* kernels and only exclusions inside the cut-off lead to exclusion
* forces. Since each atom pair is treated at most once in the non-bonded
* kernels, it doesn't matter if the exclusions for the same atom pair
- * appear multiple times in the exclusion list. In contrast, the, old,
- * group cut-off scheme loops over a list of exclusions, so there each
- * excluded pair should appear exactly once.
+ * appear multiple times in the exclusion list.
*/
rt->bExclRequired = (ir->cutoff_scheme == ecutsGROUP &&
inputrecExclForces(ir));
{
errorReasons.emplace_back("Lennard-Jones PME");
}
- if (ir.cutoff_scheme == ecutsGROUP)
- {
- errorReasons.emplace_back("group cutoff scheme");
- }
if (!EI_DYNAMICS(ir.eI))
{
errorReasons.emplace_back("not a dynamical integrator");
gmx_bool bUseGPU,
gmx_bool *bPrinting)
{
- GMX_RELEASE_ASSERT(ir.cutoff_scheme != ecutsGROUP, "PME tuning is not supported with cutoff-scheme=group (because it contains bugs)");
pme_load_balancing_t *pme_lb;
real spm, sp;
warning(wi, buf);
}
- /* If using the group scheme, make sure charge groups are made whole to avoid errors
- * in calculating charge group size later on
- */
- if (ir->cutoff_scheme == ecutsGROUP && ir->ePBC != epbcNONE)
- {
- // Need temporary rvec for coordinates
- do_pbc_first_mtop(nullptr, ir->ePBC, state->box, sys, state->x.rvec_array());
- }
-
/* Do more checks, mostly related to constraints */
if (bVerbose)
{
if (ir->cutoff_scheme == ecutsGROUP)
{
- warning_note(wi,
- "The group cutoff scheme is deprecated since GROMACS 5.0 and will be removed in a future "
- "release when all interaction forms are supported for the verlet scheme. The verlet "
- "scheme already scales better, and it is compatible with GPUs and other accelerators.");
-
- if (ir->rlist > 0 && ir->rlist < ir->rcoulomb)
- {
- gmx_fatal(FARGS, "rcoulomb must not be greater than rlist (twin-range schemes are not supported)");
- }
- if (ir->rlist > 0 && ir->rlist < ir->rvdw)
- {
- gmx_fatal(FARGS, "rvdw must not be greater than rlist (twin-range schemes are not supported)");
- }
-
- if (ir->rlist == 0 && ir->ePBC != epbcNONE)
- {
- warning_error(wi, "Can not have an infinite cut-off with PBC");
- }
+ gmx_fatal(FARGS,
+ "The group cutoff scheme has been removed since GROMACS 2020. "
+ "Please use the Verlet cutoff scheme.");
}
-
if (ir->cutoff_scheme == ecutsVERLET)
{
real rc_max;
CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
}
}
- else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
- {
- if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
- {
- sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
- eel_names[ir->coulombtype]);
- CHECK(ir->rlist > ir->rcoulomb);
- }
- }
if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
{
eel_names[ir->coulombtype]);
CHECK(ir->rcoulomb > ir->rlist);
}
- else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
- {
- if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
- {
- sprintf(err_buf,
- "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist.\n"
- "For optimal energy conservation,consider using\n"
- "a potential modifier.", eel_names[ir->coulombtype]);
- CHECK(ir->rcoulomb != ir->rlist);
- }
- }
}
if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
warning_note(wi, warn_buf);
}
}
- else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
- {
- if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
- {
- sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
- CHECK(ir->rlist > ir->rvdw);
- }
- }
if (ir->vdwtype == evdwPME)
{
}
}
- if (ir->cutoff_scheme == ecutsGROUP)
- {
- if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
- (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)))
- {
- warning_note(wi, "With exact cut-offs, rlist should be "
- "larger than rcoulomb and rvdw, so that there "
- "is a buffer region for particle motion "
- "between neighborsearch steps");
- }
-
- if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlist <= ir->rcoulomb)
- {
- sprintf(warn_buf, "For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rcoulomb.");
- warning_note(wi, warn_buf);
- }
- if (ir_vdw_switched(ir) && (ir->rlist <= ir->rvdw))
- {
- sprintf(warn_buf, "For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw.");
- warning_note(wi, warn_buf);
- }
- }
-
if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
{
warning_note(wi, "You have selected user tables with dispersion correction, the dispersion will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction between rvdw_switch and rvdw will not be double counted). Make sure that you really want dispersion correction to -C6/r^6.");
warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
}
- /* ENERGY CONSERVATION */
- if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
- {
- if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
- {
- sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
- evdw_names[evdwSHIFT]);
- warning_note(wi, warn_buf);
- }
- if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
- {
- sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
- eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
- warning_note(wi, warn_buf);
- }
- }
-
/* IMPLICIT SOLVENT */
if (ir->coulombtype == eelGB_NOTUSED)
{
{
sprintf(warn_buf,
"%s did not specify a value for the .mdp option "
- "\"cutoff-scheme\". Probably it was first intended for use "
- "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
- "introduced, but the group scheme was still the default. "
- "The default is now the Verlet scheme, so you will observe "
- "different behaviour.", mdparin);
+ "\"cutoff-scheme\". As of GROMACS 2020, the Verlet scheme "
+ "is the only cutoff scheme supported. This may affect your "
+ "simulation if you are using an old mdp file that assumes use "
+ "of the (removed) group cutoff scheme.", mdparin);
warning_note(wi, warn_buf);
}
{
errorReasons.emplace_back("No supported bonded interactions are present");
}
- if (ir.cutoff_scheme == ecutsGROUP)
- {
- errorReasons.emplace_back("group cutoff scheme");
- }
if (!EI_DYNAMICS(ir.eI))
{
errorReasons.emplace_back("not a dynamical integrator");
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. */
*/
void update_forcerec(t_forcerec *fr, matrix box);
-gmx_bool uses_simple_tables(int cutoff_scheme,
- const nonbonded_verlet_t *nbv);
-/* Returns whether simple tables (i.e. not for use with GPUs) are used
- * with the type of kernel indicated.
- */
-
void free_gpu_resources(t_forcerec *fr,
const gmx::PhysicalNodeCommunicator &physicalNodeCommunicator);
* that the numbers need to be adjusted.
*/
-/* Cost of a pair interaction in the "group" cut-off scheme */
-static const double c_group_fq = 18.0;
-static const double c_group_qlj_cut = 18.0;
-static const double c_group_qlj_tab = 24.0;
-static const double c_group_lj_cut = 12.0;
-static const double c_group_lj_tab = 21.0;
-/* Cost of 1 water with one Q/LJ atom */
-static const double c_group_qljw_cut = 24.0;
-static const double c_group_qljw_tab = 27.0;
-/* Cost of 1 water with one Q atom or with 1/3 water (LJ negligible) */
-static const double c_group_qw = 21.0;
-
/* Cost of a pair interaction in the "Verlet" cut-off scheme, QEXP is Ewald */
static const double c_nbnxn_lj = 2.5;
static const double c_nbnxn_qrf_lj = 2.9;
}
}
-static void pp_group_load(const gmx_mtop_t *mtop, const t_inputrec *ir,
- const matrix box,
- int *nq_tot, int *nlj_tot,
- double *cost_pp,
- gmx_bool *bChargePerturbed, gmx_bool *bTypePerturbed)
-{
- int atnr, cg, a0, ncqlj, ncq, nclj;
- gmx_bool bBHAM, bLJcut, bWater, bQ, bLJ;
- int nw, nqlj, nq, nlj;
- double fq, fqlj, flj, fqljw, fqw;
-
- bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
-
- bLJcut = ((ir->vdwtype == evdwCUT) && !bBHAM);
-
- /* Computational cost of bonded, non-bonded and PME calculations.
- * This will be machine dependent.
- * The numbers here are accurate for Intel Core2 and AMD Athlon 64
- * in single precision. In double precision PME mesh is slightly cheaper,
- * although not so much that the numbers need to be adjusted.
- */
- fq = c_group_fq;
- fqlj = (bLJcut ? c_group_qlj_cut : c_group_qlj_tab);
- flj = (bLJcut ? c_group_lj_cut : c_group_lj_tab);
- /* Cost of 1 water with one Q/LJ atom */
- fqljw = (bLJcut ? c_group_qljw_cut : c_group_qljw_tab);
- /* Cost of 1 water with one Q atom or with 1/3 water (LJ negligible) */
- fqw = c_group_qw;
-
- gmx::ArrayRef<const t_iparams> iparams = mtop->ffparams.iparams;
- atnr = mtop->ffparams.atnr;
- nw = 0;
- nqlj = 0;
- nq = 0;
- nlj = 0;
- *bChargePerturbed = FALSE;
- *bTypePerturbed = FALSE;
- for (const gmx_molblock_t &molb : mtop->molblock)
- {
- const gmx_moltype_t *molt = &mtop->moltype[molb.type];
- const t_atom *atom = molt->atoms.atom;
- int a = 0;
- for (cg = 0; cg < molt->cgs.nr; cg++)
- {
- bWater = !bBHAM;
- ncqlj = 0;
- ncq = 0;
- nclj = 0;
- a0 = a;
- while (a < molt->cgs.index[cg+1])
- {
- bQ = (atom[a].q != 0 || atom[a].qB != 0);
- bLJ = (iparams[(atnr+1)*atom[a].type].lj.c6 != 0 ||
- iparams[(atnr+1)*atom[a].type].lj.c12 != 0);
- if (atom[a].q != atom[a].qB)
- {
- *bChargePerturbed = TRUE;
- }
- if (atom[a].type != atom[a].typeB)
- {
- *bTypePerturbed = TRUE;
- }
- /* This if this atom fits into water optimization */
- if (!((a == a0 && bQ && bLJ) ||
- (a == a0+1 && bQ && !bLJ) ||
- (a == a0+2 && bQ && !bLJ && atom[a].q == atom[a-1].q) ||
- (a == a0+3 && !bQ && bLJ)))
- {
- bWater = FALSE;
- }
- if (bQ && bLJ)
- {
- ncqlj++;
- }
- else
- {
- if (bQ)
- {
- ncq++;
- }
- if (bLJ)
- {
- nclj++;
- }
- }
- a++;
- }
- if (bWater)
- {
- nw += molb.nmol;
- }
- else
- {
- nqlj += molb.nmol*ncqlj;
- nq += molb.nmol*ncq;
- nlj += molb.nmol*nclj;
- }
- }
- }
-
- *nq_tot = nq + nqlj + nw*3;
- *nlj_tot = nlj + nqlj + nw;
-
- if (debug)
- {
- fprintf(debug, "nw %d nqlj %d nq %d nlj %d\n", nw, nqlj, nq, nlj);
- }
-
- /* For the PP non-bonded cost it is (unrealistically) assumed
- * that all atoms are distributed homogeneously in space.
- * Factor 3 is used because a water molecule has 3 atoms
- * (and TIP4P effectively has 3 interactions with (water) atoms)).
- */
- *cost_pp = 0.5*(fqljw*nw*nqlj +
- fqw *nw*(3*nw + nq) +
- fqlj *nqlj*nqlj +
- fq *nq*(3*nw + nqlj + nq) +
- flj *nlj*(nw + nqlj + nlj))
- *4/3*M_PI*ir->rlist*ir->rlist*ir->rlist/det(box);
-
- *cost_pp *= simd_cycle_factor(bHaveSIMD);
-}
-
static void pp_verlet_load(const gmx_mtop_t *mtop, const t_inputrec *ir,
const matrix box,
int *nq_tot, int *nlj_tot,
cost_bond = c_bond*(ndistance_c *simd_cycle_factor(FALSE) +
ndistance_simd*simd_cycle_factor(bHaveSIMD));
- if (ir->cutoff_scheme == ecutsGROUP)
- {
- pp_group_load(mtop, ir, box,
- &nq_tot, &nlj_tot, &cost_pp,
- &bChargePerturbed, &bTypePerturbed);
- }
- else
- {
- pp_verlet_load(mtop, ir, box,
- &nq_tot, &nlj_tot, &cost_pp,
- &bChargePerturbed, &bTypePerturbed);
- }
+ pp_verlet_load(mtop, ir, box,
+ &nq_tot, &nlj_tot, &cost_pp,
+ &bChargePerturbed, &bTypePerturbed);
cost_redist = 0;
cost_spread = 0;
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff