/*! \brief Print Coulomb Ewald citations and set ewald coefficients */
static void initCoulombEwaldParameters(FILE* fp,
- const t_inputrec* ir,
+ const t_inputrec& ir,
bool systemHasNetCharge,
interaction_const_t* ic)
{
- if (!EEL_PME_EWALD(ir->coulombtype))
+ if (!EEL_PME_EWALD(ir.coulombtype))
{
return;
}
{
fprintf(fp, "Will do PME sum in reciprocal space for electrostatic interactions.\n");
- if (ir->coulombtype == eelP3M_AD)
+ if (ir.coulombtype == eelP3M_AD)
{
please_cite(fp, "Hockney1988");
please_cite(fp, "Ballenegger2012");
please_cite(fp, "Essmann95a");
}
- if (ir->ewald_geometry == eewg3DC)
+ if (ir.ewald_geometry == eewg3DC)
{
if (fp)
{
}
}
- ic->ewaldcoeff_q = calc_ewaldcoeff_q(ir->rcoulomb, ir->ewald_rtol);
+ 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);
}
/*! \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))
+ if (!EVDW_PME(ir.vdwtype))
{
return;
}
fprintf(fp, "Will do PME sum in reciprocal space for LJ dispersion interactions.\n");
please_cite(fp, "Essmann95a");
}
- ic->ewaldcoeff_lj = calc_ewaldcoeff_lj(ir->rvdw, ir->ewald_rtol_lj);
+ 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);
*/
static void init_interaction_const(FILE* fp,
interaction_const_t** interaction_const,
- const t_inputrec* ir,
+ const t_inputrec& ir,
const gmx_mtop_t* mtop,
bool systemHasNetCharge)
{
ic->vdwEwaldTables = std::make_unique<EwaldCorrectionTables>();
/* Lennard-Jones */
- ic->vdwtype = ir->vdwtype;
- ic->vdw_modifier = ir->vdw_modifier;
+ ic->vdwtype = ir.vdwtype;
+ ic->vdw_modifier = ir.vdw_modifier;
ic->reppow = mtop->ffparams.reppow;
- ic->rvdw = cutoff_inf(ir->rvdw);
- ic->rvdw_switch = ir->rvdw_switch;
- ic->ljpme_comb_rule = ir->ljpme_combination_rule;
+ ic->rvdw = cutoff_inf(ir.rvdw);
+ ic->rvdw_switch = ir.rvdw_switch;
+ ic->ljpme_comb_rule = ir.ljpme_combination_rule;
ic->useBuckingham = (mtop->ffparams.functype[0] == F_BHAM);
if (ic->useBuckingham)
{
}
/* Electrostatics */
- ic->eeltype = ir->coulombtype;
- ic->coulomb_modifier = ir->coulomb_modifier;
- ic->rcoulomb = cutoff_inf(ir->rcoulomb);
- ic->rcoulomb_switch = ir->rcoulomb_switch;
- ic->epsilon_r = ir->epsilon_r;
+ ic->eeltype = ir.coulombtype;
+ ic->coulomb_modifier = ir.coulomb_modifier;
+ ic->rcoulomb = cutoff_inf(ir.rcoulomb);
+ ic->rcoulomb_switch = ir.rcoulomb_switch;
+ ic->epsilon_r = ir.epsilon_r;
/* Set the Coulomb energy conversion factor */
if (ic->epsilon_r != 0)
if (EEL_RF(ic->eeltype))
{
GMX_RELEASE_ASSERT(ic->eeltype != eelGRF_NOTUSED, "GRF is no longer supported");
- ic->epsilon_rf = ir->epsilon_rf;
+ ic->epsilon_rf = ir.epsilon_rf;
calc_rffac(fp, ic->epsilon_r, ic->epsilon_rf, ic->rcoulomb, &ic->k_rf, &ic->c_rf);
}
/* For plain cut-off we might use the reaction-field kernels */
ic->epsilon_rf = ic->epsilon_r;
ic->k_rf = 0;
- if (ir->coulomb_modifier == eintmodPOTSHIFT)
+ if (ir.coulomb_modifier == eintmodPOTSHIFT)
{
ic->c_rf = 1 / ic->rcoulomb;
}
fprintf(fp, "\n");
}
- if (ir->efep != efepNO)
+ if (ir.efep != efepNO)
{
- GMX_RELEASE_ASSERT(ir->fepvals, "ir->fepvals should be set wth free-energy");
- ic->softCoreParameters = std::make_unique<interaction_const_t::SoftCoreParameters>(*ir->fepvals);
+ GMX_RELEASE_ASSERT(ir.fepvals, "ir.fepvals should be set wth free-energy");
+ ic->softCoreParameters = std::make_unique<interaction_const_t::SoftCoreParameters>(*ir.fepvals);
}
*interaction_const = ic;
void init_forcerec(FILE* fp,
const gmx::MDLogger& mdlog,
t_forcerec* fr,
- const t_inputrec* ir,
+ const t_inputrec& ir,
const gmx_mtop_t* mtop,
const t_commrec* cr,
matrix box,
/* The CMake default turns SIMD kernels on, but it might be turned off further down... */
fr->use_simd_kernels = GMX_USE_SIMD_KERNELS;
- if (check_box(ir->pbcType, box))
+ if (check_box(ir.pbcType, box))
{
- gmx_fatal(FARGS, "%s", check_box(ir->pbcType, box));
+ gmx_fatal(FARGS, "%s", check_box(ir.pbcType, box));
}
/* Test particle insertion ? */
- if (EI_TPI(ir->eI))
+ if (EI_TPI(ir.eI))
{
/* Set to the size of the molecule to be inserted (the last one) */
gmx::RangePartitioning molecules = gmx_mtop_molecules(*mtop);
fr->n_tpi = 0;
}
- if (ir->coulombtype == eelRF_NEC_UNSUPPORTED || ir->coulombtype == eelGRF_NOTUSED)
+ 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)
+ if (ir.bAdress)
{
gmx_fatal(FARGS, "AdResS simulations are no longer supported");
}
- if (ir->useTwinRange)
+ if (ir.useTwinRange)
{
gmx_fatal(FARGS, "Twin-range simulations are no longer supported");
}
/* Copy the user determined parameters */
- fr->userint1 = ir->userint1;
- fr->userint2 = ir->userint2;
- fr->userint3 = ir->userint3;
- fr->userint4 = ir->userint4;
- fr->userreal1 = ir->userreal1;
- fr->userreal2 = ir->userreal2;
- fr->userreal3 = ir->userreal3;
- fr->userreal4 = ir->userreal4;
+ fr->userint1 = ir.userint1;
+ fr->userint2 = ir.userint2;
+ fr->userint3 = ir.userint3;
+ fr->userint4 = ir.userint4;
+ fr->userreal1 = ir.userreal1;
+ fr->userreal2 = ir.userreal2;
+ fr->userreal3 = ir.userreal3;
+ fr->userreal4 = ir.userreal4;
/* Shell stuff */
- fr->fc_stepsize = ir->fc_stepsize;
+ fr->fc_stepsize = ir.fc_stepsize;
/* Free energy */
- fr->efep = ir->efep;
+ fr->efep = ir.efep;
if ((getenv("GMX_DISABLE_SIMD_KERNELS") != nullptr) || (getenv("GMX_NOOPTIMIZEDKERNELS") != nullptr))
{
fr->bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
/* Neighbour searching stuff */
- fr->pbcType = ir->pbcType;
+ fr->pbcType = ir.pbcType;
/* Determine if we will do PBC for distances in bonded interactions */
if (fr->pbcType == PbcType::No)
}
else
{
- const bool useEwaldSurfaceCorrection =
- (EEL_PME_EWALD(ir->coulombtype) && ir->epsilon_surface != 0);
+ const bool useEwaldSurfaceCorrection = (EEL_PME_EWALD(ir.coulombtype) && ir.epsilon_surface != 0);
const bool haveOrientationRestraints = (gmx_mtop_ftype_count(mtop, F_ORIRES) > 0);
if (!DOMAINDECOMP(cr))
{
if (useEwaldSurfaceCorrection || haveOrientationRestraints)
{
fr->wholeMoleculeTransform =
- std::make_unique<gmx::WholeMoleculeTransform>(*mtop, ir->pbcType);
+ std::make_unique<gmx::WholeMoleculeTransform>(*mtop, ir.pbcType);
}
}
else
}
}
- 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->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;
/* 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, fr->rlist, ir->tabext);
+ init_interaction_const_tables(fp, fr->ic, fr->rlist, ir.tabext);
const interaction_const_t* ic = fr->ic;
/* TODO: Replace this Ewald table or move it into interaction_const_t */
- if (ir->coulombtype == eelEWALD)
+ if (ir.coulombtype == eelEWALD)
{
init_ewald_tab(&(fr->ewald_table), ir, fp);
}
*/
if (EEL_USER(fr->ic->eeltype))
{
- gmx_fatal(FARGS, "Electrostatics type %s is currently not supported", eel_names[ir->coulombtype]);
+ gmx_fatal(FARGS, "Electrostatics type %s is currently not supported", eel_names[ir.coulombtype]);
}
fr->bvdwtab = FALSE;
fr->fudgeQQ = mtop->ffparams.fudgeQQ;
// Multiple time stepping
- fr->useMts = ir->useMts;
+ fr->useMts = ir.useMts;
if (fr->useMts)
{
- GMX_ASSERT(gmx::checkMtsRequirements(*ir).empty(),
- "All MTS requirements should be met here");
+ GMX_ASSERT(gmx::checkMtsRequirements(ir).empty(), "All MTS requirements should be met here");
}
- const bool haveDirectVirialContributionsFast =
- 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;
+ const bool haveDirectVirialContributionsFast = 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;
const bool haveDirectVirialContributionsSlow = EEL_FULL(ic->eeltype) || EVDW_PME(ic->vdwtype);
for (int i = 0; i < (fr->useMts ? 2 : 1); i++)
{
}
/* Copy the energy group exclusions */
- fr->egp_flags = ir->opts.egp_flags;
+ fr->egp_flags = ir.opts.egp_flags;
/* Van der Waals stuff */
if ((ic->vdwtype != evdwCUT) && (ic->vdwtype != evdwUSER) && !fr->bBHAM)
gmx_fatal(FARGS, "The Verlet cutoff-scheme does not (yet) support Buckingham");
}
- if (ir->implicit_solvent)
+ if (ir.implicit_solvent)
{
gmx_fatal(FARGS, "Implict solvation is no longer supported.");
}
* in that case grompp should already have checked that we do not need
* normal tables and we only generate tables for 1-4 interactions.
*/
- real rtab = ir->rlist + ir->tabext;
+ real rtab = ir.rlist + ir.tabext;
/* We want to use unmodified tables for 1-4 coulombic
* interactions, so we must in general have an extra set of
}
/* Wall stuff */
- fr->nwall = ir->nwall;
- if (ir->nwall && ir->wall_type == ewtTABLE)
+ fr->nwall = ir.nwall;
+ if (ir.nwall && ir.wall_type == ewtTABLE)
{
make_wall_tables(fp, ir, tabfn, &mtop->groups, fr);
}
{
// Add one ListedForces object for each MTS level
bool isFirstLevel = true;
- for (const auto& mtsLevel : ir->mtsLevels)
+ for (const auto& mtsLevel : ir.mtsLevels)
{
ListedForces::InteractionSelection interactionSelection;
const auto& forceGroups = mtsLevel.forceGroups;
}
// QM/MM initialization if requested
- if (ir->bQMMM)
+ if (ir.bQMMM)
{
gmx_incons("QM/MM was requested, but is no longer available in GROMACS");
}
fr->nthread_ewc = gmx_omp_nthreads_get(emntBonded);
snew(fr->ewc_t, fr->nthread_ewc);
- if (ir->eDispCorr != edispcNO)
+ if (ir.eDispCorr != edispcNO)
{
fr->dispersionCorrection = std::make_unique<DispersionCorrection>(
- *mtop, *ir, fr->bBHAM, fr->ntype, fr->nbfp, *fr->ic, tabfn);
+ *mtop, ir, fr->bBHAM, fr->ntype, fr->nbfp, *fr->ic, tabfn);
fr->dispersionCorrection->print(mdlog);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff