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.
- */
- nbl->table_elec =
- new t_forcetable(GMX_TABLE_INTERACTION_ELEC,
- 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);
-
- nbl->table_vdw =
- new t_forcetable(GMX_TABLE_INTERACTION_VDWREP_VDWDISP,
- 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
}
}
-gmx_bool uses_simple_tables(int cutoff_scheme,
- const nonbonded_verlet_t *nbv)
-{
- gmx_bool bUsesSimpleTables = TRUE;
-
- switch (cutoff_scheme)
- {
- case ecutsGROUP:
- bUsesSimpleTables = TRUE;
- break;
- case ecutsVERLET:
- GMX_RELEASE_ASSERT(nullptr != nbv, "A non-bonded verlet object is required with the Verlet cutoff-scheme");
- bUsesSimpleTables = nbv->pairlistIsSimple();
- break;
- default:
- gmx_incons("unimplemented");
- }
- return bUsesSimpleTables;
-}
-
static void init_ewald_f_table(interaction_const_t *ic,
real rtab)
{
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;
- }
}
else
{
gmx_bool bNoSolvOpt,
real print_force)
{
- 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 egp_flags;
-
/* By default we turn SIMD kernels on, but it might be turned off further down... */
fr->use_simd_kernels = TRUE;
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)
{
* 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;
}
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))
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;
- }
- 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;
- }
- }
- }
- }
- }
/* 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, nullptr);
- m = 1;
- }
- else
- {
- m = 0;
- }
- if (negptable > 0)
- {
- /* Read the special tables for certain energy group pairs */
- gmx::ArrayRef<const int> nm_ind = mtop->groups.groups[SimulationAtomGroupType::EnergyOutput];
- 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))
- {
- /* Read the table file with the two energy groups names appended */
- make_nbf_tables(fp, ic, rtab, tabfn,
- *mtop->groups.groupNames[nm_ind[egi]],
- *mtop->groups.groupNames[nm_ind[egj]],
- nullptr);
- m++;
- }
- }
- }
- }
- }
-
/* We want to use unmodified tables for 1-4 coulombic
* interactions, so we must in general have an extra set of
* tables. */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff