLE(cginfo[cgm+cg]);
749 SET_CGINFO_EXCL_INTRA(cginfo[cgm+cg]);
753 SET_CGINFO_EXCL_INTER(cginfo[cgm+cg]);
755 if (a1 - a0 > MAX_CHARGEGROUP_SIZE)
757 /* The size in cginfo is currently only read with DD */
758 gmx_fatal(FARGS, "A charge group has size %d which is larger than the limit of %d atoms", a1-a0, MAX_CHARGEGROUP_SIZE);
762 SET_CGINFO_HAS_VDW(cginfo[cgm+cg]);
766 SET_CGINFO_HAS_Q(cginfo[cgm+cg]);
768 if (bHavePerturbedAtoms && fr->efep != efepNO)
770 SET_CGINFO_FEP(cginfo[cgm+cg]);
771 *bFEP_NonBonded = TRUE;
773 /* Store the charge group size */
774 SET_CGINFO_NATOMS(cginfo[cgm+cg], a1-a0);
776 if (!bExclIntraAll || bExclInter)
778 *bExcl_IntraCGAll_InterCGNone = FALSE;
785 cg_offset += molb->nmol*cgs->nr;
786 a_offset += molb->nmol*cgs->index[cgs->nr];
791 /* the solvent optimizer is called after the QM is initialized,
792 * because we don't want to have the QM subsystemto become an
796 check_solvent(fplog, mtop, fr, cginfo_mb);
798 if (getenv("GMX_NO_SOLV_OPT"))
802 fprintf(fplog, "Found environment variable GMX_NO_SOLV_OPT.\n"
803 "Disabling all solvent optimization\n");
805 fr->solvent_opt = esolNO;
809 fr->solvent_opt = esolNO;
811 if (!fr->solvent_opt)
813 for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
815 for (cg = 0; cg < cginfo_mb[mb].cg_mod; cg++)
817 SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[cg], esolNO);
825 static int *cginfo_expand(int nmb, cginfo_mb_t *cgi_mb)
830 ncg = cgi_mb[nmb-1].cg_end;
833 for (cg = 0; cg < ncg; cg++)
835 while (cg >= cgi_mb[mb].cg_end)
840 cgi_mb[mb].cginfo[(cg - cgi_mb[mb].cg_start) % cgi_mb[mb].cg_mod];
846 static void done_cginfo_mb(cginfo_mb_t *cginfo_mb, int numMolBlocks)
848 if (cginfo_mb == nullptr)
852 for (int mb = 0; mb < numMolBlocks; ++mb)
854 sfree(cginfo_mb[mb].cginfo);
859 /* Sets the sum of charges (squared) and C6 in the system in fr.
860 * Returns whether the system has a net charge.
862 static bool set_chargesum(FILE *log, t_forcerec *fr, const gmx_mtop_t *mtop)
864 /*This now calculates sum for q and c6*/
865 double qsum, q2sum, q, c6sum, c6;
870 for (const gmx_molblock_t &molb : mtop->molblock)
872 int nmol = molb.nmol;
873 const t_atoms *atoms = &mtop->moltype[molb.type].atoms;
874 for (int i = 0; i < atoms->nr; i++)
876 q = atoms->atom[i].q;
879 c6 = mtop->ffparams.iparams[atoms->atom[i].type*(mtop->ffparams.atnr+1)].lj.c6;
884 fr->q2sum[0] = q2sum;
885 fr->c6sum[0] = c6sum;
887 if (fr->efep != efepNO)
892 for (const gmx_molblock_t &molb : mtop->molblock)
894 int nmol = molb.nmol;
895 const t_atoms *atoms = &mtop->moltype[molb.type].atoms;
896 for (int i = 0; i < atoms->nr; i++)
898 q = atoms->atom[i].qB;
901 c6 = mtop->ffparams.iparams[atoms->atom[i].typeB*(mtop->ffparams.atnr+1)].lj.c6;
905 fr->q2sum[1] = q2sum;
906 fr->c6sum[1] = c6sum;
911 fr->qsum[1] = fr->qsum[0];
912 fr->q2sum[1] = fr->q2sum[0];
913 fr->c6sum[1] = fr->c6sum[0];
917 if (fr->efep == efepNO)
919 fprintf(log, "System total charge: %.3f\n", fr->qsum[0]);
923 fprintf(log, "System total charge, top. A: %.3f top. B: %.3f\n",
924 fr->qsum[0], fr->qsum[1]);
928 /* A cut-off of 1e-4 is used to catch rounding errors due to ascii input */
929 return (std::abs(fr->qsum[0]) > 1e-4 ||
930 std::abs(fr->qsum[1]) > 1e-4);
933 void update_forcerec(t_forcerec *fr, matrix box)
935 if (fr->ic->eeltype == eelGRF)
937 calc_rffac(nullptr, fr->ic->eeltype, fr->ic->epsilon_r, fr->ic->epsilon_rf,
938 fr->ic->rcoulomb, fr->temp, fr->zsquare, box,
939 &fr->ic->k_rf, &fr->ic->c_rf);
943 static real calcBuckinghamBMax(FILE *fplog, const gmx_mtop_t *mtop)
945 const t_atoms *at1, *at2;
946 int i, j, tpi, tpj, ntypes;
951 fprintf(fplog, "Determining largest Buckingham b parameter for table\n");
953 ntypes = mtop->ffparams.atnr;
957 for (size_t mt1 = 0; mt1 < mtop->moltype.size(); mt1++)
959 at1 = &mtop->moltype[mt1].atoms;
960 for (i = 0; (i < at1->nr); i++)
962 tpi = at1->atom[i].type;
965 gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", i, tpi, ntypes);
968 for (size_t mt2 = mt1; mt2 < mtop->moltype.size(); mt2++)
970 at2 = &mtop->moltype[mt2].atoms;
971 for (j = 0; (j < at2->nr); j++)
973 tpj = at2->atom[j].type;
976 gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", j, tpj, ntypes);
978 b = mtop->ffparams.iparams[tpi*ntypes + tpj].bham.b;
983 if ((b < bmin) || (bmin == -1))
993 fprintf(fplog, "Buckingham b parameters, min: %g, max: %g\n",
1000 static void make_nbf_tables(FILE *fp,
1001 const interaction_const_t *ic, real rtab,
1002 const char *tabfn, char *eg1, char *eg2,
1008 if (tabfn == nullptr)
1012 fprintf(debug, "No table file name passed, can not read table, can not do non-bonded interactions\n");
1017 sprintf(buf, "%s", tabfn);
1020 /* Append the two energy group names */
1021 sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "_%s_%s.%s",
1022 eg1, eg2, ftp2ext(efXVG));
1024 nbl->table_elec_vdw = make_tables(fp, ic, buf, rtab, 0);
1025 /* Copy the contents of the table to separate coulomb and LJ tables too,
1026 * to improve cache performance.
1028 /* For performance reasons we want
1029 * the table data to be aligned to 16-byte. The pointers could be freed
1030 * but currently aren't.
1032 snew(nbl->table_elec, 1);
1033 nbl->table_elec->interaction = GMX_TABLE_INTERACTION_ELEC;
1034 nbl->table_elec->format = nbl->table_elec_vdw->format;
1035 nbl->table_elec->r = nbl->table_elec_vdw->r;
1036 nbl->table_elec->n = nbl->table_elec_vdw->n;
1037 nbl->table_elec->scale = nbl->table_elec_vdw->scale;
1038 nbl->table_elec->formatsize = nbl->table_elec_vdw->formatsize;
1039 nbl->table_elec->ninteractions = 1;
1040 nbl->table_elec->stride = nbl->table_elec->formatsize * nbl->table_elec->ninteractions;
1041 snew_aligned(nbl->table_elec->data, nbl->table_elec->stride*(nbl->table_elec->n+1), 32);
1043 snew(nbl->table_vdw, 1);
1044 nbl->table_vdw->interaction = GMX_TABLE_INTERACTION_VDWREP_VDWDISP;
1045 nbl->table_vdw->format = nbl->table_elec_vdw->format;
1046 nbl->table_vdw->r = nbl->table_elec_vdw->r;
1047 nbl->table_vdw->n = nbl->table_elec_vdw->n;
1048 nbl->table_vdw->scale = nbl->table_elec_vdw->scale;
1049 nbl->table_vdw->formatsize = nbl->table_elec_vdw->formatsize;
1050 nbl->table_vdw->ninteractions = 2;
1051 nbl->table_vdw->stride = nbl->table_vdw->formatsize * nbl->table_vdw->ninteractions;
1052 snew_aligned(nbl->table_vdw->data, nbl->table_vdw->stride*(nbl->table_vdw->n+1), 32);
1054 /* NOTE: Using a single i-loop here leads to mix-up of data in table_vdw
1055 * with (at least) gcc 6.2, 6.3 and 6.4 when compiled with -O3 and AVX
1057 for (i = 0; i <= nbl->table_elec_vdw->n; i++)
1059 for (j = 0; j < 4; j++)
1061 nbl->table_elec->data[4*i+j] = nbl->table_elec_vdw->data[12*i+j];
1064 for (i = 0; i <= nbl->table_elec_vdw->n; i++)
1066 for (j = 0; j < 8; j++)
1068 nbl->table_vdw->data[8*i+j] = nbl->table_elec_vdw->data[12*i+4+j];
1073 /*!\brief If there's bonded interactions of type \c ftype1 or \c
1074 * ftype2 present in the topology, build an array of the number of
1075 * interactions present for each bonded interaction index found in the
1078 * \c ftype1 or \c ftype2 may be set to -1 to disable seeking for a
1079 * valid type with that parameter.
1081 * \c count will be reallocated as necessary to fit the largest bonded
1082 * interaction index found, and its current size will be returned in
1083 * \c ncount. It will contain zero for every bonded interaction index
1084 * for which no interactions are present in the topology.
1086 static void count_tables(int ftype1, int ftype2, const gmx_mtop_t *mtop,
1087 int *ncount, int **count)
1089 int ftype, i, j, tabnr;
1091 // Loop over all moleculetypes
1092 for (const gmx_moltype_t &molt : mtop->moltype)
1094 // Loop over all interaction types
1095 for (ftype = 0; ftype < F_NRE; ftype++)
1097 // If the current interaction type is one of the types whose tables we're trying to count...
1098 if (ftype == ftype1 || ftype == ftype2)
1100 const InteractionList &il = molt.ilist[ftype];
1101 const int stride = 1 + NRAL(ftype);
1102 // ... and there are actually some interactions for this type
1103 for (i = 0; i < il.size(); i += stride)
1105 // Find out which table index the user wanted
1106 tabnr = mtop->ffparams.iparams[il.iatoms[i]].tab.table;
1109 gmx_fatal(FARGS, "A bonded table number is smaller than 0: %d\n", tabnr);
1111 // Make room for this index in the data structure
1112 if (tabnr >= *ncount)
1114 srenew(*count, tabnr+1);
1115 for (j = *ncount; j < tabnr+1; j++)
1121 // Record that this table index is used and must have a valid file
1129 /*!\brief If there's bonded interactions of flavour \c tabext and type
1130 * \c ftype1 or \c ftype2 present in the topology, seek them in the
1131 * list of filenames passed to mdrun, and make bonded tables from
1134 * \c ftype1 or \c ftype2 may be set to -1 to disable seeking for a
1135 * valid type with that parameter.
1137 * A fatal error occurs if no matching filename is found.
1139 static bondedtable_t *make_bonded_tables(FILE *fplog,
1140 int ftype1, int ftype2,
1141 const gmx_mtop_t *mtop,
1142 gmx::ArrayRef<const std::string> tabbfnm,
1152 count_tables(ftype1, ftype2, mtop, &ncount, &count);
1154 // Are there any relevant tabulated bond interactions?
1158 for (int i = 0; i < ncount; i++)
1160 // Do any interactions exist that requires this table?
1163 // This pattern enforces the current requirement that
1164 // table filenames end in a characteristic sequence
1165 // before the file type extension, and avoids table 13
1166 // being recognized and used for table 1.
1167 std::string patternToFind = gmx::formatString("_%s%d.%s", tabext, i, ftp2ext(efXVG));
1168 bool madeTable = false;
1169 for (gmx::index j = 0; j < tabbfnm.ssize() && !madeTable; ++j)
1171 if (gmx::endsWith(tabbfnm[j], patternToFind))
1173 // Finally read the table from the file found
1174 tab[i] = make_bonded_table(fplog, tabbfnm[j].c_str(), NRAL(ftype1)-2);
1180 bool isPlural = (ftype2 != -1);
1181 gmx_fatal(FARGS, "Tabulated interaction of type '%s%s%s' with index %d cannot be used because no table file whose name matched '%s' was passed via the gmx mdrun -tableb command-line option.",
1182 interaction_function[ftype1].longname,
1183 isPlural ? "' or '" : "",
1184 isPlural ? interaction_function[ftype2].longname : "",
1186 patternToFind.c_str());
1196 void forcerec_set_ranges(t_forcerec *fr,
1197 int ncg_home, int ncg_force,
1199 int natoms_force_constr, int natoms_f_novirsum)
1204 /* fr->ncg_force is unused in the standard code,
1205 * but it can be useful for modified code dealing with charge groups.
1207 fr->ncg_force = ncg_force;
1208 fr->natoms_force = natoms_force;
1209 fr->natoms_force_constr = natoms_force_constr;
1211 if (fr->natoms_force_constr > fr->nalloc_force)
1213 fr->nalloc_force = over_alloc_dd(fr->natoms_force_constr);
1216 if (fr->haveDirectVirialContributions)
1218 fr->forceBufferForDirectVirialContributions->resize(natoms_f_novirsum);
1222 static real cutoff_inf(real cutoff)
1226 cutoff = GMX_CUTOFF_INF;
1232 /*! \brief Print Coulomb Ewald citations and set ewald coefficients */
1233 static void initCoulombEwaldParameters(FILE *fp, const t_inputrec *ir,
1234 bool systemHasNetCharge,
1235 interaction_const_t *ic)
1237 if (!EEL_PME_EWALD(ir->coulombtype))
1244 fprintf(fp, "Will do PME sum in reciprocal space for electrostatic interactions.\n");
1246 if (ir->coulombtype == eelP3M_AD)
1248 please_cite(fp, "Hockney1988");
1249 please_cite(fp, "Ballenegger2012");
1253 please_cite(fp, "Essmann95a");
1256 if (ir->ewald_geometry == eewg3DC)
1260 fprintf(fp, "Using the Ewald3DC correction for systems with a slab geometry%s.\n",
1261 systemHasNetCharge ? " and net charge" : "");
1263 please_cite(fp, "In-Chul99a");
1264 if (systemHasNetCharge)
1266 please_cite(fp, "Ballenegger2009");
1271 ic->ewaldcoeff_q = calc_ewaldcoeff_q(ir->rcoulomb, ir->ewald_rtol);
1274 fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for Ewald\n",
1275 1/ic->ewaldcoeff_q);
1278 if (ic->coulomb_modifier == eintmodPOTSHIFT)
1280 GMX_RELEASE_ASSERT(ic->rcoulomb != 0, "Cutoff radius cannot be zero");
1281 ic->sh_ewald = std::erfc(ic->ewaldcoeff_q*ic->rcoulomb) / ic->rcoulomb;
1289 /*! \brief Print Van der Waals Ewald citations and set ewald coefficients */
1290 static void initVdwEwaldParameters(FILE *fp, const t_inputrec *ir,
1291 interaction_const_t *ic)
1293 if (!EVDW_PME(ir->vdwtype))
1300 fprintf(fp, "Will do PME sum in reciprocal space for LJ dispersion interactions.\n");
1301 please_cite(fp, "Essmann95a");
1303 ic->ewaldcoeff_lj = calc_ewaldcoeff_lj(ir->rvdw, ir->ewald_rtol_lj);
1306 fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for LJ Ewald\n",
1307 1/ic->ewaldcoeff_lj);
1310 if (ic->vdw_modifier == eintmodPOTSHIFT)
1312 real crc2 = gmx::square(ic->ewaldcoeff_lj*ic->rvdw);
1313 ic->sh_lj_ewald = (std::exp(-crc2)*(1 + crc2 + 0.5*crc2*crc2) - 1)/gmx::power6(ic->rvdw);
1317 ic->sh_lj_ewald = 0;
1321 gmx_bool uses_simple_tables(int cutoff_scheme,
1322 const nonbonded_verlet_t *nbv)
1324 gmx_bool bUsesSimpleTables = TRUE;
1326 switch (cutoff_scheme)
1329 bUsesSimpleTables = TRUE;
1332 GMX_RELEASE_ASSERT(nullptr != nbv, "A non-bonded verlet object is required with the Verlet cutoff-scheme");
1333 bUsesSimpleTables = nbv->pairlistIsSimple();
1336 gmx_incons("unimplemented");
1338 return bUsesSimpleTables;
1341 static void init_ewald_f_table(interaction_const_t *ic,
1346 /* Get the Ewald table spacing based on Coulomb and/or LJ
1347 * Ewald coefficients and rtol.
1349 ic->tabq_scale = ewald_spline3_table_scale(ic);
1351 if (ic->cutoff_scheme == ecutsVERLET)
1353 maxr = ic->rcoulomb;
1357 maxr = std::max(ic->rcoulomb, rtab);
1359 ic->tabq_size = static_cast<int>(maxr*ic->tabq_scale) + 2;
1361 sfree_aligned(ic->tabq_coul_FDV0);
1362 sfree_aligned(ic->tabq_coul_F);
1363 sfree_aligned(ic->tabq_coul_V);
1365 sfree_aligned(ic->tabq_vdw_FDV0);
1366 sfree_aligned(ic->tabq_vdw_F);
1367 sfree_aligned(ic->tabq_vdw_V);
1369 if (EEL_PME_EWALD(ic->eeltype))
1371 /* Create the original table data in FDV0 */
1372 snew_aligned(ic->tabq_coul_FDV0, ic->tabq_size*4, 32);
1373 snew_aligned(ic->tabq_coul_F, ic->tabq_size, 32);
1374 snew_aligned(ic->tabq_coul_V, ic->tabq_size, 32);
1375 table_spline3_fill_ewald_lr(ic->tabq_coul_F, ic->tabq_coul_V, ic->tabq_coul_FDV0,
1376 ic->tabq_size, 1/ic->tabq_scale, ic->ewaldcoeff_q, v_q_ewald_lr);
1379 if (EVDW_PME(ic->vdwtype))
1381 snew_aligned(ic->tabq_vdw_FDV0, ic->tabq_size*4, 32);
1382 snew_aligned(ic->tabq_vdw_F, ic->tabq_size, 32);
1383 snew_aligned(ic->tabq_vdw_V, ic->tabq_size, 32);
1384 table_spline3_fill_ewald_lr(ic->tabq_vdw_F, ic->tabq_vdw_V, ic->tabq_vdw_FDV0,
1385 ic->tabq_size, 1/ic->tabq_scale, ic->ewaldcoeff_lj, v_lj_ewald_lr);
1389 void init_interaction_const_tables(FILE *fp,
1390 interaction_const_t *ic,
1393 if (EEL_PME_EWALD(ic->eeltype) || EVDW_PME(ic->vdwtype))
1395 init_ewald_f_table(ic, rtab);
1399 fprintf(fp, "Initialized non-bonded Ewald correction tables, spacing: %.2e size: %d\n\n",
1400 1/ic->tabq_scale, ic->tabq_size);
1405 static void clear_force_switch_constants(shift_consts_t *sc)
1412 static void force_switch_constants(real p,
1416 /* Here we determine the coefficient for shifting the force to zero
1417 * between distance rsw and the cut-off rc.
1418 * For a potential of r^-p, we have force p*r^-(p+1).
1419 * But to save flops we absorb p in the coefficient.
1421 * force/p = r^-(p+1) + c2*r^2 + c3*r^3
1422 * potential = r^-p + c2/3*r^3 + c3/4*r^4 + cpot
1424 sc->c2 = ((p + 1)*rsw - (p + 4)*rc)/(pow(rc, p + 2)*gmx::square(rc - rsw));
1425 sc->c3 = -((p + 1)*rsw - (p + 3)*rc)/(pow(rc, p + 2)*gmx::power3(rc - rsw));
1426 sc->cpot = -pow(rc, -p) + p*sc->c2/3*gmx::power3(rc - rsw) + p*sc->c3/4*gmx::power4(rc - rsw);
1429 static void potential_switch_constants(real rsw, real rc,
1430 switch_consts_t *sc)
1432 /* The switch function is 1 at rsw and 0 at rc.
1433 * The derivative and second derivate are zero at both ends.
1434 * rsw = max(r - r_switch, 0)
1435 * sw = 1 + c3*rsw^3 + c4*rsw^4 + c5*rsw^5
1436 * dsw = 3*c3*rsw^2 + 4*c4*rsw^3 + 5*c5*rsw^4
1437 * force = force*dsw - potential*sw
1440 sc->c3 = -10/gmx::power3(rc - rsw);
1441 sc->c4 = 15/gmx::power4(rc - rsw);
1442 sc->c5 = -6/gmx::power5(rc - rsw);
1445 /*! \brief Construct interaction constants
1447 * This data is used (particularly) by search and force code for
1448 * short-range interactions. Many of these are constant for the whole
1449 * simulation; some are constant only after PME tuning completes.
1452 init_interaction_const(FILE *fp,
1453 interaction_const_t **interaction_const,
1454 const t_inputrec *ir,
1455 const gmx_mtop_t *mtop,
1456 bool systemHasNetCharge)
1458 interaction_const_t *ic;
1462 ic->cutoff_scheme = ir->cutoff_scheme;
1464 /* Just allocate something so we can free it */
1465 snew_aligned(ic->tabq_coul_FDV0, 16, 32);
1466 snew_aligned(ic->tabq_coul_F, 16, 32);
1467 snew_aligned(ic->tabq_coul_V, 16, 32);
1470 ic->vdwtype = ir->vdwtype;
1471 ic->vdw_modifier = ir->vdw_modifier;
1472 ic->reppow = mtop->ffparams.reppow;
1473 ic->rvdw = cutoff_inf(ir->rvdw);
1474 ic->rvdw_switch = ir->rvdw_switch;
1475 ic->ljpme_comb_rule = ir->ljpme_combination_rule;
1476 ic->useBuckingham = (mtop->ffparams.functype[0] == F_BHAM);
1477 if (ic->useBuckingham)
1479 ic->buckinghamBMax = calcBuckinghamBMax(fp, mtop);
1482 initVdwEwaldParameters(fp, ir, ic);
1484 clear_force_switch_constants(&ic->dispersion_shift);
1485 clear_force_switch_constants(&ic->repulsion_shift);
1487 switch (ic->vdw_modifier)
1489 case eintmodPOTSHIFT:
1490 /* Only shift the potential, don't touch the force */
1491 ic->dispersion_shift.cpot = -1.0/gmx::power6(ic->rvdw);
1492 ic->repulsion_shift.cpot = -1.0/gmx::power12(ic->rvdw);
1494 case eintmodFORCESWITCH:
1495 /* Switch the force, switch and shift the potential */
1496 force_switch_constants(6.0, ic->rvdw_switch, ic->rvdw,
1497 &ic->dispersion_shift);
1498 force_switch_constants(12.0, ic->rvdw_switch, ic->rvdw,
1499 &ic->repulsion_shift);
1501 case eintmodPOTSWITCH:
1502 /* Switch the potential and force */
1503 potential_switch_constants(ic->rvdw_switch, ic->rvdw,
1507 case eintmodEXACTCUTOFF:
1508 /* Nothing to do here */
1511 gmx_incons("unimplemented potential modifier");
1514 ic->sh_invrc6 = -ic->dispersion_shift.cpot;
1516 /* Electrostatics */
1517 ic->eeltype = ir->coulombtype;
1518 ic->coulomb_modifier = ir->coulomb_modifier;
1519 ic->rcoulomb = cutoff_inf(ir->rcoulomb);
1520 ic->rcoulomb_switch = ir->rcoulomb_switch;
1521 ic->epsilon_r = ir->epsilon_r;
1523 /* Set the Coulomb energy conversion factor */
1524 if (ic->epsilon_r != 0)
1526 ic->epsfac = ONE_4PI_EPS0/ic->epsilon_r;
1530 /* eps = 0 is infinite dieletric: no Coulomb interactions */
1534 /* Reaction-field */
1535 if (EEL_RF(ic->eeltype))
1537 ic->epsilon_rf = ir->epsilon_rf;
1538 /* Generalized reaction field parameters are updated every step */
1539 if (ic->eeltype != eelGRF)
1541 calc_rffac(fp, ic->eeltype, ic->epsilon_r, ic->epsilon_rf,
1542 ic->rcoulomb, 0, 0, nullptr,
1543 &ic->k_rf, &ic->c_rf);
1546 if (ir->cutoff_scheme == ecutsGROUP && ic->eeltype == eelRF_ZERO)
1548 /* grompp should have done this, but this scheme is obsolete */
1549 ic->coulomb_modifier = eintmodEXACTCUTOFF;
1554 /* For plain cut-off we might use the reaction-field kernels */
1555 ic->epsilon_rf = ic->epsilon_r;
1557 if (ir->coulomb_modifier == eintmodPOTSHIFT)
1559 ic->c_rf = 1/ic->rcoulomb;
1567 initCoulombEwaldParameters(fp, ir, systemHasNetCharge, ic);
1571 real dispersion_shift;
1573 dispersion_shift = ic->dispersion_shift.cpot;
1574 if (EVDW_PME(ic->vdwtype))
1576 dispersion_shift -= ic->sh_lj_ewald;
1578 fprintf(fp, "Potential shift: LJ r^-12: %.3e r^-6: %.3e",
1579 ic->repulsion_shift.cpot, dispersion_shift);
1581 if (ic->eeltype == eelCUT)
1583 fprintf(fp, ", Coulomb %.e", -ic->c_rf);
1585 else if (EEL_PME(ic->eeltype))
1587 fprintf(fp, ", Ewald %.3e", -ic->sh_ewald);
1592 *interaction_const = ic;
1596 done_interaction_const(interaction_const_t *interaction_const)
1598 sfree_aligned(interaction_const->tabq_coul_FDV0);
1599 sfree_aligned(interaction_const->tabq_coul_F);
1600 sfree_aligned(interaction_const->tabq_coul_V);
1601 sfree(interaction_const);
1604 void init_forcerec(FILE *fp,
1605 const gmx::MDLogger &mdlog,
1608 const t_inputrec *ir,
1609 const gmx_mtop_t *mtop,
1610 const t_commrec *cr,
1614 gmx::ArrayRef<const std::string> tabbfnm,
1615 const gmx_hw_info_t &hardwareInfo,
1616 const gmx_device_info_t *deviceInfo,
1617 const bool useGpuForBonded,
1618 gmx_bool bNoSolvOpt,
1621 int m, negp_pp, negptable, egi, egj;
1626 gmx_bool bGenericKernelOnly;
1627 gmx_bool needGroupSchemeTables, bSomeNormalNbListsAreInUse;
1628 gmx_bool bFEP_NonBonded;
1629 int *nm_ind, egp_flags;
1631 /* By default we turn SIMD kernels on, but it might be turned off further down... */
1632 fr->use_simd_kernels = TRUE;
1634 if (check_box(ir->ePBC, box))
1636 gmx_fatal(FARGS, "%s", check_box(ir->ePBC, box));
1639 /* Test particle insertion ? */
1642 /* Set to the size of the molecule to be inserted (the last one) */
1643 /* Because of old style topologies, we have to use the last cg
1644 * instead of the last molecule type.
1646 cgs = &mtop->moltype[mtop->molblock.back().type].cgs;
1647 fr->n_tpi = cgs->index[cgs->nr] - cgs->index[cgs->nr-1];
1648 gmx::RangePartitioning molecules = gmx_mtop_molecules(*mtop);
1649 if (fr->n_tpi != molecules.block(molecules.numBlocks() - 1).size())
1651 gmx_fatal(FARGS, "The molecule to insert can not consist of multiple charge groups.\nMake it a single charge group.");
1659 if (ir->coulombtype == eelRF_NEC_UNSUPPORTED)
1661 gmx_fatal(FARGS, "%s electrostatics is no longer supported",
1662 eel_names[ir->coulombtype]);
1667 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1669 if (ir->useTwinRange)
1671 gmx_fatal(FARGS, "Twin-range simulations are no longer supported");
1673 /* Copy the user determined parameters */
1674 fr->userint1 = ir->userint1;
1675 fr->userint2 = ir->userint2;
1676 fr->userint3 = ir->userint3;
1677 fr->userint4 = ir->userint4;
1678 fr->userreal1 = ir->userreal1;
1679 fr->userreal2 = ir->userreal2;
1680 fr->userreal3 = ir->userreal3;
1681 fr->userreal4 = ir->userreal4;
1684 fr->fc_stepsize = ir->fc_stepsize;
1687 fr->efep = ir->efep;
1688 fr->sc_alphavdw = ir->fepvals->sc_alpha;
1689 if (ir->fepvals->bScCoul)
1691 fr->sc_alphacoul = ir->fepvals->sc_alpha;
1692 fr->sc_sigma6_min = gmx::power6(ir->fepvals->sc_sigma_min);
1696 fr->sc_alphacoul = 0;
1697 fr->sc_sigma6_min = 0; /* only needed when bScCoul is on */
1699 fr->sc_power = ir->fepvals->sc_power;
1700 fr->sc_r_power = ir->fepvals->sc_r_power;
1701 fr->sc_sigma6_def = gmx::power6(ir->fepvals->sc_sigma);
1703 env = getenv("GMX_SCSIGMA_MIN");
1707 sscanf(env, "%20lf", &dbl);
1708 fr->sc_sigma6_min = gmx::power6(dbl);
1711 fprintf(fp, "Setting the minimum soft core sigma to %g nm\n", dbl);
1715 fr->bNonbonded = TRUE;
1716 if (getenv("GMX_NO_NONBONDED") != nullptr)
1718 /* turn off non-bonded calculations */
1719 fr->bNonbonded = FALSE;
1720 GMX_LOG(mdlog.warning).asParagraph().appendText(
1721 "Found environment variable GMX_NO_NONBONDED.\n"
1722 "Disabling nonbonded calculations.");
1725 bGenericKernelOnly = FALSE;
1727 /* We now check in the NS code whether a particular combination of interactions
1728 * can be used with water optimization, and disable it if that is not the case.
1731 if (getenv("GMX_NB_GENERIC") != nullptr)
1736 "Found environment variable GMX_NB_GENERIC.\n"
1737 "Disabling all interaction-specific nonbonded kernels, will only\n"
1738 "use the slow generic ones in src/gmxlib/nonbonded/nb_generic.c\n\n");
1740 bGenericKernelOnly = TRUE;
1743 if (bGenericKernelOnly)
1748 if ( (getenv("GMX_DISABLE_SIMD_KERNELS") != nullptr) || (getenv("GMX_NOOPTIMIZEDKERNELS") != nullptr) )
1750 fr->use_simd_kernels = FALSE;
1754 "\nFound environment variable GMX_DISABLE_SIMD_KERNELS.\n"
1755 "Disabling the usage of any SIMD-specific non-bonded & bonded kernel routines\n"
1756 "(e.g. SSE2/SSE4.1/AVX).\n\n");
1760 fr->bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
1762 /* Neighbour searching stuff */
1763 fr->cutoff_scheme = ir->cutoff_scheme;
1764 fr->bGrid = (ir->ns_type == ensGRID);
1765 fr->ePBC = ir->ePBC;
1767 if (fr->cutoff_scheme == ecutsGROUP)
1769 const char *note = "NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be\n"
1770 "removed in a future release when 'verlet' supports all interaction forms.\n";
1774 fprintf(stderr, "\n%s\n", note);
1778 fprintf(fp, "\n%s\n", note);
1782 /* Determine if we will do PBC for distances in bonded interactions */
1783 if (fr->ePBC == epbcNONE)
1785 fr->bMolPBC = FALSE;
1789 if (!DOMAINDECOMP(cr))
1793 bSHAKE = (ir->eConstrAlg == econtSHAKE &&
1794 (gmx_mtop_ftype_count(mtop, F_CONSTR) > 0 ||
1795 gmx_mtop_ftype_count(mtop, F_CONSTRNC) > 0));
1797 /* The group cut-off scheme and SHAKE assume charge groups
1798 * are whole, but not using molpbc is faster in most cases.
1799 * With intermolecular interactions we need PBC for calculating
1800 * distances between atoms in different molecules.
1802 if ((fr->cutoff_scheme == ecutsGROUP || bSHAKE) &&
1803 !mtop->bIntermolecularInteractions)
1805 fr->bMolPBC = ir->bPeriodicMols;
1807 if (bSHAKE && fr->bMolPBC)
1809 gmx_fatal(FARGS, "SHAKE is not supported with periodic molecules");
1814 /* Not making molecules whole is faster in most cases,
1815 * but With orientation restraints we need whole molecules.
1817 fr->bMolPBC = (fcd->orires.nr == 0);
1819 if (getenv("GMX_USE_GRAPH") != nullptr)
1821 fr->bMolPBC = FALSE;
1824 GMX_LOG(mdlog.warning).asParagraph().appendText("GMX_USE_GRAPH is set, using the graph for bonded interactions");
1827 if (mtop->bIntermolecularInteractions)
1829 GMX_LOG(mdlog.warning).asParagraph().appendText("WARNING: Molecules linked by intermolecular interactions have to reside in the same periodic image, otherwise artifacts will occur!");
1833 GMX_RELEASE_ASSERT(fr->bMolPBC || !mtop->bIntermolecularInteractions, "We need to use PBC within molecules with inter-molecular interactions");
1835 if (bSHAKE && fr->bMolPBC)
1837 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");
1843 fr->bMolPBC = dd_bonded_molpbc(cr->dd, fr->ePBC);
1847 fr->rc_scaling = ir->refcoord_scaling;
1848 copy_rvec(ir->posres_com, fr->posres_com);
1849 copy_rvec(ir->posres_comB, fr->posres_comB);
1850 fr->rlist = cutoff_inf(ir->rlist);
1851 fr->ljpme_combination_rule = ir->ljpme_combination_rule;
1853 /* This now calculates sum for q and c6*/
1854 bool systemHasNetCharge = set_chargesum(fp, fr, mtop);
1856 /* fr->ic is used both by verlet and group kernels (to some extent) now */
1857 init_interaction_const(fp, &fr->ic, ir, mtop, systemHasNetCharge);
1858 init_interaction_const_tables(fp, fr->ic, ir->rlist + ir->tabext);
1860 const interaction_const_t *ic = fr->ic;
1862 /* TODO: Replace this Ewald table or move it into interaction_const_t */
1863 if (ir->coulombtype == eelEWALD)
1865 init_ewald_tab(&(fr->ewald_table), ir, fp);
1868 /* Electrostatics: Translate from interaction-setting-in-mdp-file to kernel interaction format */
1869 switch (ic->eeltype)
1872 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_COULOMB;
1877 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD;
1881 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD;
1882 GMX_RELEASE_ASSERT(ic->coulomb_modifier == eintmodEXACTCUTOFF, "With the group scheme RF-zero needs the exact cut-off modifier");
1891 case eelPMEUSERSWITCH:
1892 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_CUBICSPLINETABLE;
1898 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_EWALD;
1902 gmx_fatal(FARGS, "Unsupported electrostatic interaction: %s", eel_names[ic->eeltype]);
1904 fr->nbkernel_elec_modifier = ic->coulomb_modifier;
1906 /* Vdw: Translate from mdp settings to kernel format */
1907 switch (ic->vdwtype)
1912 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_BUCKINGHAM;
1916 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_LENNARDJONES;
1920 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_LJEWALD;
1926 case evdwENCADSHIFT:
1927 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
1931 gmx_fatal(FARGS, "Unsupported vdw interaction: %s", evdw_names[ic->vdwtype]);
1933 fr->nbkernel_vdw_modifier = ic->vdw_modifier;
1935 if (ir->cutoff_scheme == ecutsGROUP)
1937 fr->bvdwtab = ((ic->vdwtype != evdwCUT || !gmx_within_tol(ic->reppow, 12.0, 10*GMX_DOUBLE_EPS))
1938 && !EVDW_PME(ic->vdwtype));
1939 /* We have special kernels for standard Ewald and PME, but the pme-switch ones are tabulated above */
1940 fr->bcoultab = !(ic->eeltype == eelCUT ||
1941 ic->eeltype == eelEWALD ||
1942 ic->eeltype == eelPME ||
1943 ic->eeltype == eelP3M_AD ||
1944 ic->eeltype == eelRF ||
1945 ic->eeltype == eelRF_ZERO);
1947 /* If the user absolutely wants different switch/shift settings for coul/vdw, it is likely
1948 * going to be faster to tabulate the interaction than calling the generic kernel.
1949 * However, if generic kernels have been requested we keep things analytically.
1951 if (fr->nbkernel_elec_modifier == eintmodPOTSWITCH &&
1952 fr->nbkernel_vdw_modifier == eintmodPOTSWITCH &&
1953 !bGenericKernelOnly)
1955 if ((ic->rcoulomb_switch != ic->rvdw_switch) || (ic->rcoulomb != ic->rvdw))
1957 fr->bcoultab = TRUE;
1958 /* Once we tabulate electrostatics, we can use the switch function for LJ,
1959 * which would otherwise need two tables.
1963 else if ((fr->nbkernel_elec_modifier == eintmodPOTSHIFT && fr->nbkernel_vdw_modifier == eintmodPOTSHIFT) ||
1964 ((fr->nbkernel_elec_interaction == GMX_NBKERNEL_ELEC_REACTIONFIELD &&
1965 fr->nbkernel_elec_modifier == eintmodEXACTCUTOFF &&
1966 (fr->nbkernel_vdw_modifier == eintmodPOTSWITCH || fr->nbkernel_vdw_modifier == eintmodPOTSHIFT))))
1968 if ((ic->rcoulomb != ic->rvdw) && (!bGenericKernelOnly))
1970 fr->bcoultab = TRUE;
1974 if (fr->nbkernel_elec_modifier == eintmodFORCESWITCH)
1976 fr->bcoultab = TRUE;
1978 if (fr->nbkernel_vdw_modifier == eintmodFORCESWITCH)
1983 if (getenv("GMX_REQUIRE_TABLES"))
1986 fr->bcoultab = TRUE;
1991 fprintf(fp, "Table routines are used for coulomb: %s\n",
1992 gmx::boolToString(fr->bcoultab));
1993 fprintf(fp, "Table routines are used for vdw: %s\n",
1994 gmx::boolToString(fr->bvdwtab));
1999 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
2000 fr->nbkernel_vdw_modifier = eintmodNONE;
2004 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_CUBICSPLINETABLE;
2005 fr->nbkernel_elec_modifier = eintmodNONE;
2009 if (ir->cutoff_scheme == ecutsVERLET)
2011 if (!gmx_within_tol(ic->reppow, 12.0, 10*GMX_DOUBLE_EPS))
2013 gmx_fatal(FARGS, "Cut-off scheme %s only supports LJ repulsion power 12", ecutscheme_names[ir->cutoff_scheme]);
2015 /* Older tpr files can contain Coulomb user tables with the Verlet cutoff-scheme,
2016 * while mdrun does not (and never did) support this.
2018 if (EEL_USER(fr->ic->eeltype))
2020 gmx_fatal(FARGS, "Combination of %s and cutoff scheme %s is not supported",
2021 eel_names[ir->coulombtype], ecutscheme_names[ir->cutoff_scheme]);
2024 fr->bvdwtab = FALSE;
2025 fr->bcoultab = FALSE;
2028 /* 1-4 interaction electrostatics */
2029 fr->fudgeQQ = mtop->ffparams.fudgeQQ;
2031 /* Parameters for generalized RF */
2035 if (ic->eeltype == eelGRF)
2037 init_generalized_rf(fp, mtop, ir, fr);
2040 fr->haveDirectVirialContributions =
2041 (EEL_FULL(ic->eeltype) || EVDW_PME(ic->vdwtype) ||
2042 fr->forceProviders->hasForceProvider() ||
2043 gmx_mtop_ftype_count(mtop, F_POSRES) > 0 ||
2044 gmx_mtop_ftype_count(mtop, F_FBPOSRES) > 0 ||
2050 if (fr->haveDirectVirialContributions)
2052 fr->forceBufferForDirectVirialContributions = new std::vector<gmx::RVec>;
2055 if (fr->cutoff_scheme == ecutsGROUP &&
2056 ncg_mtop(mtop) > fr->cg_nalloc && !DOMAINDECOMP(cr))
2058 /* Count the total number of charge groups */
2059 fr->cg_nalloc = ncg_mtop(mtop);
2060 srenew(fr->cg_cm, fr->cg_nalloc);
2062 if (fr->shift_vec == nullptr)
2064 snew(fr->shift_vec, SHIFTS);
2067 if (fr->fshift == nullptr)
2069 snew(fr->fshift, SHIFTS);
2072 if (fr->nbfp == nullptr)
2074 fr->ntype = mtop->ffparams.atnr;
2075 fr->nbfp = mk_nbfp(&mtop->ffparams, fr->bBHAM);
2076 if (EVDW_PME(ic->vdwtype))
2078 fr->ljpme_c6grid = make_ljpme_c6grid(&mtop->ffparams, fr);
2082 /* Copy the energy group exclusions */
2083 fr->egp_flags = ir->opts.egp_flags;
2085 /* Van der Waals stuff */
2086 if ((ic->vdwtype != evdwCUT) && (ic->vdwtype != evdwUSER) && !fr->bBHAM)
2088 if (ic->rvdw_switch >= ic->rvdw)
2090 gmx_fatal(FARGS, "rvdw_switch (%f) must be < rvdw (%f)",
2091 ic->rvdw_switch, ic->rvdw);
2095 fprintf(fp, "Using %s Lennard-Jones, switch between %g and %g nm\n",
2096 (ic->eeltype == eelSWITCH) ? "switched" : "shifted",
2097 ic->rvdw_switch, ic->rvdw);
2101 if (fr->bBHAM && EVDW_PME(ic->vdwtype))
2103 gmx_fatal(FARGS, "LJ PME not supported with Buckingham");
2106 if (fr->bBHAM && (ic->vdwtype == evdwSHIFT || ic->vdwtype == evdwSWITCH))
2108 gmx_fatal(FARGS, "Switch/shift interaction not supported with Buckingham");
2111 if (fr->bBHAM && fr->cutoff_scheme == ecutsVERLET)
2113 gmx_fatal(FARGS, "Verlet cutoff-scheme is not supported with Buckingham");
2116 if (fp && fr->cutoff_scheme == ecutsGROUP)
2118 fprintf(fp, "Cut-off's: NS: %g Coulomb: %g %s: %g\n",
2119 fr->rlist, ic->rcoulomb, fr->bBHAM ? "BHAM" : "LJ", ic->rvdw);
2122 fr->eDispCorr = ir->eDispCorr;
2123 fr->numAtomsForDispersionCorrection = mtop->natoms;
2124 if (ir->eDispCorr != edispcNO)
2126 set_avcsixtwelve(fp, fr, mtop);
2129 if (ir->implicit_solvent)
2131 gmx_fatal(FARGS, "Implict solvation is no longer supported.");
2134 /* Construct tables for the group scheme. A little unnecessary to
2135 * make both vdw and coul tables sometimes, but what the
2136 * heck. Note that both cutoff schemes construct Ewald tables in
2137 * init_interaction_const_tables. */
2138 needGroupSchemeTables = (ir->cutoff_scheme == ecutsGROUP &&
2139 (fr->bcoultab || fr->bvdwtab));
2141 negp_pp = ir->opts.ngener - ir->nwall;
2143 if (!needGroupSchemeTables)
2145 bSomeNormalNbListsAreInUse = TRUE;
2150 bSomeNormalNbListsAreInUse = FALSE;
2151 for (egi = 0; egi < negp_pp; egi++)
2153 for (egj = egi; egj < negp_pp; egj++)
2155 egp_flags = ir->opts.egp_flags[GID(egi, egj, ir->opts.ngener)];
2156 if (!(egp_flags & EGP_EXCL))
2158 if (egp_flags & EGP_TABLE)
2164 bSomeNormalNbListsAreInUse = TRUE;
2169 if (bSomeNormalNbListsAreInUse)
2171 fr->nnblists = negptable + 1;
2175 fr->nnblists = negptable;
2177 if (fr->nnblists > 1)
2179 snew(fr->gid2nblists, ir->opts.ngener*ir->opts.ngener);
2183 snew(fr->nblists, fr->nnblists);
2185 /* This code automatically gives table length tabext without cut-off's,
2186 * in that case grompp should already have checked that we do not need
2187 * normal tables and we only generate tables for 1-4 interactions.
2189 rtab = ir->rlist + ir->tabext;
2191 if (needGroupSchemeTables)
2193 /* make tables for ordinary interactions */
2194 if (bSomeNormalNbListsAreInUse)
2196 make_nbf_tables(fp, ic, rtab, tabfn, nullptr, nullptr, &fr->nblists[0]);
2205 /* Read the special tables for certain energy group pairs */
2206 nm_ind = mtop->groups.grps[egcENER].nm_ind;
2207 for (egi = 0; egi < negp_pp; egi++)
2209 for (egj = egi; egj < negp_pp; egj++)
2211 egp_flags = ir->opts.egp_flags[GID(egi, egj, ir->opts.ngener)];
2212 if ((egp_flags & EGP_TABLE) && !(egp_flags & EGP_EXCL))
2214 if (fr->nnblists > 1)
2216 fr->gid2nblists[GID(egi, egj, ir->opts.ngener)] = m;
2218 /* Read the table file with the two energy groups names appended */
2219 make_nbf_tables(fp, ic, rtab, tabfn,
2220 *mtop->groups.grpname[nm_ind[egi]],
2221 *mtop->groups.grpname[nm_ind[egj]],
2225 else if (fr->nnblists > 1)
2227 fr->gid2nblists[GID(egi, egj, ir->opts.ngener)] = 0;
2234 /* Tables might not be used for the potential modifier
2235 * interactions per se, but we still need them to evaluate
2236 * switch/shift dispersion corrections in this case. */
2237 if (fr->eDispCorr != edispcNO)
2239 fr->dispersionCorrectionTable = makeDispersionCorrectionTable(fp, ic, rtab, tabfn);
2242 /* We want to use unmodified tables for 1-4 coulombic
2243 * interactions, so we must in general have an extra set of
2245 if (gmx_mtop_ftype_count(mtop, F_LJ14) > 0 ||
2246 gmx_mtop_ftype_count(mtop, F_LJC14_Q) > 0 ||
2247 gmx_mtop_ftype_count(mtop, F_LJC_PAIRS_NB) > 0)
2249 fr->pairsTable = make_tables(fp, ic, tabpfn, rtab,
2250 GMX_MAKETABLES_14ONLY);
2254 fr->nwall = ir->nwall;
2255 if (ir->nwall && ir->wall_type == ewtTABLE)
2257 make_wall_tables(fp, ir, tabfn, &mtop->groups, fr);
2260 if (fcd && !tabbfnm.empty())
2262 // Need to catch std::bad_alloc
2263 // TODO Don't need to catch this here, when merging with master branch
2266 fcd->bondtab = make_bonded_tables(fp,
2267 F_TABBONDS, F_TABBONDSNC,
2268 mtop, tabbfnm, "b");
2269 fcd->angletab = make_bonded_tables(fp,
2271 mtop, tabbfnm, "a");
2272 fcd->dihtab = make_bonded_tables(fp,
2274 mtop, tabbfnm, "d");
2276 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
2282 fprintf(debug, "No fcdata or table file name passed, can not read table, can not do bonded interactions\n");
2286 // QM/MM initialization if requested
2287 fr->bQMMM = ir->bQMMM;
2290 // Initialize QM/MM if supported
2293 GMX_LOG(mdlog.info).asParagraph().
2294 appendText("Large parts of the QM/MM support is deprecated, and may be removed in a future "
2295 "version. Please get in touch with the developers if you find the support useful, "
2296 "as help is needed if the functionality is to continue to be available.");
2297 fr->qr = mk_QMMMrec();
2298 init_QMMMrec(cr, mtop, ir, fr);
2302 gmx_incons("QM/MM was requested, but is only available when GROMACS "
2303 "is configured with QM/MM support");
2307 /* Set all the static charge group info */
2308 fr->cginfo_mb = init_cginfo_mb(fp, mtop, fr, bNoSolvOpt,
2310 &fr->bExcl_IntraCGAll_InterCGNone);
2311 if (DOMAINDECOMP(cr))
2313 fr->cginfo = nullptr;
2317 fr->cginfo = cginfo_expand(mtop->molblock.size(), fr->cginfo_mb);
2320 if (!DOMAINDECOMP(cr))
2322 forcerec_set_ranges(fr, ncg_mtop(mtop), ncg_mtop(mtop),
2323 mtop->natoms, mtop->natoms, mtop->natoms);
2326 fr->print_force = print_force;
2329 /* coarse load balancing vars */
2334 /* Initialize neighbor search */
2336 init_ns(fp, cr, fr->ns, fr, mtop);
2338 /* Initialize the thread working data for bonded interactions */
2339 init_bonded_threading(fp, mtop->groups.grps[egcENER].nr,
2340 &fr->bondedThreading);
2342 fr->nthread_ewc = gmx_omp_nthreads_get(emntBonded);
2343 snew(fr->ewc_t, fr->nthread_ewc);
2345 if (fr->cutoff_scheme == ecutsVERLET)
2347 // We checked the cut-offs in grompp, but double-check here.
2348 // We have PME+LJcutoff kernels for rcoulomb>rvdw.
2349 if (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == eelCUT)
2351 GMX_RELEASE_ASSERT(ir->rcoulomb >= ir->rvdw, "With Verlet lists and PME we should have rcoulomb>=rvdw");
2355 GMX_RELEASE_ASSERT(ir->rcoulomb == ir->rvdw, "With Verlet lists and no PME rcoulomb and rvdw should be identical");
2358 fr->nbv = Nbnxm::init_nb_verlet(mdlog, bFEP_NonBonded, ir, fr,
2359 cr, hardwareInfo, deviceInfo,
2362 if (useGpuForBonded)
2364 auto stream = DOMAINDECOMP(cr) ?
2365 Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, Nbnxm::InteractionLocality::NonLocal) :
2366 Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv, Nbnxm::InteractionLocality::Local);
2367 // TODO the heap allocation is only needed while
2368 // t_forcerec lacks a constructor.
2369 fr->gpuBonded = new gmx::GpuBonded(mtop->ffparams,
2376 /* Here we switch from using mdlog, which prints the newline before
2377 * the paragraph, to our old fprintf logging, which prints the newline
2378 * after the paragraph, so we should add a newline here.
2383 if (ir->eDispCorr != edispcNO)
2385 calc_enervirdiff(fp, ir->eDispCorr, fr);
2389 /* Frees GPU memory and sets a tMPI node barrier.
2391 * Note that this function needs to be called even if GPUs are not used
2392 * in this run because the PME ranks have no knowledge of whether GPUs
2393 * are used or not, but all ranks need to enter the barrier below.
2394 * \todo Remove physical node barrier from this function after making sure
2395 * that it's not needed anymore (with a shared GPU run).
2397 void free_gpu_resources(t_forcerec *fr,
2398 const gmx::PhysicalNodeCommunicator &physicalNodeCommunicator)
2400 bool isPPrankUsingGPU = (fr != nullptr) && (fr->nbv != nullptr) && fr->nbv->useGpu();
2402 /* stop the GPU profiler (only CUDA) */
2405 if (isPPrankUsingGPU)
2407 /* Free data in GPU memory and pinned memory before destroying the GPU context */
2410 delete fr->gpuBonded;
2411 fr->gpuBonded = nullptr;
2414 /* With tMPI we need to wait for all ranks to finish deallocation before
2415 * destroying the CUDA context in free_gpu() as some tMPI ranks may be sharing
2418 * This is not a concern in OpenCL where we use one context per rank which
2419 * is freed in nbnxn_gpu_free().
2421 * Note: it is safe to not call the barrier on the ranks which do not use GPU,
2422 * but it is easier and more futureproof to call it on the whole node.
2426 physicalNodeCommunicator.barrier();
2430 void done_forcerec(t_forcerec *fr, int numMolBlocks, int numEnergyGroups)
2434 // PME-only ranks don't have a forcerec
2437 // cginfo is dynamically allocated if no domain decomposition
2438 if (fr->cginfo != nullptr)
2442 done_cginfo_mb(fr->cginfo_mb, numMolBlocks);
2444 done_interaction_const(fr->ic);
2445 sfree(fr->shift_vec);
2448 done_ns(fr->ns, numEnergyGroups);
2450 tear_down_bonded_threading(fr->bondedThreading);
2451 GMX_RELEASE_ASSERT(fr->gpuBonded == nullptr, "Should have been deleted earlier, when used");
2452 fr->bondedThreading = nullptr;