* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
* Copyright (c) 2013,2014,2015,2016,2017 by the GROMACS development team.
- * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
+ * 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 "grompp.h"
+#include <array>
#include <cerrno>
#include <climits>
#include <cmath>
#include <sys/types.h>
-#include "gromacs/awh/read_params.h"
+#include "gromacs/applied_forces/awh/read_params.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/ewald/ewald_utils.h"
#include "gromacs/ewald/pme.h"
#include "gromacs/mdlib/calc_verletbuf.h"
#include "gromacs/mdlib/compute_io.h"
#include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/md_support.h"
#include "gromacs/mdlib/perf_est.h"
#include "gromacs/mdlib/vsite.h"
#include "gromacs/mdrun/mdmodules.h"
#include "gromacs/utility/listoflists.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/loggerbuilder.h"
-#include "gromacs/utility/mdmodulenotification.h"
+#include "gromacs/utility/mdmodulesnotifiers.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/snprintf.h"
InteractionOfType::InteractionOfType(gmx::ArrayRef<const int> atoms,
gmx::ArrayRef<const real> params,
const std::string& name) :
- atoms_(atoms.begin(), atoms.end()),
- interactionTypeName_(name)
+ atoms_(atoms.begin(), atoms.end()), interactionTypeName_(name)
{
GMX_RELEASE_ASSERT(
params.size() <= forceParam_.size(),
gmx::formatString("Cannot have more parameters than the maximum number possible (%d)", MAXFORCEPARAM)
.c_str());
- auto forceParamIt = forceParam_.begin();
+ std::array<real, MAXFORCEPARAM>::iterator forceParamIt = forceParam_.begin();
for (const auto param : params)
{
*forceParamIt++ = param;
GMX_LOG(logger.warning)
.asParagraph()
.appendTextFormatted(
- "atom name %d in %s and %s does not match (%s - %s)", i + 1,
- fn1, fn2, *(tat->atomname[j]), *(at->atomname[i]));
+ "atom name %d in %s and %s does not match (%s - %s)",
+ i + 1,
+ fn1,
+ fn2,
+ *(tat->atomname[j]),
+ *(at->atomname[i]));
}
else if (nmismatch == c_maxNumberOfMismatches)
{
"oscillational period of %.1e ps, which is less than %d times the time step of "
"%.1e ps.\n"
"%s",
- *w_moltype->name, w_a1 + 1, *w_moltype->atoms.atomname[w_a1], w_a2 + 1,
- *w_moltype->atoms.atomname[w_a2], std::sqrt(w_period2),
- bWarn ? min_steps_warn : min_steps_note, dt,
+ *w_moltype->name,
+ w_a1 + 1,
+ *w_moltype->atoms.atomname[w_a1],
+ w_a2 + 1,
+ *w_moltype->atoms.atomname[w_a2],
+ std::sqrt(w_period2),
+ bWarn ? min_steps_warn : min_steps_note,
+ dt,
bWater ? "Maybe you asked for fexible water."
: "Maybe you forgot to change the constraints mdp option.");
if (bWarn)
{
const t_atom& local = atomP.atom();
int i = atomP.globalAtomNumber();
- if (local.ptype == eptShell || local.ptype == eptBond || local.ptype == eptVSite)
+ if (local.ptype == ParticleType::Shell || local.ptype == ParticleType::Bond
+ || local.ptype == ParticleType::VSite)
{
clear_rvec(v[i]);
}
for (const AtomProxy atomP : AtomRange(*mtop))
{
const t_atom& local = atomP.atom();
- if (local.ptype == eptShell || local.ptype == eptBond)
+ if (local.ptype == ParticleType::Shell || local.ptype == ParticleType::Bond)
{
nshells++;
}
std::vector<MoleculeInformation>* mi,
std::unique_ptr<MoleculeInformation>* intermolecular_interactions,
gmx::ArrayRef<InteractionsOfType> interactions,
- int* comb,
+ CombinationRule* comb,
double* reppow,
real* fudgeQQ,
gmx_bool bMorse,
bool ffParametrizedWithHBondConstraints;
/* TOPOLOGY processing */
- sys->name = do_top(bVerbose, topfile, topppfile, opts, bZero, &(sys->symtab), interactions,
- comb, reppow, fudgeQQ, atypes, mi, intermolecular_interactions, ir,
- &molblock, &ffParametrizedWithHBondConstraints, wi, logger);
+ sys->name = do_top(bVerbose,
+ topfile,
+ topppfile,
+ opts,
+ bZero,
+ &(sys->symtab),
+ interactions,
+ comb,
+ reppow,
+ fudgeQQ,
+ atypes,
+ mi,
+ intermolecular_interactions,
+ ir,
+ &molblock,
+ &ffParametrizedWithHBondConstraints,
+ wi,
+ logger);
sys->molblock.clear();
convert_harmonics(*mi, atypes);
}
- if (ir->eDisre == edrNone)
+ if (ir->eDisre == DistanceRestraintRefinement::None)
{
i = rm_interactions(F_DISRES, *mi);
if (i > 0)
* constraints only. Do not print note with large timesteps or vsites.
*/
if (opts->nshake == eshALLBONDS && ffParametrizedWithHBondConstraints && ir->delta_t < 0.0026
- && gmx_mtop_ftype_count(sys, F_VSITE3FD) == 0)
+ && gmx_mtop_ftype_count(*sys, F_VSITE3FD) == 0)
{
set_warning_line(wi, "unknown", -1);
warning_note(wi,
gmx_fatal(FARGS,
"number of coordinates in coordinate file (%s, %d)\n"
" does not match topology (%s, %d)",
- confin, state->natoms, topfile, sys->natoms);
+ confin,
+ state->natoms,
+ topfile,
+ sys->natoms);
}
/* It would be nice to get rid of the copies below, but we don't know
* a priori if the number of atoms in confin matches what we expect.
*/
- state->flags |= (1 << estX);
+ state->flags |= enumValueToBitMask(StateEntry::X);
if (v != nullptr)
{
- state->flags |= (1 << estV);
+ state->flags |= enumValueToBitMask(StateEntry::V);
}
state_change_natoms(state, state->natoms);
std::copy(x, x + state->natoms, state->x.data());
"%d non-matching atom name%s\n"
"atom names from %s will be used\n"
"atom names from %s will be ignored\n",
- nmismatch, (nmismatch == 1) ? "" : "s", topfile, confin);
+ nmismatch,
+ (nmismatch == 1) ? "" : "s",
+ topfile,
+ confin);
warning(wi, warningMessage.c_str());
}
opts->seed = static_cast<int>(gmx::makeRandomSeed());
GMX_LOG(logger.info).asParagraph().appendTextFormatted("Setting gen_seed to %d", opts->seed);
}
- state->flags |= (1 << estV);
+ state->flags |= enumValueToBitMask(StateEntry::V);
maxwell_speed(opts->tempi, opts->seed, sys, state->v.rvec_array(), logger);
stop_cm(logger, state->natoms, mass, state->x.rvec_array(), state->v.rvec_array());
GMX_LOG(logger.info).asParagraph().appendTextFormatted("Using frame at t = %g ps", use_time);
GMX_LOG(logger.info).asParagraph().appendTextFormatted("Starting time for run is %g ps", ir->init_t);
- if ((ir->epc != epcNO || ir->etc == etcNOSEHOOVER) && ener)
+ if ((ir->epc != PressureCoupling::No || ir->etc == TemperatureCoupling::NoseHoover) && ener)
{
get_enx_state(ener, use_time, sys->groups, ir, state);
preserve_box_shape(ir, state->box_rel, state->boxv);
gmx::ArrayRef<const MoleculeInformation> molinfo,
gmx_bool bTopB,
const char* fn,
- int rc_scaling,
+ RefCoordScaling rc_scaling,
PbcType pbcType,
rvec com,
warninp* wi,
std::string warningMessage = gmx::formatString(
"The number of atoms in %s (%d) does not match the number of atoms in the topology "
"(%d). Will assume that the first %d atoms in the topology and %s match.",
- fn, natoms, mtop->natoms, std::min(mtop->natoms, natoms), fn);
+ fn,
+ natoms,
+ mtop->natoms,
+ std::min(mtop->natoms, natoms),
+ fn);
warning(wi, warningMessage.c_str());
}
npbcdim = numPbcDimensions(pbcType);
GMX_RELEASE_ASSERT(npbcdim <= DIM, "Invalid npbcdim");
clear_rvec(com);
- if (rc_scaling != erscNO)
+ if (rc_scaling != RefCoordScaling::No)
{
copy_mat(box, invbox);
for (int j = npbcdim; j < DIM; j++)
gmx_fatal(FARGS,
"Position restraint atom index (%d) in moltype '%s' is larger than "
"number of atoms in %s (%d).\n",
- ai + 1, *molinfo[molb.type].name, fn, natoms);
+ ai + 1,
+ *molinfo[molb.type].name,
+ fn,
+ natoms);
}
hadAtom[ai] = TRUE;
- if (rc_scaling == erscCOM)
+ if (rc_scaling == RefCoordScaling::Com)
{
/* Determine the center of mass of the posres reference coordinates */
for (int j = 0; j < npbcdim; j++)
gmx_fatal(FARGS,
"Position restraint atom index (%d) in moltype '%s' is larger than "
"number of atoms in %s (%d).\n",
- ai + 1, *molinfo[molb.type].name, fn, natoms);
+ ai + 1,
+ *molinfo[molb.type].name,
+ fn,
+ natoms);
}
- if (rc_scaling == erscCOM && !hadAtom[ai])
+ if (rc_scaling == RefCoordScaling::Com && !hadAtom[ai])
{
/* Determine the center of mass of the posres reference coordinates */
for (int j = 0; j < npbcdim; j++)
}
a += nat_molb;
}
- if (rc_scaling == erscCOM)
+ if (rc_scaling == RefCoordScaling::Com)
{
if (totmass == 0)
{
.asParagraph()
.appendTextFormatted(
"The center of mass of the position restraint coord's is %6.3f %6.3f %6.3f",
- com[XX], com[YY], com[ZZ]);
+ com[XX],
+ com[YY],
+ com[ZZ]);
}
- if (rc_scaling != erscNO)
+ if (rc_scaling != RefCoordScaling::No)
{
GMX_ASSERT(npbcdim <= DIM, "Only DIM dimensions can have PBC");
{
for (int j = 0; j < npbcdim; j++)
{
- if (rc_scaling == erscALL)
+ if (rc_scaling == RefCoordScaling::All)
{
/* Convert from Cartesian to crystal coordinates */
xp[i][j] *= invbox[j][j];
xp[i][j] += invbox[k][j] * xp[i][k];
}
}
- else if (rc_scaling == erscCOM)
+ else if (rc_scaling == RefCoordScaling::Com)
{
/* Subtract the center of mass */
xp[i][j] -= com[j];
}
}
- if (rc_scaling == erscCOM)
+ if (rc_scaling == RefCoordScaling::Com)
{
/* Convert the COM from Cartesian to crystal coordinates */
for (int j = 0; j < npbcdim; j++)
gmx::ArrayRef<const MoleculeInformation> mi,
const char* fnA,
const char* fnB,
- int rc_scaling,
+ RefCoordScaling rc_scaling,
PbcType pbcType,
rvec com,
rvec comB,
}
for (i = 0; i < ir->nwall; i++)
{
- ir->wall_atomtype[i] = at->atomTypeFromName(opts->wall_atomtype[i]);
- if (ir->wall_atomtype[i] == NOTSET)
+ auto atomType = at->atomTypeFromName(opts->wall_atomtype[i]);
+ if (!atomType.has_value())
{
std::string warningMessage = gmx::formatString(
"Specified wall atom type %s is not defined", opts->wall_atomtype[i]);
warning_error(wi, warningMessage.c_str());
}
+ else
+ {
+ ir->wall_atomtype[i] = *atomType;
+ }
}
}
for (i = 0; i < atoms->nr; i++)
{
/* Vsite ptype might not be set here yet, so also check the mass */
- if ((atoms->atom[i].ptype == eptAtom || atoms->atom[i].ptype == eptNucleus) && atoms->atom[i].m > 0)
+ if ((atoms->atom[i].ptype == ParticleType::Atom || atoms->atom[i].ptype == ParticleType::Nucleus)
+ && atoms->atom[i].m > 0)
{
nmass++;
}
for (i = 0; i < 2 * grid_spacing; i++)
{
- spline1d(dx, &(tmp_grid[2 * grid_spacing * i]), 2 * grid_spacing, tmp_u.data(),
+ spline1d(dx,
+ &(tmp_grid[2 * grid_spacing * i]),
+ 2 * grid_spacing,
+ tmp_u.data(),
&(tmp_t2[2 * grid_spacing * i]));
}
for (k = 0; k < 2 * grid_spacing; k++)
{
- interpolate1d(xmin, dx, &(tmp_grid[2 * grid_spacing * k]),
- &(tmp_t2[2 * grid_spacing * k]), psi, &tmp_yy[k], &tmp_y1[k]);
+ interpolate1d(xmin,
+ dx,
+ &(tmp_grid[2 * grid_spacing * k]),
+ &(tmp_t2[2 * grid_spacing * k]),
+ psi,
+ &tmp_yy[k],
+ &tmp_y1[k]);
}
spline1d(dx, tmp_yy.data(), 2 * grid_spacing, tmp_u.data(), tmp_u2.data());
"Molecule type '%s' has %d constraints.\n"
"For stability and efficiency there should not be more constraints than "
"internal number of degrees of freedom: %d.\n",
- *mi[molb.type].name, count_mol, nrdf_internal(&mi[molb.type].atoms));
+ *mi[molb.type].name,
+ count_mol,
+ nrdf_internal(&mi[molb.type].atoms));
warning(wi, warningMessage.c_str());
}
count += molb.nmol * count_mol;
nrdf += ir->opts.nrdf[g];
}
- return sum_mv2 / (nrdf * BOLTZ);
+ return sum_mv2 / (nrdf * gmx::c_boltz);
}
static real get_max_reference_temp(const t_inputrec* ir, warninp* wi)
int numDanglingAtoms = 0;
for (int a = 0; a < atoms->nr; a++)
{
- if (atoms->atom[a].ptype != eptVSite && count[a] == 0)
+ if (atoms->atom[a].ptype != ParticleType::VSite && count[a] == 0)
{
if (bVerbose)
{
.appendTextFormatted(
"Atom %d '%s' in moleculetype '%s' is not bound by a potential or "
"constraint to any other atom in the same moleculetype.",
- a + 1, *atoms->atomname[a], *molt->name);
+ a + 1,
+ *atoms->atomname[a],
+ *molt->name);
}
numDanglingAtoms++;
}
"issues in a simulation, this often means that the user forgot to add a "
"bond/potential/constraint or put multiple molecules in the same moleculetype "
"definition by mistake. Run with -v to get information for each atom.",
- *molt->name, numDanglingAtoms);
+ *molt->name,
+ numDanglingAtoms);
warning_note(wi, warningMessage.c_str());
}
}
/*! \brief Checks if the Verlet buffer and constraint accuracy is sufficient for decoupled dynamic modes.
*
- * When decoupled modes are present and the accuray in insufficient,
+ * When decoupled modes are present and the accuracy in insufficient,
* this routine issues a warning if the accuracy is insufficient.
*/
static void checkDecoupledModeAccuracy(const gmx_mtop_t* mtop, const t_inputrec* ir, warninp* wi)
const int lincsOrderThreshold = 4;
const real shakeToleranceThreshold = 0.005 * ir->delta_t;
- bool lincsWithSufficientTolerance = (ir->eConstrAlg == econtLINCS && ir->nLincsIter >= lincsIterationThreshold
- && ir->nProjOrder >= lincsOrderThreshold);
- bool shakeWithSufficientTolerance =
- (ir->eConstrAlg == econtSHAKE && ir->shake_tol <= 1.1 * shakeToleranceThreshold);
- if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol <= 1.1 * bufferToleranceThreshold
+ bool lincsWithSufficientTolerance =
+ (ir->eConstrAlg == ConstraintAlgorithm::Lincs
+ && ir->nLincsIter >= lincsIterationThreshold && ir->nProjOrder >= lincsOrderThreshold);
+ bool shakeWithSufficientTolerance = (ir->eConstrAlg == ConstraintAlgorithm::Shake
+ && ir->shake_tol <= 1.1 * shakeToleranceThreshold);
+ if (ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol <= 1.1 * bufferToleranceThreshold
&& (lincsWithSufficientTolerance || shakeWithSufficientTolerance))
{
return;
"and with masses that differ by more than a factor of %g. This means "
"that there are likely dynamic modes that are only very weakly coupled.",
massFactorThreshold);
- if (ir->cutoff_scheme == ecutsVERLET)
+ if (ir->cutoff_scheme == CutoffScheme::Verlet)
{
message += gmx::formatString(
" To ensure good equipartitioning, you need to either not use "
"hydrogens) or use integrator = %s or decrease one or more tolerances: "
"verlet-buffer-tolerance <= %g, LINCS iterations >= %d, LINCS order "
">= %d or SHAKE tolerance <= %g",
- ei_names[eiSD1], bufferToleranceThreshold, lincsIterationThreshold,
- lincsOrderThreshold, shakeToleranceThreshold);
+ enumValueToString(IntegrationAlgorithm::SD1),
+ bufferToleranceThreshold,
+ lincsIterationThreshold,
+ lincsOrderThreshold,
+ shakeToleranceThreshold);
}
else
{
" To ensure good equipartitioning, we suggest to switch to the %s "
"cutoff-scheme, since that allows for better control over the Verlet "
"buffer size and thus over the energy drift.",
- ecutscheme_names[ecutsVERLET]);
+ enumValueToString(CutoffScheme::Verlet));
}
warning(wi, message);
}
.asParagraph()
.appendTextFormatted(
"Determining Verlet buffer for a tolerance of %g kJ/mol/ps at %g K",
- ir->verletbuf_tol, buffer_temp);
+ ir->verletbuf_tol,
+ buffer_temp);
/* Calculate the buffer size for simple atom vs atoms list */
VerletbufListSetup listSetup1x1;
listSetup1x1.cluster_size_i = 1;
listSetup1x1.cluster_size_j = 1;
- const real rlist_1x1 = calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1,
- buffer_temp, listSetup1x1);
+ const real rlist_1x1 = calcVerletBufferSize(
+ *mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1, buffer_temp, listSetup1x1);
/* Set the pair-list buffer size in ir */
VerletbufListSetup listSetup4x4 = verletbufGetSafeListSetup(ListSetupType::CpuNoSimd);
- ir->rlist = calcVerletBufferSize(*mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1,
- buffer_temp, listSetup4x4);
+ ir->rlist = calcVerletBufferSize(
+ *mtop, det(box), *ir, ir->nstlist, ir->nstlist - 1, buffer_temp, listSetup4x4);
const int n_nonlin_vsite = gmx::countNonlinearVsites(*mtop);
if (n_nonlin_vsite > 0)
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted(
- "Calculated rlist for %dx%d atom pair-list as %.3f nm, buffer size %.3f nm", 1,
- 1, rlist_1x1, rlist_1x1 - std::max(ir->rvdw, ir->rcoulomb));
+ "Calculated rlist for %dx%d atom pair-list as %.3f nm, buffer size %.3f nm",
+ 1,
+ 1,
+ rlist_1x1,
+ rlist_1x1 - std::max(ir->rvdw, ir->rcoulomb));
GMX_LOG(logger.info)
.asParagraph()
.appendTextFormatted(
"Set rlist, assuming %dx%d atom pair-list, to %.3f nm, buffer size %.3f nm",
- listSetup4x4.cluster_size_i, listSetup4x4.cluster_size_j, ir->rlist,
+ listSetup4x4.cluster_size_i,
+ listSetup4x4.cluster_size_j,
+ ir->rlist,
ir->rlist - std::max(ir->rvdw, ir->rcoulomb));
GMX_LOG(logger.info)
"The pair-list cut-off (%g nm) is longer than half the shortest box vector or "
"longer than the smallest box diagonal element (%g nm). Increase the box size or "
"decrease nstlist or increase verlet-buffer-tolerance.",
- ir->rlist, std::sqrt(max_cutoff2(ir->pbcType, box)));
+ ir->rlist,
+ std::sqrt(max_cutoff2(ir->pbcType, box)));
}
}
"Then a coordinate file is read and velocities can be generated",
"from a Maxwellian distribution if requested.",
"[THISMODULE] also reads parameters for [gmx-mdrun] ",
- "(eg. number of MD steps, time step, cut-off), and others such as",
- "NEMD parameters, which are corrected so that the net acceleration",
- "is zero.",
+ "(eg. number of MD steps, time step, cut-off).",
"Eventually a binary file is produced that can serve as the sole input",
"file for the MD program.[PAR]",
"interpret the output messages before attempting to bypass them with",
"this option."
};
- t_gromppopts* opts;
std::vector<MoleculeInformation> mi;
std::unique_ptr<MoleculeInformation> intermolecular_interactions;
- int nvsite, comb;
+ int nvsite;
+ CombinationRule comb;
real fudgeQQ;
double reppow;
const char* mdparin;
{ efEDR, "-e", nullptr, ffOPTRD },
/* This group is needed by the VMD viewer as the start configuration for IMD sessions: */
{ efGRO, "-imd", "imdgroup", ffOPTWR },
- { efTRN, "-ref", "rotref", ffOPTRW | ffALLOW_MISSING } };
+ { efTRN, "-ref", "rotref", ffOPTRW | ffALLOW_MISSING },
+ /* This group is needed by the QMMM MDModule: */
+ { efQMI, "-qmi", nullptr, ffOPTRD } };
#define NFILE asize(fnm)
/* Command line options */
gmx::MDModules mdModules;
t_inputrec irInstance;
t_inputrec* ir = &irInstance;
- snew(opts, 1);
+ t_gromppopts optsInstance;
+ t_gromppopts* opts = &optsInstance;
snew(opts->include, STRLEN);
snew(opts->define, STRLEN);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
- // Now that the MdModules have their options assigned from get_ir, subscribe
+ // Now that the MDModules have their options assigned from get_ir, subscribe
// to eventual notifications during pre-processing their data
mdModules.subscribeToPreProcessingNotifications();
+ // Notify MDModules of existing logger
+ mdModules.notifiers().preProcessingNotifier_.notify(logger);
+
+ // Notify MDModules of existing warninp
+ mdModules.notifiers().preProcessingNotifier_.notify(wi);
+
+ // Notify QMMM MDModule of external QM input file command-line option
+ {
+ gmx::QMInputFileName qmInputFileName = { ftp2bSet(efQMI, NFILE, fnm), ftp2fn(efQMI, NFILE, fnm) };
+ mdModules.notifiers().preProcessingNotifier_.notify(qmInputFileName);
+ }
if (bVerbose)
{
.asParagraph()
.appendTextFormatted("checking input for internal consistency...");
}
- check_ir(mdparin, mdModules.notifier(), ir, opts, wi);
+ check_ir(mdparin, mdModules.notifiers(), ir, opts, wi);
if (ir->ld_seed == -1)
{
}
t_state state;
- new_status(fn, opt2fn_null("-pp", NFILE, fnm), opt2fn("-c", NFILE, fnm), opts, ir, bZero,
- bGenVel, bVerbose, &state, &atypes, &sys, &mi, &intermolecular_interactions,
- interactions, &comb, &reppow, &fudgeQQ, opts->bMorse, wi, logger);
+ new_status(fn,
+ opt2fn_null("-pp", NFILE, fnm),
+ opt2fn("-c", NFILE, fnm),
+ opts,
+ ir,
+ bZero,
+ bGenVel,
+ bVerbose,
+ &state,
+ &atypes,
+ &sys,
+ &mi,
+ &intermolecular_interactions,
+ interactions,
+ &comb,
+ &reppow,
+ &fudgeQQ,
+ opts->bMorse,
+ wi,
+ logger);
if (debug)
{
}
}
- if ((count_constraints(&sys, mi, wi) != 0) && (ir->eConstrAlg == econtSHAKE))
+ if ((count_constraints(&sys, mi, wi) != 0) && (ir->eConstrAlg == ConstraintAlgorithm::Shake))
{
- if (ir->eI == eiCG || ir->eI == eiLBFGS)
+ if (ir->eI == IntegrationAlgorithm::CG || ir->eI == IntegrationAlgorithm::LBFGS)
{
std::string warningMessage =
- gmx::formatString("Can not do %s with %s, use %s", EI(ir->eI),
- econstr_names[econtSHAKE], econstr_names[econtLINCS]);
+ gmx::formatString("Can not do %s with %s, use %s",
+ enumValueToString(ir->eI),
+ enumValueToString(ConstraintAlgorithm::Shake),
+ enumValueToString(ConstraintAlgorithm::Lincs));
warning_error(wi, warningMessage);
}
if (ir->bPeriodicMols)
{
std::string warningMessage =
gmx::formatString("Can not do periodic molecules with %s, use %s",
- econstr_names[econtSHAKE], econstr_names[econtLINCS]);
+ enumValueToString(ConstraintAlgorithm::Shake),
+ enumValueToString(ConstraintAlgorithm::Lincs));
warning_error(wi, warningMessage);
}
}
- if (EI_SD(ir->eI) && ir->etc != etcNO)
+ if (EI_SD(ir->eI) && ir->etc != TemperatureCoupling::No)
{
warning_note(wi, "Temperature coupling is ignored with SD integrators.");
}
if (nint_ftype(&sys, mi, F_POSRES) > 0 || nint_ftype(&sys, mi, F_FBPOSRES) > 0)
{
- if (ir->epc == epcPARRINELLORAHMAN || ir->epc == epcMTTK)
+ if (ir->epc == PressureCoupling::ParrinelloRahman || ir->epc == PressureCoupling::Mttk)
{
std::string warningMessage = gmx::formatString(
"You are combining position restraints with %s pressure coupling, which can "
"lead to instabilities. If you really want to combine position restraints with "
"pressure coupling, we suggest to use %s pressure coupling instead.",
- EPCOUPLTYPE(ir->epc), EPCOUPLTYPE(epcBERENDSEN));
+ enumValueToString(ir->epc),
+ enumValueToString(PressureCoupling::Berendsen));
warning_note(wi, warningMessage);
}
}
GMX_LOG(logger.info).asParagraph().appendText(message);
}
- gen_posres(&sys, mi, fn, fnB, ir->refcoord_scaling, ir->pbcType, ir->posres_com,
- ir->posres_comB, wi, logger);
+ gen_posres(&sys, mi, fn, fnB, ir->refcoord_scaling, ir->pbcType, ir->posres_com, ir->posres_comB, wi, logger);
}
/* If we are using CMAP, setup the pre-interpolation grid */
if (interactions[F_CMAP].ncmap() > 0)
{
- init_cmap_grid(&sys.ffparams.cmap_grid, interactions[F_CMAP].cmapAngles,
+ init_cmap_grid(&sys.ffparams.cmap_grid,
+ interactions[F_CMAP].cmapAngles,
interactions[F_CMAP].cmakeGridSpacing);
- setup_cmap(interactions[F_CMAP].cmakeGridSpacing, interactions[F_CMAP].cmapAngles,
- interactions[F_CMAP].cmap, &sys.ffparams.cmap_grid);
+ setup_cmap(interactions[F_CMAP].cmakeGridSpacing,
+ interactions[F_CMAP].cmapAngles,
+ interactions[F_CMAP].cmap,
+ &sys.ffparams.cmap_grid);
}
set_wall_atomtype(&atypes, opts, ir, wi, logger);
}
const int ntype = atypes.size();
- convertInteractionsOfType(ntype, interactions, mi, intermolecular_interactions.get(), comb,
- reppow, fudgeQQ, &sys);
+ convertInteractionsOfType(
+ ntype, interactions, mi, intermolecular_interactions.get(), comb, reppow, fudgeQQ, &sys);
if (debug)
{
/* check masses */
check_mol(&sys, wi);
+ if (haveFepPerturbedMassesInSettles(sys))
+ {
+ warning_error(wi,
+ "SETTLE is not implemented for atoms whose mass is perturbed. "
+ "You might instead use normal constraints.");
+ }
+
checkForUnboundAtoms(&sys, bVerbose, wi, logger);
- if (EI_DYNAMICS(ir->eI) && ir->eI != eiBD)
+ if (EI_DYNAMICS(ir->eI) && ir->eI != IntegrationAlgorithm::BD)
{
check_bonds_timestep(&sys, ir->delta_t, wi);
}
{
GMX_LOG(logger.info).asParagraph().appendTextFormatted("initialising group options...");
}
- do_index(mdparin, ftp2fn_null(efNDX, NFILE, fnm), &sys, bVerbose, mdModules.notifier(), ir, wi);
+ do_index(mdparin, ftp2fn_null(efNDX, NFILE, fnm), &sys, bVerbose, mdModules.notifiers(), ir, wi);
+
+ // Notify topology to MdModules for pre-processing after all indexes were built
+ mdModules.notifiers().preProcessingNotifier_.notify(&sys);
- if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0)
+ if (ir->cutoff_scheme == CutoffScheme::Verlet && ir->verletbuf_tol > 0)
{
if (EI_DYNAMICS(ir->eI) && inputrec2nboundeddim(ir) == 3)
{
real buffer_temp;
- if (EI_MD(ir->eI) && ir->etc == etcNO)
+ if (EI_MD(ir->eI) && ir->etc == TemperatureCoupling::No)
{
if (bGenVel)
{
buffer_temp = get_max_reference_temp(ir, wi);
}
- if (EI_MD(ir->eI) && ir->etc == etcNO && buffer_temp == 0)
+ if (EI_MD(ir->eI) && ir->etc == TemperatureCoupling::No && buffer_temp == 0)
{
/* NVE with initial T=0: we add a fixed ratio to rlist.
* Since we don't actually use verletbuf_tol, we set it to -1
* Note that we can't warn when nsteps=0, since we don't
* know how many steps the user intends to run.
*/
- if (EI_MD(ir->eI) && ir->etc == etcNO && ir->nstlist > 1 && ir->nsteps > 0)
+ if (EI_MD(ir->eI) && ir->etc == TemperatureCoupling::No && ir->nstlist > 1 && ir->nsteps > 0)
{
const real driftTolerance = 0.01;
/* We use 2 DOF per atom = 2kT pot+kin energy,
* to be on the safe side with constraints.
*/
const real totalEnergyDriftPerAtomPerPicosecond =
- 2 * BOLTZ * buffer_temp / (ir->nsteps * ir->delta_t);
+ 2 * gmx::c_boltz * buffer_temp / (ir->nsteps * ir->delta_t);
if (ir->verletbuf_tol > 1.1 * driftTolerance * totalEnergyDriftPerAtomPerPicosecond)
{
"NVE simulation of length %g ps, which can give a final drift of "
"%d%%. For conserving energy to %d%% when using constraints, you "
"might need to set verlet-buffer-tolerance to %.1e.",
- ir->verletbuf_tol, ir->nsteps * ir->delta_t,
+ ir->verletbuf_tol,
+ ir->nsteps * ir->delta_t,
gmx::roundToInt(ir->verletbuf_tol / totalEnergyDriftPerAtomPerPicosecond * 100),
gmx::roundToInt(100 * driftTolerance),
driftTolerance * totalEnergyDriftPerAtomPerPicosecond);
pr_symtab(debug, 0, "After close", &sys.symtab);
}
- if (ir->eI == eiMimic)
+ if (ir->eI == IntegrationAlgorithm::Mimic)
{
generate_qmexcl(&sys, ir, logger);
}
.asParagraph()
.appendTextFormatted("getting data from old trajectory ...");
}
- cont_status(ftp2fn(efTRN, NFILE, fnm), ftp2fn_null(efEDR, NFILE, fnm), bNeedVel, bGenVel,
- fr_time, ir, &state, &sys, oenv, logger);
+ cont_status(ftp2fn(efTRN, NFILE, fnm),
+ ftp2fn_null(efEDR, NFILE, fnm),
+ bNeedVel,
+ bGenVel,
+ fr_time,
+ ir,
+ &state,
+ &sys,
+ oenv,
+ logger);
}
if (ir->pbcType == PbcType::XY && ir->nwall != 2)
{
/* Calculate the optimal grid dimensions */
matrix scaledBox;
- EwaldBoxZScaler boxScaler(*ir);
+ EwaldBoxZScaler boxScaler(inputrecPbcXY2Walls(ir), ir->wall_ewald_zfac);
boxScaler.scaleBox(state.box, scaledBox);
if (ir->nkx > 0 && ir->nky > 0 && ir->nkz > 0)
wi, "Some of the Fourier grid sizes are set, but all of them need to be set.");
}
const int minGridSize = minimalPmeGridSize(ir->pme_order);
- calcFftGrid(stdout, scaledBox, ir->fourier_spacing, minGridSize, &(ir->nkx), &(ir->nky),
- &(ir->nkz));
+ calcFftGrid(stdout, scaledBox, ir->fourier_spacing, minGridSize, &(ir->nkx), &(ir->nky), &(ir->nkz));
if (ir->nkx < minGridSize || ir->nky < minGridSize || ir->nkz < minGridSize)
{
warning_error(wi,
/* MRS: eventually figure out better logic for initializing the fep
values that makes declaring the lambda and declaring the state not
potentially conflict if not handled correctly. */
- if (ir->efep != efepNO)
+ if (ir->efep != FreeEnergyPerturbationType::No)
{
state.fep_state = ir->fepvals->init_fep_state;
- for (i = 0; i < efptNR; i++)
+ for (i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
{
/* init_lambda trumps state definitions*/
if (ir->fepvals->init_lambda >= 0)
}
else
{
- if (ir->fepvals->all_lambda[i] == nullptr)
+ if (ir->fepvals->all_lambda[i].empty())
{
gmx_fatal(FARGS, "Values of lambda not set for a free energy calculation!");
}
if (ir->bPull)
{
- pull = set_pull_init(ir, &sys, state.x.rvec_array(), state.box, state.lambda[efptMASS], wi);
+ pull = set_pull_init(
+ ir, sys, state.x, state.box, state.lambda[FreeEnergyPerturbationCouplingType::Mass], wi);
}
/* Modules that supply external potential for pull coordinates
if (ir->bDoAwh)
{
tensor compressibility = { { 0 } };
- if (ir->epc != epcNO)
+ if (ir->epc != PressureCoupling::No)
{
copy_mat(ir->compress, compressibility);
}
- setStateDependentAwhParams(ir->awhParams, ir->pull, pull, state.box, ir->pbcType,
- compressibility, &ir->opts, wi);
+ setStateDependentAwhParams(
+ ir->awhParams.get(),
+ *ir->pull,
+ pull,
+ state.box,
+ ir->pbcType,
+ compressibility,
+ &ir->opts,
+ ir->efep != FreeEnergyPerturbationType::No ? ir->fepvals->all_lambda[static_cast<int>(
+ FreeEnergyPerturbationCouplingType::Fep)][ir->fepvals->init_fep_state]
+ : 0,
+ sys,
+ wi);
}
if (ir->bPull)
if (ir->bRot)
{
- set_reference_positions(ir->rot, state.x.rvec_array(), state.box,
- opt2fn("-ref", NFILE, fnm), opt2bSet("-ref", NFILE, fnm), wi);
+ set_reference_positions(ir->rot,
+ state.x.rvec_array(),
+ state.box,
+ opt2fn("-ref", NFILE, fnm),
+ opt2bSet("-ref", NFILE, fnm),
+ wi);
}
/* reset_multinr(sys); */
* charges. This will double the cost, but the optimal performance will
* then probably be at a slightly larger cut-off and grid spacing.
*/
- if ((ir->efep == efepNO && ratio > 1.0 / 2.0) || (ir->efep != efepNO && ratio > 2.0 / 3.0))
+ if ((ir->efep == FreeEnergyPerturbationType::No && ratio > 1.0 / 2.0)
+ || (ir->efep != FreeEnergyPerturbationType::No && ratio > 2.0 / 3.0))
{
warning_note(
wi,
"The optimal PME mesh load for parallel simulations is below 0.5\n"
"and for highly parallel simulations between 0.25 and 0.33,\n"
"for higher performance, increase the cut-off and the PME grid spacing.\n");
- if (ir->efep != efepNO)
+ if (ir->efep != FreeEnergyPerturbationType::No)
{
warning_note(wi,
"For free energy simulations, the optimal load limit increases from "
}
}
+ // Hand over box and coordiantes to MdModules before they evaluate their final parameters
+ {
+ gmx::CoordinatesAndBoxPreprocessed coordinatesAndBoxPreprocessed;
+ coordinatesAndBoxPreprocessed.coordinates_ = state.x.arrayRefWithPadding();
+ copy_mat(state.box, coordinatesAndBoxPreprocessed.box_);
+ coordinatesAndBoxPreprocessed.pbc_ = ir->pbcType;
+ mdModules.notifiers().preProcessingNotifier_.notify(coordinatesAndBoxPreprocessed);
+ }
+
// Add the md modules internal parameters that are not mdp options
// e.g., atom indices
{
gmx::KeyValueTreeBuilder internalParameterBuilder;
- mdModules.notifier().preProcessingNotifications_.notify(internalParameterBuilder.rootObject());
+ mdModules.notifiers().preProcessingNotifier_.notify(internalParameterBuilder.rootObject());
ir->internalParameters =
std::make_unique<gmx::KeyValueTreeObject>(internalParameterBuilder.build());
}
+ if (ir->comm_mode != ComRemovalAlgorithm::No)
+ {
+ const int nstglobalcomm = computeGlobalCommunicationPeriod(ir);
+ if (ir->nstcomm % nstglobalcomm != 0)
+ {
+ warning_note(
+ wi,
+ gmx::formatString(
+ "COM removal frequency is set to (%d).\n"
+ "Other settings require a global communication frequency of %d.\n"
+ "Note that this will require additional global communication steps,\n"
+ "which will reduce performance when using multiple ranks.\n"
+ "Consider setting nstcomm to a multiple of %d.",
+ ir->nstcomm,
+ nstglobalcomm,
+ nstglobalcomm));
+ }
+ }
+
if (bVerbose)
{
GMX_LOG(logger.info).asParagraph().appendTextFormatted("writing run input file...");
}
done_warning(wi, FARGS);
- write_tpx_state(ftp2fn(efTPR, NFILE, fnm), ir, &state, &sys);
+ write_tpx_state(ftp2fn(efTPR, NFILE, fnm), ir, &state, sys);
/* Output IMD group, if bIMD is TRUE */
- gmx::write_IMDgroup_to_file(ir->bIMD, ir, &state, &sys, NFILE, fnm);
+ gmx::write_IMDgroup_to_file(ir->bIMD, ir, &state, sys, NFILE, fnm);
sfree(opts->define);
sfree(opts->wall_atomtype[0]);
sfree(opts->wall_atomtype[1]);
sfree(opts->include);
- sfree(opts);
+ sfree(opts->couple_moltype);
+
for (auto& mol : mi)
{
// Some of the contents of molinfo have been stolen, so
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff