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49 #include "gromacs/commandline/filenm.h"
50 #include "gromacs/domdec/domdec.h"
51 #include "gromacs/domdec/domdec_struct.h"
52 #include "gromacs/ewald/ewald.h"
53 #include "gromacs/ewald/ewald_utils.h"
54 #include "gromacs/ewald/pme_pp_comm_gpu.h"
55 #include "gromacs/fileio/filetypes.h"
56 #include "gromacs/gmxlib/network.h"
57 #include "gromacs/gmxlib/nonbonded/nonbonded.h"
58 #include "gromacs/gpu_utils/gpu_utils.h"
59 #include "gromacs/hardware/hw_info.h"
60 #include "gromacs/listed_forces/gpubonded.h"
61 #include "gromacs/listed_forces/manage_threading.h"
62 #include "gromacs/listed_forces/pairs.h"
63 #include "gromacs/math/functions.h"
64 #include "gromacs/math/units.h"
65 #include "gromacs/math/utilities.h"
66 #include "gromacs/math/vec.h"
67 #include "gromacs/mdlib/dispersioncorrection.h"
68 #include "gromacs/mdlib/force.h"
69 #include "gromacs/mdlib/forcerec_threading.h"
70 #include "gromacs/mdlib/gmx_omp_nthreads.h"
71 #include "gromacs/mdlib/md_support.h"
72 #include "gromacs/mdlib/qmmm.h"
73 #include "gromacs/mdlib/rf_util.h"
74 #include "gromacs/mdlib/wall.h"
75 #include "gromacs/mdtypes/commrec.h"
76 #include "gromacs/mdtypes/fcdata.h"
77 #include "gromacs/mdtypes/forcerec.h"
78 #include "gromacs/mdtypes/group.h"
79 #include "gromacs/mdtypes/iforceprovider.h"
80 #include "gromacs/mdtypes/inputrec.h"
81 #include "gromacs/mdtypes/interaction_const.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 std::vector<real> mk_nbfp(const gmx_ffparams_t* idef, gmx_bool bBHAM)
103 std::vector<real> nbfp;
109 nbfp.resize(3 * atnr * atnr);
111 for (int i = 0; (i < atnr); i++)
113 for (int j = 0; (j < atnr); j++, k++)
115 BHAMA(nbfp, atnr, i, j) = idef->iparams[k].bham.a;
116 BHAMB(nbfp, atnr, i, j) = idef->iparams[k].bham.b;
117 /* nbfp now includes the 6.0 derivative prefactor */
118 BHAMC(nbfp, atnr, i, j) = idef->iparams[k].bham.c * 6.0;
124 nbfp.resize(2 * atnr * atnr);
126 for (int i = 0; (i < atnr); i++)
128 for (int j = 0; (j < atnr); j++, k++)
130 /* nbfp now includes the 6.0/12.0 derivative prefactors */
131 C6(nbfp, atnr, i, j) = idef->iparams[k].lj.c6 * 6.0;
132 C12(nbfp, atnr, i, j) = idef->iparams[k].lj.c12 * 12.0;
140 static real* make_ljpme_c6grid(const gmx_ffparams_t* idef, t_forcerec* fr)
143 real c6, c6i, c6j, c12i, c12j, epsi, epsj, sigmai, sigmaj;
146 /* For LJ-PME simulations, we correct the energies with the reciprocal space
147 * inside of the cut-off. To do this the non-bonded kernels needs to have
148 * access to the C6-values used on the reciprocal grid in pme.c
152 snew(grid, 2 * atnr * atnr);
153 for (i = k = 0; (i < atnr); i++)
155 for (j = 0; (j < atnr); j++, k++)
157 c6i = idef->iparams[i * (atnr + 1)].lj.c6;
158 c12i = idef->iparams[i * (atnr + 1)].lj.c12;
159 c6j = idef->iparams[j * (atnr + 1)].lj.c6;
160 c12j = idef->iparams[j * (atnr + 1)].lj.c12;
161 c6 = std::sqrt(c6i * c6j);
162 if (fr->ljpme_combination_rule == eljpmeLB && !gmx_numzero(c6) && !gmx_numzero(c12i)
163 && !gmx_numzero(c12j))
165 sigmai = gmx::sixthroot(c12i / c6i);
166 sigmaj = gmx::sixthroot(c12j / c6j);
167 epsi = c6i * c6i / c12i;
168 epsj = c6j * c6j / c12j;
169 c6 = std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
171 /* Store the elements at the same relative positions as C6 in nbfp in order
172 * to simplify access in the kernels
174 grid[2 * (atnr * i + j)] = c6 * 6.0;
187 static std::vector<cginfo_mb_t> init_cginfo_mb(const gmx_mtop_t* mtop, const t_forcerec* fr)
192 snew(type_VDW, fr->ntype);
193 for (int ai = 0; ai < fr->ntype; ai++)
195 type_VDW[ai] = FALSE;
196 for (int j = 0; j < fr->ntype; j++)
198 type_VDW[ai] = type_VDW[ai] || fr->bBHAM || C6(fr->nbfp, fr->ntype, ai, j) != 0
199 || C12(fr->nbfp, fr->ntype, ai, j) != 0;
203 std::vector<cginfo_mb_t> cginfoPerMolblock;
205 for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
207 const gmx_molblock_t& molb = mtop->molblock[mb];
208 const gmx_moltype_t& molt = mtop->moltype[molb.type];
209 const auto& excl = molt.excls;
211 /* Check if the cginfo is identical for all molecules in this block.
212 * If so, we only need an array of the size of one molecule.
213 * Otherwise we make an array of #mol times #cgs per molecule.
216 for (int m = 0; m < molb.nmol; m++)
218 const int am = m * molt.atoms.nr;
219 for (int a = 0; a < molt.atoms.nr; a++)
221 if (getGroupType(mtop->groups, SimulationAtomGroupType::QuantumMechanics, a_offset + am + a)
222 != getGroupType(mtop->groups, SimulationAtomGroupType::QuantumMechanics, a_offset + a))
226 if (!mtop->groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics].empty())
228 if (mtop->groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics][a_offset + am + a]
229 != mtop->groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics][a_offset + a])
237 cginfo_mb_t cginfo_mb;
238 cginfo_mb.cg_start = a_offset;
239 cginfo_mb.cg_end = a_offset + molb.nmol * molt.atoms.nr;
240 cginfo_mb.cg_mod = (bId ? 1 : molb.nmol) * molt.atoms.nr;
241 cginfo_mb.cginfo.resize(cginfo_mb.cg_mod);
242 gmx::ArrayRef<int> cginfo = cginfo_mb.cginfo;
244 /* Set constraints flags for constrained atoms */
245 snew(a_con, molt.atoms.nr);
246 for (int ftype = 0; ftype < F_NRE; ftype++)
248 if (interaction_function[ftype].flags & IF_CONSTRAINT)
250 const int nral = NRAL(ftype);
251 for (int ia = 0; ia < molt.ilist[ftype].size(); ia += 1 + nral)
255 for (a = 0; a < nral; a++)
257 a_con[molt.ilist[ftype].iatoms[ia + 1 + a]] =
258 (ftype == F_SETTLE ? acSETTLE : acCONSTRAINT);
264 for (int m = 0; m < (bId ? 1 : molb.nmol); m++)
266 const int molculeOffsetInBlock = m * molt.atoms.nr;
267 for (int a = 0; a < molt.atoms.nr; a++)
269 const t_atom& atom = molt.atoms.atom[a];
270 int& atomInfo = cginfo[molculeOffsetInBlock + a];
272 /* Store the energy group in cginfo */
273 int gid = getGroupType(mtop->groups, SimulationAtomGroupType::EnergyOutput,
274 a_offset + molculeOffsetInBlock + a);
275 SET_CGINFO_GID(atomInfo, gid);
277 bool bHaveVDW = (type_VDW[atom.type] || type_VDW[atom.typeB]);
278 bool bHaveQ = (atom.q != 0 || atom.qB != 0);
280 bool haveExclusions = false;
281 /* Loop over all the exclusions of atom ai */
282 for (const int j : excl[a])
286 haveExclusions = true;
293 case acCONSTRAINT: SET_CGINFO_CONSTR(atomInfo); break;
294 case acSETTLE: SET_CGINFO_SETTLE(atomInfo); break;
299 SET_CGINFO_EXCL_INTER(atomInfo);
303 SET_CGINFO_HAS_VDW(atomInfo);
307 SET_CGINFO_HAS_Q(atomInfo);
309 if (fr->efep != efepNO && PERTURBED(atom))
311 SET_CGINFO_FEP(atomInfo);
318 cginfoPerMolblock.push_back(cginfo_mb);
320 a_offset += molb.nmol * molt.atoms.nr;
324 return cginfoPerMolblock;
327 static std::vector<int> cginfo_expand(const int nmb, gmx::ArrayRef<const cginfo_mb_t> cgi_mb)
329 const int ncg = cgi_mb[nmb - 1].cg_end;
331 std::vector<int> cginfo(ncg);
334 for (int cg = 0; cg < ncg; cg++)
336 while (cg >= cgi_mb[mb].cg_end)
340 cginfo[cg] = cgi_mb[mb].cginfo[(cg - cgi_mb[mb].cg_start) % cgi_mb[mb].cg_mod];
346 /* Sets the sum of charges (squared) and C6 in the system in fr.
347 * Returns whether the system has a net charge.
349 static bool set_chargesum(FILE* log, t_forcerec* fr, const gmx_mtop_t* mtop)
351 /*This now calculates sum for q and c6*/
352 double qsum, q2sum, q, c6sum, c6;
357 for (const gmx_molblock_t& molb : mtop->molblock)
359 int nmol = molb.nmol;
360 const t_atoms* atoms = &mtop->moltype[molb.type].atoms;
361 for (int i = 0; i < atoms->nr; i++)
363 q = atoms->atom[i].q;
365 q2sum += nmol * q * q;
366 c6 = mtop->ffparams.iparams[atoms->atom[i].type * (mtop->ffparams.atnr + 1)].lj.c6;
371 fr->q2sum[0] = q2sum;
372 fr->c6sum[0] = c6sum;
374 if (fr->efep != efepNO)
379 for (const gmx_molblock_t& molb : mtop->molblock)
381 int nmol = molb.nmol;
382 const t_atoms* atoms = &mtop->moltype[molb.type].atoms;
383 for (int i = 0; i < atoms->nr; i++)
385 q = atoms->atom[i].qB;
387 q2sum += nmol * q * q;
388 c6 = mtop->ffparams.iparams[atoms->atom[i].typeB * (mtop->ffparams.atnr + 1)].lj.c6;
392 fr->q2sum[1] = q2sum;
393 fr->c6sum[1] = c6sum;
398 fr->qsum[1] = fr->qsum[0];
399 fr->q2sum[1] = fr->q2sum[0];
400 fr->c6sum[1] = fr->c6sum[0];
404 if (fr->efep == efepNO)
406 fprintf(log, "System total charge: %.3f\n", fr->qsum[0]);
410 fprintf(log, "System total charge, top. A: %.3f top. B: %.3f\n", fr->qsum[0], fr->qsum[1]);
414 /* A cut-off of 1e-4 is used to catch rounding errors due to ascii input */
415 return (std::abs(fr->qsum[0]) > 1e-4 || std::abs(fr->qsum[1]) > 1e-4);
418 static real calcBuckinghamBMax(FILE* fplog, const gmx_mtop_t* mtop)
420 const t_atoms *at1, *at2;
421 int i, j, tpi, tpj, ntypes;
426 fprintf(fplog, "Determining largest Buckingham b parameter for table\n");
428 ntypes = mtop->ffparams.atnr;
432 for (size_t mt1 = 0; mt1 < mtop->moltype.size(); mt1++)
434 at1 = &mtop->moltype[mt1].atoms;
435 for (i = 0; (i < at1->nr); i++)
437 tpi = at1->atom[i].type;
440 gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", i, tpi, ntypes);
443 for (size_t mt2 = mt1; mt2 < mtop->moltype.size(); mt2++)
445 at2 = &mtop->moltype[mt2].atoms;
446 for (j = 0; (j < at2->nr); j++)
448 tpj = at2->atom[j].type;
451 gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", j, tpj, ntypes);
453 b = mtop->ffparams.iparams[tpi * ntypes + tpj].bham.b;
458 if ((b < bmin) || (bmin == -1))
468 fprintf(fplog, "Buckingham b parameters, min: %g, max: %g\n", bmin, bham_b_max);
474 /*!\brief If there's bonded interactions of type \c ftype1 or \c
475 * ftype2 present in the topology, build an array of the number of
476 * interactions present for each bonded interaction index found in the
479 * \c ftype1 or \c ftype2 may be set to -1 to disable seeking for a
480 * valid type with that parameter.
482 * \c count will be reallocated as necessary to fit the largest bonded
483 * interaction index found, and its current size will be returned in
484 * \c ncount. It will contain zero for every bonded interaction index
485 * for which no interactions are present in the topology.
487 static void count_tables(int ftype1, int ftype2, const gmx_mtop_t* mtop, int* ncount, int** count)
489 int ftype, i, j, tabnr;
491 // Loop over all moleculetypes
492 for (const gmx_moltype_t& molt : mtop->moltype)
494 // Loop over all interaction types
495 for (ftype = 0; ftype < F_NRE; ftype++)
497 // If the current interaction type is one of the types whose tables we're trying to count...
498 if (ftype == ftype1 || ftype == ftype2)
500 const InteractionList& il = molt.ilist[ftype];
501 const int stride = 1 + NRAL(ftype);
502 // ... and there are actually some interactions for this type
503 for (i = 0; i < il.size(); i += stride)
505 // Find out which table index the user wanted
506 tabnr = mtop->ffparams.iparams[il.iatoms[i]].tab.table;
509 gmx_fatal(FARGS, "A bonded table number is smaller than 0: %d\n", tabnr);
511 // Make room for this index in the data structure
512 if (tabnr >= *ncount)
514 srenew(*count, tabnr + 1);
515 for (j = *ncount; j < tabnr + 1; j++)
521 // Record that this table index is used and must have a valid file
529 /*!\brief If there's bonded interactions of flavour \c tabext and type
530 * \c ftype1 or \c ftype2 present in the topology, seek them in the
531 * list of filenames passed to mdrun, and make bonded tables from
534 * \c ftype1 or \c ftype2 may be set to -1 to disable seeking for a
535 * valid type with that parameter.
537 * A fatal error occurs if no matching filename is found.
539 static bondedtable_t* make_bonded_tables(FILE* fplog,
542 const gmx_mtop_t* mtop,
543 gmx::ArrayRef<const std::string> tabbfnm,
553 count_tables(ftype1, ftype2, mtop, &ncount, &count);
555 // Are there any relevant tabulated bond interactions?
559 for (int i = 0; i < ncount; i++)
561 // Do any interactions exist that requires this table?
564 // This pattern enforces the current requirement that
565 // table filenames end in a characteristic sequence
566 // before the file type extension, and avoids table 13
567 // being recognized and used for table 1.
568 std::string patternToFind = gmx::formatString("_%s%d.%s", tabext, i, ftp2ext(efXVG));
569 bool madeTable = false;
570 for (gmx::index j = 0; j < tabbfnm.ssize() && !madeTable; ++j)
572 if (gmx::endsWith(tabbfnm[j], patternToFind))
574 // Finally read the table from the file found
575 tab[i] = make_bonded_table(fplog, tabbfnm[j].c_str(), NRAL(ftype1) - 2);
581 bool isPlural = (ftype2 != -1);
583 "Tabulated interaction of type '%s%s%s' with index %d cannot be used "
584 "because no table file whose name matched '%s' was passed via the "
585 "gmx mdrun -tableb command-line option.",
586 interaction_function[ftype1].longname, isPlural ? "' or '" : "",
587 isPlural ? interaction_function[ftype2].longname : "", i,
588 patternToFind.c_str());
598 void forcerec_set_ranges(t_forcerec* fr, int natoms_force, int natoms_force_constr, int natoms_f_novirsum)
600 fr->natoms_force = natoms_force;
601 fr->natoms_force_constr = natoms_force_constr;
603 if (fr->natoms_force_constr > fr->nalloc_force)
605 fr->nalloc_force = over_alloc_dd(fr->natoms_force_constr);
608 if (fr->haveDirectVirialContributions)
610 fr->forceBufferForDirectVirialContributions.resize(natoms_f_novirsum);
614 static real cutoff_inf(real cutoff)
618 cutoff = GMX_CUTOFF_INF;
624 /*! \brief Print Coulomb Ewald citations and set ewald coefficients */
625 static void initCoulombEwaldParameters(FILE* fp,
626 const t_inputrec* ir,
627 bool systemHasNetCharge,
628 interaction_const_t* ic)
630 if (!EEL_PME_EWALD(ir->coulombtype))
637 fprintf(fp, "Will do PME sum in reciprocal space for electrostatic interactions.\n");
639 if (ir->coulombtype == eelP3M_AD)
641 please_cite(fp, "Hockney1988");
642 please_cite(fp, "Ballenegger2012");
646 please_cite(fp, "Essmann95a");
649 if (ir->ewald_geometry == eewg3DC)
653 fprintf(fp, "Using the Ewald3DC correction for systems with a slab geometry%s.\n",
654 systemHasNetCharge ? " and net charge" : "");
656 please_cite(fp, "In-Chul99a");
657 if (systemHasNetCharge)
659 please_cite(fp, "Ballenegger2009");
664 ic->ewaldcoeff_q = calc_ewaldcoeff_q(ir->rcoulomb, ir->ewald_rtol);
667 fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for Ewald\n", 1 / ic->ewaldcoeff_q);
670 if (ic->coulomb_modifier == eintmodPOTSHIFT)
672 GMX_RELEASE_ASSERT(ic->rcoulomb != 0, "Cutoff radius cannot be zero");
673 ic->sh_ewald = std::erfc(ic->ewaldcoeff_q * ic->rcoulomb) / ic->rcoulomb;
681 /*! \brief Print Van der Waals Ewald citations and set ewald coefficients */
682 static void initVdwEwaldParameters(FILE* fp, const t_inputrec* ir, interaction_const_t* ic)
684 if (!EVDW_PME(ir->vdwtype))
691 fprintf(fp, "Will do PME sum in reciprocal space for LJ dispersion interactions.\n");
692 please_cite(fp, "Essmann95a");
694 ic->ewaldcoeff_lj = calc_ewaldcoeff_lj(ir->rvdw, ir->ewald_rtol_lj);
697 fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for LJ Ewald\n", 1 / ic->ewaldcoeff_lj);
700 if (ic->vdw_modifier == eintmodPOTSHIFT)
702 real crc2 = gmx::square(ic->ewaldcoeff_lj * ic->rvdw);
703 ic->sh_lj_ewald = (std::exp(-crc2) * (1 + crc2 + 0.5 * crc2 * crc2) - 1) / gmx::power6(ic->rvdw);
711 /* Generate Coulomb and/or Van der Waals Ewald long-range correction tables
713 * Tables are generated for one or both, depending on if the pointers
714 * are non-null. The spacing for both table sets is the same and obeys
715 * both accuracy requirements, when relevant.
717 static void init_ewald_f_table(const interaction_const_t& ic,
718 EwaldCorrectionTables* coulombTables,
719 EwaldCorrectionTables* vdwTables)
721 const bool useCoulombTable = (EEL_PME_EWALD(ic.eeltype) && coulombTables != nullptr);
722 const bool useVdwTable = (EVDW_PME(ic.vdwtype) && vdwTables != nullptr);
724 /* Get the Ewald table spacing based on Coulomb and/or LJ
725 * Ewald coefficients and rtol.
727 const real tableScale = ewald_spline3_table_scale(ic, useCoulombTable, useVdwTable);
729 const int tableSize = static_cast<int>(ic.rcoulomb * tableScale) + 2;
734 generateEwaldCorrectionTables(tableSize, tableScale, ic.ewaldcoeff_q, v_q_ewald_lr);
739 *vdwTables = generateEwaldCorrectionTables(tableSize, tableScale, ic.ewaldcoeff_lj, v_lj_ewald_lr);
743 void init_interaction_const_tables(FILE* fp, interaction_const_t* ic)
745 if (EEL_PME_EWALD(ic->eeltype))
747 init_ewald_f_table(*ic, ic->coulombEwaldTables.get(), nullptr);
750 fprintf(fp, "Initialized non-bonded Coulomb Ewald tables, spacing: %.2e size: %zu\n\n",
751 1 / ic->coulombEwaldTables->scale, ic->coulombEwaldTables->tableF.size());
756 static void clear_force_switch_constants(shift_consts_t* sc)
763 static void force_switch_constants(real p, real rsw, real rc, shift_consts_t* sc)
765 /* Here we determine the coefficient for shifting the force to zero
766 * between distance rsw and the cut-off rc.
767 * For a potential of r^-p, we have force p*r^-(p+1).
768 * But to save flops we absorb p in the coefficient.
770 * force/p = r^-(p+1) + c2*r^2 + c3*r^3
771 * potential = r^-p + c2/3*r^3 + c3/4*r^4 + cpot
773 sc->c2 = ((p + 1) * rsw - (p + 4) * rc) / (pow(rc, p + 2) * gmx::square(rc - rsw));
774 sc->c3 = -((p + 1) * rsw - (p + 3) * rc) / (pow(rc, p + 2) * gmx::power3(rc - rsw));
775 sc->cpot = -pow(rc, -p) + p * sc->c2 / 3 * gmx::power3(rc - rsw)
776 + p * sc->c3 / 4 * gmx::power4(rc - rsw);
779 static void potential_switch_constants(real rsw, real rc, switch_consts_t* sc)
781 /* The switch function is 1 at rsw and 0 at rc.
782 * The derivative and second derivate are zero at both ends.
783 * rsw = max(r - r_switch, 0)
784 * sw = 1 + c3*rsw^3 + c4*rsw^4 + c5*rsw^5
785 * dsw = 3*c3*rsw^2 + 4*c4*rsw^3 + 5*c5*rsw^4
786 * force = force*dsw - potential*sw
789 sc->c3 = -10 / gmx::power3(rc - rsw);
790 sc->c4 = 15 / gmx::power4(rc - rsw);
791 sc->c5 = -6 / gmx::power5(rc - rsw);
794 /*! \brief Construct interaction constants
796 * This data is used (particularly) by search and force code for
797 * short-range interactions. Many of these are constant for the whole
798 * simulation; some are constant only after PME tuning completes.
800 static void init_interaction_const(FILE* fp,
801 interaction_const_t** interaction_const,
802 const t_inputrec* ir,
803 const gmx_mtop_t* mtop,
804 bool systemHasNetCharge)
806 interaction_const_t* ic = new interaction_const_t;
808 ic->cutoff_scheme = ir->cutoff_scheme;
810 ic->coulombEwaldTables = std::make_unique<EwaldCorrectionTables>();
813 ic->vdwtype = ir->vdwtype;
814 ic->vdw_modifier = ir->vdw_modifier;
815 ic->reppow = mtop->ffparams.reppow;
816 ic->rvdw = cutoff_inf(ir->rvdw);
817 ic->rvdw_switch = ir->rvdw_switch;
818 ic->ljpme_comb_rule = ir->ljpme_combination_rule;
819 ic->useBuckingham = (mtop->ffparams.functype[0] == F_BHAM);
820 if (ic->useBuckingham)
822 ic->buckinghamBMax = calcBuckinghamBMax(fp, mtop);
825 initVdwEwaldParameters(fp, ir, ic);
827 clear_force_switch_constants(&ic->dispersion_shift);
828 clear_force_switch_constants(&ic->repulsion_shift);
830 switch (ic->vdw_modifier)
832 case eintmodPOTSHIFT:
833 /* Only shift the potential, don't touch the force */
834 ic->dispersion_shift.cpot = -1.0 / gmx::power6(ic->rvdw);
835 ic->repulsion_shift.cpot = -1.0 / gmx::power12(ic->rvdw);
837 case eintmodFORCESWITCH:
838 /* Switch the force, switch and shift the potential */
839 force_switch_constants(6.0, ic->rvdw_switch, ic->rvdw, &ic->dispersion_shift);
840 force_switch_constants(12.0, ic->rvdw_switch, ic->rvdw, &ic->repulsion_shift);
842 case eintmodPOTSWITCH:
843 /* Switch the potential and force */
844 potential_switch_constants(ic->rvdw_switch, ic->rvdw, &ic->vdw_switch);
847 case eintmodEXACTCUTOFF:
848 /* Nothing to do here */
850 default: gmx_incons("unimplemented potential modifier");
854 ic->eeltype = ir->coulombtype;
855 ic->coulomb_modifier = ir->coulomb_modifier;
856 ic->rcoulomb = cutoff_inf(ir->rcoulomb);
857 ic->rcoulomb_switch = ir->rcoulomb_switch;
858 ic->epsilon_r = ir->epsilon_r;
860 /* Set the Coulomb energy conversion factor */
861 if (ic->epsilon_r != 0)
863 ic->epsfac = ONE_4PI_EPS0 / ic->epsilon_r;
867 /* eps = 0 is infinite dieletric: no Coulomb interactions */
872 if (EEL_RF(ic->eeltype))
874 GMX_RELEASE_ASSERT(ic->eeltype != eelGRF_NOTUSED, "GRF is no longer supported");
875 ic->epsilon_rf = ir->epsilon_rf;
877 calc_rffac(fp, ic->epsilon_r, ic->epsilon_rf, ic->rcoulomb, &ic->k_rf, &ic->c_rf);
881 /* For plain cut-off we might use the reaction-field kernels */
882 ic->epsilon_rf = ic->epsilon_r;
884 if (ir->coulomb_modifier == eintmodPOTSHIFT)
886 ic->c_rf = 1 / ic->rcoulomb;
894 initCoulombEwaldParameters(fp, ir, systemHasNetCharge, ic);
898 real dispersion_shift;
900 dispersion_shift = ic->dispersion_shift.cpot;
901 if (EVDW_PME(ic->vdwtype))
903 dispersion_shift -= ic->sh_lj_ewald;
905 fprintf(fp, "Potential shift: LJ r^-12: %.3e r^-6: %.3e", ic->repulsion_shift.cpot, dispersion_shift);
907 if (ic->eeltype == eelCUT)
909 fprintf(fp, ", Coulomb %.e", -ic->c_rf);
911 else if (EEL_PME(ic->eeltype))
913 fprintf(fp, ", Ewald %.3e", -ic->sh_ewald);
918 *interaction_const = ic;
921 bool areMoleculesDistributedOverPbc(const t_inputrec& ir, const gmx_mtop_t& mtop, const gmx::MDLogger& mdlog)
923 bool areMoleculesDistributedOverPbc = false;
925 if (ir.pbcType != PbcType::No)
927 /* Not making molecules whole is faster in most cases,
928 * but with orientation restraints or non-tinfoil boundary
929 * conditions we need whole molecules.
931 const bool useEwaldSurfaceCorrection = (EEL_PME_EWALD(ir.coulombtype) && ir.epsilon_surface != 0);
932 areMoleculesDistributedOverPbc =
933 (gmx_mtop_ftype_count(mtop, F_ORIRES) == 0 && !useEwaldSurfaceCorrection);
935 if (getenv("GMX_USE_GRAPH") != nullptr)
937 areMoleculesDistributedOverPbc = false;
939 GMX_LOG(mdlog.warning)
942 "GMX_USE_GRAPH is set, using the graph for bonded "
945 if (mtop.bIntermolecularInteractions)
947 GMX_LOG(mdlog.warning)
950 "WARNING: Molecules linked by intermolecular interactions "
951 "have to reside in the same periodic image, otherwise "
952 "artifacts will occur!");
956 GMX_RELEASE_ASSERT(areMoleculesDistributedOverPbc || !mtop.bIntermolecularInteractions,
957 "We need to use PBC within molecules with inter-molecular interactions");
960 return areMoleculesDistributedOverPbc;
963 void init_forcerec(FILE* fp,
964 const gmx::MDLogger& mdlog,
967 const t_inputrec* ir,
968 const gmx_mtop_t* mtop,
973 gmx::ArrayRef<const std::string> tabbfnm,
976 /* By default we turn SIMD kernels on, but it might be turned off further down... */
977 fr->use_simd_kernels = TRUE;
979 if (check_box(ir->pbcType, box))
981 gmx_fatal(FARGS, "%s", check_box(ir->pbcType, box));
984 /* Test particle insertion ? */
987 /* Set to the size of the molecule to be inserted (the last one) */
988 gmx::RangePartitioning molecules = gmx_mtop_molecules(*mtop);
989 fr->n_tpi = molecules.block(molecules.numBlocks() - 1).size();
996 if (ir->coulombtype == eelRF_NEC_UNSUPPORTED || ir->coulombtype == eelGRF_NOTUSED)
998 gmx_fatal(FARGS, "%s electrostatics is no longer supported", eel_names[ir->coulombtype]);
1003 gmx_fatal(FARGS, "AdResS simulations are no longer supported");
1005 if (ir->useTwinRange)
1007 gmx_fatal(FARGS, "Twin-range simulations are no longer supported");
1009 /* Copy the user determined parameters */
1010 fr->userint1 = ir->userint1;
1011 fr->userint2 = ir->userint2;
1012 fr->userint3 = ir->userint3;
1013 fr->userint4 = ir->userint4;
1014 fr->userreal1 = ir->userreal1;
1015 fr->userreal2 = ir->userreal2;
1016 fr->userreal3 = ir->userreal3;
1017 fr->userreal4 = ir->userreal4;
1020 fr->fc_stepsize = ir->fc_stepsize;
1023 fr->efep = ir->efep;
1024 fr->sc_alphavdw = ir->fepvals->sc_alpha;
1025 if (ir->fepvals->bScCoul)
1027 fr->sc_alphacoul = ir->fepvals->sc_alpha;
1028 fr->sc_sigma6_min = gmx::power6(ir->fepvals->sc_sigma_min);
1032 fr->sc_alphacoul = 0;
1033 fr->sc_sigma6_min = 0; /* only needed when bScCoul is on */
1035 fr->sc_power = ir->fepvals->sc_power;
1036 fr->sc_r_power = ir->fepvals->sc_r_power;
1037 fr->sc_sigma6_def = gmx::power6(ir->fepvals->sc_sigma);
1039 char* env = getenv("GMX_SCSIGMA_MIN");
1043 sscanf(env, "%20lf", &dbl);
1044 fr->sc_sigma6_min = gmx::power6(dbl);
1047 fprintf(fp, "Setting the minimum soft core sigma to %g nm\n", dbl);
1051 fr->bNonbonded = TRUE;
1052 if (getenv("GMX_NO_NONBONDED") != nullptr)
1054 /* turn off non-bonded calculations */
1055 fr->bNonbonded = FALSE;
1056 GMX_LOG(mdlog.warning)
1059 "Found environment variable GMX_NO_NONBONDED.\n"
1060 "Disabling nonbonded calculations.");
1063 if ((getenv("GMX_DISABLE_SIMD_KERNELS") != nullptr) || (getenv("GMX_NOOPTIMIZEDKERNELS") != nullptr))
1065 fr->use_simd_kernels = FALSE;
1069 "\nFound environment variable GMX_DISABLE_SIMD_KERNELS.\n"
1070 "Disabling the usage of any SIMD-specific non-bonded & bonded kernel routines\n"
1071 "(e.g. SSE2/SSE4.1/AVX).\n\n");
1075 fr->bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
1077 /* Neighbour searching stuff */
1078 fr->cutoff_scheme = ir->cutoff_scheme;
1079 fr->pbcType = ir->pbcType;
1081 /* Determine if we will do PBC for distances in bonded interactions */
1082 if (fr->pbcType == PbcType::No)
1084 fr->bMolPBC = FALSE;
1088 const bool useEwaldSurfaceCorrection =
1089 (EEL_PME_EWALD(ir->coulombtype) && ir->epsilon_surface != 0);
1090 if (!DOMAINDECOMP(cr))
1092 fr->bMolPBC = areMoleculesDistributedOverPbc(*ir, *mtop, mdlog);
1093 // The assert below is equivalent to fcd->orires.nr != gmx_mtop_ftype_count(mtop, F_ORIRES)
1094 GMX_RELEASE_ASSERT(!fr->bMolPBC || fcd->orires.nr == 0,
1095 "Molecules broken over PBC exist in a simulation including "
1096 "orientation restraints. "
1097 "This likely means that the global topology and the force constant "
1098 "data have gotten out of sync.");
1102 fr->bMolPBC = dd_bonded_molpbc(cr->dd, fr->pbcType);
1104 if (useEwaldSurfaceCorrection && !dd_moleculesAreAlwaysWhole(*cr->dd))
1107 "You requested dipole correction (epsilon_surface > 0), but molecules "
1109 "over periodic boundary conditions by the domain decomposition. "
1110 "Run without domain decomposition instead.");
1114 if (useEwaldSurfaceCorrection)
1116 GMX_RELEASE_ASSERT((!DOMAINDECOMP(cr) && !fr->bMolPBC)
1117 || (DOMAINDECOMP(cr) && dd_moleculesAreAlwaysWhole(*cr->dd)),
1118 "Molecules can not be broken by PBC with epsilon_surface > 0");
1122 fr->rc_scaling = ir->refcoord_scaling;
1123 copy_rvec(ir->posres_com, fr->posres_com);
1124 copy_rvec(ir->posres_comB, fr->posres_comB);
1125 fr->rlist = cutoff_inf(ir->rlist);
1126 fr->ljpme_combination_rule = ir->ljpme_combination_rule;
1128 /* This now calculates sum for q and c6*/
1129 bool systemHasNetCharge = set_chargesum(fp, fr, mtop);
1131 /* fr->ic is used both by verlet and group kernels (to some extent) now */
1132 init_interaction_const(fp, &fr->ic, ir, mtop, systemHasNetCharge);
1133 init_interaction_const_tables(fp, fr->ic);
1135 const interaction_const_t* ic = fr->ic;
1137 /* TODO: Replace this Ewald table or move it into interaction_const_t */
1138 if (ir->coulombtype == eelEWALD)
1140 init_ewald_tab(&(fr->ewald_table), ir, fp);
1143 /* Electrostatics: Translate from interaction-setting-in-mdp-file to kernel interaction format */
1144 switch (ic->eeltype)
1146 case eelCUT: fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_COULOMB; break;
1149 case eelRF_ZERO: fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD; break;
1157 case eelPMEUSERSWITCH:
1158 fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_CUBICSPLINETABLE;
1163 case eelEWALD: fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_EWALD; break;
1166 gmx_fatal(FARGS, "Unsupported electrostatic interaction: %s", eel_names[ic->eeltype]);
1168 fr->nbkernel_elec_modifier = ic->coulomb_modifier;
1170 /* Vdw: Translate from mdp settings to kernel format */
1171 switch (ic->vdwtype)
1176 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_BUCKINGHAM;
1180 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_LENNARDJONES;
1183 case evdwPME: fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_LJEWALD; break;
1188 case evdwENCADSHIFT:
1189 fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
1192 default: gmx_fatal(FARGS, "Unsupported vdw interaction: %s", evdw_names[ic->vdwtype]);
1194 fr->nbkernel_vdw_modifier = ic->vdw_modifier;
1196 if (ir->cutoff_scheme == ecutsVERLET)
1198 if (!gmx_within_tol(ic->reppow, 12.0, 10 * GMX_DOUBLE_EPS))
1200 gmx_fatal(FARGS, "Cut-off scheme %s only supports LJ repulsion power 12",
1201 ecutscheme_names[ir->cutoff_scheme]);
1203 /* Older tpr files can contain Coulomb user tables with the Verlet cutoff-scheme,
1204 * while mdrun does not (and never did) support this.
1206 if (EEL_USER(fr->ic->eeltype))
1208 gmx_fatal(FARGS, "Combination of %s and cutoff scheme %s is not supported",
1209 eel_names[ir->coulombtype], ecutscheme_names[ir->cutoff_scheme]);
1212 fr->bvdwtab = FALSE;
1213 fr->bcoultab = FALSE;
1216 /* 1-4 interaction electrostatics */
1217 fr->fudgeQQ = mtop->ffparams.fudgeQQ;
1219 fr->haveDirectVirialContributions =
1220 (EEL_FULL(ic->eeltype) || EVDW_PME(ic->vdwtype) || fr->forceProviders->hasForceProvider()
1221 || gmx_mtop_ftype_count(mtop, F_POSRES) > 0 || gmx_mtop_ftype_count(mtop, F_FBPOSRES) > 0
1222 || ir->nwall > 0 || ir->bPull || ir->bRot || ir->bIMD);
1224 if (fr->shift_vec == nullptr)
1226 snew(fr->shift_vec, SHIFTS);
1229 fr->shiftForces.resize(SHIFTS);
1231 if (fr->nbfp.empty())
1233 fr->ntype = mtop->ffparams.atnr;
1234 fr->nbfp = mk_nbfp(&mtop->ffparams, fr->bBHAM);
1235 if (EVDW_PME(ic->vdwtype))
1237 fr->ljpme_c6grid = make_ljpme_c6grid(&mtop->ffparams, fr);
1241 /* Copy the energy group exclusions */
1242 fr->egp_flags = ir->opts.egp_flags;
1244 /* Van der Waals stuff */
1245 if ((ic->vdwtype != evdwCUT) && (ic->vdwtype != evdwUSER) && !fr->bBHAM)
1247 if (ic->rvdw_switch >= ic->rvdw)
1249 gmx_fatal(FARGS, "rvdw_switch (%f) must be < rvdw (%f)", ic->rvdw_switch, ic->rvdw);
1253 fprintf(fp, "Using %s Lennard-Jones, switch between %g and %g nm\n",
1254 (ic->eeltype == eelSWITCH) ? "switched" : "shifted", ic->rvdw_switch, ic->rvdw);
1258 if (fr->bBHAM && EVDW_PME(ic->vdwtype))
1260 gmx_fatal(FARGS, "LJ PME not supported with Buckingham");
1263 if (fr->bBHAM && (ic->vdwtype == evdwSHIFT || ic->vdwtype == evdwSWITCH))
1265 gmx_fatal(FARGS, "Switch/shift interaction not supported with Buckingham");
1268 if (fr->bBHAM && fr->cutoff_scheme == ecutsVERLET)
1270 gmx_fatal(FARGS, "Verlet cutoff-scheme is not supported with Buckingham");
1273 if (fp && fr->cutoff_scheme == ecutsGROUP)
1275 fprintf(fp, "Cut-off's: NS: %g Coulomb: %g %s: %g\n", fr->rlist, ic->rcoulomb,
1276 fr->bBHAM ? "BHAM" : "LJ", ic->rvdw);
1279 if (ir->implicit_solvent)
1281 gmx_fatal(FARGS, "Implict solvation is no longer supported.");
1285 /* This code automatically gives table length tabext without cut-off's,
1286 * in that case grompp should already have checked that we do not need
1287 * normal tables and we only generate tables for 1-4 interactions.
1289 real rtab = ir->rlist + ir->tabext;
1291 /* We want to use unmodified tables for 1-4 coulombic
1292 * interactions, so we must in general have an extra set of
1294 if (gmx_mtop_ftype_count(mtop, F_LJ14) > 0 || gmx_mtop_ftype_count(mtop, F_LJC14_Q) > 0
1295 || gmx_mtop_ftype_count(mtop, F_LJC_PAIRS_NB) > 0)
1297 fr->pairsTable = make_tables(fp, ic, tabpfn, rtab, GMX_MAKETABLES_14ONLY);
1301 fr->nwall = ir->nwall;
1302 if (ir->nwall && ir->wall_type == ewtTABLE)
1304 make_wall_tables(fp, ir, tabfn, &mtop->groups, fr);
1307 if (fcd && !tabbfnm.empty())
1309 // Need to catch std::bad_alloc
1310 // TODO Don't need to catch this here, when merging with master branch
1313 fcd->bondtab = make_bonded_tables(fp, F_TABBONDS, F_TABBONDSNC, mtop, tabbfnm, "b");
1314 fcd->angletab = make_bonded_tables(fp, F_TABANGLES, -1, mtop, tabbfnm, "a");
1315 fcd->dihtab = make_bonded_tables(fp, F_TABDIHS, -1, mtop, tabbfnm, "d");
1317 GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
1324 "No fcdata or table file name passed, can not read table, can not do bonded "
1329 // QM/MM initialization if requested
1330 fr->bQMMM = ir->bQMMM;
1333 // Initialize QM/MM if supported
1339 "Large parts of the QM/MM support is deprecated, and may be removed in "
1341 "version. Please get in touch with the developers if you find the "
1343 "as help is needed if the functionality is to continue to be "
1345 fr->qr = mk_QMMMrec();
1346 init_QMMMrec(cr, mtop, ir, fr);
1351 "QM/MM was requested, but is only available when GROMACS "
1352 "is configured with QM/MM support");
1356 /* Set all the static charge group info */
1357 fr->cginfo_mb = init_cginfo_mb(mtop, fr);
1358 if (!DOMAINDECOMP(cr))
1360 fr->cginfo = cginfo_expand(mtop->molblock.size(), fr->cginfo_mb);
1363 if (!DOMAINDECOMP(cr))
1365 forcerec_set_ranges(fr, mtop->natoms, mtop->natoms, mtop->natoms);
1368 fr->print_force = print_force;
1370 /* Initialize the thread working data for bonded interactions */
1371 fr->bondedThreading = init_bonded_threading(
1372 fp, mtop->groups.groups[SimulationAtomGroupType::EnergyOutput].size());
1374 fr->nthread_ewc = gmx_omp_nthreads_get(emntBonded);
1375 snew(fr->ewc_t, fr->nthread_ewc);
1377 if (ir->eDispCorr != edispcNO)
1379 fr->dispersionCorrection = std::make_unique<DispersionCorrection>(
1380 *mtop, *ir, fr->bBHAM, fr->ntype, fr->nbfp, *fr->ic, tabfn);
1381 fr->dispersionCorrection->print(mdlog);
1386 /* Here we switch from using mdlog, which prints the newline before
1387 * the paragraph, to our old fprintf logging, which prints the newline
1388 * after the paragraph, so we should add a newline here.
1394 t_forcerec::t_forcerec() = default;
1396 t_forcerec::~t_forcerec()
1398 /* Note: This code will disappear when types are converted to C++ */
1401 tear_down_bonded_threading(bondedThreading);