#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_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
{
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
{
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
{
{
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);
}
}
}
{
fepvals->all_lambda[g].resize(fepvals->n_lambda);
serializer->doDoubleArray(fepvals->all_lambda[g].data(), fepvals->n_lambda);
- serializer->doBoolArray(
- fepvals->separate_dvdl.begin(),
- gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, real>::size());
+ serializer->doBoolArray(fepvals->separate_dvdl.begin(), fepvals->separate_dvdl.size());
}
else if (fepvals->init_lambda >= 0)
{
{
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 */
if ((file_version >= 83 && file_version < 90) || file_version >= 92)
}
}
-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);
- if (serializer->reading())
- {
- int temp = 0;
- serializer->doInt(&temp);
- awhBiasParams->bUserData = static_cast<bool>(temp);
- }
- else
- {
- int temp = static_cast<int>(awhBiasParams->bUserData);
- serializer->doInt(&temp);
- }
- 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)
-{
- 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, PullingAlgorithm ePullOld)
{
PullGroupGeometry eGeomOld = PullGroupGeometry::Count;
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)
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)
{
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)
{
- serializer->doInt(&removedOptsNgacc);
+ ir->opts.ngacc = 0;
+ }
+ else
+ {
+ 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);
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());
}
}
}
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