#include <memory>
#include <vector>
+#include "gromacs/applied_forces/awh/read_params.h"
#include "gromacs/fileio/filetypes.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/gmxfio_xdr.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/inmemoryserializer.h"
+#include "gromacs/utility/iserializer.h"
#include "gromacs/utility/keyvaluetreebuilder.h"
#include "gromacs/utility/keyvaluetreeserializer.h"
#include "gromacs/utility/smalloc.h"
* merging with mainstream GROMACS, set this tag string back to
* TPX_TAG_RELEASE, and instead add an element to tpxv.
*/
-static const char* tpx_tag = TPX_TAG_RELEASE;
+static const std::string tpx_tag = TPX_TAG_RELEASE;
/*! \brief Enum of values that describe the contents of a tpr file
* whose format matches a version number
tpxv_VSite1, /**< Added 1 type virtual site */
tpxv_MTS, /**< Added multiple time stepping */
tpxv_RemovedConstantAcceleration, /**< Removed support for constant acceleration NEMD. */
+ tpxv_TransformationPullCoord, /**< Support for transformation pull coordinates */
+ tpxv_SoftcoreGapsys, /**< Added gapsys softcore function */
+ tpxv_ReaddedConstantAcceleration, /**< Re-added support for constant acceleration NEMD. */
+ tpxv_RemoveTholeRfac, /**< Remove unused rfac parameter from thole listed force */
tpxv_Count /**< the total number of tpxv versions */
};
};
#define NFTUPD asize(ftupd)
-/* Needed for backward compatibility */
-#define MAXNODES 256
-
/**************************************************************
*
* Now the higer level routines that do io of the structures and arrays
static void do_pull_coord(gmx::ISerializer* serializer,
t_pull_coord* pcrd,
int file_version,
- int ePullOld,
- int eGeomOld,
+ PullingAlgorithm ePullOld,
+ PullGroupGeometry eGeomOld,
ivec dimOld)
{
if (file_version >= tpxv_PullCoordNGroup)
{
- serializer->doInt(&pcrd->eType);
+ serializer->doEnumAsInt(&pcrd->eType);
if (file_version >= tpxv_PullExternalPotential)
{
- if (pcrd->eType == epullEXTERNAL)
+ if (pcrd->eType == PullingAlgorithm::External)
{
- std::string buf;
- if (serializer->reading())
- {
- serializer->doString(&buf);
- pcrd->externalPotentialProvider = gmx_strdup(buf.c_str());
- }
- else
- {
- buf = pcrd->externalPotentialProvider;
- serializer->doString(&buf);
- }
+ serializer->doString(&pcrd->externalPotentialProvider);
}
else
{
* changing the tpx version. This requires checks when printing the
* geometry string and a check and fatal_error in init_pull.
*/
- serializer->doInt(&pcrd->eGeom);
+ serializer->doEnumAsInt(&pcrd->eGeom);
serializer->doInt(&pcrd->ngroup);
if (pcrd->ngroup <= c_pullCoordNgroupMax)
{
pcrd->ngroup = 0;
}
serializer->doIvec(&pcrd->dim.as_vec());
+ if (file_version >= tpxv_TransformationPullCoord)
+ {
+ serializer->doString(&pcrd->expression);
+ }
+ else
+ {
+ if (serializer->reading())
+ {
+ pcrd->expression.clear();
+ }
+ }
}
else
{
serializer->doInt(&pcrd->group[1]);
if (file_version >= tpxv_PullCoordTypeGeom)
{
- pcrd->ngroup = (pcrd->eGeom == epullgDIRRELATIVE ? 4 : 2);
- serializer->doInt(&pcrd->eType);
- serializer->doInt(&pcrd->eGeom);
+ pcrd->ngroup = (pcrd->eGeom == PullGroupGeometry::DirectionRelative ? 4 : 2);
+ serializer->doEnumAsInt(&pcrd->eType);
+ serializer->doEnumAsInt(&pcrd->eGeom);
if (pcrd->ngroup == 4)
{
serializer->doInt(&pcrd->group[2]);
{
if (n_lambda > 0)
{
- if (serializer->reading())
- {
- snew(expand->init_lambda_weights, n_lambda);
- }
- serializer->doRealArray(expand->init_lambda_weights, n_lambda);
+ expand->init_lambda_weights.resize(n_lambda);
+ serializer->doRealArray(expand->init_lambda_weights.data(), n_lambda);
serializer->doBool(&expand->bInit_weights);
}
serializer->doInt(&expand->nstexpanded);
- serializer->doInt(&expand->elmcmove);
- serializer->doInt(&expand->elamstats);
+ serializer->doEnumAsInt(&expand->elmcmove);
+ serializer->doEnumAsInt(&expand->elamstats);
serializer->doInt(&expand->lmc_repeats);
serializer->doInt(&expand->gibbsdeltalam);
serializer->doInt(&expand->lmc_forced_nstart);
serializer->doReal(&expand->wl_ratio);
serializer->doReal(&expand->init_wl_delta);
serializer->doBool(&expand->bWLoneovert);
- serializer->doInt(&expand->elmceq);
+ serializer->doEnumAsInt(&expand->elmceq);
serializer->doInt(&expand->equil_steps);
serializer->doInt(&expand->equil_samples);
serializer->doInt(&expand->equil_n_at_lam);
{
if (file_version >= 79)
{
- serializer->doInt(&simtemp->eSimTempScale);
+ serializer->doEnumAsInt(&simtemp->eSimTempScale);
serializer->doReal(&simtemp->simtemp_high);
serializer->doReal(&simtemp->simtemp_low);
if (n_lambda > 0)
{
if (serializer->reading())
{
- snew(simtemp->temperatures, n_lambda);
+ simtemp->temperatures.resize(n_lambda);
}
- serializer->doRealArray(simtemp->temperatures, n_lambda);
+ serializer->doRealArray(simtemp->temperatures.data(), n_lambda);
}
}
}
static void do_fepvals(gmx::ISerializer* serializer, t_lambda* fepvals, int file_version)
{
/* i is defined in the ndo_double macro; use g to iterate. */
- int g;
real rdum;
/* free energy values */
if (file_version >= 79)
{
serializer->doInt(&fepvals->n_lambda);
- if (serializer->reading())
- {
- snew(fepvals->all_lambda, efptNR);
- }
- for (g = 0; g < efptNR; g++)
+ for (auto g : keysOf(fepvals->all_lambda))
{
if (fepvals->n_lambda > 0)
{
- if (serializer->reading())
- {
- snew(fepvals->all_lambda[g], fepvals->n_lambda);
- }
- serializer->doDoubleArray(fepvals->all_lambda[g], fepvals->n_lambda);
- serializer->doBoolArray(fepvals->separate_dvdl, efptNR);
+ fepvals->all_lambda[g].resize(fepvals->n_lambda);
+ serializer->doDoubleArray(fepvals->all_lambda[g].data(), fepvals->n_lambda);
+ serializer->doBoolArray(fepvals->separate_dvdl.begin(), fepvals->separate_dvdl.size());
}
else if (fepvals->init_lambda >= 0)
{
- fepvals->separate_dvdl[efptFEP] = TRUE;
+ fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
}
}
}
serializer->doInt(&fepvals->n_lambda);
if (serializer->reading())
{
- int g;
-
- snew(fepvals->all_lambda, efptNR);
/* still allocate the all_lambda array's contents. */
- for (g = 0; g < efptNR; g++)
+ for (auto g : keysOf(fepvals->all_lambda))
{
if (fepvals->n_lambda > 0)
{
- snew(fepvals->all_lambda[g], fepvals->n_lambda);
+ fepvals->all_lambda[g].resize(fepvals->n_lambda);
}
}
}
- serializer->doDoubleArray(fepvals->all_lambda[efptFEP], fepvals->n_lambda);
+ serializer->doDoubleArray(fepvals->all_lambda[FreeEnergyPerturbationCouplingType::Fep].data(),
+ fepvals->n_lambda);
if (fepvals->init_lambda >= 0)
{
- int g, h;
-
- fepvals->separate_dvdl[efptFEP] = TRUE;
+ fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
if (serializer->reading())
{
/* copy the contents of the efptFEP lambda component to all
the other components */
- for (g = 0; g < efptNR; g++)
+ for (auto g : keysOf(fepvals->all_lambda))
{
- for (h = 0; h < fepvals->n_lambda; h++)
+ for (int h = 0; h < fepvals->n_lambda; h++)
{
- if (g != efptFEP)
+ if (g != FreeEnergyPerturbationCouplingType::Fep)
{
- fepvals->all_lambda[g][h] = fepvals->all_lambda[efptFEP][h];
+ fepvals->all_lambda[g][h] =
+ fepvals->all_lambda[FreeEnergyPerturbationCouplingType::Fep][h];
}
}
}
}
else
{
- fepvals->n_lambda = 0;
- fepvals->all_lambda = nullptr;
+ fepvals->n_lambda = 0;
if (fepvals->init_lambda >= 0)
{
- fepvals->separate_dvdl[efptFEP] = TRUE;
+ fepvals->separate_dvdl[FreeEnergyPerturbationCouplingType::Fep] = TRUE;
}
}
serializer->doReal(&fepvals->sc_alpha);
if (file_version >= 73)
{
- serializer->doInt(&fepvals->separate_dhdl_file);
- serializer->doInt(&fepvals->dhdl_derivatives);
+ serializer->doEnumAsInt(&fepvals->separate_dhdl_file);
+ serializer->doEnumAsInt(&fepvals->dhdl_derivatives);
}
else
{
- fepvals->separate_dhdl_file = esepdhdlfileYES;
- fepvals->dhdl_derivatives = edhdlderivativesYES;
+ fepvals->separate_dhdl_file = SeparateDhdlFile::Yes;
+ fepvals->dhdl_derivatives = DhDlDerivativeCalculation::Yes;
}
if (file_version >= 71)
{
}
if (file_version >= 79)
{
- serializer->doInt(&fepvals->edHdLPrintEnergy);
+ serializer->doEnumAsInt(&fepvals->edHdLPrintEnergy);
}
else
{
- fepvals->edHdLPrintEnergy = edHdLPrintEnergyNO;
+ fepvals->edHdLPrintEnergy = FreeEnergyPrintEnergy::No;
+ }
+ if (file_version >= tpxv_SoftcoreGapsys)
+ {
+ serializer->doInt(reinterpret_cast<int*>(&fepvals->softcoreFunction));
+ serializer->doReal(&fepvals->scGapsysScaleLinpointLJ);
+ serializer->doReal(&fepvals->scGapsysScaleLinpointQ);
+ serializer->doReal(&fepvals->scGapsysSigmaLJ);
+ }
+ else
+ {
+ fepvals->softcoreFunction = SoftcoreType::Beutler;
+ fepvals->scGapsysScaleLinpointLJ = 0.85;
+ fepvals->scGapsysScaleLinpointQ = 0.3;
+ fepvals->scGapsysSigmaLJ = 0.3;
}
/* handle lambda_neighbors */
}
}
-static void do_awhBias(gmx::ISerializer* serializer, gmx::AwhBiasParams* awhBiasParams, int gmx_unused file_version)
-{
- serializer->doInt(&awhBiasParams->eTarget);
- serializer->doDouble(&awhBiasParams->targetBetaScaling);
- serializer->doDouble(&awhBiasParams->targetCutoff);
- serializer->doInt(&awhBiasParams->eGrowth);
- serializer->doInt(&awhBiasParams->bUserData);
- serializer->doDouble(&awhBiasParams->errorInitial);
- serializer->doInt(&awhBiasParams->ndim);
- serializer->doInt(&awhBiasParams->shareGroup);
- serializer->doBool(&awhBiasParams->equilibrateHistogram);
-
- if (serializer->reading())
- {
- snew(awhBiasParams->dimParams, awhBiasParams->ndim);
- }
-
- for (int d = 0; d < awhBiasParams->ndim; d++)
- {
- gmx::AwhDimParams* dimParams = &awhBiasParams->dimParams[d];
-
- serializer->doInt(&dimParams->eCoordProvider);
- serializer->doInt(&dimParams->coordIndex);
- serializer->doDouble(&dimParams->origin);
- serializer->doDouble(&dimParams->end);
- serializer->doDouble(&dimParams->period);
- serializer->doDouble(&dimParams->forceConstant);
- serializer->doDouble(&dimParams->diffusion);
- serializer->doDouble(&dimParams->coordValueInit);
- serializer->doDouble(&dimParams->coverDiameter);
- }
-}
-
-static void do_awh(gmx::ISerializer* serializer, gmx::AwhParams* awhParams, int gmx_unused file_version)
+static void do_pull(gmx::ISerializer* serializer, pull_params_t* pull, int file_version, PullingAlgorithm ePullOld)
{
- serializer->doInt(&awhParams->numBias);
- serializer->doInt(&awhParams->nstOut);
- serializer->doInt64(&awhParams->seed);
- serializer->doInt(&awhParams->nstSampleCoord);
- serializer->doInt(&awhParams->numSamplesUpdateFreeEnergy);
- serializer->doInt(&awhParams->ePotential);
- serializer->doBool(&awhParams->shareBiasMultisim);
-
- if (awhParams->numBias > 0)
- {
- if (serializer->reading())
- {
- snew(awhParams->awhBiasParams, awhParams->numBias);
- }
-
- for (int k = 0; k < awhParams->numBias; k++)
- {
- do_awhBias(serializer, &awhParams->awhBiasParams[k], file_version);
- }
- }
-}
-
-static void do_pull(gmx::ISerializer* serializer, pull_params_t* pull, int file_version, int ePullOld)
-{
- int eGeomOld = -1;
- ivec dimOld;
- int g;
+ PullGroupGeometry eGeomOld = PullGroupGeometry::Count;
+ ivec dimOld;
+ int g;
if (file_version >= 95)
{
{
real dum;
- serializer->doInt(&eGeomOld);
+ serializer->doEnumAsInt(&eGeomOld);
serializer->doIvec(&dimOld);
/* The inner cylinder radius, now removed */
serializer->doReal(&dum);
if (file_version < 95)
{
/* epullgPOS for position pulling, before epullgDIRPBC was removed */
- if (eGeomOld == epullgDIRPBC)
+ if (eGeomOld == PullGroupGeometry::DirectionPBC)
{
gmx_fatal(FARGS, "pull-geometry=position is no longer supported");
}
- if (eGeomOld > epullgDIRPBC)
+ if (eGeomOld > PullGroupGeometry::DirectionPBC)
{
- eGeomOld -= 1;
+ switch (eGeomOld)
+ {
+ case (PullGroupGeometry::DirectionRelative):
+ eGeomOld = PullGroupGeometry::DirectionPBC;
+ break;
+ case (PullGroupGeometry::Angle):
+ eGeomOld = PullGroupGeometry::DirectionRelative;
+ break;
+ case (PullGroupGeometry::Dihedral): eGeomOld = PullGroupGeometry::Angle; break;
+ case (PullGroupGeometry::AngleAxis): eGeomOld = PullGroupGeometry::Dihedral; break;
+ case (PullGroupGeometry::Count): eGeomOld = PullGroupGeometry::AngleAxis; break;
+ default: GMX_RELEASE_ASSERT(false, "Unhandled old pull type");
+ }
}
for (g = 0; g < pull->ngroup; g++)
for (g = 0; g < pull->ncoord; g++)
{
do_pull_coord(serializer, &pull->coord[g], file_version, ePullOld, eGeomOld, dimOld);
+ if (serializer->reading())
+ {
+ pull->coord[g].coordIndex = g;
+ }
}
}
if (file_version >= tpxv_PullAverage)
static void do_rotgrp(gmx::ISerializer* serializer, t_rotgrp* rotg)
{
- serializer->doInt(&rotg->eType);
- serializer->doInt(&rotg->bMassW);
+ serializer->doEnumAsInt(&rotg->eType);
+ if (serializer->reading())
+ {
+ int temp = 0;
+ serializer->doInt(&temp);
+ rotg->bMassW = static_cast<bool>(temp);
+ }
+ else
+ {
+ int temp = static_cast<int>(rotg->bMassW);
+ serializer->doInt(&temp);
+ }
serializer->doInt(&rotg->nat);
if (serializer->reading())
{
serializer->doReal(&rotg->slab_dist);
serializer->doReal(&rotg->min_gaussian);
serializer->doReal(&rotg->eps);
- serializer->doInt(&rotg->eFittype);
+ serializer->doEnumAsInt(&rotg->eFittype);
serializer->doInt(&rotg->PotAngle_nstep);
serializer->doReal(&rotg->PotAngle_step);
}
serializer->doIntArray(g->ind, g->nat);
/* Requested counts for compartments A and B */
- serializer->doIntArray(g->nmolReq, eCompNR);
+ serializer->doIntArray(g->nmolReq.data(), static_cast<int>(Compartment::Count));
}
static void do_swapcoords_tpx(gmx::ISerializer* serializer, t_swapcoords* swap, int file_version)
swap->ngrp = 5;
snew(swap->grp, swap->ngrp);
- swap->grp[eGrpSplit0].molname = gmx_strdup("split0"); // group 0: split0
- swap->grp[eGrpSplit1].molname = gmx_strdup("split1"); // group 1: split1
- swap->grp[eGrpSolvent].molname = gmx_strdup("solvent"); // group 2: solvent
- swap->grp[3].molname = gmx_strdup("anions"); // group 3: anions
- swap->grp[4].molname = gmx_strdup("cations"); // group 4: cations
+ swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].molname = gmx_strdup("split0"); // group 0: split0
+ swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].molname = gmx_strdup("split1"); // group 1: split1
+ swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].molname =
+ gmx_strdup("solvent"); // group 2: solvent
+ swap->grp[3].molname = gmx_strdup("anions"); // group 3: anions
+ swap->grp[4].molname = gmx_strdup("cations"); // group 4: cations
serializer->doInt(&swap->grp[3].nat);
- serializer->doInt(&swap->grp[eGrpSolvent].nat);
- serializer->doInt(&swap->grp[eGrpSplit0].nat);
+ serializer->doInt(&swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].nat);
+ serializer->doInt(&swap->grp[static_cast<int>(SwapGroupSplittingType::Split0)].nat);
serializer->doBool(&swap->massw_split[eChannel0]);
- serializer->doInt(&swap->grp[eGrpSplit1].nat);
+ serializer->doInt(&swap->grp[static_cast<int>(SwapGroupSplittingType::Split1)].nat);
serializer->doBool(&swap->massw_split[eChannel1]);
serializer->doInt(&swap->nstswap);
serializer->doInt(&swap->nAverage);
// The order[] array keeps compatibility with older .tpr files
// by reading in the groups in the classic order
{
- const int order[4] = { 3, eGrpSolvent, eGrpSplit0, eGrpSplit1 };
+ const int order[4] = { 3,
+ static_cast<int>(SwapGroupSplittingType::Solvent),
+ static_cast<int>(SwapGroupSplittingType::Split0),
+ static_cast<int>(SwapGroupSplittingType::Split1) };
for (int ig = 0; ig < 4; ig++)
{
gmx::KeyValueTreeObjectBuilder paramsObj = paramsBuilder.rootObject();
/* Basic inputrec stuff */
- serializer->doInt(&ir->eI);
+ serializer->doEnumAsInt(&ir->eI);
if (file_version >= 62)
{
serializer->doInt64(&ir->nsteps);
}
if (file_version >= 81)
{
- serializer->doInt(&ir->cutoff_scheme);
+ serializer->doEnumAsInt(&ir->cutoff_scheme);
if (file_version < 94)
{
- ir->cutoff_scheme = 1 - ir->cutoff_scheme;
+ // Need to invert the scheme order
+ switch (ir->cutoff_scheme)
+ {
+ case (CutoffScheme::Group): ir->cutoff_scheme = CutoffScheme::Verlet; break;
+ case (CutoffScheme::Verlet): ir->cutoff_scheme = CutoffScheme::Group; break;
+ default: GMX_RELEASE_ASSERT(false, "Unhandled cutoff scheme type");
+ }
}
}
else
{
- ir->cutoff_scheme = ecutsGROUP;
+ ir->cutoff_scheme = CutoffScheme::Group;
}
serializer->doInt(&idum); /* used to be ns_type; not used anymore */
serializer->doInt(&ir->nstlist);
serializer->doReal(&ir->rtpi);
serializer->doInt(&ir->nstcomm);
- serializer->doInt(&ir->comm_mode);
+ serializer->doEnumAsInt(&ir->comm_mode);
/* ignore nstcheckpoint */
if (file_version < tpxv_RemoveObsoleteParameters1)
int dummy_nstcalclr = -1;
serializer->doInt(&dummy_nstcalclr);
}
- serializer->doInt(&ir->coulombtype);
+ serializer->doEnumAsInt(&ir->coulombtype);
if (file_version >= 81)
{
- serializer->doInt(&ir->coulomb_modifier);
+ serializer->doEnumAsInt(&ir->coulomb_modifier);
}
else
{
- ir->coulomb_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
+ ir->coulomb_modifier = (ir->cutoff_scheme == CutoffScheme::Verlet ? InteractionModifiers::PotShift
+ : InteractionModifiers::None);
}
serializer->doReal(&ir->rcoulomb_switch);
serializer->doReal(&ir->rcoulomb);
- serializer->doInt(&ir->vdwtype);
+ serializer->doEnumAsInt(&ir->vdwtype);
if (file_version >= 81)
{
- serializer->doInt(&ir->vdw_modifier);
+ serializer->doEnumAsInt(&ir->vdw_modifier);
}
else
{
- ir->vdw_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
+ ir->vdw_modifier = (ir->cutoff_scheme == CutoffScheme::Verlet ? InteractionModifiers::PotShift
+ : InteractionModifiers::None);
}
serializer->doReal(&ir->rvdw_switch);
serializer->doReal(&ir->rvdw);
- serializer->doInt(&ir->eDispCorr);
+ serializer->doEnumAsInt(&ir->eDispCorr);
serializer->doReal(&ir->epsilon_r);
serializer->doReal(&ir->epsilon_rf);
serializer->doReal(&ir->tabext);
{
ir->ewald_rtol_lj = ir->ewald_rtol;
}
- serializer->doInt(&ir->ewald_geometry);
+ serializer->doEnumAsInt(&ir->ewald_geometry);
serializer->doReal(&ir->epsilon_surface);
/* ignore bOptFFT */
if (file_version >= 93)
{
- serializer->doInt(&ir->ljpme_combination_rule);
+ serializer->doEnumAsInt(&ir->ljpme_combination_rule);
}
serializer->doBool(&ir->bContinuation);
serializer->doEnumAsInt(&ir->etc);
ir->nsttcouple = ir->nstcalcenergy;
}
serializer->doEnumAsInt(&ir->epc);
- serializer->doInt(&ir->epct);
+ serializer->doEnumAsInt(&ir->epct);
if (file_version >= 71)
{
serializer->doInt(&ir->nstpcouple);
serializer->doRvec(&ir->compress[XX]);
serializer->doRvec(&ir->compress[YY]);
serializer->doRvec(&ir->compress[ZZ]);
- serializer->doInt(&ir->refcoord_scaling);
+ serializer->doEnumAsInt(&ir->refcoord_scaling);
serializer->doRvec(&ir->posres_com);
serializer->doRvec(&ir->posres_comB);
serializer->doReal(&ir->shake_tol);
- serializer->doInt(&ir->efep);
- do_fepvals(serializer, ir->fepvals, file_version);
+ serializer->doEnumAsInt(&ir->efep);
+ if (serializer->reading())
+ {
+ ir->fepvals = std::make_unique<t_lambda>();
+ }
+ do_fepvals(serializer, ir->fepvals.get(), file_version);
if (file_version >= 79)
{
}
if (ir->bSimTemp)
{
- do_simtempvals(serializer, ir->simtempvals, ir->fepvals->n_lambda, file_version);
+ if (serializer->reading())
+ {
+ ir->simtempvals = std::make_unique<t_simtemp>();
+ }
+ do_simtempvals(serializer, ir->simtempvals.get(), ir->fepvals->n_lambda, file_version);
}
if (file_version >= 79)
}
if (ir->bExpanded)
{
- do_expandedvals(serializer, ir->expandedvals, ir->fepvals, file_version);
+ if (serializer->reading())
+ {
+ ir->expandedvals = std::make_unique<t_expanded>();
+ }
+ do_expandedvals(serializer, ir->expandedvals.get(), ir->fepvals.get(), file_version);
}
- serializer->doInt(&ir->eDisre);
- serializer->doInt(&ir->eDisreWeighting);
+ serializer->doEnumAsInt(&ir->eDisre);
+ serializer->doEnumAsInt(&ir->eDisreWeighting);
serializer->doBool(&ir->bDisreMixed);
serializer->doReal(&ir->dr_fc);
serializer->doReal(&ir->dr_tau);
serializer->doBool(&ir->bShakeSOR);
serializer->doInt(&ir->niter);
serializer->doReal(&ir->fc_stepsize);
- serializer->doInt(&ir->eConstrAlg);
+ serializer->doEnumAsInt(&ir->eConstrAlg);
serializer->doInt(&ir->nProjOrder);
serializer->doReal(&ir->LincsWarnAngle);
serializer->doInt(&ir->nLincsIter);
/* pull stuff */
{
- int ePullOld = 0;
+ PullingAlgorithm ePullOld = PullingAlgorithm::Umbrella;
if (file_version >= tpxv_PullCoordTypeGeom)
{
}
else
{
- serializer->doInt(&ePullOld);
- ir->bPull = (ePullOld > 0);
+ serializer->doEnumAsInt(&ePullOld);
+ ir->bPull = (ePullOld != PullingAlgorithm::Umbrella);
/* We removed the first ePull=ePullNo for the enum */
- ePullOld -= 1;
+ switch (ePullOld)
+ {
+ case (PullingAlgorithm::Umbrella): break; // this is equal to not using pulling
+ case (PullingAlgorithm::Constraint): ePullOld = PullingAlgorithm::Umbrella; break;
+ case (PullingAlgorithm::ConstantForce):
+ ePullOld = PullingAlgorithm::Constraint;
+ break;
+ case (PullingAlgorithm::FlatBottom):
+ ePullOld = PullingAlgorithm::ConstantForce;
+ break;
+ case (PullingAlgorithm::FlatBottomHigh):
+ ePullOld = PullingAlgorithm::FlatBottom;
+ break;
+ case (PullingAlgorithm::External):
+ ePullOld = PullingAlgorithm::FlatBottomHigh;
+ break;
+ case (PullingAlgorithm::Count): ePullOld = PullingAlgorithm::External; break;
+ default: GMX_RELEASE_ASSERT(false, "Unhandled old pull algorithm");
+ }
}
if (ir->bPull)
{
{
if (serializer->reading())
{
- snew(ir->awhParams, 1);
+ ir->awhParams = std::make_unique<gmx::AwhParams>(serializer);
+ }
+ else
+ {
+ ir->awhParams->serialize(serializer);
}
- do_awh(serializer, ir->awhParams, file_version);
}
}
else
{
ir->opts.nhchainlength = 1;
}
- int removedOptsNgacc = 0;
- if (serializer->reading() && file_version < tpxv_RemovedConstantAcceleration)
+ if (serializer->reading() && file_version >= tpxv_RemovedConstantAcceleration
+ && file_version < tpxv_ReaddedConstantAcceleration)
+ {
+ ir->opts.ngacc = 0;
+ }
+ else
{
- serializer->doInt(&removedOptsNgacc);
+ serializer->doInt(&ir->opts.ngacc);
}
serializer->doInt(&ir->opts.ngfrz);
serializer->doInt(&ir->opts.ngener);
snew(ir->opts.anneal_temp, ir->opts.ngtc);
snew(ir->opts.tau_t, ir->opts.ngtc);
snew(ir->opts.nFreeze, ir->opts.ngfrz);
+ snew(ir->opts.acceleration, ir->opts.ngacc);
snew(ir->opts.egp_flags, ir->opts.ngener * ir->opts.ngener);
}
if (ir->opts.ngtc > 0)
{
serializer->doIvecArray(ir->opts.nFreeze, ir->opts.ngfrz);
}
- if (serializer->reading() && file_version < tpxv_RemovedConstantAcceleration && removedOptsNgacc > 0)
+ if (ir->opts.ngacc > 0)
{
- std::vector<gmx::RVec> dummy;
- dummy.resize(removedOptsNgacc);
- serializer->doRvecArray(reinterpret_cast<rvec*>(dummy.data()), removedOptsNgacc);
- ir->useConstantAcceleration = std::any_of(dummy.begin(), dummy.end(), [](const gmx::RVec& vec) {
- return vec[XX] != 0.0 || vec[YY] != 0.0 || vec[ZZ] != 0.0;
- });
+ serializer->doRvecArray(ir->opts.acceleration, ir->opts.ngacc);
}
- else
+ if (serializer->reading())
{
ir->useConstantAcceleration = false;
+ for (int g = 0; g < ir->opts.ngacc; g++)
+ {
+ if (norm2(ir->opts.acceleration[g]) != 0)
+ {
+ ir->useConstantAcceleration = true;
+ }
+ }
}
serializer->doIntArray(ir->opts.egp_flags, ir->opts.ngener * ir->opts.ngener);
/* First read the lists with annealing and npoints for each group */
- serializer->doIntArray(ir->opts.annealing, ir->opts.ngtc);
+ serializer->doEnumArrayAsInt(ir->opts.annealing, ir->opts.ngtc);
serializer->doIntArray(ir->opts.anneal_npoints, ir->opts.ngtc);
for (j = 0; j < (ir->opts.ngtc); j++)
{
/* Walls */
{
serializer->doInt(&ir->nwall);
- serializer->doInt(&ir->wall_type);
+ serializer->doEnumAsInt(&ir->wall_type);
serializer->doReal(&ir->wall_r_linpot);
serializer->doInt(&ir->wall_atomtype[0]);
serializer->doInt(&ir->wall_atomtype[1]);
/* Swap ions */
if (file_version >= tpxv_ComputationalElectrophysiology)
{
- serializer->doInt(&ir->eSwapCoords);
- if (ir->eSwapCoords != eswapNO)
+ serializer->doEnumAsInt(&ir->eSwapCoords);
+ if (ir->eSwapCoords != SwapType::No)
{
if (serializer->reading())
{
serializer->doReal(&iparams->thole.a);
serializer->doReal(&iparams->thole.alpha1);
serializer->doReal(&iparams->thole.alpha2);
- serializer->doReal(&iparams->thole.rfac);
+ if (file_version < tpxv_RemoveTholeRfac)
+ {
+ real noRfac = 0;
+ serializer->doReal(&noRfac);
+ }
+
break;
case F_LJ:
serializer->doReal(&iparams->lj.c6);
serializer->doReal(&atom->qB);
serializer->doUShort(&atom->type);
serializer->doUShort(&atom->typeB);
- serializer->doInt(&atom->ptype);
+ serializer->doEnumAsInt(&atom->ptype);
serializer->doInt(&atom->resind);
serializer->doInt(&atom->atomnumber);
if (serializer->reading())
static void set_disres_npair(gmx_mtop_t* mtop)
{
- gmx_mtop_ilistloop_t iloop;
- int nmol;
-
gmx::ArrayRef<t_iparams> ip = mtop->ffparams.iparams;
- iloop = gmx_mtop_ilistloop_init(mtop);
- while (const InteractionLists* ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
+ for (const auto ilist : IListRange(*mtop))
{
- const InteractionList& il = (*ilist)[F_DISRES];
+ const InteractionList& il = ilist.list()[F_DISRES];
if (!il.empty())
{
}
do_groups(serializer, &mtop->groups, &(mtop->symtab));
- if (file_version < tpxv_RemovedConstantAcceleration)
- {
- mtop->groups.groups[SimulationAtomGroupType::AccelerationUnused].clear();
- mtop->groups.groupNumbers[SimulationAtomGroupType::AccelerationUnused].clear();
- }
mtop->haveMoleculeIndices = true;
serializer->doString(&buf);
gmx_fio_setprecision(fio, tpx->isDouble);
serializer->doInt(&precision);
- fileTag = gmx::formatString("%s", tpx_tag);
+ fileTag = tpx_tag;
}
/* Check versions! */
if (fileTag != tpx_tag)
{
- fprintf(stderr, "Note: file tpx tag '%s', software tpx tag '%s'\n", fileTag.c_str(), tpx_tag);
+ fprintf(stderr, "Note: file tpx tag '%s', software tpx tag '%s'\n", fileTag.c_str(), tpx_tag.c_str());
/* We only support reading tpx files with the same tag as the code
* or tpx files with the release tag and with lower version number.
tpx->fileVersion,
fileTag.c_str(),
tpx_version,
- tpx_tag);
+ tpx_tag.c_str());
}
}
}
// of the tpx file.
if (tpx->bX)
{
- state->flags |= (1 << estX);
+ state->flags |= enumValueToBitMask(StateEntry::X);
}
if (tpx->bV)
{
- state->flags |= (1 << estV);
+ state->flags |= enumValueToBitMask(StateEntry::V);
}
state_change_natoms(state, tpx->natoms);
}
{
if (serializer->reading())
{
- state->flags |= (1 << estX);
+ state->flags |= enumValueToBitMask(StateEntry::X);
}
serializer->doRvecArray(x, tpx->natoms);
}
{
if (serializer->reading())
{
- state->flags |= (1 << estV);
+ state->flags |= enumValueToBitMask(StateEntry::V);
}
if (!v)
{
{
if (tpx->fileVersion < 57)
{
- if (!mtop->moltype[0].ilist[F_DISRES].empty())
- {
- ir->eDisre = edrSimple;
- }
- else
- {
- ir->eDisre = edrNone;
- }
+ ir->eDisre = !mtop->moltype[0].ilist[F_DISRES].empty()
+ ? DistanceRestraintRefinement::Simple
+ : DistanceRestraintRefinement::None;
}
}
}
header.natoms = state.natoms;
header.ngtc = state.ngtc;
header.fep_state = state.fep_state;
- header.lambda = state.lambda[efptFEP];
+ header.lambda = state.lambda[FreeEnergyPerturbationCouplingType::Fep];
header.bIr = ir != nullptr;
header.bTop = mtop != nullptr;
- header.bX = (state.flags & (1 << estX)) != 0;
- header.bV = (state.flags & (1 << estV)) != 0;
+ header.bX = (state.flags & enumValueToBitMask(StateEntry::X)) != 0;
+ header.bV = (state.flags & enumValueToBitMask(StateEntry::V)) != 0;
header.bF = false;
header.bBox = true;
header.fileVersion = tpx_version;
return tpx;
}
-void write_tpx_state(const char* fn, const t_inputrec* ir, const t_state* state, const gmx_mtop_t* mtop)
+void write_tpx_state(const char* fn, const t_inputrec* ir, const t_state* state, const gmx_mtop_t& mtop)
{
/* To write a state, we first need to write the state information to a buffer before
* we append the raw bytes to the file. For this, the header information needs to be
t_fileio* fio;
- TpxFileHeader tpx = populateTpxHeader(*state, ir, mtop);
+ TpxFileHeader tpx = populateTpxHeader(*state, ir, &mtop);
// Long-term we should move to use little endian in files to avoid extra byte swapping,
// but since we just used the default XDR format (which is big endian) for the TPR
// header it would cause third-party libraries reading our raw data to tear their hair
const_cast<t_state*>(state),
nullptr,
nullptr,
- const_cast<gmx_mtop_t*>(mtop));
+ const_cast<gmx_mtop_t*>(&mtop));
std::vector<char> tprBody = tprBodySerializer.finishAndGetBuffer();
tpx.sizeOfTprBody = tprBody.size();
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff