*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013-2020, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017, The GROMACS development team.
+ * Copyright (c) 2018,2019,2020,2021, 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 <cstdlib>
#include <algorithm>
+#include <memory>
#include <string>
-#include "gromacs/awh/read_params.h"
+#include "gromacs/applied_forces/awh/read_params.h"
#include "gromacs/fileio/readinp.h"
#include "gromacs/fileio/warninp.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/mdrun/mdmodules.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
+#include "gromacs/mdtypes/multipletimestepping.h"
#include "gromacs/mdtypes/pull_params.h"
#include "gromacs/options/options.h"
#include "gromacs/options/treesupport.h"
* message.
*/
-typedef struct t_inputrec_strings
+struct gmx_inputrec_strings
{
char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN], acc[STRLEN], accgrps[STRLEN], freeze[STRLEN],
frdim[STRLEN], energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN],
x_compressed_groups[STRLEN], couple_moltype[STRLEN], orirefitgrp[STRLEN],
egptable[STRLEN], egpexcl[STRLEN], wall_atomtype[STRLEN], wall_density[STRLEN],
deform[STRLEN], QMMM[STRLEN], imd_grp[STRLEN];
- char fep_lambda[efptNR][STRLEN];
- char lambda_weights[STRLEN];
- char** pull_grp;
- char** rot_grp;
- char anneal[STRLEN], anneal_npoints[STRLEN], anneal_time[STRLEN], anneal_temp[STRLEN];
- char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN], bSH[STRLEN],
- CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN], SAoff[STRLEN], SAsteps[STRLEN];
-
-} gmx_inputrec_strings;
+ char fep_lambda[efptNR][STRLEN];
+ char lambda_weights[STRLEN];
+ std::vector<std::string> pullGroupNames;
+ std::vector<std::string> rotateGroupNames;
+ char anneal[STRLEN], anneal_npoints[STRLEN], anneal_time[STRLEN], anneal_temp[STRLEN];
+};
-static gmx_inputrec_strings* is = nullptr;
+static gmx_inputrec_strings* inputrecStrings = nullptr;
void init_inputrec_strings()
{
- if (is)
+ if (inputrecStrings)
{
gmx_incons(
"Attempted to call init_inputrec_strings before calling done_inputrec_strings. "
"Only one inputrec (i.e. .mdp file) can be parsed at a time.");
}
- snew(is, 1);
+ inputrecStrings = new gmx_inputrec_strings();
}
void done_inputrec_strings()
{
- sfree(is);
- is = nullptr;
+ delete inputrecStrings;
+ inputrecStrings = nullptr;
}
}
}
+static void checkMtsRequirement(const t_inputrec& ir, const char* param, const int nstValue, warninp_t wi)
+{
+ GMX_RELEASE_ASSERT(ir.mtsLevels.size() >= 2, "Need at least two levels for MTS");
+ const int mtsFactor = ir.mtsLevels.back().stepFactor;
+ if (nstValue % mtsFactor != 0)
+ {
+ auto message = gmx::formatString(
+ "With MTS, %s = %d should be a multiple of mts-factor = %d", param, nstValue, mtsFactor);
+ warning_error(wi, message.c_str());
+ }
+}
+
+static void setupMtsLevels(gmx::ArrayRef<gmx::MtsLevel> mtsLevels,
+ const t_inputrec& ir,
+ const t_gromppopts& opts,
+ warninp_t wi)
+{
+ /* MD-VV has no MTS support yet.
+ * SD1 needs different scaling coefficients for the different MTS forces
+ * and the different forces are currently not available in ForceBuffers.
+ */
+ if (ir.eI != eiMD)
+ {
+ auto message = gmx::formatString(
+ "Multiple time stepping is only supported with integrator %s", ei_names[eiMD]);
+ warning_error(wi, message.c_str());
+ }
+ if (opts.numMtsLevels != 2)
+ {
+ warning_error(wi, "Only mts-levels = 2 is supported");
+ }
+ else
+ {
+ const std::vector<std::string> inputForceGroups = gmx::splitString(opts.mtsLevel2Forces);
+ auto& forceGroups = mtsLevels[1].forceGroups;
+ for (const auto& inputForceGroup : inputForceGroups)
+ {
+ bool found = false;
+ int nameIndex = 0;
+ for (const auto& forceGroupName : gmx::mtsForceGroupNames)
+ {
+ if (gmx::equalCaseInsensitive(inputForceGroup, forceGroupName))
+ {
+ forceGroups.set(nameIndex);
+ found = true;
+ }
+ nameIndex++;
+ }
+ if (!found)
+ {
+ auto message =
+ gmx::formatString("Unknown MTS force group '%s'", inputForceGroup.c_str());
+ warning_error(wi, message.c_str());
+ }
+ }
+
+ if (mtsLevels[1].stepFactor <= 1)
+ {
+ gmx_fatal(FARGS, "mts-factor should be larger than 1");
+ }
+
+ // Make the level 0 use the complement of the force groups of group 1
+ mtsLevels[0].forceGroups = ~mtsLevels[1].forceGroups;
+ mtsLevels[0].stepFactor = 1;
+
+ if ((EEL_FULL(ir.coulombtype) || EVDW_PME(ir.vdwtype))
+ && !mtsLevels[1].forceGroups[static_cast<int>(gmx::MtsForceGroups::LongrangeNonbonded)])
+ {
+ warning_error(wi,
+ "With long-range electrostatics and/or LJ treatment, the long-range part "
+ "has to be part of the mts-level2-forces");
+ }
+
+ if (ir.nstcalcenergy > 0)
+ {
+ checkMtsRequirement(ir, "nstcalcenergy", ir.nstcalcenergy, wi);
+ }
+ checkMtsRequirement(ir, "nstenergy", ir.nstenergy, wi);
+ checkMtsRequirement(ir, "nstlog", ir.nstlog, wi);
+ if (ir.efep != efepNO)
+ {
+ checkMtsRequirement(ir, "nstdhdl", ir.fepvals->nstdhdl, wi);
+ }
+
+ if (ir.bPull)
+ {
+ const int pullMtsLevel = gmx::forceGroupMtsLevel(ir.mtsLevels, gmx::MtsForceGroups::Pull);
+ if (ir.pull->nstxout % ir.mtsLevels[pullMtsLevel].stepFactor != 0)
+ {
+ warning_error(wi, "pull-nstxout should be a multiple of mts-factor");
+ }
+ if (ir.pull->nstfout % ir.mtsLevels[pullMtsLevel].stepFactor != 0)
+ {
+ warning_error(wi, "pull-nstfout should be a multiple of mts-factor");
+ }
+ }
+ }
+}
+
void check_ir(const char* mdparin,
const gmx::MdModulesNotifier& mdModulesNotifier,
t_inputrec* ir,
{
ir->nstpcouple = ir_optimal_nstpcouple(ir);
}
+ if (ir->useMts && ir->nstpcouple % ir->mtsLevels.back().stepFactor != 0)
+ {
+ warning_error(wi,
+ "With multiple time stepping, nstpcouple should be a mutiple of "
+ "mts-factor");
+ }
}
if (ir->nstcalcenergy > 0)
// Inquire all MdModules, if their parameters match with the energy
// calculation frequency
gmx::EnergyCalculationFrequencyErrors energyCalculationFrequencyErrors(ir->nstcalcenergy);
- mdModulesNotifier.notifier_.notify(&energyCalculationFrequencyErrors);
+ mdModulesNotifier.preProcessingNotifications_.notify(&energyCalculationFrequencyErrors);
// Emit all errors from the energy calculation frequency checks
for (const std::string& energyFrequencyErrorMessage :
/* TPI STUFF */
if (EI_TPI(ir->eI))
{
- sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
- CHECK(ir->ePBC != epbcXYZ);
+ sprintf(err_buf, "TPI only works with pbc = %s", c_pbcTypeNames[PbcType::Xyz].c_str());
+ CHECK(ir->pbcType != PbcType::Xyz);
sprintf(err_buf, "with TPI nstlist should be larger than zero");
CHECK(ir->nstlist <= 0);
sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2", fep->sc_power);
CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
- sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
+ sprintf(err_buf,
+ "The soft-core sc-r-power is %d and can only be 6. (sc-r-power 48 is no longer "
+ "supported.)",
static_cast<int>(fep->sc_r_power));
- CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
+ CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0);
sprintf(err_buf,
"Can't use positive delta-lambda (%g) if initial state/lambda does not start at "
}
/* PBC/WALLS */
- sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
- CHECK(ir->nwall && ir->ePBC != epbcXY);
+ sprintf(err_buf, "walls only work with pbc=%s", c_pbcTypeNames[PbcType::XY].c_str());
+ CHECK(ir->nwall && ir->pbcType != PbcType::XY);
/* VACUUM STUFF */
- if (ir->ePBC != epbcXYZ && ir->nwall != 2)
+ if (ir->pbcType != PbcType::Xyz && ir->nwall != 2)
{
- if (ir->ePBC == epbcNONE)
+ if (ir->pbcType == PbcType::No)
{
if (ir->epc != epcNO)
{
}
else
{
- sprintf(err_buf, "Can not have pressure coupling with pbc=%s", epbc_names[ir->ePBC]);
+ sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
+ c_pbcTypeNames[ir->pbcType].c_str());
CHECK(ir->epc != epcNO);
}
- sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
+ sprintf(err_buf, "Can not have Ewald with pbc=%s", c_pbcTypeNames[ir->pbcType].c_str());
CHECK(EEL_FULL(ir->coulombtype));
- sprintf(err_buf, "Can not have dispersion correction with pbc=%s", epbc_names[ir->ePBC]);
+ sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
+ c_pbcTypeNames[ir->pbcType].c_str());
CHECK(ir->eDispCorr != edispcNO);
}
"with coulombtype = %s or coulombtype = %s\n"
"without periodic boundary conditions (pbc = %s) and\n"
"rcoulomb and rvdw set to zero",
- eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
+ eel_names[eelCUT], eel_names[eelUSER], c_pbcTypeNames[PbcType::No].c_str());
CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER))
- || (ir->ePBC != epbcNONE) || (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
+ || (ir->pbcType != PbcType::No) || (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
if (ir->nstlist > 0)
{
"Can not remove the rotation around the center of mass with periodic "
"molecules");
CHECK(ir->bPeriodicMols);
- if (ir->ePBC != epbcNONE)
+ if (ir->pbcType != PbcType::No)
{
warning(wi,
"Removing the rotation around the center of mass in a periodic system, "
}
}
- if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
+ if (EI_STATE_VELOCITY(ir->eI) && !EI_SD(ir->eI) && ir->pbcType == PbcType::No && ir->comm_mode != ecmANGULAR)
{
sprintf(warn_buf,
"Tumbling and flying ice-cubes: We are not removing rotation around center of mass "
{
if (ir->ewald_geometry == eewg3D)
{
- sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s", epbc_names[ir->ePBC],
- eewg_names[eewg3DC]);
+ sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
+ c_pbcTypeNames[ir->pbcType].c_str(), eewg_names[eewg3DC]);
warning(wi, warn_buf);
}
/* This check avoids extra pbc coding for exclusion corrections */
sprintf(err_buf, "wall-ewald-zfac should be >= 2");
CHECK(ir->wall_ewald_zfac < 2);
}
- if ((ir->ewald_geometry == eewg3DC) && (ir->ePBC != epbcXY) && EEL_FULL(ir->coulombtype))
+ if ((ir->ewald_geometry == eewg3DC) && (ir->pbcType != PbcType::XY) && EEL_FULL(ir->coulombtype))
{
sprintf(warn_buf, "With %s and ewald_geometry = %s you should use pbc = %s",
- eel_names[ir->coulombtype], eewg_names[eewg3DC], epbc_names[epbcXY]);
+ eel_names[ir->coulombtype], eewg_names[eewg3DC], c_pbcTypeNames[PbcType::XY].c_str());
warning(wi, warn_buf);
}
if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
if (ir->bQMMM)
{
- warning_error(wi, "QMMM is currently not supported");
- if (!EI_DYNAMICS(ir->eI))
- {
- char buf[STRLEN];
- sprintf(buf, "QMMM is only supported with dynamics, not with integrator %s", ei_names[ir->eI]);
- warning_error(wi, buf);
- }
+ warning_error(wi, "The QMMM integration you are trying to use is no longer supported");
}
if (ir->bAdress)
}
- /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
- if (fep->sc_r_power == 48)
- {
- if (fep->sc_alpha > 0.1)
- {
- gmx_fatal(FARGS,
- "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004",
- fep->sc_alpha);
- }
- }
-
/* now read in the weights */
parse_n_real(weights, &nweights, &(expand->init_lambda_weights), wi);
if (nweights == 0)
GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
}
-static void convertYesNos(warninp_t /*wi*/,
- gmx::ArrayRef<const std::string> inputs,
- const char* /*name*/,
- gmx_bool* outputs)
-{
- int i = 0;
- for (const auto& input : inputs)
- {
- outputs[i] = gmx::equalCaseInsensitive(input, "Y", 1);
- ++i;
- }
-}
-
template<typename T>
void convertInts(warninp_t wi, gmx::ArrayRef<const std::string> inputs, const char* name, T* outputs)
{
gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %zu", ir->nwall,
wallAtomTypes.size());
}
+ GMX_RELEASE_ASSERT(ir->nwall < 3, "Invalid number of walls");
for (int i = 0; i < ir->nwall; i++)
{
opts->wall_atomtype[i] = gmx_strdup(wallAtomTypes[i].c_str());
printStringNoNewline(
&inp, "Part index is updated automatically on checkpointing (keeps files separate)");
ir->simulation_part = get_eint(&inp, "simulation-part", 1, wi);
+ printStringNoNewline(&inp, "Multiple time-stepping");
+ ir->useMts = (get_eeenum(&inp, "mts", yesno_names, wi) != 0);
+ if (ir->useMts)
+ {
+ opts->numMtsLevels = get_eint(&inp, "mts-levels", 2, wi);
+ ir->mtsLevels.resize(2);
+ gmx::MtsLevel& mtsLevel = ir->mtsLevels[1];
+ opts->mtsLevel2Forces = setStringEntry(&inp, "mts-level2-forces",
+ "longrange-nonbonded nonbonded pair dihedral");
+ mtsLevel.stepFactor = get_eint(&inp, "mts-level2-factor", 2, wi);
+
+ // We clear after reading without dynamics to not force the user to remove MTS mdp options
+ if (!EI_DYNAMICS(ir->eI))
+ {
+ ir->useMts = false;
+ ir->mtsLevels.clear();
+ }
+ }
printStringNoNewline(&inp, "mode for center of mass motion removal");
ir->comm_mode = get_eeenum(&inp, "comm-mode", ecm_names, wi);
printStringNoNewline(&inp, "number of steps for center of mass motion removal");
ir->nstcomm = get_eint(&inp, "nstcomm", 100, wi);
printStringNoNewline(&inp, "group(s) for center of mass motion removal");
- setStringEntry(&inp, "comm-grps", is->vcm, nullptr);
+ setStringEntry(&inp, "comm-grps", inputrecStrings->vcm, nullptr);
printStringNewline(&inp, "LANGEVIN DYNAMICS OPTIONS");
printStringNoNewline(&inp, "Friction coefficient (amu/ps) and random seed");
printStringNoNewline(&inp, "This selects the subset of atoms for the compressed");
printStringNoNewline(&inp, "trajectory file. You can select multiple groups. By");
printStringNoNewline(&inp, "default, all atoms will be written.");
- setStringEntry(&inp, "compressed-x-grps", is->x_compressed_groups, nullptr);
+ setStringEntry(&inp, "compressed-x-grps", inputrecStrings->x_compressed_groups, nullptr);
printStringNoNewline(&inp, "Selection of energy groups");
- setStringEntry(&inp, "energygrps", is->energy, nullptr);
+ setStringEntry(&inp, "energygrps", inputrecStrings->energy, nullptr);
/* Neighbor searching */
printStringNewline(&inp, "NEIGHBORSEARCHING PARAMETERS");
printStringNoNewline(&inp, "nblist update frequency");
ir->nstlist = get_eint(&inp, "nstlist", 10, wi);
printStringNoNewline(&inp, "Periodic boundary conditions: xyz, no, xy");
- ir->ePBC = get_eeenum(&inp, "pbc", epbc_names, wi);
+ // TODO This conversion should be removed when proper std:string handling will be added to get_eeenum(...), etc.
+ std::vector<const char*> pbcTypesNamesChar;
+ for (const auto& pbcTypeName : c_pbcTypeNames)
+ {
+ pbcTypesNamesChar.push_back(pbcTypeName.c_str());
+ }
+ ir->pbcType = static_cast<PbcType>(get_eeenum(&inp, "pbc", pbcTypesNamesChar.data(), wi));
ir->bPeriodicMols = get_eeenum(&inp, "periodic-molecules", yesno_names, wi) != 0;
printStringNoNewline(&inp,
"Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
printStringNoNewline(&inp, "Extension of the potential lookup tables beyond the cut-off");
ir->tabext = get_ereal(&inp, "table-extension", 1.0, wi);
printStringNoNewline(&inp, "Separate tables between energy group pairs");
- setStringEntry(&inp, "energygrp-table", is->egptable, nullptr);
+ setStringEntry(&inp, "energygrp-table", inputrecStrings->egptable, nullptr);
printStringNoNewline(&inp, "Spacing for the PME/PPPM FFT grid");
ir->fourier_spacing = get_ereal(&inp, "fourierspacing", 0.12, wi);
printStringNoNewline(&inp, "FFT grid size, when a value is 0 fourierspacing will be used");
ir->opts.nhchainlength = get_eint(&inp, "nh-chain-length", 10, wi);
ir->bPrintNHChains = (get_eeenum(&inp, "print-nose-hoover-chain-variables", yesno_names, wi) != 0);
printStringNoNewline(&inp, "Groups to couple separately");
- setStringEntry(&inp, "tc-grps", is->tcgrps, nullptr);
+ setStringEntry(&inp, "tc-grps", inputrecStrings->tcgrps, nullptr);
printStringNoNewline(&inp, "Time constant (ps) and reference temperature (K)");
- setStringEntry(&inp, "tau-t", is->tau_t, nullptr);
- setStringEntry(&inp, "ref-t", is->ref_t, nullptr);
+ setStringEntry(&inp, "tau-t", inputrecStrings->tau_t, nullptr);
+ setStringEntry(&inp, "ref-t", inputrecStrings->ref_t, nullptr);
printStringNoNewline(&inp, "pressure coupling");
ir->epc = get_eeenum(&inp, "pcoupl", epcoupl_names, wi);
ir->epct = get_eeenum(&inp, "pcoupltype", epcoupltype_names, wi);
/* QMMM */
printStringNewline(&inp, "OPTIONS FOR QMMM calculations");
ir->bQMMM = (get_eeenum(&inp, "QMMM", yesno_names, wi) != 0);
- printStringNoNewline(&inp, "Groups treated Quantum Mechanically");
- setStringEntry(&inp, "QMMM-grps", is->QMMM, nullptr);
- printStringNoNewline(&inp, "QM method");
- setStringEntry(&inp, "QMmethod", is->QMmethod, nullptr);
- printStringNoNewline(&inp, "QMMM scheme");
- ir->QMMMscheme = get_eeenum(&inp, "QMMMscheme", eQMMMscheme_names, wi);
- printStringNoNewline(&inp, "QM basisset");
- setStringEntry(&inp, "QMbasis", is->QMbasis, nullptr);
- printStringNoNewline(&inp, "QM charge");
- setStringEntry(&inp, "QMcharge", is->QMcharge, nullptr);
- printStringNoNewline(&inp, "QM multiplicity");
- setStringEntry(&inp, "QMmult", is->QMmult, nullptr);
- printStringNoNewline(&inp, "Surface Hopping");
- setStringEntry(&inp, "SH", is->bSH, nullptr);
- printStringNoNewline(&inp, "CAS space options");
- setStringEntry(&inp, "CASorbitals", is->CASorbitals, nullptr);
- setStringEntry(&inp, "CASelectrons", is->CASelectrons, nullptr);
- setStringEntry(&inp, "SAon", is->SAon, nullptr);
- setStringEntry(&inp, "SAoff", is->SAoff, nullptr);
- setStringEntry(&inp, "SAsteps", is->SAsteps, nullptr);
- printStringNoNewline(&inp, "Scale factor for MM charges");
- ir->scalefactor = get_ereal(&inp, "MMChargeScaleFactor", 1.0, wi);
+ printStringNoNewline(&inp, "Groups treated with MiMiC");
+ setStringEntry(&inp, "QMMM-grps", inputrecStrings->QMMM, nullptr);
/* Simulated annealing */
printStringNewline(&inp, "SIMULATED ANNEALING");
printStringNoNewline(&inp, "Type of annealing for each temperature group (no/single/periodic)");
- setStringEntry(&inp, "annealing", is->anneal, nullptr);
+ setStringEntry(&inp, "annealing", inputrecStrings->anneal, nullptr);
printStringNoNewline(&inp,
"Number of time points to use for specifying annealing in each group");
- setStringEntry(&inp, "annealing-npoints", is->anneal_npoints, nullptr);
+ setStringEntry(&inp, "annealing-npoints", inputrecStrings->anneal_npoints, nullptr);
printStringNoNewline(&inp, "List of times at the annealing points for each group");
- setStringEntry(&inp, "annealing-time", is->anneal_time, nullptr);
+ setStringEntry(&inp, "annealing-time", inputrecStrings->anneal_time, nullptr);
printStringNoNewline(&inp, "Temp. at each annealing point, for each group.");
- setStringEntry(&inp, "annealing-temp", is->anneal_temp, nullptr);
+ setStringEntry(&inp, "annealing-temp", inputrecStrings->anneal_temp, nullptr);
/* Startup run */
printStringNewline(&inp, "GENERATE VELOCITIES FOR STARTUP RUN");
printStringNewline(&inp, "ENERGY GROUP EXCLUSIONS");
printStringNoNewline(
&inp, "Pairs of energy groups for which all non-bonded interactions are excluded");
- setStringEntry(&inp, "energygrp-excl", is->egpexcl, nullptr);
+ setStringEntry(&inp, "energygrp-excl", inputrecStrings->egpexcl, nullptr);
/* Walls */
printStringNewline(&inp, "WALLS");
ir->nwall = get_eint(&inp, "nwall", 0, wi);
ir->wall_type = get_eeenum(&inp, "wall-type", ewt_names, wi);
ir->wall_r_linpot = get_ereal(&inp, "wall-r-linpot", -1, wi);
- setStringEntry(&inp, "wall-atomtype", is->wall_atomtype, nullptr);
- setStringEntry(&inp, "wall-density", is->wall_density, nullptr);
+ setStringEntry(&inp, "wall-atomtype", inputrecStrings->wall_atomtype, nullptr);
+ setStringEntry(&inp, "wall-density", inputrecStrings->wall_density, nullptr);
ir->wall_ewald_zfac = get_ereal(&inp, "wall-ewald-zfac", 3, wi);
/* COM pulling */
ir->bPull = (get_eeenum(&inp, "pull", yesno_names, wi) != 0);
if (ir->bPull)
{
- snew(ir->pull, 1);
- is->pull_grp = read_pullparams(&inp, ir->pull, wi);
+ ir->pull = std::make_unique<pull_params_t>();
+ inputrecStrings->pullGroupNames = read_pullparams(&inp, ir->pull.get(), wi);
+
+ if (ir->useMts)
+ {
+ for (int c = 0; c < ir->pull->ncoord; c++)
+ {
+ if (ir->pull->coord[c].eType == epullCONSTRAINT)
+ {
+ warning_error(wi,
+ "Constraint COM pulling is not supported in combination with "
+ "multiple time stepping");
+ break;
+ }
+ }
+ }
}
/* AWH biasing
- NOTE: needs COM pulling input */
+ NOTE: needs COM pulling or free energy input */
printStringNewline(&inp, "AWH biasing");
ir->bDoAwh = (get_eeenum(&inp, "awh", yesno_names, wi) != 0);
if (ir->bDoAwh)
{
- if (ir->bPull)
- {
- ir->awhParams = gmx::readAndCheckAwhParams(&inp, ir, wi);
- }
- else
- {
- gmx_fatal(FARGS, "AWH biasing is only compatible with COM pulling turned on");
- }
+ ir->awhParams = gmx::readAwhParams(&inp, wi);
}
/* Enforced rotation */
if (ir->bRot)
{
snew(ir->rot, 1);
- is->rot_grp = read_rotparams(&inp, ir->rot, wi);
+ inputrecStrings->rotateGroupNames = read_rotparams(&inp, ir->rot, wi);
}
/* Interactive MD */
ir->bIMD = FALSE;
printStringNewline(&inp, "Group to display and/or manipulate in interactive MD session");
- setStringEntry(&inp, "IMD-group", is->imd_grp, nullptr);
- if (is->imd_grp[0] != '\0')
+ setStringEntry(&inp, "IMD-group", inputrecStrings->imd_grp, nullptr);
+ if (inputrecStrings->imd_grp[0] != '\0')
{
snew(ir->imd, 1);
ir->bIMD = TRUE;
printStringNoNewline(&inp, "Orientation restraints force constant and tau for time averaging");
ir->orires_fc = get_ereal(&inp, "orire-fc", 0.0, wi);
ir->orires_tau = get_ereal(&inp, "orire-tau", 0.0, wi);
- setStringEntry(&inp, "orire-fitgrp", is->orirefitgrp, nullptr);
+ setStringEntry(&inp, "orire-fitgrp", inputrecStrings->orirefitgrp, nullptr);
printStringNoNewline(&inp, "Output frequency for trace(SD) and S to energy file");
ir->nstorireout = get_eint(&inp, "nstorireout", 100, wi);
/* free energy variables */
printStringNewline(&inp, "Free energy variables");
ir->efep = get_eeenum(&inp, "free-energy", efep_names, wi);
- setStringEntry(&inp, "couple-moltype", is->couple_moltype, nullptr);
+ setStringEntry(&inp, "couple-moltype", inputrecStrings->couple_moltype, nullptr);
opts->couple_lam0 = get_eeenum(&inp, "couple-lambda0", couple_lam, wi);
opts->couple_lam1 = get_eeenum(&inp, "couple-lambda1", couple_lam, wi);
opts->bCoupleIntra = (get_eeenum(&inp, "couple-intramol", yesno_names, wi) != 0);
fep->init_fep_state = get_eint(&inp, "init-lambda-state", -1, wi);
fep->delta_lambda = get_ereal(&inp, "delta-lambda", 0.0, wi);
fep->nstdhdl = get_eint(&inp, "nstdhdl", 50, wi);
- setStringEntry(&inp, "fep-lambdas", is->fep_lambda[efptFEP], nullptr);
- setStringEntry(&inp, "mass-lambdas", is->fep_lambda[efptMASS], nullptr);
- setStringEntry(&inp, "coul-lambdas", is->fep_lambda[efptCOUL], nullptr);
- setStringEntry(&inp, "vdw-lambdas", is->fep_lambda[efptVDW], nullptr);
- setStringEntry(&inp, "bonded-lambdas", is->fep_lambda[efptBONDED], nullptr);
- setStringEntry(&inp, "restraint-lambdas", is->fep_lambda[efptRESTRAINT], nullptr);
- setStringEntry(&inp, "temperature-lambdas", is->fep_lambda[efptTEMPERATURE], nullptr);
+ setStringEntry(&inp, "fep-lambdas", inputrecStrings->fep_lambda[efptFEP], nullptr);
+ setStringEntry(&inp, "mass-lambdas", inputrecStrings->fep_lambda[efptMASS], nullptr);
+ setStringEntry(&inp, "coul-lambdas", inputrecStrings->fep_lambda[efptCOUL], nullptr);
+ setStringEntry(&inp, "vdw-lambdas", inputrecStrings->fep_lambda[efptVDW], nullptr);
+ setStringEntry(&inp, "bonded-lambdas", inputrecStrings->fep_lambda[efptBONDED], nullptr);
+ setStringEntry(&inp, "restraint-lambdas", inputrecStrings->fep_lambda[efptRESTRAINT], nullptr);
+ setStringEntry(&inp, "temperature-lambdas", inputrecStrings->fep_lambda[efptTEMPERATURE], nullptr);
fep->lambda_neighbors = get_eint(&inp, "calc-lambda-neighbors", 1, wi);
- setStringEntry(&inp, "init-lambda-weights", is->lambda_weights, nullptr);
+ setStringEntry(&inp, "init-lambda-weights", inputrecStrings->lambda_weights, nullptr);
fep->edHdLPrintEnergy = get_eeenum(&inp, "dhdl-print-energy", edHdLPrintEnergy_names, wi);
fep->sc_alpha = get_ereal(&inp, "sc-alpha", 0.0, wi);
fep->sc_power = get_eint(&inp, "sc-power", 1, wi);
/* Non-equilibrium MD stuff */
printStringNewline(&inp, "Non-equilibrium MD stuff");
- setStringEntry(&inp, "acc-grps", is->accgrps, nullptr);
- setStringEntry(&inp, "accelerate", is->acc, nullptr);
- setStringEntry(&inp, "freezegrps", is->freeze, nullptr);
- setStringEntry(&inp, "freezedim", is->frdim, nullptr);
+ setStringEntry(&inp, "acc-grps", inputrecStrings->accgrps, nullptr);
+ setStringEntry(&inp, "accelerate", inputrecStrings->acc, nullptr);
+ setStringEntry(&inp, "freezegrps", inputrecStrings->freeze, nullptr);
+ setStringEntry(&inp, "freezedim", inputrecStrings->frdim, nullptr);
ir->cos_accel = get_ereal(&inp, "cos-acceleration", 0, wi);
- setStringEntry(&inp, "deform", is->deform, nullptr);
+ setStringEntry(&inp, "deform", inputrecStrings->deform, nullptr);
/* simulated tempering variables */
printStringNewline(&inp, "simulated tempering variables");
/* User defined thingies */
printStringNewline(&inp, "User defined thingies");
- setStringEntry(&inp, "user1-grps", is->user1, nullptr);
- setStringEntry(&inp, "user2-grps", is->user2, nullptr);
+ setStringEntry(&inp, "user1-grps", inputrecStrings->user1, nullptr);
+ setStringEntry(&inp, "user2-grps", inputrecStrings->user2, nullptr);
ir->userint1 = get_eint(&inp, "userint1", 0, wi);
ir->userint2 = get_eint(&inp, "userint2", 0, wi);
ir->userint3 = get_eint(&inp, "userint3", 0, wi);
}
opts->couple_moltype = nullptr;
- if (strlen(is->couple_moltype) > 0)
+ if (strlen(inputrecStrings->couple_moltype) > 0)
{
if (ir->efep != efepNO)
{
- opts->couple_moltype = gmx_strdup(is->couple_moltype);
+ opts->couple_moltype = gmx_strdup(inputrecStrings->couple_moltype);
if (opts->couple_lam0 == opts->couple_lam1)
{
warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
/* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
if (ir->efep != efepNO)
{
- if (fep->delta_lambda > 0)
+ if (fep->delta_lambda != 0)
{
ir->efep = efepSLOWGROWTH;
}
{
ir->bExpanded = TRUE;
}
- do_fep_params(ir, is->fep_lambda, is->lambda_weights, wi);
+ do_fep_params(ir, inputrecStrings->fep_lambda, inputrecStrings->lambda_weights, wi);
if (ir->bSimTemp) /* done after fep params */
{
do_simtemp_params(ir);
/* WALL PARAMETERS */
- do_wall_params(ir, is->wall_atomtype, is->wall_density, opts, wi);
+ do_wall_params(ir, inputrecStrings->wall_atomtype, inputrecStrings->wall_density, opts, wi);
/* ORIENTATION RESTRAINT PARAMETERS */
- if (opts->bOrire && gmx::splitString(is->orirefitgrp).size() != 1)
+ if (opts->bOrire && gmx::splitString(inputrecStrings->orirefitgrp).size() != 1)
{
warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
}
}
double gmx_unused canary;
- int ndeform = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf %lf", &(dumdub[0][0]), &(dumdub[0][1]),
- &(dumdub[0][2]), &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]), &canary);
+ int ndeform = sscanf(inputrecStrings->deform, "%lf %lf %lf %lf %lf %lf %lf", &(dumdub[0][0]),
+ &(dumdub[0][1]), &(dumdub[0][2]), &(dumdub[0][3]), &(dumdub[0][4]),
+ &(dumdub[0][5]), &canary);
- if (strlen(is->deform) > 0 && ndeform != 6)
+ if (strlen(inputrecStrings->deform) > 0 && ndeform != 6)
{
- warning_error(
- wi, gmx::formatString(
- "Cannot parse exactly 6 box deformation velocities from string '%s'", is->deform)
- .c_str());
+ warning_error(wi,
+ gmx::formatString(
+ "Cannot parse exactly 6 box deformation velocities from string '%s'",
+ inputrecStrings->deform)
+ .c_str());
}
for (i = 0; i < 3; i++)
{
}
}
- sfree(dumstr[0]);
- sfree(dumstr[1]);
-}
-
-static int search_QMstring(const char* s, int ng, const char* gn[])
-{
- /* same as normal search_string, but this one searches QM strings */
- int i;
+ /* Set up MTS levels, this needs to happen before checking AWH parameters */
+ if (ir->useMts)
+ {
+ setupMtsLevels(ir->mtsLevels, *ir, *opts, wi);
+ }
- for (i = 0; (i < ng); i++)
+ if (ir->bDoAwh)
{
- if (gmx_strcasecmp(s, gn[i]) == 0)
- {
- return i;
- }
+ gmx::checkAwhParams(ir->awhParams, ir, wi);
}
- gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
-} /* search_QMstring */
+ sfree(dumstr[0]);
+ sfree(dumstr[1]);
+}
/* We would like gn to be const as well, but C doesn't allow this */
/* TODO this is utility functionality (search for the index of a
* belong to different TC or VCM groups it is anyhow difficult
* to determine the optimal nrdf assignment.
*/
- pull = ir->pull;
+ pull = ir->pull.get();
for (int i = 0; i < pull->ncoord; i++)
{
pgrp = &pull->group[pull->coord[i].group[j]];
- if (pgrp->nat > 0)
+ if (!pgrp->ind.empty())
{
/* Subtract 1/2 dof from each group */
int ai = pgrp->ind[0];
set_warning_line(wi, mdparin, -1);
- auto temperatureCouplingTauValues = gmx::splitString(is->tau_t);
- auto temperatureCouplingReferenceValues = gmx::splitString(is->ref_t);
- auto temperatureCouplingGroupNames = gmx::splitString(is->tcgrps);
+ auto temperatureCouplingTauValues = gmx::splitString(inputrecStrings->tau_t);
+ auto temperatureCouplingReferenceValues = gmx::splitString(inputrecStrings->ref_t);
+ auto temperatureCouplingGroupNames = gmx::splitString(inputrecStrings->tcgrps);
if (temperatureCouplingTauValues.size() != temperatureCouplingGroupNames.size()
|| temperatureCouplingReferenceValues.size() != temperatureCouplingGroupNames.size())
{
}
/* Simulated annealing for each group. There are nr groups */
- auto simulatedAnnealingGroupNames = gmx::splitString(is->anneal);
+ auto simulatedAnnealingGroupNames = gmx::splitString(inputrecStrings->anneal);
if (simulatedAnnealingGroupNames.size() == 1
&& gmx::equalCaseInsensitive(simulatedAnnealingGroupNames[0], "N", 1))
{
if (bAnneal)
{
/* Read the other fields too */
- auto simulatedAnnealingPoints = gmx::splitString(is->anneal_npoints);
+ auto simulatedAnnealingPoints = gmx::splitString(inputrecStrings->anneal_npoints);
if (simulatedAnnealingPoints.size() != simulatedAnnealingGroupNames.size())
{
gmx_fatal(FARGS, "Found %zu annealing-npoints values for %zu groups\n",
numSimulatedAnnealingFields += ir->opts.anneal_npoints[i];
}
- auto simulatedAnnealingTimes = gmx::splitString(is->anneal_time);
+ auto simulatedAnnealingTimes = gmx::splitString(inputrecStrings->anneal_time);
if (simulatedAnnealingTimes.size() != numSimulatedAnnealingFields)
{
gmx_fatal(FARGS, "Found %zu annealing-time values, wanted %zu\n",
simulatedAnnealingTimes.size(), numSimulatedAnnealingFields);
}
- auto simulatedAnnealingTemperatures = gmx::splitString(is->anneal_temp);
+ auto simulatedAnnealingTemperatures = gmx::splitString(inputrecStrings->anneal_temp);
if (simulatedAnnealingTemperatures.size() != numSimulatedAnnealingFields)
{
gmx_fatal(FARGS, "Found %zu annealing-temp values, wanted %zu\n",
{
for (int i = 1; i < ir->pull->ngroup; i++)
{
- const int gid = search_string(is->pull_grp[i], defaultIndexGroups->nr, gnames);
+ const int gid = search_string(inputrecStrings->pullGroupNames[i].c_str(),
+ defaultIndexGroups->nr, gnames);
GMX_ASSERT(defaultIndexGroups, "Must have initialized default index groups");
atomGroupRangeValidation(natoms, gid, *defaultIndexGroups);
}
- make_pull_groups(ir->pull, is->pull_grp, defaultIndexGroups, gnames);
+ process_pull_groups(ir->pull->group, inputrecStrings->pullGroupNames, defaultIndexGroups, gnames);
- make_pull_coords(ir->pull);
+ checkPullCoords(ir->pull->group, ir->pull->coord);
}
if (ir->bRot)
{
- make_rotation_groups(ir->rot, is->rot_grp, defaultIndexGroups, gnames);
+ make_rotation_groups(ir->rot, inputrecStrings->rotateGroupNames, defaultIndexGroups, gnames);
}
if (ir->eSwapCoords != eswapNO)
/* Make indices for IMD session */
if (ir->bIMD)
{
- make_IMD_group(ir->imd, is->imd_grp, defaultIndexGroups, gnames);
+ make_IMD_group(ir->imd, inputrecStrings->imd_grp, defaultIndexGroups, gnames);
}
gmx::IndexGroupsAndNames defaultIndexGroupsAndNames(
*defaultIndexGroups, gmx::arrayRefFromArray(gnames, defaultIndexGroups->nr));
- notifier.notifier_.notify(defaultIndexGroupsAndNames);
+ notifier.preProcessingNotifications_.notify(defaultIndexGroupsAndNames);
- auto accelerations = gmx::splitString(is->acc);
- auto accelerationGroupNames = gmx::splitString(is->accgrps);
+ auto accelerations = gmx::splitString(inputrecStrings->acc);
+ auto accelerationGroupNames = gmx::splitString(inputrecStrings->accgrps);
if (accelerationGroupNames.size() * DIM != accelerations.size())
{
gmx_fatal(FARGS, "Invalid Acceleration input: %zu groups and %zu acc. values",
convertRvecs(wi, accelerations, "anneal-time", ir->opts.acc);
- auto freezeDims = gmx::splitString(is->frdim);
- auto freezeGroupNames = gmx::splitString(is->freeze);
+ auto freezeDims = gmx::splitString(inputrecStrings->frdim);
+ auto freezeGroupNames = gmx::splitString(inputrecStrings->freeze);
if (freezeDims.size() != DIM * freezeGroupNames.size())
{
gmx_fatal(FARGS, "Invalid Freezing input: %zu groups and %zu freeze values",
}
}
- auto energyGroupNames = gmx::splitString(is->energy);
+ auto energyGroupNames = gmx::splitString(inputrecStrings->energy);
do_numbering(natoms, groups, energyGroupNames, defaultIndexGroups, gnames,
SimulationAtomGroupType::EnergyOutput, restnm, egrptpALL_GENREST, bVerbose, wi);
add_wall_energrps(groups, ir->nwall, symtab);
ir->opts.ngener = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
- auto vcmGroupNames = gmx::splitString(is->vcm);
+ auto vcmGroupNames = gmx::splitString(inputrecStrings->vcm);
do_numbering(natoms, groups, vcmGroupNames, defaultIndexGroups, gnames,
SimulationAtomGroupType::MassCenterVelocityRemoval, restnm,
vcmGroupNames.empty() ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
/* Now we have filled the freeze struct, so we can calculate NRDF */
calc_nrdf(mtop, ir, gnames);
- auto user1GroupNames = gmx::splitString(is->user1);
+ auto user1GroupNames = gmx::splitString(inputrecStrings->user1);
do_numbering(natoms, groups, user1GroupNames, defaultIndexGroups, gnames,
SimulationAtomGroupType::User1, restnm, egrptpALL_GENREST, bVerbose, wi);
- auto user2GroupNames = gmx::splitString(is->user2);
+ auto user2GroupNames = gmx::splitString(inputrecStrings->user2);
do_numbering(natoms, groups, user2GroupNames, defaultIndexGroups, gnames,
SimulationAtomGroupType::User2, restnm, egrptpALL_GENREST, bVerbose, wi);
- auto compressedXGroupNames = gmx::splitString(is->x_compressed_groups);
+ auto compressedXGroupNames = gmx::splitString(inputrecStrings->x_compressed_groups);
do_numbering(natoms, groups, compressedXGroupNames, defaultIndexGroups, gnames,
SimulationAtomGroupType::CompressedPositionOutput, restnm, egrptpONE, bVerbose, wi);
- auto orirefFitGroupNames = gmx::splitString(is->orirefitgrp);
+ auto orirefFitGroupNames = gmx::splitString(inputrecStrings->orirefitgrp);
do_numbering(natoms, groups, orirefFitGroupNames, defaultIndexGroups, gnames,
SimulationAtomGroupType::OrientationRestraintsFit, restnm, egrptpALL_GENREST,
bVerbose, wi);
- /* QMMM input processing */
- auto qmGroupNames = gmx::splitString(is->QMMM);
- auto qmMethods = gmx::splitString(is->QMmethod);
- auto qmBasisSets = gmx::splitString(is->QMbasis);
- if (ir->eI != eiMimic)
- {
- if (qmMethods.size() != qmGroupNames.size() || qmBasisSets.size() != qmGroupNames.size())
- {
- gmx_fatal(FARGS,
- "Invalid QMMM input: %zu groups %zu basissets"
- " and %zu methods\n",
- qmGroupNames.size(), qmBasisSets.size(), qmMethods.size());
- }
- /* group rest, if any, is always MM! */
- do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
- SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
- nr = qmGroupNames.size(); /*atoms->grps[egcQMMM].nr;*/
- ir->opts.ngQM = qmGroupNames.size();
- snew(ir->opts.QMmethod, nr);
- snew(ir->opts.QMbasis, nr);
- for (i = 0; i < nr; i++)
- {
- /* input consists of strings: RHF CASSCF PM3 .. These need to be
- * converted to the corresponding enum in names.c
- */
- ir->opts.QMmethod[i] = search_QMstring(qmMethods[i].c_str(), eQMmethodNR, eQMmethod_names);
- ir->opts.QMbasis[i] = search_QMstring(qmBasisSets[i].c_str(), eQMbasisNR, eQMbasis_names);
- }
- auto qmMultiplicities = gmx::splitString(is->QMmult);
- auto qmCharges = gmx::splitString(is->QMcharge);
- auto qmbSH = gmx::splitString(is->bSH);
- snew(ir->opts.QMmult, nr);
- snew(ir->opts.QMcharge, nr);
- snew(ir->opts.bSH, nr);
- convertInts(wi, qmMultiplicities, "QMmult", ir->opts.QMmult);
- convertInts(wi, qmCharges, "QMcharge", ir->opts.QMcharge);
- convertYesNos(wi, qmbSH, "bSH", ir->opts.bSH);
-
- auto CASelectrons = gmx::splitString(is->CASelectrons);
- auto CASorbitals = gmx::splitString(is->CASorbitals);
- snew(ir->opts.CASelectrons, nr);
- snew(ir->opts.CASorbitals, nr);
- convertInts(wi, CASelectrons, "CASelectrons", ir->opts.CASelectrons);
- convertInts(wi, CASorbitals, "CASOrbitals", ir->opts.CASorbitals);
-
- auto SAon = gmx::splitString(is->SAon);
- auto SAoff = gmx::splitString(is->SAoff);
- auto SAsteps = gmx::splitString(is->SAsteps);
- snew(ir->opts.SAon, nr);
- snew(ir->opts.SAoff, nr);
- snew(ir->opts.SAsteps, nr);
- convertInts(wi, SAon, "SAon", ir->opts.SAon);
- convertInts(wi, SAoff, "SAoff", ir->opts.SAoff);
- convertInts(wi, SAsteps, "SAsteps", ir->opts.SAsteps);
- }
- else
+ /* MiMiC QMMM input processing */
+ auto qmGroupNames = gmx::splitString(inputrecStrings->QMMM);
+ if (qmGroupNames.size() > 1)
{
- /* MiMiC */
- if (qmGroupNames.size() > 1)
- {
- gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
- }
- /* group rest, if any, is always MM! */
- do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
- SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
-
- ir->opts.ngQM = qmGroupNames.size();
+ gmx_fatal(FARGS, "Currently, having more than one QM group in MiMiC is not supported");
}
+ /* group rest, if any, is always MM! */
+ do_numbering(natoms, groups, qmGroupNames, defaultIndexGroups, gnames,
+ SimulationAtomGroupType::QuantumMechanics, restnm, egrptpALL_GENREST, bVerbose, wi);
+ ir->opts.ngQM = qmGroupNames.size();
- /* end of QMMM input */
+ /* end of MiMiC QMMM input */
if (bVerbose)
{
nr = groups->groups[SimulationAtomGroupType::EnergyOutput].size();
snew(ir->opts.egp_flags, nr * nr);
- bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
+ bExcl = do_egp_flag(ir, groups, "energygrp-excl", inputrecStrings->egpexcl, EGP_EXCL);
if (bExcl && ir->cutoff_scheme == ecutsVERLET)
{
warning_error(wi, "Energy group exclusions are currently not supported");
warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
}
- bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
+ bTable = do_egp_flag(ir, groups, "energygrp-table", inputrecStrings->egptable, EGP_TABLE);
if (bTable && !(ir->vdwtype == evdwUSER) && !(ir->coulombtype == eelUSER)
&& !(ir->coulombtype == eelPMEUSER) && !(ir->coulombtype == eelPMEUSERSWITCH))
{
void triple_check(const char* mdparin, t_inputrec* ir, gmx_mtop_t* sys, warninp_t wi)
{
+ // Not meeting MTS requirements should have resulted in a fatal error, so we can assert here
+ gmx::assertMtsRequirements(*ir);
+
char err_buf[STRLEN];
int i, m, c, nmol;
bool bCharge, bAcc;
char warn_buf[STRLEN];
const char* ptr;
- ptr = check_box(ir->ePBC, box);
+ ptr = check_box(ir->pbcType, box);
if (ptr)
{
warning_error(wi, ptr);
ir->LincsWarnAngle = 90.0;
}
- if (ir->ePBC != epbcNONE)
+ if (ir->pbcType != PbcType::No)
{
if (ir->nstlist == 0)
{
"With nstlist=0 atoms are only put into the box at step 0, therefore drifting "
"atoms might cause the simulation to crash.");
}
- if (gmx::square(ir->rlist) >= max_cutoff2(ir->ePBC, box))
+ if (gmx::square(ir->rlist) >= max_cutoff2(ir->pbcType, box))
{
sprintf(warn_buf,
"ERROR: The cut-off length is longer than half the shortest box vector or "
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff