*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013-2019, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include <cstring>
#include <algorithm>
+#include <memory>
#include "gromacs/commandline/filenm.h"
-#include "gromacs/compat/make_unique.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/ewald/ewald.h"
-#include "gromacs/ewald/ewald-utils.h"
+#include "gromacs/ewald/ewald_utils.h"
+#include "gromacs/ewald/pme_pp_comm_gpu.h"
#include "gromacs/fileio/filetypes.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nonbonded/nonbonded.h"
#include "gromacs/gpu_utils/gpu_utils.h"
#include "gromacs/hardware/hw_info.h"
-#include "gromacs/listed-forces/gpubonded.h"
-#include "gromacs/listed-forces/manage-threading.h"
-#include "gromacs/listed-forces/pairs.h"
+#include "gromacs/listed_forces/gpubonded.h"
+#include "gromacs/listed_forces/manage_threading.h"
+#include "gromacs/listed_forces/pairs.h"
#include "gromacs/math/functions.h"
#include "gromacs/math/units.h"
#include "gromacs/math/utilities.h"
#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/dispersioncorrection.h"
#include "gromacs/mdlib/force.h"
-#include "gromacs/mdlib/forcerec-threading.h"
+#include "gromacs/mdlib/forcerec_threading.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdlib/md_support.h"
-#include "gromacs/mdlib/nb_verlet.h"
-#include "gromacs/mdlib/nbnxn_atomdata.h"
-#include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
-#include "gromacs/mdlib/nbnxn_grid.h"
-#include "gromacs/mdlib/nbnxn_internal.h"
-#include "gromacs/mdlib/nbnxn_search.h"
-#include "gromacs/mdlib/nbnxn_simd.h"
-#include "gromacs/mdlib/nbnxn_tuning.h"
-#include "gromacs/mdlib/nbnxn_util.h"
-#include "gromacs/mdlib/ns.h"
#include "gromacs/mdlib/qmmm.h"
#include "gromacs/mdlib/rf_util.h"
-#include "gromacs/mdlib/sim_util.h"
#include "gromacs/mdlib/wall.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/fcdata.h"
#include "gromacs/mdtypes/iforceprovider.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/nbnxm/gpu_data_mgmt.h"
+#include "gromacs/nbnxm/nbnxm.h"
+#include "gromacs/nbnxm/nbnxm_geometry.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/simd/simd.h"
#include "gromacs/tables/forcetable.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/trajectory/trajectoryframe.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/strconvert.h"
-#include "nbnxn_gpu_jit_support.h"
+/*! \brief environment variable to enable GPU P2P communication */
+static const bool c_enableGpuPmePpComms =
+ (getenv("GMX_GPU_PME_PP_COMMS") != nullptr) && GMX_THREAD_MPI && (GMX_GPU == GMX_GPU_CUDA);
-t_forcerec *mk_forcerec()
+static real* mk_nbfp(const gmx_ffparams_t* idef, gmx_bool bBHAM)
{
- t_forcerec *fr;
-
- snew(fr, 1);
-
- return fr;
-}
-
-static real *mk_nbfp(const gmx_ffparams_t *idef, gmx_bool bBHAM)
-{
- real *nbfp;
+ real* nbfp;
int i, j, k, atnr;
atnr = idef->atnr;
if (bBHAM)
{
- snew(nbfp, 3*atnr*atnr);
+ snew(nbfp, 3 * atnr * atnr);
for (i = k = 0; (i < atnr); i++)
{
for (j = 0; (j < atnr); j++, k++)
BHAMA(nbfp, atnr, i, j) = idef->iparams[k].bham.a;
BHAMB(nbfp, atnr, i, j) = idef->iparams[k].bham.b;
/* nbfp now includes the 6.0 derivative prefactor */
- BHAMC(nbfp, atnr, i, j) = idef->iparams[k].bham.c*6.0;
+ BHAMC(nbfp, atnr, i, j) = idef->iparams[k].bham.c * 6.0;
}
}
}
else
{
- snew(nbfp, 2*atnr*atnr);
+ snew(nbfp, 2 * atnr * atnr);
for (i = k = 0; (i < atnr); i++)
{
for (j = 0; (j < atnr); j++, k++)
{
/* nbfp now includes the 6.0/12.0 derivative prefactors */
- C6(nbfp, atnr, i, j) = idef->iparams[k].lj.c6*6.0;
- C12(nbfp, atnr, i, j) = idef->iparams[k].lj.c12*12.0;
+ C6(nbfp, atnr, i, j) = idef->iparams[k].lj.c6 * 6.0;
+ C12(nbfp, atnr, i, j) = idef->iparams[k].lj.c12 * 12.0;
}
}
}
return nbfp;
}
-static real *make_ljpme_c6grid(const gmx_ffparams_t *idef, t_forcerec *fr)
+static real* make_ljpme_c6grid(const gmx_ffparams_t* idef, t_forcerec* fr)
{
- int i, j, k, atnr;
- real c6, c6i, c6j, c12i, c12j, epsi, epsj, sigmai, sigmaj;
- real *grid;
+ int i, j, k, atnr;
+ real c6, c6i, c6j, c12i, c12j, epsi, epsj, sigmai, sigmaj;
+ real* grid;
/* For LJ-PME simulations, we correct the energies with the reciprocal space
* inside of the cut-off. To do this the non-bonded kernels needs to have
*/
atnr = idef->atnr;
- snew(grid, 2*atnr*atnr);
+ snew(grid, 2 * atnr * atnr);
for (i = k = 0; (i < atnr); i++)
{
for (j = 0; (j < atnr); j++, k++)
{
- c6i = idef->iparams[i*(atnr+1)].lj.c6;
- c12i = idef->iparams[i*(atnr+1)].lj.c12;
- c6j = idef->iparams[j*(atnr+1)].lj.c6;
- c12j = idef->iparams[j*(atnr+1)].lj.c12;
+ c6i = idef->iparams[i * (atnr + 1)].lj.c6;
+ c12i = idef->iparams[i * (atnr + 1)].lj.c12;
+ c6j = idef->iparams[j * (atnr + 1)].lj.c6;
+ c12j = idef->iparams[j * (atnr + 1)].lj.c12;
c6 = std::sqrt(c6i * c6j);
- if (fr->ljpme_combination_rule == eljpmeLB
- && !gmx_numzero(c6) && !gmx_numzero(c12i) && !gmx_numzero(c12j))
+ if (fr->ljpme_combination_rule == eljpmeLB && !gmx_numzero(c6) && !gmx_numzero(c12i)
+ && !gmx_numzero(c12j))
{
sigmai = gmx::sixthroot(c12i / c6i);
sigmaj = gmx::sixthroot(c12j / c6j);
epsi = c6i * c6i / c12i;
epsj = c6j * c6j / c12j;
- c6 = std::sqrt(epsi * epsj) * gmx::power6(0.5*(sigmai+sigmaj));
+ c6 = std::sqrt(epsi * epsj) * gmx::power6(0.5 * (sigmai + sigmaj));
}
/* Store the elements at the same relative positions as C6 in nbfp in order
* to simplify access in the kernels
*/
- grid[2*(atnr*i+j)] = c6*6.0;
+ grid[2 * (atnr * i + j)] = c6 * 6.0;
}
}
return grid;
}
-static real *mk_nbfp_combination_rule(const gmx_ffparams_t *idef, int comb_rule)
-{
- real *nbfp;
- int i, j, atnr;
- real c6i, c6j, c12i, c12j, epsi, epsj, sigmai, sigmaj;
- real c6, c12;
-
- atnr = idef->atnr;
- snew(nbfp, 2*atnr*atnr);
- for (i = 0; i < atnr; ++i)
- {
- for (j = 0; j < atnr; ++j)
- {
- c6i = idef->iparams[i*(atnr+1)].lj.c6;
- c12i = idef->iparams[i*(atnr+1)].lj.c12;
- c6j = idef->iparams[j*(atnr+1)].lj.c6;
- c12j = idef->iparams[j*(atnr+1)].lj.c12;
- c6 = std::sqrt(c6i * c6j);
- c12 = std::sqrt(c12i * c12j);
- if (comb_rule == eCOMB_ARITHMETIC
- && !gmx_numzero(c6) && !gmx_numzero(c12))
- {
- sigmai = gmx::sixthroot(c12i / c6i);
- sigmaj = gmx::sixthroot(c12j / c6j);
- epsi = c6i * c6i / c12i;
- epsj = c6j * c6j / c12j;
- c6 = std::sqrt(epsi * epsj) * gmx::power6(0.5*(sigmai+sigmaj));
- c12 = std::sqrt(epsi * epsj) * gmx::power12(0.5*(sigmai+sigmaj));
- }
- C6(nbfp, atnr, i, j) = c6*6.0;
- C12(nbfp, atnr, i, j) = c12*12.0;
- }
- }
- return nbfp;
-}
-
-/* This routine sets fr->solvent_opt to the most common solvent in the
- * system, e.g. esolSPC or esolTIP4P. It will also mark each charge group in
- * the fr->solvent_type array with the correct type (or esolNO).
- *
- * Charge groups that fulfill the conditions but are not identical to the
- * most common one will be marked as esolNO in the solvent_type array.
- *
- * TIP3p is identical to SPC for these purposes, so we call it
- * SPC in the arrays (Apologies to Bill Jorgensen ;-)
- *
- * NOTE: QM particle should not
- * become an optimized solvent. Not even if there is only one charge
- * group in the Qm
- */
-
-typedef struct
-{
- int model;
- int count;
- int vdwtype[4];
- real charge[4];
-} solvent_parameters_t;
-
-static void
-check_solvent_cg(const gmx_moltype_t *molt,
- int cg0,
- int nmol,
- const unsigned char *qm_grpnr,
- const t_grps *qm_grps,
- t_forcerec * fr,
- int *n_solvent_parameters,
- solvent_parameters_t **solvent_parameters_p,
- int cginfo,
- int *cg_sp)
-{
- t_atom *atom;
- int j, k;
- int j0, j1, nj;
- gmx_bool perturbed;
- gmx_bool has_vdw[4];
- gmx_bool match;
- real tmp_charge[4] = { 0.0 }; /* init to zero to make gcc4.8 happy */
- int tmp_vdwtype[4] = { 0 }; /* init to zero to make gcc4.8 happy */
- int tjA;
- gmx_bool qm;
- solvent_parameters_t *solvent_parameters;
-
- /* We use a list with parameters for each solvent type.
- * Every time we discover a new molecule that fulfills the basic
- * conditions for a solvent we compare with the previous entries
- * in these lists. If the parameters are the same we just increment
- * the counter for that type, and otherwise we create a new type
- * based on the current molecule.
- *
- * Once we've finished going through all molecules we check which
- * solvent is most common, and mark all those molecules while we
- * clear the flag on all others.
- */
-
- solvent_parameters = *solvent_parameters_p;
-
- /* Mark the cg first as non optimized */
- *cg_sp = -1;
-
- /* Check if this cg has no exclusions with atoms in other charge groups
- * and all atoms inside the charge group excluded.
- * We only have 3 or 4 atom solvent loops.
- */
- if (GET_CGINFO_EXCL_INTER(cginfo) ||
- !GET_CGINFO_EXCL_INTRA(cginfo))
- {
- return;
- }
-
- /* Get the indices of the first atom in this charge group */
- j0 = molt->cgs.index[cg0];
- j1 = molt->cgs.index[cg0+1];
-
- /* Number of atoms in our molecule */
- nj = j1 - j0;
-
- if (debug)
- {
- fprintf(debug,
- "Moltype '%s': there are %d atoms in this charge group\n",
- *molt->name, nj);
- }
-
- /* Check if it could be an SPC (3 atoms) or TIP4p (4) water,
- * otherwise skip it.
- */
- if (nj < 3 || nj > 4)
- {
- return;
- }
-
- /* Check if we are doing QM on this group */
- qm = FALSE;
- if (qm_grpnr != nullptr)
- {
- for (j = j0; j < j1 && !qm; j++)
- {
- qm = (qm_grpnr[j] < qm_grps->nr - 1);
- }
- }
- /* Cannot use solvent optimization with QM */
- if (qm)
- {
- return;
- }
-
- atom = molt->atoms.atom;
-
- /* Still looks like a solvent, time to check parameters */
-
- /* If it is perturbed (free energy) we can't use the solvent loops,
- * so then we just skip to the next molecule.
- */
- perturbed = FALSE;
-
- for (j = j0; j < j1 && !perturbed; j++)
- {
- perturbed = PERTURBED(atom[j]);
- }
-
- if (perturbed)
- {
- return;
- }
-
- /* Now it's only a question if the VdW and charge parameters
- * are OK. Before doing the check we compare and see if they are
- * identical to a possible previous solvent type.
- * First we assign the current types and charges.
- */
- for (j = 0; j < nj; j++)
- {
- tmp_vdwtype[j] = atom[j0+j].type;
- tmp_charge[j] = atom[j0+j].q;
- }
-
- /* Does it match any previous solvent type? */
- for (k = 0; k < *n_solvent_parameters; k++)
- {
- match = TRUE;
-
-
- /* We can only match SPC with 3 atoms and TIP4p with 4 atoms */
- if ( (solvent_parameters[k].model == esolSPC && nj != 3) ||
- (solvent_parameters[k].model == esolTIP4P && nj != 4) )
- {
- match = FALSE;
- }
-
- /* Check that types & charges match for all atoms in molecule */
- for (j = 0; j < nj && match; j++)
- {
- if (tmp_vdwtype[j] != solvent_parameters[k].vdwtype[j])
- {
- match = FALSE;
- }
- if (tmp_charge[j] != solvent_parameters[k].charge[j])
- {
- match = FALSE;
- }
- }
- if (match)
- {
- /* Congratulations! We have a matched solvent.
- * Flag it with this type for later processing.
- */
- *cg_sp = k;
- solvent_parameters[k].count += nmol;
-
- /* We are done with this charge group */
- return;
- }
- }
-
- /* If we get here, we have a tentative new solvent type.
- * Before we add it we must check that it fulfills the requirements
- * of the solvent optimized loops. First determine which atoms have
- * VdW interactions.
- */
- for (j = 0; j < nj; j++)
- {
- has_vdw[j] = FALSE;
- tjA = tmp_vdwtype[j];
-
- /* Go through all other tpes and see if any have non-zero
- * VdW parameters when combined with this one.
- */
- for (k = 0; k < fr->ntype && (!has_vdw[j]); k++)
- {
- /* We already checked that the atoms weren't perturbed,
- * so we only need to check state A now.
- */
- if (fr->bBHAM)
- {
- has_vdw[j] = (has_vdw[j] ||
- (BHAMA(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
- (BHAMB(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
- (BHAMC(fr->nbfp, fr->ntype, tjA, k) != 0.0));
- }
- else
- {
- /* Standard LJ */
- has_vdw[j] = (has_vdw[j] ||
- (C6(fr->nbfp, fr->ntype, tjA, k) != 0.0) ||
- (C12(fr->nbfp, fr->ntype, tjA, k) != 0.0));
- }
- }
- }
-
- /* Now we know all we need to make the final check and assignment. */
- if (nj == 3)
- {
- /* So, is it an SPC?
- * For this we require thatn all atoms have charge,
- * the charges on atom 2 & 3 should be the same, and only
- * atom 1 might have VdW.
- */
- if (!has_vdw[1] &&
- !has_vdw[2] &&
- tmp_charge[0] != 0 &&
- tmp_charge[1] != 0 &&
- tmp_charge[2] == tmp_charge[1])
- {
- srenew(solvent_parameters, *n_solvent_parameters+1);
- solvent_parameters[*n_solvent_parameters].model = esolSPC;
- solvent_parameters[*n_solvent_parameters].count = nmol;
- for (k = 0; k < 3; k++)
- {
- solvent_parameters[*n_solvent_parameters].vdwtype[k] = tmp_vdwtype[k];
- solvent_parameters[*n_solvent_parameters].charge[k] = tmp_charge[k];
- }
-
- *cg_sp = *n_solvent_parameters;
- (*n_solvent_parameters)++;
- }
- }
- else if (nj == 4)
- {
- /* Or could it be a TIP4P?
- * For this we require thatn atoms 2,3,4 have charge, but not atom 1.
- * Only atom 1 mght have VdW.
- */
- if (!has_vdw[1] &&
- !has_vdw[2] &&
- !has_vdw[3] &&
- tmp_charge[0] == 0 &&
- tmp_charge[1] != 0 &&
- tmp_charge[2] == tmp_charge[1] &&
- tmp_charge[3] != 0)
- {
- srenew(solvent_parameters, *n_solvent_parameters+1);
- solvent_parameters[*n_solvent_parameters].model = esolTIP4P;
- solvent_parameters[*n_solvent_parameters].count = nmol;
- for (k = 0; k < 4; k++)
- {
- solvent_parameters[*n_solvent_parameters].vdwtype[k] = tmp_vdwtype[k];
- solvent_parameters[*n_solvent_parameters].charge[k] = tmp_charge[k];
- }
-
- *cg_sp = *n_solvent_parameters;
- (*n_solvent_parameters)++;
- }
- }
-
- *solvent_parameters_p = solvent_parameters;
-}
-
-static void
-check_solvent(FILE * fp,
- const gmx_mtop_t * mtop,
- t_forcerec * fr,
- cginfo_mb_t *cginfo_mb)
+enum
{
- const t_block * cgs;
- const gmx_moltype_t *molt;
- int mol, cg_mol, at_offset, am, cgm, i, nmol_ch, nmol;
- int n_solvent_parameters;
- solvent_parameters_t *solvent_parameters;
- int **cg_sp;
- int bestsp, bestsol;
-
- if (debug)
- {
- fprintf(debug, "Going to determine what solvent types we have.\n");
- }
-
- n_solvent_parameters = 0;
- solvent_parameters = nullptr;
- /* Allocate temporary array for solvent type */
- snew(cg_sp, mtop->molblock.size());
-
- at_offset = 0;
- for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
- {
- molt = &mtop->moltype[mtop->molblock[mb].type];
- cgs = &molt->cgs;
- /* Here we have to loop over all individual molecules
- * because we need to check for QMMM particles.
- */
- snew(cg_sp[mb], cginfo_mb[mb].cg_mod);
- nmol_ch = cginfo_mb[mb].cg_mod/cgs->nr;
- nmol = mtop->molblock[mb].nmol/nmol_ch;
- for (mol = 0; mol < nmol_ch; mol++)
- {
- cgm = mol*cgs->nr;
- am = mol*cgs->index[cgs->nr];
- for (cg_mol = 0; cg_mol < cgs->nr; cg_mol++)
- {
- check_solvent_cg(molt, cg_mol, nmol,
- mtop->groups.grpnr[egcQMMM] ?
- mtop->groups.grpnr[egcQMMM]+at_offset+am : nullptr,
- &mtop->groups.grps[egcQMMM],
- fr,
- &n_solvent_parameters, &solvent_parameters,
- cginfo_mb[mb].cginfo[cgm+cg_mol],
- &cg_sp[mb][cgm+cg_mol]);
- }
- }
- at_offset += cgs->index[cgs->nr];
- }
-
- /* Puh! We finished going through all charge groups.
- * Now find the most common solvent model.
- */
-
- /* Most common solvent this far */
- bestsp = -2;
- for (i = 0; i < n_solvent_parameters; i++)
- {
- if (bestsp == -2 ||
- solvent_parameters[i].count > solvent_parameters[bestsp].count)
- {
- bestsp = i;
- }
- }
-
- if (bestsp >= 0)
- {
- bestsol = solvent_parameters[bestsp].model;
- }
- else
- {
- bestsol = esolNO;
- }
-
- fr->nWatMol = 0;
- for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
- {
- cgs = &mtop->moltype[mtop->molblock[mb].type].cgs;
- nmol = (mtop->molblock[mb].nmol*cgs->nr)/cginfo_mb[mb].cg_mod;
- for (i = 0; i < cginfo_mb[mb].cg_mod; i++)
- {
- if (cg_sp[mb][i] == bestsp)
- {
- SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[i], bestsol);
- fr->nWatMol += nmol;
- }
- else
- {
- SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[i], esolNO);
- }
- }
- sfree(cg_sp[mb]);
- }
- sfree(cg_sp);
-
- if (bestsol != esolNO && fp != nullptr)
- {
- fprintf(fp, "\nEnabling %s-like water optimization for %d molecules.\n\n",
- esol_names[bestsol],
- solvent_parameters[bestsp].count);
- }
-
- sfree(solvent_parameters);
- fr->solvent_opt = bestsol;
-}
-
-enum {
- acNONE = 0, acCONSTRAINT, acSETTLE
+ acNONE = 0,
+ acCONSTRAINT,
+ acSETTLE
};
-static cginfo_mb_t *init_cginfo_mb(FILE *fplog, const gmx_mtop_t *mtop,
- t_forcerec *fr, gmx_bool bNoSolvOpt,
- gmx_bool *bFEP_NonBonded,
- gmx_bool *bExcl_IntraCGAll_InterCGNone)
+static cginfo_mb_t* init_cginfo_mb(const gmx_mtop_t* mtop, const t_forcerec* fr, gmx_bool* bFEP_NonBonded)
{
- const t_block *cgs;
- const t_blocka *excl;
- const gmx_moltype_t *molt;
- const gmx_molblock_t *molb;
- cginfo_mb_t *cginfo_mb;
- gmx_bool *type_VDW;
- int *cginfo;
- int cg_offset, a_offset;
- int m, cg, a0, a1, gid, ai, j, aj, excl_nalloc;
- int *a_con;
- int ftype;
- int ia;
- gmx_bool bId, *bExcl, bExclIntraAll, bExclInter, bHaveVDW, bHaveQ, bHavePerturbedAtoms;
+ cginfo_mb_t* cginfo_mb;
+ gmx_bool* type_VDW;
+ int* cginfo;
+ int* a_con;
snew(cginfo_mb, mtop->molblock.size());
snew(type_VDW, fr->ntype);
- for (ai = 0; ai < fr->ntype; ai++)
+ for (int ai = 0; ai < fr->ntype; ai++)
{
type_VDW[ai] = FALSE;
- for (j = 0; j < fr->ntype; j++)
+ for (int j = 0; j < fr->ntype; j++)
{
- type_VDW[ai] = type_VDW[ai] ||
- fr->bBHAM ||
- C6(fr->nbfp, fr->ntype, ai, j) != 0 ||
- C12(fr->nbfp, fr->ntype, ai, j) != 0;
+ type_VDW[ai] = type_VDW[ai] || fr->bBHAM || C6(fr->nbfp, fr->ntype, ai, j) != 0
+ || C12(fr->nbfp, fr->ntype, ai, j) != 0;
}
}
- *bFEP_NonBonded = FALSE;
- *bExcl_IntraCGAll_InterCGNone = TRUE;
+ *bFEP_NonBonded = FALSE;
- excl_nalloc = 10;
- snew(bExcl, excl_nalloc);
- cg_offset = 0;
- a_offset = 0;
+ int a_offset = 0;
for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
{
- molb = &mtop->molblock[mb];
- molt = &mtop->moltype[molb->type];
- cgs = &molt->cgs;
- excl = &molt->excls;
+ const gmx_molblock_t& molb = mtop->molblock[mb];
+ const gmx_moltype_t& molt = mtop->moltype[molb.type];
+ const t_blocka& excl = molt.excls;
/* Check if the cginfo is identical for all molecules in this block.
* If so, we only need an array of the size of one molecule.
* Otherwise we make an array of #mol times #cgs per molecule.
*/
- bId = TRUE;
- for (m = 0; m < molb->nmol; m++)
+ gmx_bool bId = TRUE;
+ for (int m = 0; m < molb.nmol; m++)
{
- int am = m*cgs->index[cgs->nr];
- for (cg = 0; cg < cgs->nr; cg++)
+ const int am = m * molt.atoms.nr;
+ for (int a = 0; a < molt.atoms.nr; a++)
{
- a0 = cgs->index[cg];
- a1 = cgs->index[cg+1];
- if (getGroupType(&mtop->groups, egcENER, a_offset+am+a0) !=
- getGroupType(&mtop->groups, egcENER, a_offset +a0))
+ if (getGroupType(mtop->groups, SimulationAtomGroupType::QuantumMechanics, a_offset + am + a)
+ != getGroupType(mtop->groups, SimulationAtomGroupType::QuantumMechanics, a_offset + a))
{
bId = FALSE;
}
- if (mtop->groups.grpnr[egcQMMM] != nullptr)
+ if (!mtop->groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics].empty())
{
- for (ai = a0; ai < a1; ai++)
+ if (mtop->groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics][a_offset + am + a]
+ != mtop->groups.groupNumbers[SimulationAtomGroupType::QuantumMechanics][a_offset + a])
{
- if (mtop->groups.grpnr[egcQMMM][a_offset+am+ai] !=
- mtop->groups.grpnr[egcQMMM][a_offset +ai])
- {
- bId = FALSE;
- }
+ bId = FALSE;
}
}
}
}
- cginfo_mb[mb].cg_start = cg_offset;
- cginfo_mb[mb].cg_end = cg_offset + molb->nmol*cgs->nr;
- cginfo_mb[mb].cg_mod = (bId ? 1 : molb->nmol)*cgs->nr;
+ cginfo_mb[mb].cg_start = a_offset;
+ cginfo_mb[mb].cg_end = a_offset + molb.nmol * molt.atoms.nr;
+ cginfo_mb[mb].cg_mod = (bId ? 1 : molb.nmol) * molt.atoms.nr;
snew(cginfo_mb[mb].cginfo, cginfo_mb[mb].cg_mod);
cginfo = cginfo_mb[mb].cginfo;
/* Set constraints flags for constrained atoms */
- snew(a_con, molt->atoms.nr);
- for (ftype = 0; ftype < F_NRE; ftype++)
+ snew(a_con, molt.atoms.nr);
+ for (int ftype = 0; ftype < F_NRE; ftype++)
{
if (interaction_function[ftype].flags & IF_CONSTRAINT)
{
- int nral;
-
- nral = NRAL(ftype);
- for (ia = 0; ia < molt->ilist[ftype].size(); ia += 1+nral)
+ const int nral = NRAL(ftype);
+ for (int ia = 0; ia < molt.ilist[ftype].size(); ia += 1 + nral)
{
int a;
for (a = 0; a < nral; a++)
{
- a_con[molt->ilist[ftype].iatoms[ia+1+a]] =
- (ftype == F_SETTLE ? acSETTLE : acCONSTRAINT);
+ a_con[molt.ilist[ftype].iatoms[ia + 1 + a]] =
+ (ftype == F_SETTLE ? acSETTLE : acCONSTRAINT);
}
}
}
}
- for (m = 0; m < (bId ? 1 : molb->nmol); m++)
+ for (int m = 0; m < (bId ? 1 : molb.nmol); m++)
{
- int cgm = m*cgs->nr;
- int am = m*cgs->index[cgs->nr];
- for (cg = 0; cg < cgs->nr; cg++)
+ const int molculeOffsetInBlock = m * molt.atoms.nr;
+ for (int a = 0; a < molt.atoms.nr; a++)
{
- a0 = cgs->index[cg];
- a1 = cgs->index[cg+1];
+ const t_atom& atom = molt.atoms.atom[a];
+ int& atomInfo = cginfo[molculeOffsetInBlock + a];
/* Store the energy group in cginfo */
- gid = getGroupType(&mtop->groups, egcENER, a_offset+am+a0);
- SET_CGINFO_GID(cginfo[cgm+cg], gid);
+ int gid = getGroupType(mtop->groups, SimulationAtomGroupType::EnergyOutput,
+ a_offset + molculeOffsetInBlock + a);
+ SET_CGINFO_GID(atomInfo, gid);
- /* Check the intra/inter charge group exclusions */
- if (a1-a0 > excl_nalloc)
- {
- excl_nalloc = a1 - a0;
- srenew(bExcl, excl_nalloc);
- }
- /* bExclIntraAll: all intra cg interactions excluded
- * bExclInter: any inter cg interactions excluded
- */
- bExclIntraAll = TRUE;
- bExclInter = FALSE;
- bHaveVDW = FALSE;
- bHaveQ = FALSE;
- bHavePerturbedAtoms = FALSE;
- for (ai = a0; ai < a1; ai++)
- {
- /* Check VDW and electrostatic interactions */
- bHaveVDW = bHaveVDW || (type_VDW[molt->atoms.atom[ai].type] ||
- type_VDW[molt->atoms.atom[ai].typeB]);
- bHaveQ = bHaveQ || (molt->atoms.atom[ai].q != 0 ||
- molt->atoms.atom[ai].qB != 0);
-
- bHavePerturbedAtoms = bHavePerturbedAtoms || (PERTURBED(molt->atoms.atom[ai]) != 0);
-
- /* Clear the exclusion list for atom ai */
- for (aj = a0; aj < a1; aj++)
- {
- bExcl[aj-a0] = FALSE;
- }
- /* Loop over all the exclusions of atom ai */
- for (j = excl->index[ai]; j < excl->index[ai+1]; j++)
- {
- aj = excl->a[j];
- if (aj < a0 || aj >= a1)
- {
- bExclInter = TRUE;
- }
- else
- {
- bExcl[aj-a0] = TRUE;
- }
- }
- /* Check if ai excludes a0 to a1 */
- for (aj = a0; aj < a1; aj++)
- {
- if (!bExcl[aj-a0])
- {
- bExclIntraAll = FALSE;
- }
- }
+ bool bHaveVDW = (type_VDW[atom.type] || type_VDW[atom.typeB]);
+ bool bHaveQ = (atom.q != 0 || atom.qB != 0);
- switch (a_con[ai])
+ bool haveExclusions = false;
+ /* Loop over all the exclusions of atom ai */
+ for (int j = excl.index[a]; j < excl.index[a + 1]; j++)
+ {
+ if (excl.a[j] != a)
{
- case acCONSTRAINT:
- SET_CGINFO_CONSTR(cginfo[cgm+cg]);
- break;
- case acSETTLE:
- SET_CGINFO_SETTLE(cginfo[cgm+cg]);
- break;
- default:
- break;
+ haveExclusions = true;
+ break;
}
}
- if (bExclIntraAll)
- {
- SET_CGINFO_EXCL_INTRA(cginfo[cgm+cg]);
- }
- if (bExclInter)
+
+ switch (a_con[a])
{
- SET_CGINFO_EXCL_INTER(cginfo[cgm+cg]);
+ case acCONSTRAINT: SET_CGINFO_CONSTR(atomInfo); break;
+ case acSETTLE: SET_CGINFO_SETTLE(atomInfo); break;
+ default: break;
}
- if (a1 - a0 > MAX_CHARGEGROUP_SIZE)
+ if (haveExclusions)
{
- /* The size in cginfo is currently only read with DD */
- gmx_fatal(FARGS, "A charge group has size %d which is larger than the limit of %d atoms", a1-a0, MAX_CHARGEGROUP_SIZE);
+ SET_CGINFO_EXCL_INTER(atomInfo);
}
if (bHaveVDW)
{
- SET_CGINFO_HAS_VDW(cginfo[cgm+cg]);
+ SET_CGINFO_HAS_VDW(atomInfo);
}
if (bHaveQ)
{
- SET_CGINFO_HAS_Q(cginfo[cgm+cg]);
+ SET_CGINFO_HAS_Q(atomInfo);
}
- if (bHavePerturbedAtoms && fr->efep != efepNO)
+ if (fr->efep != efepNO && PERTURBED(atom))
{
- SET_CGINFO_FEP(cginfo[cgm+cg]);
+ SET_CGINFO_FEP(atomInfo);
*bFEP_NonBonded = TRUE;
}
- /* Store the charge group size */
- SET_CGINFO_NATOMS(cginfo[cgm+cg], a1-a0);
-
- if (!bExclIntraAll || bExclInter)
- {
- *bExcl_IntraCGAll_InterCGNone = FALSE;
- }
}
}
sfree(a_con);
- cg_offset += molb->nmol*cgs->nr;
- a_offset += molb->nmol*cgs->index[cgs->nr];
+ a_offset += molb.nmol * molt.atoms.nr;
}
sfree(type_VDW);
- sfree(bExcl);
-
- /* the solvent optimizer is called after the QM is initialized,
- * because we don't want to have the QM subsystemto become an
- * optimized solvent
- */
-
- check_solvent(fplog, mtop, fr, cginfo_mb);
-
- if (getenv("GMX_NO_SOLV_OPT"))
- {
- if (fplog)
- {
- fprintf(fplog, "Found environment variable GMX_NO_SOLV_OPT.\n"
- "Disabling all solvent optimization\n");
- }
- fr->solvent_opt = esolNO;
- }
- if (bNoSolvOpt)
- {
- fr->solvent_opt = esolNO;
- }
- if (!fr->solvent_opt)
- {
- for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
- {
- for (cg = 0; cg < cginfo_mb[mb].cg_mod; cg++)
- {
- SET_CGINFO_SOLOPT(cginfo_mb[mb].cginfo[cg], esolNO);
- }
- }
- }
return cginfo_mb;
}
-static int *cginfo_expand(int nmb, cginfo_mb_t *cgi_mb)
+static std::vector<int> cginfo_expand(const int nmb, const cginfo_mb_t* cgi_mb)
{
- int ncg, mb, cg;
- int *cginfo;
+ const int ncg = cgi_mb[nmb - 1].cg_end;
- ncg = cgi_mb[nmb-1].cg_end;
- snew(cginfo, ncg);
- mb = 0;
- for (cg = 0; cg < ncg; cg++)
+ std::vector<int> cginfo(ncg);
+
+ int mb = 0;
+ for (int cg = 0; cg < ncg; cg++)
{
while (cg >= cgi_mb[mb].cg_end)
{
mb++;
}
- cginfo[cg] =
- cgi_mb[mb].cginfo[(cg - cgi_mb[mb].cg_start) % cgi_mb[mb].cg_mod];
+ cginfo[cg] = cgi_mb[mb].cginfo[(cg - cgi_mb[mb].cg_start) % cgi_mb[mb].cg_mod];
}
return cginfo;
}
-static void done_cginfo_mb(cginfo_mb_t *cginfo_mb, int numMolBlocks)
+static void done_cginfo_mb(cginfo_mb_t* cginfo_mb, int numMolBlocks)
{
if (cginfo_mb == nullptr)
{
/* Sets the sum of charges (squared) and C6 in the system in fr.
* Returns whether the system has a net charge.
*/
-static bool set_chargesum(FILE *log, t_forcerec *fr, const gmx_mtop_t *mtop)
+static bool set_chargesum(FILE* log, t_forcerec* fr, const gmx_mtop_t* mtop)
{
/*This now calculates sum for q and c6*/
- double qsum, q2sum, q, c6sum, c6;
+ double qsum, q2sum, q, c6sum, c6;
- qsum = 0;
- q2sum = 0;
- c6sum = 0;
- for (const gmx_molblock_t &molb : mtop->molblock)
+ qsum = 0;
+ q2sum = 0;
+ c6sum = 0;
+ for (const gmx_molblock_t& molb : mtop->molblock)
{
int nmol = molb.nmol;
- const t_atoms *atoms = &mtop->moltype[molb.type].atoms;
+ const t_atoms* atoms = &mtop->moltype[molb.type].atoms;
for (int i = 0; i < atoms->nr; i++)
{
- q = atoms->atom[i].q;
- qsum += nmol*q;
- q2sum += nmol*q*q;
- c6 = mtop->ffparams.iparams[atoms->atom[i].type*(mtop->ffparams.atnr+1)].lj.c6;
- c6sum += nmol*c6;
+ q = atoms->atom[i].q;
+ qsum += nmol * q;
+ q2sum += nmol * q * q;
+ c6 = mtop->ffparams.iparams[atoms->atom[i].type * (mtop->ffparams.atnr + 1)].lj.c6;
+ c6sum += nmol * c6;
}
}
- fr->qsum[0] = qsum;
- fr->q2sum[0] = q2sum;
- fr->c6sum[0] = c6sum;
+ fr->qsum[0] = qsum;
+ fr->q2sum[0] = q2sum;
+ fr->c6sum[0] = c6sum;
if (fr->efep != efepNO)
{
- qsum = 0;
- q2sum = 0;
- c6sum = 0;
- for (const gmx_molblock_t &molb : mtop->molblock)
+ qsum = 0;
+ q2sum = 0;
+ c6sum = 0;
+ for (const gmx_molblock_t& molb : mtop->molblock)
{
int nmol = molb.nmol;
- const t_atoms *atoms = &mtop->moltype[molb.type].atoms;
+ const t_atoms* atoms = &mtop->moltype[molb.type].atoms;
for (int i = 0; i < atoms->nr; i++)
{
- q = atoms->atom[i].qB;
- qsum += nmol*q;
- q2sum += nmol*q*q;
- c6 = mtop->ffparams.iparams[atoms->atom[i].typeB*(mtop->ffparams.atnr+1)].lj.c6;
- c6sum += nmol*c6;
+ q = atoms->atom[i].qB;
+ qsum += nmol * q;
+ q2sum += nmol * q * q;
+ c6 = mtop->ffparams.iparams[atoms->atom[i].typeB * (mtop->ffparams.atnr + 1)].lj.c6;
+ c6sum += nmol * c6;
}
- fr->qsum[1] = qsum;
- fr->q2sum[1] = q2sum;
- fr->c6sum[1] = c6sum;
+ fr->qsum[1] = qsum;
+ fr->q2sum[1] = q2sum;
+ fr->c6sum[1] = c6sum;
}
}
else
{
- fr->qsum[1] = fr->qsum[0];
- fr->q2sum[1] = fr->q2sum[0];
- fr->c6sum[1] = fr->c6sum[0];
+ fr->qsum[1] = fr->qsum[0];
+ fr->q2sum[1] = fr->q2sum[0];
+ fr->c6sum[1] = fr->c6sum[0];
}
if (log)
{
}
else
{
- fprintf(log, "System total charge, top. A: %.3f top. B: %.3f\n",
- fr->qsum[0], fr->qsum[1]);
+ fprintf(log, "System total charge, top. A: %.3f top. B: %.3f\n", fr->qsum[0], fr->qsum[1]);
}
}
/* A cut-off of 1e-4 is used to catch rounding errors due to ascii input */
- return (std::abs(fr->qsum[0]) > 1e-4 ||
- std::abs(fr->qsum[1]) > 1e-4);
-}
-
-void update_forcerec(t_forcerec *fr, matrix box)
-{
- if (fr->ic->eeltype == eelGRF)
- {
- calc_rffac(nullptr, fr->ic->eeltype, fr->ic->epsilon_r, fr->ic->epsilon_rf,
- fr->ic->rcoulomb, fr->temp, fr->zsquare, box,
- &fr->ic->k_rf, &fr->ic->c_rf);
- }
+ return (std::abs(fr->qsum[0]) > 1e-4 || std::abs(fr->qsum[1]) > 1e-4);
}
-void set_avcsixtwelve(FILE *fplog, t_forcerec *fr, const gmx_mtop_t *mtop)
-{
- const t_atoms *atoms, *atoms_tpi;
- const t_blocka *excl;
- int nmolc, i, j, tpi, tpj, j1, j2, k, nexcl, q;
- int64_t npair, npair_ij, tmpi, tmpj;
- double csix, ctwelve;
- int ntp, *typecount;
- gmx_bool bBHAM;
- real *nbfp;
- real *nbfp_comb = nullptr;
-
- ntp = fr->ntype;
- bBHAM = fr->bBHAM;
- nbfp = fr->nbfp;
-
- /* For LJ-PME, we want to correct for the difference between the
- * actual C6 values and the C6 values used by the LJ-PME based on
- * combination rules. */
-
- if (EVDW_PME(fr->ic->vdwtype))
- {
- nbfp_comb = mk_nbfp_combination_rule(&mtop->ffparams,
- (fr->ljpme_combination_rule == eljpmeLB) ? eCOMB_ARITHMETIC : eCOMB_GEOMETRIC);
- for (tpi = 0; tpi < ntp; ++tpi)
- {
- for (tpj = 0; tpj < ntp; ++tpj)
- {
- C6(nbfp_comb, ntp, tpi, tpj) =
- C6(nbfp, ntp, tpi, tpj) - C6(nbfp_comb, ntp, tpi, tpj);
- C12(nbfp_comb, ntp, tpi, tpj) = C12(nbfp, ntp, tpi, tpj);
- }
- }
- nbfp = nbfp_comb;
- }
- for (q = 0; q < (fr->efep == efepNO ? 1 : 2); q++)
- {
- csix = 0;
- ctwelve = 0;
- npair = 0;
- nexcl = 0;
- if (!fr->n_tpi)
- {
- /* Count the types so we avoid natoms^2 operations */
- snew(typecount, ntp);
- gmx_mtop_count_atomtypes(mtop, q, typecount);
-
- for (tpi = 0; tpi < ntp; tpi++)
- {
- for (tpj = tpi; tpj < ntp; tpj++)
- {
- tmpi = typecount[tpi];
- tmpj = typecount[tpj];
- if (tpi != tpj)
- {
- npair_ij = tmpi*tmpj;
- }
- else
- {
- npair_ij = tmpi*(tmpi - 1)/2;
- }
- if (bBHAM)
- {
- /* nbfp now includes the 6.0 derivative prefactor */
- csix += npair_ij*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
- }
- else
- {
- /* nbfp now includes the 6.0/12.0 derivative prefactors */
- csix += npair_ij* C6(nbfp, ntp, tpi, tpj)/6.0;
- ctwelve += npair_ij* C12(nbfp, ntp, tpi, tpj)/12.0;
- }
- npair += npair_ij;
- }
- }
- sfree(typecount);
- /* Subtract the excluded pairs.
- * The main reason for substracting exclusions is that in some cases
- * some combinations might never occur and the parameters could have
- * any value. These unused values should not influence the dispersion
- * correction.
- */
- for (const gmx_molblock_t &molb : mtop->molblock)
- {
- int nmol = molb.nmol;
- atoms = &mtop->moltype[molb.type].atoms;
- excl = &mtop->moltype[molb.type].excls;
- for (int i = 0; (i < atoms->nr); i++)
- {
- if (q == 0)
- {
- tpi = atoms->atom[i].type;
- }
- else
- {
- tpi = atoms->atom[i].typeB;
- }
- j1 = excl->index[i];
- j2 = excl->index[i+1];
- for (j = j1; j < j2; j++)
- {
- k = excl->a[j];
- if (k > i)
- {
- if (q == 0)
- {
- tpj = atoms->atom[k].type;
- }
- else
- {
- tpj = atoms->atom[k].typeB;
- }
- if (bBHAM)
- {
- /* nbfp now includes the 6.0 derivative prefactor */
- csix -= nmol*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
- }
- else
- {
- /* nbfp now includes the 6.0/12.0 derivative prefactors */
- csix -= nmol*C6 (nbfp, ntp, tpi, tpj)/6.0;
- ctwelve -= nmol*C12(nbfp, ntp, tpi, tpj)/12.0;
- }
- nexcl += molb.nmol;
- }
- }
- }
- }
- }
- else
- {
- /* Only correct for the interaction of the test particle
- * with the rest of the system.
- */
- atoms_tpi =
- &mtop->moltype[mtop->molblock.back().type].atoms;
-
- npair = 0;
- for (size_t mb = 0; mb < mtop->molblock.size(); mb++)
- {
- const gmx_molblock_t &molb = mtop->molblock[mb];
- atoms = &mtop->moltype[molb.type].atoms;
- for (j = 0; j < atoms->nr; j++)
- {
- nmolc = molb.nmol;
- /* Remove the interaction of the test charge group
- * with itself.
- */
- if (mb == mtop->molblock.size() - 1)
- {
- nmolc--;
-
- if (mb == 0 && molb.nmol == 1)
- {
- gmx_fatal(FARGS, "Old format tpr with TPI, please generate a new tpr file");
- }
- }
- if (q == 0)
- {
- tpj = atoms->atom[j].type;
- }
- else
- {
- tpj = atoms->atom[j].typeB;
- }
- for (i = 0; i < fr->n_tpi; i++)
- {
- if (q == 0)
- {
- tpi = atoms_tpi->atom[i].type;
- }
- else
- {
- tpi = atoms_tpi->atom[i].typeB;
- }
- if (bBHAM)
- {
- /* nbfp now includes the 6.0 derivative prefactor */
- csix += nmolc*BHAMC(nbfp, ntp, tpi, tpj)/6.0;
- }
- else
- {
- /* nbfp now includes the 6.0/12.0 derivative prefactors */
- csix += nmolc*C6 (nbfp, ntp, tpi, tpj)/6.0;
- ctwelve += nmolc*C12(nbfp, ntp, tpi, tpj)/12.0;
- }
- npair += nmolc;
- }
- }
- }
- }
- if (npair - nexcl <= 0 && fplog)
- {
- fprintf(fplog, "\nWARNING: There are no atom pairs for dispersion correction\n\n");
- csix = 0;
- ctwelve = 0;
- }
- else
- {
- csix /= npair - nexcl;
- ctwelve /= npair - nexcl;
- }
- if (debug)
- {
- fprintf(debug, "Counted %d exclusions\n", nexcl);
- fprintf(debug, "Average C6 parameter is: %10g\n", csix);
- fprintf(debug, "Average C12 parameter is: %10g\n", ctwelve);
- }
- fr->avcsix[q] = csix;
- fr->avctwelve[q] = ctwelve;
- }
-
- if (EVDW_PME(fr->ic->vdwtype))
- {
- sfree(nbfp_comb);
- }
-
- if (fplog != nullptr)
- {
- if (fr->eDispCorr == edispcAllEner ||
- fr->eDispCorr == edispcAllEnerPres)
- {
- fprintf(fplog, "Long Range LJ corr.: <C6> %10.4e, <C12> %10.4e\n",
- fr->avcsix[0], fr->avctwelve[0]);
- }
- else
- {
- fprintf(fplog, "Long Range LJ corr.: <C6> %10.4e\n", fr->avcsix[0]);
- }
- }
-}
-
-
-static real calcBuckinghamBMax(FILE *fplog, const gmx_mtop_t *mtop)
+static real calcBuckinghamBMax(FILE* fplog, const gmx_mtop_t* mtop)
{
const t_atoms *at1, *at2;
int i, j, tpi, tpj, ntypes;
{
gmx_fatal(FARGS, "Atomtype[%d] = %d, maximum = %d", j, tpj, ntypes);
}
- b = mtop->ffparams.iparams[tpi*ntypes + tpj].bham.b;
+ b = mtop->ffparams.iparams[tpi * ntypes + tpj].bham.b;
if (b > bham_b_max)
{
bham_b_max = b;
}
if (fplog)
{
- fprintf(fplog, "Buckingham b parameters, min: %g, max: %g\n",
- bmin, bham_b_max);
+ fprintf(fplog, "Buckingham b parameters, min: %g, max: %g\n", bmin, bham_b_max);
}
return bham_b_max;
}
-static void make_nbf_tables(FILE *fp,
- const interaction_const_t *ic, real rtab,
- const char *tabfn, char *eg1, char *eg2,
- t_nblists *nbl)
-{
- char buf[STRLEN];
- int i, j;
-
- if (tabfn == nullptr)
- {
- if (debug)
- {
- fprintf(debug, "No table file name passed, can not read table, can not do non-bonded interactions\n");
- }
- return;
- }
-
- sprintf(buf, "%s", tabfn);
- if (eg1 && eg2)
- {
- /* Append the two energy group names */
- sprintf(buf + strlen(tabfn) - strlen(ftp2ext(efXVG)) - 1, "_%s_%s.%s",
- eg1, eg2, ftp2ext(efXVG));
- }
- nbl->table_elec_vdw = make_tables(fp, ic, buf, rtab, 0);
- /* Copy the contents of the table to separate coulomb and LJ tables too,
- * to improve cache performance.
- */
- /* For performance reasons we want
- * the table data to be aligned to 16-byte. The pointers could be freed
- * but currently aren't.
- */
- snew(nbl->table_elec, 1);
- nbl->table_elec->interaction = GMX_TABLE_INTERACTION_ELEC;
- nbl->table_elec->format = nbl->table_elec_vdw->format;
- nbl->table_elec->r = nbl->table_elec_vdw->r;
- nbl->table_elec->n = nbl->table_elec_vdw->n;
- nbl->table_elec->scale = nbl->table_elec_vdw->scale;
- nbl->table_elec->formatsize = nbl->table_elec_vdw->formatsize;
- nbl->table_elec->ninteractions = 1;
- nbl->table_elec->stride = nbl->table_elec->formatsize * nbl->table_elec->ninteractions;
- snew_aligned(nbl->table_elec->data, nbl->table_elec->stride*(nbl->table_elec->n+1), 32);
-
- snew(nbl->table_vdw, 1);
- nbl->table_vdw->interaction = GMX_TABLE_INTERACTION_VDWREP_VDWDISP;
- nbl->table_vdw->format = nbl->table_elec_vdw->format;
- nbl->table_vdw->r = nbl->table_elec_vdw->r;
- nbl->table_vdw->n = nbl->table_elec_vdw->n;
- nbl->table_vdw->scale = nbl->table_elec_vdw->scale;
- nbl->table_vdw->formatsize = nbl->table_elec_vdw->formatsize;
- nbl->table_vdw->ninteractions = 2;
- nbl->table_vdw->stride = nbl->table_vdw->formatsize * nbl->table_vdw->ninteractions;
- snew_aligned(nbl->table_vdw->data, nbl->table_vdw->stride*(nbl->table_vdw->n+1), 32);
-
- /* NOTE: Using a single i-loop here leads to mix-up of data in table_vdw
- * with (at least) gcc 6.2, 6.3 and 6.4 when compiled with -O3 and AVX
- */
- for (i = 0; i <= nbl->table_elec_vdw->n; i++)
- {
- for (j = 0; j < 4; j++)
- {
- nbl->table_elec->data[4*i+j] = nbl->table_elec_vdw->data[12*i+j];
- }
- }
- for (i = 0; i <= nbl->table_elec_vdw->n; i++)
- {
- for (j = 0; j < 8; j++)
- {
- nbl->table_vdw->data[8*i+j] = nbl->table_elec_vdw->data[12*i+4+j];
- }
- }
-}
-
/*!\brief If there's bonded interactions of type \c ftype1 or \c
* ftype2 present in the topology, build an array of the number of
* interactions present for each bonded interaction index found in the
* \c ncount. It will contain zero for every bonded interaction index
* for which no interactions are present in the topology.
*/
-static void count_tables(int ftype1, int ftype2, const gmx_mtop_t *mtop,
- int *ncount, int **count)
+static void count_tables(int ftype1, int ftype2, const gmx_mtop_t* mtop, int* ncount, int** count)
{
- int ftype, i, j, tabnr;
+ int ftype, i, j, tabnr;
// Loop over all moleculetypes
- for (const gmx_moltype_t &molt : mtop->moltype)
+ for (const gmx_moltype_t& molt : mtop->moltype)
{
// Loop over all interaction types
for (ftype = 0; ftype < F_NRE; ftype++)
// If the current interaction type is one of the types whose tables we're trying to count...
if (ftype == ftype1 || ftype == ftype2)
{
- const InteractionList &il = molt.ilist[ftype];
+ const InteractionList& il = molt.ilist[ftype];
const int stride = 1 + NRAL(ftype);
// ... and there are actually some interactions for this type
for (i = 0; i < il.size(); i += stride)
// Make room for this index in the data structure
if (tabnr >= *ncount)
{
- srenew(*count, tabnr+1);
- for (j = *ncount; j < tabnr+1; j++)
+ srenew(*count, tabnr + 1);
+ for (j = *ncount; j < tabnr + 1; j++)
{
(*count)[j] = 0;
}
- *ncount = tabnr+1;
+ *ncount = tabnr + 1;
}
// Record that this table index is used and must have a valid file
(*count)[tabnr]++;
*
* A fatal error occurs if no matching filename is found.
*/
-static bondedtable_t *make_bonded_tables(FILE *fplog,
- int ftype1, int ftype2,
- const gmx_mtop_t *mtop,
+static bondedtable_t* make_bonded_tables(FILE* fplog,
+ int ftype1,
+ int ftype2,
+ const gmx_mtop_t* mtop,
gmx::ArrayRef<const std::string> tabbfnm,
- const char *tabext)
+ const char* tabext)
{
int ncount, *count;
- bondedtable_t *tab;
+ bondedtable_t* tab;
tab = nullptr;
// being recognized and used for table 1.
std::string patternToFind = gmx::formatString("_%s%d.%s", tabext, i, ftp2ext(efXVG));
bool madeTable = false;
- for (gmx::index j = 0; j < tabbfnm.size() && !madeTable; ++j)
+ for (gmx::index j = 0; j < tabbfnm.ssize() && !madeTable; ++j)
{
if (gmx::endsWith(tabbfnm[j], patternToFind))
{
// Finally read the table from the file found
- tab[i] = make_bonded_table(fplog, tabbfnm[j].c_str(), NRAL(ftype1)-2);
+ tab[i] = make_bonded_table(fplog, tabbfnm[j].c_str(), NRAL(ftype1) - 2);
madeTable = true;
}
}
if (!madeTable)
{
bool isPlural = (ftype2 != -1);
- 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.",
- interaction_function[ftype1].longname,
- isPlural ? "' or '" : "",
- isPlural ? interaction_function[ftype2].longname : "",
- i,
+ 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.",
+ interaction_function[ftype1].longname, isPlural ? "' or '" : "",
+ isPlural ? interaction_function[ftype2].longname : "", i,
patternToFind.c_str());
}
}
return tab;
}
-void forcerec_set_ranges(t_forcerec *fr,
- int ncg_home, int ncg_force,
- int natoms_force,
- int natoms_force_constr, int natoms_f_novirsum)
+void forcerec_set_ranges(t_forcerec* fr, int natoms_force, int natoms_force_constr, int natoms_f_novirsum)
{
- fr->cg0 = 0;
- fr->hcg = ncg_home;
-
- /* fr->ncg_force is unused in the standard code,
- * but it can be useful for modified code dealing with charge groups.
- */
- fr->ncg_force = ncg_force;
fr->natoms_force = natoms_force;
fr->natoms_force_constr = natoms_force_constr;
if (fr->haveDirectVirialContributions)
{
- fr->forceBufferForDirectVirialContributions->resize(natoms_f_novirsum);
+ fr->forceBufferForDirectVirialContributions.resize(natoms_f_novirsum);
}
}
static real cutoff_inf(real cutoff)
-{
- if (cutoff == 0)
- {
- cutoff = GMX_CUTOFF_INF;
- }
-
- return cutoff;
-}
-
-gmx_bool can_use_allvsall(const t_inputrec *ir, gmx_bool bPrintNote, const t_commrec *cr, FILE *fp)
-{
- gmx_bool bAllvsAll;
-
- bAllvsAll =
- (
- ir->rlist == 0 &&
- ir->rcoulomb == 0 &&
- ir->rvdw == 0 &&
- ir->ePBC == epbcNONE &&
- ir->vdwtype == evdwCUT &&
- ir->coulombtype == eelCUT &&
- ir->efep == efepNO &&
- getenv("GMX_NO_ALLVSALL") == nullptr
- );
-
- if (bAllvsAll && ir->opts.ngener > 1)
- {
- const char *note = "NOTE: Can not use all-vs-all force loops, because there are multiple energy monitor groups; you might get significantly higher performance when using only a single energy monitor group.\n";
-
- if (bPrintNote)
- {
- if (fp != nullptr)
- {
- fprintf(fp, "\n%s\n", note);
- }
- }
- bAllvsAll = FALSE;
- }
-
- if (bAllvsAll && fp && MASTER(cr))
- {
- fprintf(fp, "\nUsing SIMD all-vs-all kernels.\n\n");
- }
-
- return bAllvsAll;
-}
-
-
-gmx_bool nbnxn_simd_supported(const gmx::MDLogger &mdlog,
- const t_inputrec *ir)
-{
- if (ir->vdwtype == evdwPME && ir->ljpme_combination_rule == eljpmeLB)
- {
- /* LJ PME with LB combination rule does 7 mesh operations.
- * This so slow that we don't compile SIMD non-bonded kernels
- * for that. */
- GMX_LOG(mdlog.warning).asParagraph().appendText("LJ-PME with Lorentz-Berthelot is not supported with SIMD kernels, falling back to plain C kernels");
- return FALSE;
- }
-
- return TRUE;
-}
-
-
-static void pick_nbnxn_kernel_cpu(const t_inputrec gmx_unused *ir,
- int *kernel_type,
- int *ewald_excl,
- const gmx_hw_info_t gmx_unused &hardwareInfo)
-{
- *kernel_type = nbnxnk4x4_PlainC;
- *ewald_excl = ewaldexclTable;
-
-#if GMX_SIMD
- {
-#ifdef GMX_NBNXN_SIMD_4XN
- *kernel_type = nbnxnk4xN_SIMD_4xN;
-#endif
-#ifdef GMX_NBNXN_SIMD_2XNN
- *kernel_type = nbnxnk4xN_SIMD_2xNN;
-#endif
-
-#if defined GMX_NBNXN_SIMD_2XNN && defined GMX_NBNXN_SIMD_4XN
- /* We need to choose if we want 2x(N+N) or 4xN kernels.
- * This is based on the SIMD acceleration choice and CPU information
- * detected at runtime.
- *
- * 4xN calculates more (zero) interactions, but has less pair-search
- * work and much better kernel instruction scheduling.
- *
- * Up till now we have only seen that on Intel Sandy/Ivy Bridge,
- * which doesn't have FMA, both the analytical and tabulated Ewald
- * kernels have similar pair rates for 4x8 and 2x(4+4), so we choose
- * 2x(4+4) because it results in significantly fewer pairs.
- * For RF, the raw pair rate of the 4x8 kernel is higher than 2x(4+4),
- * 10% with HT, 50% without HT. As we currently don't detect the actual
- * use of HT, use 4x8 to avoid a potential performance hit.
- * On Intel Haswell 4x8 is always faster.
- */
- *kernel_type = nbnxnk4xN_SIMD_4xN;
-
-#if !GMX_SIMD_HAVE_FMA
- if (EEL_PME_EWALD(ir->coulombtype) ||
- EVDW_PME(ir->vdwtype))
- {
- /* We have Ewald kernels without FMA (Intel Sandy/Ivy Bridge).
- * There are enough instructions to make 2x(4+4) efficient.
- */
- *kernel_type = nbnxnk4xN_SIMD_2xNN;
- }
-#endif
- if (hardwareInfo.haveAmdZen1Cpu)
- {
- /* One 256-bit FMA per cycle makes 2xNN faster */
- *kernel_type = nbnxnk4xN_SIMD_2xNN;
- }
-#endif /* GMX_NBNXN_SIMD_2XNN && GMX_NBNXN_SIMD_4XN */
-
-
- if (getenv("GMX_NBNXN_SIMD_4XN") != nullptr)
- {
-#ifdef GMX_NBNXN_SIMD_4XN
- *kernel_type = nbnxnk4xN_SIMD_4xN;
-#else
- gmx_fatal(FARGS, "SIMD 4xN kernels requested, but GROMACS has been compiled without support for these kernels");
-#endif
- }
- if (getenv("GMX_NBNXN_SIMD_2XNN") != nullptr)
- {
-#ifdef GMX_NBNXN_SIMD_2XNN
- *kernel_type = nbnxnk4xN_SIMD_2xNN;
-#else
- gmx_fatal(FARGS, "SIMD 2x(N+N) kernels requested, but GROMACS has been compiled without support for these kernels");
-#endif
- }
-
- /* Analytical Ewald exclusion correction is only an option in
- * the SIMD kernel.
- * Since table lookup's don't parallelize with SIMD, analytical
- * will probably always be faster for a SIMD width of 8 or more.
- * With FMA analytical is sometimes faster for a width if 4 as well.
- * In single precision, this is faster on Bulldozer.
- */
-#if GMX_SIMD_REAL_WIDTH >= 8 || \
- (GMX_SIMD_REAL_WIDTH >= 4 && GMX_SIMD_HAVE_FMA && !GMX_DOUBLE)
- /* On AMD Zen, tabulated Ewald kernels are faster on all 4 combinations
- * of single or double precision and 128 or 256-bit AVX2.
- */
- if (!hardwareInfo.haveAmdZen1Cpu)
- {
- *ewald_excl = ewaldexclAnalytical;
- }
-#endif
- if (getenv("GMX_NBNXN_EWALD_TABLE") != nullptr)
- {
- *ewald_excl = ewaldexclTable;
- }
- if (getenv("GMX_NBNXN_EWALD_ANALYTICAL") != nullptr)
- {
- *ewald_excl = ewaldexclAnalytical;
- }
-
- }
-#endif // GMX_SIMD
-}
-
-
-const char *lookup_nbnxn_kernel_name(int kernel_type)
-{
- const char *returnvalue = nullptr;
- switch (kernel_type)
- {
- case nbnxnkNotSet:
- returnvalue = "not set";
- break;
- case nbnxnk4x4_PlainC:
- returnvalue = "plain C";
- break;
- case nbnxnk4xN_SIMD_4xN:
- case nbnxnk4xN_SIMD_2xNN:
-#if GMX_SIMD
- returnvalue = "SIMD";
-#else // GMX_SIMD
- returnvalue = "not available";
-#endif // GMX_SIMD
- break;
- case nbnxnk8x8x8_GPU: returnvalue = "GPU"; break;
- case nbnxnk8x8x8_PlainC: returnvalue = "plain C"; break;
-
- case nbnxnkNR:
- default:
- gmx_fatal(FARGS, "Illegal kernel type selected");
- }
- return returnvalue;
-};
-
-static void pick_nbnxn_kernel(const gmx::MDLogger &mdlog,
- gmx_bool use_simd_kernels,
- const gmx_hw_info_t &hardwareInfo,
- gmx_bool bUseGPU,
- EmulateGpuNonbonded emulateGpu,
- const t_inputrec *ir,
- int *kernel_type,
- int *ewald_excl,
- gmx_bool bDoNonbonded)
-{
- assert(kernel_type);
-
- *kernel_type = nbnxnkNotSet;
- *ewald_excl = ewaldexclTable;
-
- if (emulateGpu == EmulateGpuNonbonded::Yes)
- {
- *kernel_type = nbnxnk8x8x8_PlainC;
-
- if (bDoNonbonded)
- {
- GMX_LOG(mdlog.warning).asParagraph().appendText("Emulating a GPU run on the CPU (slow)");
- }
- }
- else if (bUseGPU)
- {
- *kernel_type = nbnxnk8x8x8_GPU;
- }
-
- if (*kernel_type == nbnxnkNotSet)
- {
- if (use_simd_kernels &&
- nbnxn_simd_supported(mdlog, ir))
- {
- pick_nbnxn_kernel_cpu(ir, kernel_type, ewald_excl, hardwareInfo);
- }
- else
- {
- *kernel_type = nbnxnk4x4_PlainC;
- }
- }
-
- if (bDoNonbonded)
+{
+ if (cutoff == 0)
{
- GMX_LOG(mdlog.info).asParagraph().appendTextFormatted(
- "Using %s %dx%d nonbonded short-range kernels",
- lookup_nbnxn_kernel_name(*kernel_type),
- nbnxn_kernel_to_cluster_i_size(*kernel_type),
- nbnxn_kernel_to_cluster_j_size(*kernel_type));
-
- if (nbnxnk4x4_PlainC == *kernel_type ||
- nbnxnk8x8x8_PlainC == *kernel_type)
- {
- GMX_LOG(mdlog.warning).asParagraph().appendTextFormatted(
- "WARNING: Using the slow %s kernels. This should\n"
- "not happen during routine usage on supported platforms.",
- lookup_nbnxn_kernel_name(*kernel_type));
- }
+ cutoff = GMX_CUTOFF_INF;
}
+
+ return cutoff;
}
/*! \brief Print Coulomb Ewald citations and set ewald coefficients */
-static void initCoulombEwaldParameters(FILE *fp, const t_inputrec *ir,
- bool systemHasNetCharge,
- interaction_const_t *ic)
+static void initCoulombEwaldParameters(FILE* fp,
+ const t_inputrec* ir,
+ bool systemHasNetCharge,
+ interaction_const_t* ic)
{
if (!EEL_PME_EWALD(ir->coulombtype))
{
ic->ewaldcoeff_q = calc_ewaldcoeff_q(ir->rcoulomb, ir->ewald_rtol);
if (fp)
{
- fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for Ewald\n",
- 1/ic->ewaldcoeff_q);
+ fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for Ewald\n", 1 / ic->ewaldcoeff_q);
}
if (ic->coulomb_modifier == eintmodPOTSHIFT)
{
GMX_RELEASE_ASSERT(ic->rcoulomb != 0, "Cutoff radius cannot be zero");
- ic->sh_ewald = std::erfc(ic->ewaldcoeff_q*ic->rcoulomb) / ic->rcoulomb;
+ ic->sh_ewald = std::erfc(ic->ewaldcoeff_q * ic->rcoulomb) / ic->rcoulomb;
}
else
{
}
/*! \brief Print Van der Waals Ewald citations and set ewald coefficients */
-static void initVdwEwaldParameters(FILE *fp, const t_inputrec *ir,
- interaction_const_t *ic)
+static void initVdwEwaldParameters(FILE* fp, const t_inputrec* ir, interaction_const_t* ic)
{
if (!EVDW_PME(ir->vdwtype))
{
ic->ewaldcoeff_lj = calc_ewaldcoeff_lj(ir->rvdw, ir->ewald_rtol_lj);
if (fp)
{
- fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for LJ Ewald\n",
- 1/ic->ewaldcoeff_lj);
+ fprintf(fp, "Using a Gaussian width (1/beta) of %g nm for LJ Ewald\n", 1 / ic->ewaldcoeff_lj);
}
if (ic->vdw_modifier == eintmodPOTSHIFT)
{
- real crc2 = gmx::square(ic->ewaldcoeff_lj*ic->rvdw);
- ic->sh_lj_ewald = (std::exp(-crc2)*(1 + crc2 + 0.5*crc2*crc2) - 1)/gmx::power6(ic->rvdw);
+ real crc2 = gmx::square(ic->ewaldcoeff_lj * ic->rvdw);
+ ic->sh_lj_ewald = (std::exp(-crc2) * (1 + crc2 + 0.5 * crc2 * crc2) - 1) / gmx::power6(ic->rvdw);
}
else
{
}
}
-gmx_bool uses_simple_tables(int cutoff_scheme,
- nonbonded_verlet_t *nbv,
- int group)
-{
- gmx_bool bUsesSimpleTables = TRUE;
- int grp_index;
-
- switch (cutoff_scheme)
- {
- case ecutsGROUP:
- bUsesSimpleTables = TRUE;
- break;
- case ecutsVERLET:
- assert(nullptr != nbv);
- grp_index = (group < 0) ? 0 : (nbv->ngrp - 1);
- bUsesSimpleTables = nbnxn_kernel_pairlist_simple(nbv->grp[grp_index].kernel_type);
- break;
- default:
- gmx_incons("unimplemented");
- }
- return bUsesSimpleTables;
-}
-
-static void init_ewald_f_table(interaction_const_t *ic,
- real rtab)
+/* Generate Coulomb and/or Van der Waals Ewald long-range correction tables
+ *
+ * Tables are generated for one or both, depending on if the pointers
+ * are non-null. The spacing for both table sets is the same and obeys
+ * both accuracy requirements, when relevant.
+ */
+static void init_ewald_f_table(const interaction_const_t& ic,
+ EwaldCorrectionTables* coulombTables,
+ EwaldCorrectionTables* vdwTables)
{
- real maxr;
+ const bool useCoulombTable = (EEL_PME_EWALD(ic.eeltype) && coulombTables != nullptr);
+ const bool useVdwTable = (EVDW_PME(ic.vdwtype) && vdwTables != nullptr);
/* Get the Ewald table spacing based on Coulomb and/or LJ
* Ewald coefficients and rtol.
*/
- ic->tabq_scale = ewald_spline3_table_scale(ic);
-
- if (ic->cutoff_scheme == ecutsVERLET)
- {
- maxr = ic->rcoulomb;
- }
- else
- {
- maxr = std::max(ic->rcoulomb, rtab);
- }
- ic->tabq_size = static_cast<int>(maxr*ic->tabq_scale) + 2;
-
- sfree_aligned(ic->tabq_coul_FDV0);
- sfree_aligned(ic->tabq_coul_F);
- sfree_aligned(ic->tabq_coul_V);
+ const real tableScale = ewald_spline3_table_scale(ic, useCoulombTable, useVdwTable);
- sfree_aligned(ic->tabq_vdw_FDV0);
- sfree_aligned(ic->tabq_vdw_F);
- sfree_aligned(ic->tabq_vdw_V);
+ const int tableSize = static_cast<int>(ic.rcoulomb * tableScale) + 2;
- if (EEL_PME_EWALD(ic->eeltype))
+ if (useCoulombTable)
{
- /* Create the original table data in FDV0 */
- snew_aligned(ic->tabq_coul_FDV0, ic->tabq_size*4, 32);
- snew_aligned(ic->tabq_coul_F, ic->tabq_size, 32);
- snew_aligned(ic->tabq_coul_V, ic->tabq_size, 32);
- table_spline3_fill_ewald_lr(ic->tabq_coul_F, ic->tabq_coul_V, ic->tabq_coul_FDV0,
- ic->tabq_size, 1/ic->tabq_scale, ic->ewaldcoeff_q, v_q_ewald_lr);
+ *coulombTables =
+ generateEwaldCorrectionTables(tableSize, tableScale, ic.ewaldcoeff_q, v_q_ewald_lr);
}
- if (EVDW_PME(ic->vdwtype))
+ if (useVdwTable)
{
- snew_aligned(ic->tabq_vdw_FDV0, ic->tabq_size*4, 32);
- snew_aligned(ic->tabq_vdw_F, ic->tabq_size, 32);
- snew_aligned(ic->tabq_vdw_V, ic->tabq_size, 32);
- table_spline3_fill_ewald_lr(ic->tabq_vdw_F, ic->tabq_vdw_V, ic->tabq_vdw_FDV0,
- ic->tabq_size, 1/ic->tabq_scale, ic->ewaldcoeff_lj, v_lj_ewald_lr);
+ *vdwTables = generateEwaldCorrectionTables(tableSize, tableScale, ic.ewaldcoeff_lj, v_lj_ewald_lr);
}
}
-void init_interaction_const_tables(FILE *fp,
- interaction_const_t *ic,
- real rtab)
+void init_interaction_const_tables(FILE* fp, interaction_const_t* ic)
{
- if (EEL_PME_EWALD(ic->eeltype) || EVDW_PME(ic->vdwtype))
+ if (EEL_PME_EWALD(ic->eeltype))
{
- init_ewald_f_table(ic, rtab);
-
+ init_ewald_f_table(*ic, ic->coulombEwaldTables.get(), nullptr);
if (fp != nullptr)
{
- fprintf(fp, "Initialized non-bonded Ewald correction tables, spacing: %.2e size: %d\n\n",
- 1/ic->tabq_scale, ic->tabq_size);
+ fprintf(fp, "Initialized non-bonded Coulomb Ewald tables, spacing: %.2e size: %zu\n\n",
+ 1 / ic->coulombEwaldTables->scale, ic->coulombEwaldTables->tableF.size());
}
}
}
-static void clear_force_switch_constants(shift_consts_t *sc)
+static void clear_force_switch_constants(shift_consts_t* sc)
{
sc->c2 = 0;
sc->c3 = 0;
sc->cpot = 0;
}
-static void force_switch_constants(real p,
- real rsw, real rc,
- shift_consts_t *sc)
+static void force_switch_constants(real p, real rsw, real rc, shift_consts_t* sc)
{
/* Here we determine the coefficient for shifting the force to zero
* between distance rsw and the cut-off rc.
* force/p = r^-(p+1) + c2*r^2 + c3*r^3
* potential = r^-p + c2/3*r^3 + c3/4*r^4 + cpot
*/
- sc->c2 = ((p + 1)*rsw - (p + 4)*rc)/(pow(rc, p + 2)*gmx::square(rc - rsw));
- sc->c3 = -((p + 1)*rsw - (p + 3)*rc)/(pow(rc, p + 2)*gmx::power3(rc - rsw));
- sc->cpot = -pow(rc, -p) + p*sc->c2/3*gmx::power3(rc - rsw) + p*sc->c3/4*gmx::power4(rc - rsw);
+ sc->c2 = ((p + 1) * rsw - (p + 4) * rc) / (pow(rc, p + 2) * gmx::square(rc - rsw));
+ sc->c3 = -((p + 1) * rsw - (p + 3) * rc) / (pow(rc, p + 2) * gmx::power3(rc - rsw));
+ sc->cpot = -pow(rc, -p) + p * sc->c2 / 3 * gmx::power3(rc - rsw)
+ + p * sc->c3 / 4 * gmx::power4(rc - rsw);
}
-static void potential_switch_constants(real rsw, real rc,
- switch_consts_t *sc)
+static void potential_switch_constants(real rsw, real rc, switch_consts_t* sc)
{
/* The switch function is 1 at rsw and 0 at rc.
* The derivative and second derivate are zero at both ends.
* force = force*dsw - potential*sw
* potential *= sw
*/
- sc->c3 = -10/gmx::power3(rc - rsw);
- sc->c4 = 15/gmx::power4(rc - rsw);
- sc->c5 = -6/gmx::power5(rc - rsw);
+ sc->c3 = -10 / gmx::power3(rc - rsw);
+ sc->c4 = 15 / gmx::power4(rc - rsw);
+ sc->c5 = -6 / gmx::power5(rc - rsw);
}
/*! \brief Construct interaction constants
* short-range interactions. Many of these are constant for the whole
* simulation; some are constant only after PME tuning completes.
*/
-static void
-init_interaction_const(FILE *fp,
- interaction_const_t **interaction_const,
- const t_inputrec *ir,
- const gmx_mtop_t *mtop,
- bool systemHasNetCharge)
+static void init_interaction_const(FILE* fp,
+ interaction_const_t** interaction_const,
+ const t_inputrec* ir,
+ const gmx_mtop_t* mtop,
+ bool systemHasNetCharge)
{
- interaction_const_t *ic;
-
- snew(ic, 1);
+ interaction_const_t* ic = new interaction_const_t;
- ic->cutoff_scheme = ir->cutoff_scheme;
+ ic->cutoff_scheme = ir->cutoff_scheme;
- /* Just allocate something so we can free it */
- snew_aligned(ic->tabq_coul_FDV0, 16, 32);
- snew_aligned(ic->tabq_coul_F, 16, 32);
- snew_aligned(ic->tabq_coul_V, 16, 32);
+ ic->coulombEwaldTables = std::make_unique<EwaldCorrectionTables>();
/* Lennard-Jones */
ic->vdwtype = ir->vdwtype;
{
case eintmodPOTSHIFT:
/* Only shift the potential, don't touch the force */
- ic->dispersion_shift.cpot = -1.0/gmx::power6(ic->rvdw);
- ic->repulsion_shift.cpot = -1.0/gmx::power12(ic->rvdw);
+ ic->dispersion_shift.cpot = -1.0 / gmx::power6(ic->rvdw);
+ ic->repulsion_shift.cpot = -1.0 / gmx::power12(ic->rvdw);
break;
case eintmodFORCESWITCH:
/* Switch the force, switch and shift the potential */
- force_switch_constants(6.0, ic->rvdw_switch, ic->rvdw,
- &ic->dispersion_shift);
- force_switch_constants(12.0, ic->rvdw_switch, ic->rvdw,
- &ic->repulsion_shift);
+ force_switch_constants(6.0, ic->rvdw_switch, ic->rvdw, &ic->dispersion_shift);
+ force_switch_constants(12.0, ic->rvdw_switch, ic->rvdw, &ic->repulsion_shift);
break;
case eintmodPOTSWITCH:
/* Switch the potential and force */
- potential_switch_constants(ic->rvdw_switch, ic->rvdw,
- &ic->vdw_switch);
+ potential_switch_constants(ic->rvdw_switch, ic->rvdw, &ic->vdw_switch);
break;
case eintmodNONE:
case eintmodEXACTCUTOFF:
/* Nothing to do here */
break;
- default:
- gmx_incons("unimplemented potential modifier");
+ default: gmx_incons("unimplemented potential modifier");
}
- ic->sh_invrc6 = -ic->dispersion_shift.cpot;
-
/* Electrostatics */
ic->eeltype = ir->coulombtype;
ic->coulomb_modifier = ir->coulomb_modifier;
/* Set the Coulomb energy conversion factor */
if (ic->epsilon_r != 0)
{
- ic->epsfac = ONE_4PI_EPS0/ic->epsilon_r;
+ ic->epsfac = ONE_4PI_EPS0 / ic->epsilon_r;
}
else
{
/* Reaction-field */
if (EEL_RF(ic->eeltype))
{
+ GMX_RELEASE_ASSERT(ic->eeltype != eelGRF_NOTUSED, "GRF is no longer supported");
ic->epsilon_rf = ir->epsilon_rf;
- /* Generalized reaction field parameters are updated every step */
- if (ic->eeltype != eelGRF)
- {
- calc_rffac(fp, ic->eeltype, ic->epsilon_r, ic->epsilon_rf,
- ic->rcoulomb, 0, 0, nullptr,
- &ic->k_rf, &ic->c_rf);
- }
- if (ir->cutoff_scheme == ecutsGROUP && ic->eeltype == eelRF_ZERO)
- {
- /* grompp should have done this, but this scheme is obsolete */
- ic->coulomb_modifier = eintmodEXACTCUTOFF;
- }
+ calc_rffac(fp, ic->epsilon_r, ic->epsilon_rf, ic->rcoulomb, &ic->k_rf, &ic->c_rf);
}
else
{
ic->k_rf = 0;
if (ir->coulomb_modifier == eintmodPOTSHIFT)
{
- ic->c_rf = 1/ic->rcoulomb;
+ ic->c_rf = 1 / ic->rcoulomb;
}
else
{
- ic->c_rf = 0;
+ ic->c_rf = 0;
}
}
{
dispersion_shift -= ic->sh_lj_ewald;
}
- fprintf(fp, "Potential shift: LJ r^-12: %.3e r^-6: %.3e",
- ic->repulsion_shift.cpot, dispersion_shift);
+ fprintf(fp, "Potential shift: LJ r^-12: %.3e r^-6: %.3e", ic->repulsion_shift.cpot, dispersion_shift);
if (ic->eeltype == eelCUT)
{
*interaction_const = ic;
}
-static void
-done_interaction_const(interaction_const_t *interaction_const)
-{
- sfree_aligned(interaction_const->tabq_coul_FDV0);
- sfree_aligned(interaction_const->tabq_coul_F);
- sfree_aligned(interaction_const->tabq_coul_V);
- sfree(interaction_const);
-}
-
-static void init_nb_verlet(const gmx::MDLogger &mdlog,
- nonbonded_verlet_t **nb_verlet,
- gmx_bool bFEP_NonBonded,
- const t_inputrec *ir,
- const t_forcerec *fr,
- const t_commrec *cr,
- const gmx_hw_info_t &hardwareInfo,
- const gmx_device_info_t *deviceInfo,
- const gmx_mtop_t *mtop,
- matrix box)
-{
- nonbonded_verlet_t *nbv;
- char *env;
-
- nbnxn_alloc_t *nb_alloc;
- nbnxn_free_t *nb_free;
-
- nbv = new nonbonded_verlet_t();
-
- nbv->emulateGpu = ((getenv("GMX_EMULATE_GPU") != nullptr) ? EmulateGpuNonbonded::Yes : EmulateGpuNonbonded::No);
- nbv->bUseGPU = deviceInfo != nullptr;
-
- GMX_RELEASE_ASSERT(!(nbv->emulateGpu == EmulateGpuNonbonded::Yes && nbv->bUseGPU), "When GPU emulation is active, there cannot be a GPU assignment");
-
- nbv->nbs = nullptr;
- nbv->min_ci_balanced = 0;
-
- nbv->ngrp = (DOMAINDECOMP(cr) ? 2 : 1);
- for (int i = 0; i < nbv->ngrp; i++)
- {
- nbv->grp[i].nbl_lists.nnbl = 0;
- nbv->grp[i].kernel_type = nbnxnkNotSet;
-
- if (i == 0) /* local */
- {
- pick_nbnxn_kernel(mdlog, fr->use_simd_kernels, hardwareInfo,
- nbv->bUseGPU, nbv->emulateGpu, ir,
- &nbv->grp[i].kernel_type,
- &nbv->grp[i].ewald_excl,
- fr->bNonbonded);
- }
- else /* non-local */
- {
- /* Use the same kernel for local and non-local interactions */
- nbv->grp[i].kernel_type = nbv->grp[0].kernel_type;
- nbv->grp[i].ewald_excl = nbv->grp[0].ewald_excl;
- }
- }
-
- nbv->listParams = gmx::compat::make_unique<NbnxnListParameters>(ir->rlist);
- setupDynamicPairlistPruning(mdlog, ir, mtop, box, nbv->grp[0].kernel_type, fr->ic,
- nbv->listParams.get());
-
- nbv->nbs = gmx::compat::make_unique<nbnxn_search>(DOMAINDECOMP(cr) ? &cr->dd->nc : nullptr,
- DOMAINDECOMP(cr) ? domdec_zones(cr->dd) : nullptr,
- bFEP_NonBonded,
- gmx_omp_nthreads_get(emntPairsearch));
-
- gpu_set_host_malloc_and_free(nbv->grp[0].kernel_type == nbnxnk8x8x8_GPU,
- &nb_alloc, &nb_free);
-
- for (int i = 0; i < nbv->ngrp; i++)
- {
- nbnxn_init_pairlist_set(&nbv->grp[i].nbl_lists,
- nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type),
- /* 8x8x8 "non-simple" lists are ATM always combined */
- !nbnxn_kernel_pairlist_simple(nbv->grp[i].kernel_type),
- nb_alloc, nb_free);
- }
-
- int enbnxninitcombrule;
- if (fr->ic->vdwtype == evdwCUT &&
- (fr->ic->vdw_modifier == eintmodNONE ||
- fr->ic->vdw_modifier == eintmodPOTSHIFT) &&
- getenv("GMX_NO_LJ_COMB_RULE") == nullptr)
- {
- /* Plain LJ cut-off: we can optimize with combination rules */
- enbnxninitcombrule = enbnxninitcombruleDETECT;
- }
- else if (fr->ic->vdwtype == evdwPME)
- {
- /* LJ-PME: we need to use a combination rule for the grid */
- if (fr->ljpme_combination_rule == eljpmeGEOM)
- {
- enbnxninitcombrule = enbnxninitcombruleGEOM;
- }
- else
- {
- enbnxninitcombrule = enbnxninitcombruleLB;
- }
- }
- else
- {
- /* We use a full combination matrix: no rule required */
- enbnxninitcombrule = enbnxninitcombruleNONE;
- }
-
- snew(nbv->nbat, 1);
- int mimimumNumEnergyGroupNonbonded = ir->opts.ngener;
- if (ir->opts.ngener - ir->nwall == 1)
- {
- /* We have only one non-wall energy group, we do not need energy group
- * support in the non-bondeds kernels, since all non-bonded energy
- * contributions go to the first element of the energy group matrix.
- */
- mimimumNumEnergyGroupNonbonded = 1;
- }
- bool bSimpleList = nbnxn_kernel_pairlist_simple(nbv->grp[0].kernel_type);
- nbnxn_atomdata_init(mdlog,
- nbv->nbat,
- nbv->grp[0].kernel_type,
- enbnxninitcombrule,
- fr->ntype, fr->nbfp,
- mimimumNumEnergyGroupNonbonded,
- bSimpleList ? gmx_omp_nthreads_get(emntNonbonded) : 1,
- nb_alloc, nb_free);
-
- if (nbv->bUseGPU)
- {
- /* init the NxN GPU data; the last argument tells whether we'll have
- * both local and non-local NB calculation on GPU */
- nbnxn_gpu_init(&nbv->gpu_nbv,
- deviceInfo,
- fr->ic,
- nbv->listParams.get(),
- nbv->nbat,
- cr->nodeid,
- (nbv->ngrp > 1));
-
- if ((env = getenv("GMX_NB_MIN_CI")) != nullptr)
- {
- char *end;
-
- nbv->min_ci_balanced = strtol(env, &end, 10);
- if (!end || (*end != 0) || nbv->min_ci_balanced < 0)
- {
- gmx_fatal(FARGS, "Invalid value passed in GMX_NB_MIN_CI=%s, non-negative integer required", env);
- }
-
- if (debug)
- {
- fprintf(debug, "Neighbor-list balancing parameter: %d (passed as env. var.)\n",
- nbv->min_ci_balanced);
- }
- }
- else
- {
- nbv->min_ci_balanced = nbnxn_gpu_min_ci_balanced(nbv->gpu_nbv);
- if (debug)
- {
- fprintf(debug, "Neighbor-list balancing parameter: %d (auto-adjusted to the number of GPU multi-processors)\n",
- nbv->min_ci_balanced);
- }
- }
-
- }
-
- *nb_verlet = nbv;
-}
-
-gmx_bool usingGpu(nonbonded_verlet_t *nbv)
-{
- return nbv != nullptr && nbv->bUseGPU;
-}
-
-void init_forcerec(FILE *fp,
- const gmx::MDLogger &mdlog,
- t_forcerec *fr,
- t_fcdata *fcd,
- const t_inputrec *ir,
- const gmx_mtop_t *mtop,
- const t_commrec *cr,
- matrix box,
- const char *tabfn,
- const char *tabpfn,
- gmx::ArrayRef<const std::string> tabbfnm,
- const gmx_hw_info_t &hardwareInfo,
- const gmx_device_info_t *deviceInfo,
- const bool useGpuForBonded,
- gmx_bool bNoSolvOpt,
- real print_force)
+void init_forcerec(FILE* fp,
+ const gmx::MDLogger& mdlog,
+ t_forcerec* fr,
+ t_fcdata* fcd,
+ const t_inputrec* ir,
+ const gmx_mtop_t* mtop,
+ const t_commrec* cr,
+ matrix box,
+ const char* tabfn,
+ const char* tabpfn,
+ gmx::ArrayRef<const std::string> tabbfnm,
+ const gmx_hw_info_t& hardwareInfo,
+ const gmx_device_info_t* deviceInfo,
+ const bool useGpuForBonded,
+ const bool pmeOnlyRankUsesGpu,
+ real print_force,
+ gmx_wallcycle* wcycle)
{
- int m, negp_pp, negptable, egi, egj;
- real rtab;
- char *env;
- double dbl;
- const t_block *cgs;
- gmx_bool bGenericKernelOnly;
- gmx_bool needGroupSchemeTables, bSomeNormalNbListsAreInUse;
- gmx_bool bFEP_NonBonded;
- int *nm_ind, egp_flags;
+ real rtab;
+ char* env;
+ double dbl;
+ gmx_bool bFEP_NonBonded;
/* By default we turn SIMD kernels on, but it might be turned off further down... */
fr->use_simd_kernels = TRUE;
if (EI_TPI(ir->eI))
{
/* Set to the size of the molecule to be inserted (the last one) */
- /* Because of old style topologies, we have to use the last cg
- * instead of the last molecule type.
- */
- cgs = &mtop->moltype[mtop->molblock.back().type].cgs;
- fr->n_tpi = cgs->index[cgs->nr] - cgs->index[cgs->nr-1];
gmx::RangePartitioning molecules = gmx_mtop_molecules(*mtop);
- if (fr->n_tpi != molecules.block(molecules.numBlocks() - 1).size())
- {
- gmx_fatal(FARGS, "The molecule to insert can not consist of multiple charge groups.\nMake it a single charge group.");
- }
+ fr->n_tpi = molecules.block(molecules.numBlocks() - 1).size();
}
else
{
fr->n_tpi = 0;
}
- if (ir->coulombtype == eelRF_NEC_UNSUPPORTED)
+ if (ir->coulombtype == eelRF_NEC_UNSUPPORTED || ir->coulombtype == eelGRF_NOTUSED)
{
- gmx_fatal(FARGS, "%s electrostatics is no longer supported",
- eel_names[ir->coulombtype]);
+ gmx_fatal(FARGS, "%s electrostatics is no longer supported", eel_names[ir->coulombtype]);
}
if (ir->bAdress)
{
/* turn off non-bonded calculations */
fr->bNonbonded = FALSE;
- GMX_LOG(mdlog.warning).asParagraph().appendText(
- "Found environment variable GMX_NO_NONBONDED.\n"
- "Disabling nonbonded calculations.");
- }
-
- bGenericKernelOnly = FALSE;
-
- /* We now check in the NS code whether a particular combination of interactions
- * can be used with water optimization, and disable it if that is not the case.
- */
-
- if (getenv("GMX_NB_GENERIC") != nullptr)
- {
- if (fp != nullptr)
- {
- fprintf(fp,
- "Found environment variable GMX_NB_GENERIC.\n"
- "Disabling all interaction-specific nonbonded kernels, will only\n"
- "use the slow generic ones in src/gmxlib/nonbonded/nb_generic.c\n\n");
- }
- bGenericKernelOnly = TRUE;
- }
-
- if (bGenericKernelOnly)
- {
- bNoSolvOpt = TRUE;
+ GMX_LOG(mdlog.warning)
+ .asParagraph()
+ .appendText(
+ "Found environment variable GMX_NO_NONBONDED.\n"
+ "Disabling nonbonded calculations.");
}
- if ( (getenv("GMX_DISABLE_SIMD_KERNELS") != nullptr) || (getenv("GMX_NOOPTIMIZEDKERNELS") != nullptr) )
+ if ((getenv("GMX_DISABLE_SIMD_KERNELS") != nullptr) || (getenv("GMX_NOOPTIMIZEDKERNELS") != nullptr))
{
fr->use_simd_kernels = FALSE;
if (fp != nullptr)
fr->bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
- /* Check if we can/should do all-vs-all kernels */
- fr->bAllvsAll = can_use_allvsall(ir, FALSE, nullptr, nullptr);
- fr->AllvsAll_work = nullptr;
-
- /* All-vs-all kernels have not been implemented in 4.6 and later.
- * See Redmine #1249. */
- if (fr->bAllvsAll)
- {
- fr->bAllvsAll = FALSE;
- if (fp != nullptr)
- {
- fprintf(fp,
- "\nYour simulation settings would have triggered the efficient all-vs-all\n"
- "kernels in GROMACS 4.5, but these have not been implemented in GROMACS\n"
- "4.6 and 5.x. If performance is important, please use GROMACS 4.5.7\n"
- "or try cutoff-scheme = Verlet.\n\n");
- }
- }
-
/* Neighbour searching stuff */
fr->cutoff_scheme = ir->cutoff_scheme;
- fr->bGrid = (ir->ns_type == ensGRID);
fr->ePBC = ir->ePBC;
- if (fr->cutoff_scheme == ecutsGROUP)
- {
- const char *note = "NOTE: This file uses the deprecated 'group' cutoff_scheme. This will be\n"
- "removed in a future release when 'verlet' supports all interaction forms.\n";
-
- if (MASTER(cr))
- {
- fprintf(stderr, "\n%s\n", note);
- }
- if (fp != nullptr)
- {
- fprintf(fp, "\n%s\n", note);
- }
- }
-
/* Determine if we will do PBC for distances in bonded interactions */
if (fr->ePBC == epbcNONE)
{
}
else
{
+ const bool useEwaldSurfaceCorrection =
+ (EEL_PME_EWALD(ir->coulombtype) && ir->epsilon_surface != 0);
if (!DOMAINDECOMP(cr))
{
gmx_bool bSHAKE;
- bSHAKE = (ir->eConstrAlg == econtSHAKE &&
- (gmx_mtop_ftype_count(mtop, F_CONSTR) > 0 ||
- gmx_mtop_ftype_count(mtop, F_CONSTRNC) > 0));
+ bSHAKE = (ir->eConstrAlg == econtSHAKE
+ && (gmx_mtop_ftype_count(mtop, F_CONSTR) > 0
+ || gmx_mtop_ftype_count(mtop, F_CONSTRNC) > 0));
/* The group cut-off scheme and SHAKE assume charge groups
* are whole, but not using molpbc is faster in most cases.
* With intermolecular interactions we need PBC for calculating
* distances between atoms in different molecules.
*/
- if ((fr->cutoff_scheme == ecutsGROUP || bSHAKE) &&
- !mtop->bIntermolecularInteractions)
+ if (bSHAKE && !mtop->bIntermolecularInteractions)
{
fr->bMolPBC = ir->bPeriodicMols;
else
{
/* Not making molecules whole is faster in most cases,
- * but With orientation restraints we need whole molecules.
+ * but with orientation restraints or non-tinfoil boundary
+ * conditions we need whole molecules.
*/
- fr->bMolPBC = (fcd->orires.nr == 0);
+ fr->bMolPBC = (fcd->orires.nr == 0 && !useEwaldSurfaceCorrection);
if (getenv("GMX_USE_GRAPH") != nullptr)
{
fr->bMolPBC = FALSE;
if (fp)
{
- GMX_LOG(mdlog.warning).asParagraph().appendText("GMX_USE_GRAPH is set, using the graph for bonded interactions");
+ GMX_LOG(mdlog.warning)
+ .asParagraph()
+ .appendText(
+ "GMX_USE_GRAPH is set, using the graph for bonded "
+ "interactions");
}
if (mtop->bIntermolecularInteractions)
{
- GMX_LOG(mdlog.warning).asParagraph().appendText("WARNING: Molecules linked by intermolecular interactions have to reside in the same periodic image, otherwise artifacts will occur!");
+ GMX_LOG(mdlog.warning)
+ .asParagraph()
+ .appendText(
+ "WARNING: Molecules linked by intermolecular interactions "
+ "have to reside in the same periodic image, otherwise "
+ "artifacts will occur!");
}
}
- GMX_RELEASE_ASSERT(fr->bMolPBC || !mtop->bIntermolecularInteractions, "We need to use PBC within molecules with inter-molecular interactions");
+ GMX_RELEASE_ASSERT(
+ fr->bMolPBC || !mtop->bIntermolecularInteractions,
+ "We need to use PBC within molecules with inter-molecular interactions");
if (bSHAKE && fr->bMolPBC)
{
- 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");
+ 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");
}
}
}
else
{
fr->bMolPBC = dd_bonded_molpbc(cr->dd, fr->ePBC);
+
+ if (useEwaldSurfaceCorrection && !dd_moleculesAreAlwaysWhole(*cr->dd))
+ {
+ gmx_fatal(FARGS,
+ "You requested dipole correction (epsilon_surface > 0), but molecules "
+ "are broken "
+ "over periodic boundary conditions by the domain decomposition. "
+ "Run without domain decomposition instead.");
+ }
+ }
+
+ if (useEwaldSurfaceCorrection)
+ {
+ GMX_RELEASE_ASSERT((!DOMAINDECOMP(cr) && !fr->bMolPBC)
+ || (DOMAINDECOMP(cr) && dd_moleculesAreAlwaysWhole(*cr->dd)),
+ "Molecules can not be broken by PBC with epsilon_surface > 0");
}
}
fr->rc_scaling = ir->refcoord_scaling;
copy_rvec(ir->posres_com, fr->posres_com);
copy_rvec(ir->posres_comB, fr->posres_comB);
- fr->rlist = cutoff_inf(ir->rlist);
- fr->ljpme_combination_rule = ir->ljpme_combination_rule;
+ fr->rlist = cutoff_inf(ir->rlist);
+ fr->ljpme_combination_rule = ir->ljpme_combination_rule;
/* This now calculates sum for q and c6*/
bool systemHasNetCharge = set_chargesum(fp, fr, mtop);
/* fr->ic is used both by verlet and group kernels (to some extent) now */
init_interaction_const(fp, &fr->ic, ir, mtop, systemHasNetCharge);
- init_interaction_const_tables(fp, fr->ic, ir->rlist + ir->tabext);
+ init_interaction_const_tables(fp, fr->ic);
- const interaction_const_t *ic = fr->ic;
+ const interaction_const_t* ic = fr->ic;
/* TODO: Replace this Ewald table or move it into interaction_const_t */
if (ir->coulombtype == eelEWALD)
/* Electrostatics: Translate from interaction-setting-in-mdp-file to kernel interaction format */
switch (ic->eeltype)
{
- case eelCUT:
- fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_COULOMB;
- break;
+ case eelCUT: fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_COULOMB; break;
case eelRF:
- case eelGRF:
- fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD;
- break;
-
- case eelRF_ZERO:
- fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD;
- GMX_RELEASE_ASSERT(ic->coulomb_modifier == eintmodEXACTCUTOFF, "With the group scheme RF-zero needs the exact cut-off modifier");
- break;
+ case eelRF_ZERO: fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_REACTIONFIELD; break;
case eelSWITCH:
case eelSHIFT:
case eelPME:
case eelP3M_AD:
- case eelEWALD:
- fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_EWALD;
- break;
+ case eelEWALD: fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_EWALD; break;
default:
gmx_fatal(FARGS, "Unsupported electrostatic interaction: %s", eel_names[ic->eeltype]);
fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_LENNARDJONES;
}
break;
- case evdwPME:
- fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_LJEWALD;
- break;
+ case evdwPME: fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_LJEWALD; break;
case evdwSWITCH:
case evdwSHIFT:
fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
break;
- default:
- gmx_fatal(FARGS, "Unsupported vdw interaction: %s", evdw_names[ic->vdwtype]);
+ default: gmx_fatal(FARGS, "Unsupported vdw interaction: %s", evdw_names[ic->vdwtype]);
}
fr->nbkernel_vdw_modifier = ic->vdw_modifier;
- if (ir->cutoff_scheme == ecutsGROUP)
- {
- fr->bvdwtab = ((ic->vdwtype != evdwCUT || !gmx_within_tol(ic->reppow, 12.0, 10*GMX_DOUBLE_EPS))
- && !EVDW_PME(ic->vdwtype));
- /* We have special kernels for standard Ewald and PME, but the pme-switch ones are tabulated above */
- fr->bcoultab = !(ic->eeltype == eelCUT ||
- ic->eeltype == eelEWALD ||
- ic->eeltype == eelPME ||
- ic->eeltype == eelP3M_AD ||
- ic->eeltype == eelRF ||
- ic->eeltype == eelRF_ZERO);
-
- /* If the user absolutely wants different switch/shift settings for coul/vdw, it is likely
- * going to be faster to tabulate the interaction than calling the generic kernel.
- * However, if generic kernels have been requested we keep things analytically.
- */
- if (fr->nbkernel_elec_modifier == eintmodPOTSWITCH &&
- fr->nbkernel_vdw_modifier == eintmodPOTSWITCH &&
- !bGenericKernelOnly)
- {
- if ((ic->rcoulomb_switch != ic->rvdw_switch) || (ic->rcoulomb != ic->rvdw))
- {
- fr->bcoultab = TRUE;
- /* Once we tabulate electrostatics, we can use the switch function for LJ,
- * which would otherwise need two tables.
- */
- }
- }
- else if ((fr->nbkernel_elec_modifier == eintmodPOTSHIFT && fr->nbkernel_vdw_modifier == eintmodPOTSHIFT) ||
- ((fr->nbkernel_elec_interaction == GMX_NBKERNEL_ELEC_REACTIONFIELD &&
- fr->nbkernel_elec_modifier == eintmodEXACTCUTOFF &&
- (fr->nbkernel_vdw_modifier == eintmodPOTSWITCH || fr->nbkernel_vdw_modifier == eintmodPOTSHIFT))))
- {
- if ((ic->rcoulomb != ic->rvdw) && (!bGenericKernelOnly))
- {
- fr->bcoultab = TRUE;
- }
- }
-
- if (fr->nbkernel_elec_modifier == eintmodFORCESWITCH)
- {
- fr->bcoultab = TRUE;
- }
- if (fr->nbkernel_vdw_modifier == eintmodFORCESWITCH)
- {
- fr->bvdwtab = TRUE;
- }
-
- if (getenv("GMX_REQUIRE_TABLES"))
- {
- fr->bvdwtab = TRUE;
- fr->bcoultab = TRUE;
- }
-
- if (fp)
- {
- fprintf(fp, "Table routines are used for coulomb: %s\n",
- gmx::boolToString(fr->bcoultab));
- fprintf(fp, "Table routines are used for vdw: %s\n",
- gmx::boolToString(fr->bvdwtab));
- }
-
- if (fr->bvdwtab)
- {
- fr->nbkernel_vdw_interaction = GMX_NBKERNEL_VDW_CUBICSPLINETABLE;
- fr->nbkernel_vdw_modifier = eintmodNONE;
- }
- if (fr->bcoultab)
- {
- fr->nbkernel_elec_interaction = GMX_NBKERNEL_ELEC_CUBICSPLINETABLE;
- fr->nbkernel_elec_modifier = eintmodNONE;
- }
- }
-
if (ir->cutoff_scheme == ecutsVERLET)
{
- if (!gmx_within_tol(ic->reppow, 12.0, 10*GMX_DOUBLE_EPS))
+ if (!gmx_within_tol(ic->reppow, 12.0, 10 * GMX_DOUBLE_EPS))
{
- gmx_fatal(FARGS, "Cut-off scheme %s only supports LJ repulsion power 12", ecutscheme_names[ir->cutoff_scheme]);
+ gmx_fatal(FARGS, "Cut-off scheme %s only supports LJ repulsion power 12",
+ ecutscheme_names[ir->cutoff_scheme]);
}
/* Older tpr files can contain Coulomb user tables with the Verlet cutoff-scheme,
* while mdrun does not (and never did) support this.
/* 1-4 interaction electrostatics */
fr->fudgeQQ = mtop->ffparams.fudgeQQ;
- /* Parameters for generalized RF */
- fr->zsquare = 0.0;
- fr->temp = 0.0;
-
- if (ic->eeltype == eelGRF)
- {
- init_generalized_rf(fp, mtop, ir, fr);
- }
-
fr->haveDirectVirialContributions =
- (EEL_FULL(ic->eeltype) || EVDW_PME(ic->vdwtype) ||
- fr->forceProviders->hasForceProvider() ||
- gmx_mtop_ftype_count(mtop, F_POSRES) > 0 ||
- gmx_mtop_ftype_count(mtop, F_FBPOSRES) > 0 ||
- ir->nwall > 0 ||
- ir->bPull ||
- ir->bRot ||
- ir->bIMD);
-
- if (fr->haveDirectVirialContributions)
- {
- fr->forceBufferForDirectVirialContributions = new std::vector<gmx::RVec>;
- }
+ (EEL_FULL(ic->eeltype) || EVDW_PME(ic->vdwtype) || fr->forceProviders->hasForceProvider()
+ || gmx_mtop_ftype_count(mtop, F_POSRES) > 0 || gmx_mtop_ftype_count(mtop, F_FBPOSRES) > 0
+ || ir->nwall > 0 || ir->bPull || ir->bRot || ir->bIMD);
- if (fr->cutoff_scheme == ecutsGROUP &&
- ncg_mtop(mtop) > fr->cg_nalloc && !DOMAINDECOMP(cr))
- {
- /* Count the total number of charge groups */
- fr->cg_nalloc = ncg_mtop(mtop);
- srenew(fr->cg_cm, fr->cg_nalloc);
- }
if (fr->shift_vec == nullptr)
{
snew(fr->shift_vec, SHIFTS);
}
- if (fr->fshift == nullptr)
- {
- snew(fr->fshift, SHIFTS);
- }
+ fr->shiftForces.resize(SHIFTS);
if (fr->nbfp == nullptr)
{
fr->nbfp = mk_nbfp(&mtop->ffparams, fr->bBHAM);
if (EVDW_PME(ic->vdwtype))
{
- fr->ljpme_c6grid = make_ljpme_c6grid(&mtop->ffparams, fr);
+ fr->ljpme_c6grid = make_ljpme_c6grid(&mtop->ffparams, fr);
}
}
{
if (ic->rvdw_switch >= ic->rvdw)
{
- gmx_fatal(FARGS, "rvdw_switch (%f) must be < rvdw (%f)",
- ic->rvdw_switch, ic->rvdw);
+ gmx_fatal(FARGS, "rvdw_switch (%f) must be < rvdw (%f)", ic->rvdw_switch, ic->rvdw);
}
if (fp)
{
fprintf(fp, "Using %s Lennard-Jones, switch between %g and %g nm\n",
- (ic->eeltype == eelSWITCH) ? "switched" : "shifted",
- ic->rvdw_switch, ic->rvdw);
+ (ic->eeltype == eelSWITCH) ? "switched" : "shifted", ic->rvdw_switch, ic->rvdw);
}
}
if (fp && fr->cutoff_scheme == ecutsGROUP)
{
- fprintf(fp, "Cut-off's: NS: %g Coulomb: %g %s: %g\n",
- fr->rlist, ic->rcoulomb, fr->bBHAM ? "BHAM" : "LJ", ic->rvdw);
- }
-
- fr->eDispCorr = ir->eDispCorr;
- fr->numAtomsForDispersionCorrection = mtop->natoms;
- if (ir->eDispCorr != edispcNO)
- {
- set_avcsixtwelve(fp, fr, mtop);
+ fprintf(fp, "Cut-off's: NS: %g Coulomb: %g %s: %g\n", fr->rlist, ic->rcoulomb,
+ fr->bBHAM ? "BHAM" : "LJ", ic->rvdw);
}
if (ir->implicit_solvent)
gmx_fatal(FARGS, "Implict solvation is no longer supported.");
}
- /* Construct tables for the group scheme. A little unnecessary to
- * make both vdw and coul tables sometimes, but what the
- * heck. Note that both cutoff schemes construct Ewald tables in
- * init_interaction_const_tables. */
- needGroupSchemeTables = (ir->cutoff_scheme == ecutsGROUP &&
- (fr->bcoultab || fr->bvdwtab));
-
- negp_pp = ir->opts.ngener - ir->nwall;
- negptable = 0;
- if (!needGroupSchemeTables)
- {
- bSomeNormalNbListsAreInUse = TRUE;
- fr->nnblists = 1;
- }
- else
- {
- bSomeNormalNbListsAreInUse = FALSE;
- for (egi = 0; egi < negp_pp; egi++)
- {
- for (egj = egi; egj < negp_pp; egj++)
- {
- egp_flags = ir->opts.egp_flags[GID(egi, egj, ir->opts.ngener)];
- if (!(egp_flags & EGP_EXCL))
- {
- if (egp_flags & EGP_TABLE)
- {
- negptable++;
- }
- else
- {
- bSomeNormalNbListsAreInUse = TRUE;
- }
- }
- }
- }
- if (bSomeNormalNbListsAreInUse)
- {
- fr->nnblists = negptable + 1;
- }
- else
- {
- fr->nnblists = negptable;
- }
- if (fr->nnblists > 1)
- {
- snew(fr->gid2nblists, ir->opts.ngener*ir->opts.ngener);
- }
- }
-
- snew(fr->nblists, fr->nnblists);
/* This code automatically gives table length tabext without cut-off's,
* in that case grompp should already have checked that we do not need
*/
rtab = ir->rlist + ir->tabext;
- if (needGroupSchemeTables)
- {
- /* make tables for ordinary interactions */
- if (bSomeNormalNbListsAreInUse)
- {
- make_nbf_tables(fp, ic, rtab, tabfn, nullptr, nullptr, &fr->nblists[0]);
- m = 1;
- }
- else
- {
- m = 0;
- }
- if (negptable > 0)
- {
- /* Read the special tables for certain energy group pairs */
- nm_ind = mtop->groups.grps[egcENER].nm_ind;
- for (egi = 0; egi < negp_pp; egi++)
- {
- for (egj = egi; egj < negp_pp; egj++)
- {
- egp_flags = ir->opts.egp_flags[GID(egi, egj, ir->opts.ngener)];
- if ((egp_flags & EGP_TABLE) && !(egp_flags & EGP_EXCL))
- {
- if (fr->nnblists > 1)
- {
- fr->gid2nblists[GID(egi, egj, ir->opts.ngener)] = m;
- }
- /* Read the table file with the two energy groups names appended */
- make_nbf_tables(fp, ic, rtab, tabfn,
- *mtop->groups.grpname[nm_ind[egi]],
- *mtop->groups.grpname[nm_ind[egj]],
- &fr->nblists[m]);
- m++;
- }
- else if (fr->nnblists > 1)
- {
- fr->gid2nblists[GID(egi, egj, ir->opts.ngener)] = 0;
- }
- }
- }
- }
- }
-
- /* Tables might not be used for the potential modifier
- * interactions per se, but we still need them to evaluate
- * switch/shift dispersion corrections in this case. */
- if (fr->eDispCorr != edispcNO)
- {
- fr->dispersionCorrectionTable = makeDispersionCorrectionTable(fp, ic, rtab, tabfn);
- }
-
/* We want to use unmodified tables for 1-4 coulombic
* interactions, so we must in general have an extra set of
* tables. */
- if (gmx_mtop_ftype_count(mtop, F_LJ14) > 0 ||
- gmx_mtop_ftype_count(mtop, F_LJC14_Q) > 0 ||
- gmx_mtop_ftype_count(mtop, F_LJC_PAIRS_NB) > 0)
+ if (gmx_mtop_ftype_count(mtop, F_LJ14) > 0 || gmx_mtop_ftype_count(mtop, F_LJC14_Q) > 0
+ || gmx_mtop_ftype_count(mtop, F_LJC_PAIRS_NB) > 0)
{
- fr->pairsTable = make_tables(fp, ic, tabpfn, rtab,
- GMX_MAKETABLES_14ONLY);
+ fr->pairsTable = make_tables(fp, ic, tabpfn, rtab, GMX_MAKETABLES_14ONLY);
}
/* Wall stuff */
// TODO Don't need to catch this here, when merging with master branch
try
{
- fcd->bondtab = make_bonded_tables(fp,
- F_TABBONDS, F_TABBONDSNC,
- mtop, tabbfnm, "b");
- fcd->angletab = make_bonded_tables(fp,
- F_TABANGLES, -1,
- mtop, tabbfnm, "a");
- fcd->dihtab = make_bonded_tables(fp,
- F_TABDIHS, -1,
- mtop, tabbfnm, "d");
+ fcd->bondtab = make_bonded_tables(fp, F_TABBONDS, F_TABBONDSNC, mtop, tabbfnm, "b");
+ fcd->angletab = make_bonded_tables(fp, F_TABANGLES, -1, mtop, tabbfnm, "a");
+ fcd->dihtab = make_bonded_tables(fp, F_TABDIHS, -1, mtop, tabbfnm, "d");
}
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
else
{
if (debug)
{
- fprintf(debug, "No fcdata or table file name passed, can not read table, can not do bonded interactions\n");
+ fprintf(debug,
+ "No fcdata or table file name passed, can not read table, can not do bonded "
+ "interactions\n");
}
}
// Initialize QM/MM if supported
if (GMX_QMMM)
{
- GMX_LOG(mdlog.info).asParagraph().
- appendText("Large parts of the QM/MM support is deprecated, and may be removed in a future "
- "version. Please get in touch with the developers if you find the support useful, "
- "as help is needed if the functionality is to continue to be available.");
+ GMX_LOG(mdlog.info)
+ .asParagraph()
+ .appendText(
+ "Large parts of the QM/MM support is deprecated, and may be removed in "
+ "a future "
+ "version. Please get in touch with the developers if you find the "
+ "support useful, "
+ "as help is needed if the functionality is to continue to be "
+ "available.");
fr->qr = mk_QMMMrec();
init_QMMMrec(cr, mtop, ir, fr);
}
else
{
- gmx_incons("QM/MM was requested, but is only available when GROMACS "
- "is configured with QM/MM support");
+ gmx_incons(
+ "QM/MM was requested, but is only available when GROMACS "
+ "is configured with QM/MM support");
}
}
/* Set all the static charge group info */
- fr->cginfo_mb = init_cginfo_mb(fp, mtop, fr, bNoSolvOpt,
- &bFEP_NonBonded,
- &fr->bExcl_IntraCGAll_InterCGNone);
- if (DOMAINDECOMP(cr))
- {
- fr->cginfo = nullptr;
- }
- else
+ fr->cginfo_mb = init_cginfo_mb(mtop, fr, &bFEP_NonBonded);
+ if (!DOMAINDECOMP(cr))
{
fr->cginfo = cginfo_expand(mtop->molblock.size(), fr->cginfo_mb);
}
if (!DOMAINDECOMP(cr))
{
- forcerec_set_ranges(fr, ncg_mtop(mtop), ncg_mtop(mtop),
- mtop->natoms, mtop->natoms, mtop->natoms);
+ forcerec_set_ranges(fr, mtop->natoms, mtop->natoms, mtop->natoms);
}
fr->print_force = print_force;
-
- /* coarse load balancing vars */
- fr->t_fnbf = 0.;
- fr->t_wait = 0.;
- fr->timesteps = 0;
-
- /* Initialize neighbor search */
- snew(fr->ns, 1);
- init_ns(fp, cr, fr->ns, fr, mtop);
-
- if (thisRankHasDuty(cr, DUTY_PP))
- {
- gmx_nonbonded_setup(fr, bGenericKernelOnly);
- }
-
/* Initialize the thread working data for bonded interactions */
- init_bonded_threading(fp, mtop->groups.grps[egcENER].nr,
- &fr->bondedThreading);
+ fr->bondedThreading = init_bonded_threading(
+ fp, mtop->groups.groups[SimulationAtomGroupType::EnergyOutput].size());
fr->nthread_ewc = gmx_omp_nthreads_get(emntBonded);
snew(fr->ewc_t, fr->nthread_ewc);
// We have PME+LJcutoff kernels for rcoulomb>rvdw.
if (EEL_PME_EWALD(ir->coulombtype) && ir->vdwtype == eelCUT)
{
- GMX_RELEASE_ASSERT(ir->rcoulomb >= ir->rvdw, "With Verlet lists and PME we should have rcoulomb>=rvdw");
+ GMX_RELEASE_ASSERT(ir->rcoulomb >= ir->rvdw,
+ "With Verlet lists and PME we should have rcoulomb>=rvdw");
}
else
{
- GMX_RELEASE_ASSERT(ir->rcoulomb == ir->rvdw, "With Verlet lists and no PME rcoulomb and rvdw should be identical");
+ GMX_RELEASE_ASSERT(
+ ir->rcoulomb == ir->rvdw,
+ "With Verlet lists and no PME rcoulomb and rvdw should be identical");
}
- init_nb_verlet(mdlog, &fr->nbv, bFEP_NonBonded, ir, fr,
- cr, hardwareInfo, deviceInfo,
- mtop, box);
+ fr->nbv = Nbnxm::init_nb_verlet(mdlog, bFEP_NonBonded, ir, fr, cr, hardwareInfo, deviceInfo,
+ mtop, box, wcycle);
if (useGpuForBonded)
{
- // TODO use havePPDomainDecomposition here to simplify the code.
- auto stream = (DOMAINDECOMP(cr) && (cr->nnodes - cr->npmenodes > 1)) ?
- nbnxn_gpu_get_command_stream(fr->nbv->gpu_nbv, eintNonlocal) :
- nbnxn_gpu_get_command_stream(fr->nbv->gpu_nbv, eintLocal);
+ auto stream = havePPDomainDecomposition(cr)
+ ? Nbnxm::gpu_get_command_stream(
+ fr->nbv->gpu_nbv, gmx::InteractionLocality::NonLocal)
+ : Nbnxm::gpu_get_command_stream(fr->nbv->gpu_nbv,
+ gmx::InteractionLocality::Local);
// TODO the heap allocation is only needed while
// t_forcerec lacks a constructor.
- fr->gpuBonded = new gmx::GpuBonded(mtop->ffparams,
- stream);
+ fr->gpuBonded = new gmx::GpuBonded(mtop->ffparams, stream, wcycle);
}
}
+ if (ir->eDispCorr != edispcNO)
+ {
+ fr->dispersionCorrection = std::make_unique<DispersionCorrection>(
+ *mtop, *ir, fr->bBHAM, fr->ntype,
+ gmx::arrayRefFromArray(fr->nbfp, fr->ntype * fr->ntype * 2), *fr->ic, tabfn);
+ fr->dispersionCorrection->print(mdlog);
+ }
+
if (fp != nullptr)
{
/* Here we switch from using mdlog, which prints the newline before
fprintf(fp, "\n");
}
- if (ir->eDispCorr != edispcNO)
+ if (pmeOnlyRankUsesGpu && c_enableGpuPmePpComms)
{
- calc_enervirdiff(fp, ir->eDispCorr, fr);
+ fr->pmePpCommGpu = std::make_unique<gmx::PmePpCommGpu>(cr->mpi_comm_mysim, cr->dd->pme_nodeid);
}
}
+t_forcerec::t_forcerec() = default;
+
+t_forcerec::~t_forcerec() = default;
+
/* Frees GPU memory and sets a tMPI node barrier.
*
* Note that this function needs to be called even if GPUs are not used
* \todo Remove physical node barrier from this function after making sure
* that it's not needed anymore (with a shared GPU run).
*/
-void free_gpu_resources(t_forcerec *fr,
- const gmx::PhysicalNodeCommunicator &physicalNodeCommunicator)
+void free_gpu_resources(t_forcerec* fr,
+ const gmx::PhysicalNodeCommunicator& physicalNodeCommunicator,
+ const gmx_gpu_info_t& gpu_info)
{
- bool isPPrankUsingGPU = (fr != nullptr) && (fr->nbv != nullptr) && fr->nbv->bUseGPU;
+ bool isPPrankUsingGPU = (fr != nullptr) && (fr->nbv != nullptr) && fr->nbv->useGpu();
/* stop the GPU profiler (only CUDA) */
- stopGpuProfiler();
+ if (gpu_info.n_dev > 0)
+ {
+ stopGpuProfiler();
+ }
if (isPPrankUsingGPU)
{
- /* free nbnxn data in GPU memory */
- nbnxn_gpu_free(fr->nbv->gpu_nbv);
+ /* Free data in GPU memory and pinned memory before destroying the GPU context */
+ fr->nbv.reset();
+
delete fr->gpuBonded;
fr->gpuBonded = nullptr;
}
}
}
-void done_forcerec(t_forcerec *fr, int numMolBlocks, int numEnergyGroups)
+void done_forcerec(t_forcerec* fr, int numMolBlocks)
{
if (fr == nullptr)
{
}
done_cginfo_mb(fr->cginfo_mb, numMolBlocks);
sfree(fr->nbfp);
- done_interaction_const(fr->ic);
+ delete fr->ic;
sfree(fr->shift_vec);
- sfree(fr->fshift);
- sfree(fr->nblists);
- done_ns(fr->ns, numEnergyGroups);
sfree(fr->ewc_t);
tear_down_bonded_threading(fr->bondedThreading);
GMX_RELEASE_ASSERT(fr->gpuBonded == nullptr, "Should have been deleted earlier, when used");
fr->bondedThreading = nullptr;
- sfree(fr);
+ delete fr;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff