*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017 by 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.
/* This file is completely threadsafe - keep it that way! */
-#include "tpxio.h"
+#include "gromacs/fileio/tpxio.h"
#include <cstdio>
#include <cstdlib>
#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/mdtypes/awh_params.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/mdtypes/state.h"
#include "gromacs/pbcutil/boxutilities.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"
#include "gromacs/utility/snprintf.h"
#include "gromacs/utility/txtdump.h"
-#define TPX_TAG_RELEASE "release"
+#define TPX_TAG_RELEASE "release"
/*! \brief Tag string for the file format written to run input files
* written by this version of the code.
* 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
*/
enum tpxv
{
- tpxv_ComputationalElectrophysiology = 96, /**< support for ion/water position swaps (computational electrophysiology) */
- tpxv_Use64BitRandomSeed, /**< change ld_seed from int to int64_t */
+ tpxv_ComputationalElectrophysiology =
+ 96, /**< support for ion/water position swaps (computational electrophysiology) */
+ tpxv_Use64BitRandomSeed, /**< change ld_seed from int to int64_t */
tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, /**< potentials for supporting coarse-grained force fields */
- tpxv_InteractiveMolecularDynamics, /**< interactive molecular dynamics (IMD) */
- tpxv_RemoveObsoleteParameters1, /**< remove optimize_fft, dihre_fc, nstcheckpoint */
- tpxv_PullCoordTypeGeom, /**< add pull type and geometry per group and flat-bottom */
- tpxv_PullGeomDirRel, /**< add pull geometry direction-relative */
- tpxv_IntermolecularBondeds, /**< permit inter-molecular bonded interactions in the topology */
- tpxv_CompElWithSwapLayerOffset, /**< added parameters for improved CompEl setups */
- tpxv_CompElPolyatomicIonsAndMultipleIonTypes, /**< CompEl now can handle polyatomic ions and more than two types of ions */
- tpxv_RemoveAdress, /**< removed support for AdResS */
- tpxv_PullCoordNGroup, /**< add ngroup to pull coord */
- tpxv_RemoveTwinRange, /**< removed support for twin-range interactions */
- tpxv_ReplacePullPrintCOM12, /**< Replaced print-com-1, 2 with pull-print-com */
- tpxv_PullExternalPotential, /**< Added pull type external potential */
- tpxv_GenericParamsForElectricField, /**< Introduced KeyValueTree and moved electric field parameters */
- tpxv_AcceleratedWeightHistogram, /**< sampling with accelerated weight histogram method (AWH) */
- tpxv_RemoveImplicitSolvation, /**< removed support for implicit solvation */
- tpxv_PullPrevStepCOMAsReference, /**< Enabled using the COM of the pull group of the last frame as reference for PBC */
- tpxv_MimicQMMM, /**< Introduced support for MiMiC QM/MM interface */
- tpxv_PullAverage, /**< Added possibility to output average pull force and position */
- tpxv_GenericInternalParameters, /**< Added internal parameters for mdrun modules*/
- tpxv_VSite2FD, /**< Added 2FD type virtual site */
- tpxv_AddSizeField, /**< Added field with information about the size of the serialized tpr file in bytes, excluding the header */
- tpxv_Count /**< the total number of tpxv versions */
+ tpxv_InteractiveMolecularDynamics, /**< interactive molecular dynamics (IMD) */
+ tpxv_RemoveObsoleteParameters1, /**< remove optimize_fft, dihre_fc, nstcheckpoint */
+ tpxv_PullCoordTypeGeom, /**< add pull type and geometry per group and flat-bottom */
+ tpxv_PullGeomDirRel, /**< add pull geometry direction-relative */
+ tpxv_IntermolecularBondeds, /**< permit inter-molecular bonded interactions in the topology */
+ tpxv_CompElWithSwapLayerOffset, /**< added parameters for improved CompEl setups */
+ tpxv_CompElPolyatomicIonsAndMultipleIonTypes, /**< CompEl now can handle polyatomic ions and more than two types of ions */
+ tpxv_RemoveAdress, /**< removed support for AdResS */
+ tpxv_PullCoordNGroup, /**< add ngroup to pull coord */
+ tpxv_RemoveTwinRange, /**< removed support for twin-range interactions */
+ tpxv_ReplacePullPrintCOM12, /**< Replaced print-com-1, 2 with pull-print-com */
+ tpxv_PullExternalPotential, /**< Added pull type external potential */
+ tpxv_GenericParamsForElectricField, /**< Introduced KeyValueTree and moved electric field parameters */
+ tpxv_AcceleratedWeightHistogram, /**< sampling with accelerated weight histogram method (AWH) */
+ tpxv_RemoveImplicitSolvation, /**< removed support for implicit solvation */
+ tpxv_PullPrevStepCOMAsReference, /**< Enabled using the COM of the pull group of the last frame as reference for PBC */
+ tpxv_MimicQMMM, /**< Introduced support for MiMiC QM/MM interface */
+ tpxv_PullAverage, /**< Added possibility to output average pull force and position */
+ tpxv_GenericInternalParameters, /**< Added internal parameters for mdrun modules*/
+ tpxv_VSite2FD, /**< Added 2FD type virtual site */
+ tpxv_AddSizeField, /**< Added field with information about the size of the serialized tpr file in bytes, excluding the header */
+ tpxv_StoreNonBondedInteractionExclusionGroup, /**< Store the non bonded interaction exclusion group in the topology */
+ 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 */
};
/*! \brief Version number of the file format written to run input
static const int tpx_version = tpxv_Count - 1;
-/* This number should only be increased when you edit the TOPOLOGY section
- * or the HEADER of the tpx format.
+/*! \brief
+ * Enum keeping track of incompatible changes for older TPR versions.
+ *
+ * The enum should be updated with a new field when editing the TOPOLOGY
+ * or HEADER of the tpx format. In particular, updating ftupd or
+ * changing the fields of TprHeaderVersion often trigger such needs.
+ *
* This way we can maintain forward compatibility too for all analysis tools
* and/or external programs that only need to know the atom/residue names,
* charges, and bond connectivity.
*
* In particular, it must be increased when adding new elements to
* ftupd, so that old code can read new .tpr files.
- *
- * Updated for added field that contains the number of bytes of the tpr body, excluding the header.
*/
-static const int tpx_generation = 27;
+enum class TpxGeneration : int
+{
+ Initial = 26, //! First version is 26
+ AddSizeField, //! TPR header modified for writing as a block.
+ AddVSite1, //! ftupd changed to include VSite1 type.
+ Count //! Number of entries.
+};
+
+//! Value of Current TPR generation.
+static const int tpx_generation = static_cast<int>(TpxGeneration::Count) - 1;
/* This number should be the most recent backwards incompatible version
* I.e., if this number is 9, we cannot read tpx version 9 with this code.
static const int tpx_incompatible_version = 57; // GMX4.0 has version 58
-
/* Struct used to maintain tpx compatibility when function types are added */
-typedef struct {
+typedef struct
+{
int fvnr; /* file version number in which the function type first appeared */
int ftype; /* function type */
} t_ftupd;
* obsolete t_interaction_function types. Any data read from such
* fields is discarded. Their names have _NOLONGERUSED appended to
* them to make things clear.
+ *
+ * When adding to or making breaking changes to reading this struct,
+ * update TpxGeneration.
*/
static const t_ftupd ftupd[] = {
- { 70, F_RESTRBONDS },
+ { 70, F_RESTRBONDS },
{ tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRANGLES },
- { 76, F_LINEAR_ANGLES },
+ { 76, F_LINEAR_ANGLES },
{ tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_RESTRDIHS },
{ tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, F_CBTDIHS },
- { 65, F_CMAP },
+ { 65, F_CMAP },
{ 60, F_GB12_NOLONGERUSED },
{ 61, F_GB13_NOLONGERUSED },
{ 61, F_GB14_NOLONGERUSED },
{ 72, F_GBPOL_NOLONGERUSED },
{ 72, F_NPSOLVATION_NOLONGERUSED },
- { 93, F_LJ_RECIP },
- { 90, F_FBPOSRES },
- { 69, F_VTEMP_NOLONGERUSED},
- { 66, F_PDISPCORR },
- { 76, F_ANHARM_POL },
- { 79, F_DVDL_COUL },
- { 79, F_DVDL_VDW, },
- { 79, F_DVDL_BONDED, },
- { 79, F_DVDL_RESTRAINT },
- { 79, F_DVDL_TEMPERATURE },
- { tpxv_GenericInternalParameters, F_DENSITYFITTING },
+ { 93, F_LJ_RECIP },
+ { 76, F_ANHARM_POL },
+ { 90, F_FBPOSRES },
+ { tpxv_VSite1, F_VSITE1 },
{ tpxv_VSite2FD, F_VSITE2FD },
+ { tpxv_GenericInternalParameters, F_DENSITYFITTING },
+ { 69, F_VTEMP_NOLONGERUSED },
+ { 66, F_PDISPCORR },
+ { 79, F_DVDL_COUL },
+ {
+ 79,
+ F_DVDL_VDW,
+ },
+ {
+ 79,
+ F_DVDL_BONDED,
+ },
+ { 79, F_DVDL_RESTRAINT },
+ { 79, F_DVDL_TEMPERATURE },
};
#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_pullgrp_tpx_pre95(gmx::ISerializer *serializer,
- t_pull_group *pgrp,
- t_pull_coord *pcrd)
+static void do_pullgrp_tpx_pre95(gmx::ISerializer* serializer, t_pull_group* pgrp, t_pull_coord* pcrd)
{
rvec tmp;
- serializer->doInt(&pgrp->nat);
- if (serializer->reading())
- {
- snew(pgrp->ind, pgrp->nat);
- }
- serializer->doIntArray(pgrp->ind, pgrp->nat);
- serializer->doInt(&pgrp->nweight);
- if (serializer->reading())
- {
- snew(pgrp->weight, pgrp->nweight);
- }
- serializer->doRealArray(pgrp->weight, pgrp->nweight);
+ int numAtoms = pgrp->ind.size();
+ serializer->doInt(&numAtoms);
+ pgrp->ind.resize(numAtoms);
+ serializer->doIntArray(pgrp->ind.data(), numAtoms);
+ int numWeights = pgrp->weight.size();
+ serializer->doInt(&numWeights);
+ pgrp->weight.resize(numWeights);
+ serializer->doRealArray(pgrp->weight.data(), numWeights);
serializer->doInt(&pgrp->pbcatom);
- serializer->doRvec(&pcrd->vec);
+ serializer->doRvec(&pcrd->vec.as_vec());
clear_rvec(pcrd->origin);
serializer->doRvec(&tmp);
pcrd->init = tmp[0];
serializer->doReal(&pcrd->kB);
}
-static void do_pull_group(gmx::ISerializer *serializer, t_pull_group *pgrp)
+static void do_pull_group(gmx::ISerializer* serializer, t_pull_group* pgrp)
{
- serializer->doInt(&pgrp->nat);
- if (serializer->reading())
- {
- snew(pgrp->ind, pgrp->nat);
- }
- serializer->doIntArray(pgrp->ind, pgrp->nat);
- serializer->doInt(&pgrp->nweight);
- if (serializer->reading())
- {
- snew(pgrp->weight, pgrp->nweight);
- }
- serializer->doRealArray(pgrp->weight, pgrp->nweight);
+ int numAtoms = pgrp->ind.size();
+ serializer->doInt(&numAtoms);
+ pgrp->ind.resize(numAtoms);
+ serializer->doIntArray(pgrp->ind.data(), numAtoms);
+ int numWeights = pgrp->weight.size();
+ serializer->doInt(&numWeights);
+ pgrp->weight.resize(numWeights);
+ serializer->doRealArray(pgrp->weight.data(), numWeights);
serializer->doInt(&pgrp->pbcatom);
}
-static void do_pull_coord(gmx::ISerializer *serializer,
- t_pull_coord *pcrd,
- int file_version,
- int ePullOld, int eGeomOld, ivec dimOld)
+static void do_pull_coord(gmx::ISerializer* serializer,
+ t_pull_coord* pcrd,
+ int file_version,
+ 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
{
- pcrd->externalPotentialProvider = nullptr;
+ pcrd->externalPotentialProvider.clear();
}
}
else
{
if (serializer->reading())
{
- pcrd->externalPotentialProvider = nullptr;
+ pcrd->externalPotentialProvider.clear();
}
}
/* Note that we try to support adding new geometries without
* 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)
{
- serializer->doIntArray(pcrd->group, pcrd->ngroup);
+ serializer->doIntArray(pcrd->group.data(), pcrd->ngroup);
}
else
{
* use the groups for this coord (checks in the pull and WHAM code
* ensure this), we can ignore the groups and set ngroup=0.
*/
- int *dum;
+ int* dum;
snew(dum, pcrd->ngroup);
serializer->doIntArray(dum, pcrd->ngroup);
sfree(dum);
pcrd->ngroup = 0;
}
- serializer->doIvec(&pcrd->dim);
+ 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]);
serializer->doInt(&pcrd->group[3]);
}
- serializer->doIvec(&pcrd->dim);
+ serializer->doIvec(&pcrd->dim.as_vec());
}
else
{
copy_ivec(dimOld, pcrd->dim);
}
}
- serializer->doRvec(&pcrd->origin);
- serializer->doRvec(&pcrd->vec);
+ serializer->doRvec(&pcrd->origin.as_vec());
+ serializer->doRvec(&pcrd->vec.as_vec());
if (file_version >= tpxv_PullCoordTypeGeom)
{
serializer->doBool(&pcrd->bStart);
serializer->doReal(&pcrd->kB);
}
-static void do_expandedvals(gmx::ISerializer *serializer,
- t_expanded *expand,
- t_lambda *fepvals,
- int file_version)
+static void do_expandedvals(gmx::ISerializer* serializer, t_expanded* expand, t_lambda* fepvals, int file_version)
{
- int n_lambda = fepvals->n_lambda;
+ int n_lambda = fepvals->n_lambda;
/* reset the lambda calculation window */
fepvals->lambda_start_n = 0;
{
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);
}
}
-static void do_simtempvals(gmx::ISerializer *serializer,
- t_simtemp *simtemp,
- int n_lambda,
- int file_version)
+static void do_simtempvals(gmx::ISerializer* serializer, t_simtemp* simtemp, int n_lambda, int file_version)
{
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_imd(gmx::ISerializer *serializer, t_IMD *imd)
+static void do_imd(gmx::ISerializer* serializer, t_IMD* imd)
{
serializer->doInt(&imd->nat);
if (serializer->reading())
serializer->doIntArray(imd->ind, imd->nat);
}
-static void do_fepvals(gmx::ISerializer *serializer,
- t_lambda *fepvals,
- int file_version)
+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;
+ 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[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);
{
fepvals->sc_r_power = 6.0;
}
+ if (fepvals->sc_r_power != 6.0)
+ {
+ gmx_fatal(FARGS, "sc-r-power=48 is no longer supported");
+ }
serializer->doReal(&fepvals->sc_sigma);
if (serializer->reading())
{
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 */
if ((file_version >= 83 && file_version < 90) || file_version >= 92)
{
serializer->doInt(&fepvals->lambda_neighbors);
- if ( (fepvals->lambda_neighbors >= 0) && (fepvals->init_fep_state >= 0) &&
- (fepvals->init_lambda < 0) )
+ if ((fepvals->lambda_neighbors >= 0) && (fepvals->init_fep_state >= 0)
+ && (fepvals->init_lambda < 0))
{
- fepvals->lambda_start_n = (fepvals->init_fep_state -
- fepvals->lambda_neighbors);
- fepvals->lambda_stop_n = (fepvals->init_fep_state +
- fepvals->lambda_neighbors + 1);
+ fepvals->lambda_start_n = (fepvals->init_fep_state - fepvals->lambda_neighbors);
+ fepvals->lambda_stop_n = (fepvals->init_fep_state + fepvals->lambda_neighbors + 1);
if (fepvals->lambda_start_n < 0)
{
fepvals->lambda_start_n = 0;
}
}
-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)
-{
- 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)
+static void do_pull(gmx::ISerializer* serializer, pull_params_t* pull, int file_version, PullingAlgorithm 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);
{
pull->bSetPbcRefToPrevStepCOM = FALSE;
}
- if (serializer->reading())
- {
- snew(pull->group, pull->ngroup);
- snew(pull->coord, pull->ncoord);
- }
+ pull->group.resize(pull->ngroup);
+ pull->coord.resize(pull->ncoord);
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++)
{
/* We read and ignore a pull coordinate for group 0 */
- do_pullgrp_tpx_pre95(serializer, &pull->group[g], &pull->coord[std::max(g-1, 0)]);
+ do_pullgrp_tpx_pre95(serializer, &pull->group[g], &pull->coord[std::max(g - 1, 0)]);
if (g > 0)
{
- pull->coord[g-1].group[0] = 0;
- pull->coord[g-1].group[1] = g;
+ pull->coord[g - 1].group[0] = 0;
+ pull->coord[g - 1].group[1] = g;
}
}
- pull->bPrintCOM = (pull->group[0].nat > 0);
+ pull->bPrintCOM = (!pull->group[0].ind.empty());
}
else
{
}
for (g = 0; g < pull->ncoord; g++)
{
- do_pull_coord(serializer, &pull->coord[g],
- file_version, ePullOld, eGeomOld, dimOld);
+ 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)
{
gmx_bool v;
- v = pull->bXOutAverage;
+ v = pull->bXOutAverage;
serializer->doBool(&v);
pull->bXOutAverage = v;
v = pull->bFOutAverage;
}
-static void do_rotgrp(gmx::ISerializer *serializer,
- t_rotgrp *rotg)
+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);
}
-static void do_rot(gmx::ISerializer *serializer,
- t_rot *rot)
+static void do_rot(gmx::ISerializer* serializer, t_rot* rot)
{
int g;
}
-static void do_swapgroup(gmx::ISerializer *serializer,
- t_swapGroup *g)
+static void do_swapgroup(gmx::ISerializer* serializer, t_swapGroup* g)
{
/* Name of the group or molecule */
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)
+static void do_swapcoords_tpx(gmx::ISerializer* serializer, t_swapcoords* swap, int file_version)
{
/* Enums for better readability of the code */
- enum {
- eCompA = 0, eCompB
+ enum
+ {
+ eCompA = 0,
+ eCompB
};
- enum {
- eChannel0 = 0, eChannel1
+ enum
+ {
+ eChannel0 = 0,
+ eChannel1
};
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++)
{
serializer->doInt(&swap->grp[3].nmolReq[j]); // group 3 = anions
serializer->doInt(&swap->grp[4].nmolReq[j]); // group 4 = cations
}
- } /* End support reading older CompEl .tpr files */
+ } /* End support reading older CompEl .tpr files */
if (file_version >= tpxv_CompElWithSwapLayerOffset)
{
serializer->doReal(&swap->bulkOffset[eCompA]);
serializer->doReal(&swap->bulkOffset[eCompB]);
}
-
}
-static void do_legacy_efield(gmx::ISerializer *serializer, gmx::KeyValueTreeObjectBuilder *root)
+static void do_legacy_efield(gmx::ISerializer* serializer, gmx::KeyValueTreeObjectBuilder* root)
{
- const char *const dimName[] = { "x", "y", "z" };
+ const char* const dimName[] = { "x", "y", "z" };
- auto appliedForcesObj = root->addObject("applied-forces");
- auto efieldObj = appliedForcesObj.addObject("electric-field");
+ auto appliedForcesObj = root->addObject("applied-forces");
+ auto efieldObj = appliedForcesObj.addObject("electric-field");
// The content of the tpr file for this feature has
// been the same since gromacs 4.0 that was used for
// developing.
int n, nt;
serializer->doInt(&n);
serializer->doInt(&nt);
- std::vector<real> aa(n+1), phi(nt+1), at(nt+1), phit(nt+1);
- serializer->doRealArray(aa.data(), n);
+ std::vector<real> aa(n + 1), phi(nt + 1), at(nt + 1), phit(nt + 1);
+ serializer->doRealArray(aa.data(), n);
serializer->doRealArray(phi.data(), n);
- serializer->doRealArray(at.data(), nt);
+ serializer->doRealArray(at.data(), nt);
serializer->doRealArray(phit.data(), nt);
if (n > 0)
{
if (n > 1 || nt > 1)
{
- gmx_fatal(FARGS, "Can not handle tpr files with more than one electric field term per direction.");
+ gmx_fatal(FARGS,
+ "Can not handle tpr files with more than one electric field term per "
+ "direction.");
}
auto dimObj = efieldObj.addObject(dimName[j]);
dimObj.addValue<real>("E0", aa[0]);
}
-static void do_inputrec(gmx::ISerializer *serializer,
- t_inputrec *ir,
- int file_version)
+static void do_inputrec(gmx::ISerializer* serializer, t_inputrec* ir, int file_version)
{
int i, j, k, idum = 0;
real rdum;
if (file_version != tpx_version)
{
/* Give a warning about features that are not accessible */
- fprintf(stderr, "Note: file tpx version %d, software tpx version %d\n",
- file_version, tpx_version);
+ fprintf(stderr, "Note: file tpx version %d, software tpx version %d\n", file_version, tpx_version);
}
if (file_version == 0)
gmx::KeyValueTreeObjectBuilder paramsObj = paramsBuilder.rootObject();
/* Basic inputrec stuff */
- serializer->doInt(&ir->eI);
+ serializer->doEnumAsInt(&ir->eI);
if (file_version >= 62)
{
serializer->doInt64(&ir->nsteps);
serializer->doInt(&ir->simulation_part);
+ if (file_version >= tpxv_MTS)
+ {
+ serializer->doBool(&ir->useMts);
+ int numLevels = ir->mtsLevels.size();
+ if (ir->useMts)
+ {
+ serializer->doInt(&numLevels);
+ }
+ ir->mtsLevels.resize(numLevels);
+ for (auto& mtsLevel : ir->mtsLevels)
+ {
+ int forceGroups = mtsLevel.forceGroups.to_ulong();
+ serializer->doInt(&forceGroups);
+ mtsLevel.forceGroups = std::bitset<static_cast<int>(gmx::MtsForceGroups::Count)>(forceGroups);
+ serializer->doInt(&mtsLevel.stepFactor);
+ }
+ }
+ else
+ {
+ ir->useMts = false;
+ ir->mtsLevels.clear();
+ }
+
if (file_version >= 67)
{
serializer->doInt(&ir->nstcalcenergy);
}
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)
real dummy_rlistlong = -1;
serializer->doReal(&dummy_rlistlong);
- if (ir->rlist > 0 && (dummy_rlistlong == 0 || dummy_rlistlong > ir->rlist))
- {
- // Get mdrun to issue an error (regardless of
- // ir->cutoff_scheme).
- ir->useTwinRange = true;
- }
- else
- {
- // grompp used to set rlistlong actively. Users were
- // probably also confused and set rlistlong == rlist.
- // However, in all remaining cases, it is safe to let
- // mdrun proceed normally.
- ir->useTwinRange = false;
- }
+ ir->useTwinRange = (ir->rlist > 0 && (dummy_rlistlong == 0 || dummy_rlistlong > ir->rlist));
+ // When true, this forces mdrun to issue an error (regardless of
+ // ir->cutoff_scheme).
+ //
+ // Otherwise, grompp used to set rlistlong actively. Users
+ // were probably also confused and set rlistlong == rlist.
+ // However, in all remaining cases, it is safe to let
+ // mdrun proceed normally.
}
}
else
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->doInt(&ir->etc);
+ serializer->doEnumAsInt(&ir->etc);
/* before version 18, ir->etc was a gmx_bool (ir->btc),
* but the values 0 and 1 still mean no and
* berendsen temperature coupling, respectively.
{
ir->nsttcouple = ir->nstcalcenergy;
}
- serializer->doInt(&ir->epc);
- serializer->doInt(&ir->epct);
+ serializer->doEnumAsInt(&ir->epc);
+ 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)
{
serializer->doBool(&ir->bExpanded);
- if (ir->bExpanded)
- {
- ir->bExpanded = TRUE;
- }
- else
- {
- ir->bExpanded = FALSE;
- }
}
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->pull, 1);
+ ir->pull = std::make_unique<pull_params_t>();
}
- do_pull(serializer, ir->pull, file_version, ePullOld);
+ do_pull(serializer, ir->pull.get(), file_version, ePullOld);
}
}
{
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;
}
- serializer->doInt(&ir->opts.ngacc);
+ if (serializer->reading() && file_version >= tpxv_RemovedConstantAcceleration
+ && file_version < tpxv_ReaddedConstantAcceleration)
+ {
+ ir->opts.ngacc = 0;
+ }
+ else
+ {
+ serializer->doInt(&ir->opts.ngacc);
+ }
serializer->doInt(&ir->opts.ngfrz);
serializer->doInt(&ir->opts.ngener);
if (serializer->reading())
{
- snew(ir->opts.nrdf, ir->opts.ngtc);
- snew(ir->opts.ref_t, ir->opts.ngtc);
+ snew(ir->opts.nrdf, ir->opts.ngtc);
+ snew(ir->opts.ref_t, ir->opts.ngtc);
snew(ir->opts.annealing, ir->opts.ngtc);
snew(ir->opts.anneal_npoints, ir->opts.ngtc);
snew(ir->opts.anneal_time, ir->opts.ngtc);
snew(ir->opts.anneal_temp, ir->opts.ngtc);
- snew(ir->opts.tau_t, ir->opts.ngtc);
+ snew(ir->opts.tau_t, ir->opts.ngtc);
snew(ir->opts.nFreeze, ir->opts.ngfrz);
- snew(ir->opts.acc, ir->opts.ngacc);
- snew(ir->opts.egp_flags, ir->opts.ngener*ir->opts.ngener);
+ snew(ir->opts.acceleration, ir->opts.ngacc);
+ snew(ir->opts.egp_flags, ir->opts.ngener * ir->opts.ngener);
}
if (ir->opts.ngtc > 0)
{
}
if (ir->opts.ngacc > 0)
{
- serializer->doRvecArray(ir->opts.acc, ir->opts.ngacc);
+ serializer->doRvecArray(ir->opts.acceleration, ir->opts.ngacc);
}
- serializer->doIntArray(ir->opts.egp_flags,
- ir->opts.ngener*ir->opts.ngener);
+ 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())
{
}
}
- /* QMMM stuff */
+ /* QMMM reading - despite defunct we require reading for backwards
+ * compability and correct serialization
+ */
{
serializer->doBool(&ir->bQMMM);
- serializer->doInt(&ir->QMMMscheme);
- serializer->doReal(&ir->scalefactor);
+ int qmmmScheme;
+ serializer->doInt(&qmmmScheme);
+ real unusedScalefactor;
+ serializer->doReal(&unusedScalefactor);
+
+ // this is still used in Mimic
serializer->doInt(&ir->opts.ngQM);
- if (serializer->reading())
- {
- snew(ir->opts.QMmethod, ir->opts.ngQM);
- snew(ir->opts.QMbasis, ir->opts.ngQM);
- snew(ir->opts.QMcharge, ir->opts.ngQM);
- snew(ir->opts.QMmult, ir->opts.ngQM);
- snew(ir->opts.bSH, ir->opts.ngQM);
- snew(ir->opts.CASorbitals, ir->opts.ngQM);
- snew(ir->opts.CASelectrons, ir->opts.ngQM);
- snew(ir->opts.SAon, ir->opts.ngQM);
- snew(ir->opts.SAoff, ir->opts.ngQM);
- snew(ir->opts.SAsteps, ir->opts.ngQM);
- }
if (ir->opts.ngQM > 0 && ir->bQMMM)
{
- serializer->doIntArray(ir->opts.QMmethod, ir->opts.ngQM);
- serializer->doIntArray(ir->opts.QMbasis, ir->opts.ngQM);
- serializer->doIntArray(ir->opts.QMcharge, ir->opts.ngQM);
- serializer->doIntArray(ir->opts.QMmult, ir->opts.ngQM);
- serializer->doBoolArray(ir->opts.bSH, ir->opts.ngQM);
- serializer->doIntArray(ir->opts.CASorbitals, ir->opts.ngQM);
- serializer->doIntArray(ir->opts.CASelectrons, ir->opts.ngQM);
- serializer->doRealArray(ir->opts.SAon, ir->opts.ngQM);
- serializer->doRealArray(ir->opts.SAoff, ir->opts.ngQM);
- serializer->doIntArray(ir->opts.SAsteps, ir->opts.ngQM);
/* We leave in dummy i/o for removed parameters to avoid
- * changing the tpr format for every QMMM change.
+ * changing the tpr format.
*/
- std::vector<int> dummy(ir->opts.ngQM, 0);
- serializer->doIntArray(dummy.data(), ir->opts.ngQM);
- serializer->doIntArray(dummy.data(), ir->opts.ngQM);
+ std::vector<int> dummyIntVec(4 * ir->opts.ngQM, 0);
+ serializer->doIntArray(dummyIntVec.data(), dummyIntVec.size());
+ dummyIntVec.clear();
+
+ // std::vector<bool> has no data()
+ std::vector<char> dummyBoolVec(ir->opts.ngQM * sizeof(bool) / sizeof(char));
+ serializer->doBoolArray(reinterpret_cast<bool*>(dummyBoolVec.data()), dummyBoolVec.size());
+ dummyBoolVec.clear();
+
+ dummyIntVec.resize(2 * ir->opts.ngQM, 0);
+ serializer->doIntArray(dummyIntVec.data(), dummyIntVec.size());
+ dummyIntVec.clear();
+
+ std::vector<real> dummyRealVec(2 * ir->opts.ngQM, 0);
+ serializer->doRealArray(dummyRealVec.data(), dummyRealVec.size());
+ dummyRealVec.clear();
+
+ dummyIntVec.resize(3 * ir->opts.ngQM, 0);
+ serializer->doIntArray(dummyIntVec.data(), dummyIntVec.size());
+ dummyIntVec.clear();
}
/* end of QMMM stuff */
}
{
if (serializer->reading())
{
- paramsObj.mergeObject(
- gmx::deserializeKeyValueTree(serializer));
+ paramsObj.mergeObject(gmx::deserializeKeyValueTree(serializer));
}
else
{
{
if (serializer->reading())
{
- ir->internalParameters = std::make_unique<gmx::KeyValueTreeObject>(gmx::deserializeKeyValueTree(serializer));
+ ir->internalParameters =
+ std::make_unique<gmx::KeyValueTreeObject>(gmx::deserializeKeyValueTree(serializer));
}
else
{
}
-static void do_harm(gmx::ISerializer *serializer, t_iparams *iparams)
+static void do_harm(gmx::ISerializer* serializer, t_iparams* iparams)
{
serializer->doReal(&iparams->harmonic.rA);
serializer->doReal(&iparams->harmonic.krA);
serializer->doReal(&iparams->harmonic.krB);
}
-static void do_iparams(gmx::ISerializer *serializer,
- t_functype ftype,
- t_iparams *iparams,
- int file_version)
+static void do_iparams(gmx::ISerializer* serializer, t_functype ftype, t_iparams* iparams, int file_version)
{
- int idum;
- real rdum;
+ int idum;
+ real rdum;
switch (ftype)
{
serializer->doReal(&iparams->cubic.kb);
serializer->doReal(&iparams->cubic.kcub);
break;
- case F_CONNBONDS:
- break;
- case F_POLARIZATION:
- serializer->doReal(&iparams->polarize.alpha);
- break;
+ case F_CONNBONDS: break;
+ case F_POLARIZATION: serializer->doReal(&iparams->polarize.alpha); break;
case F_ANHARM_POL:
serializer->doReal(&iparams->anharm_polarize.alpha);
serializer->doReal(&iparams->anharm_polarize.drcut);
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(&iparams->fbposres.r);
serializer->doReal(&iparams->fbposres.k);
break;
- case F_CBTDIHS:
- serializer->doRealArray(iparams->cbtdihs.cbtcA, NR_CBTDIHS);
- break;
+ case F_CBTDIHS: serializer->doRealArray(iparams->cbtdihs.cbtcA, NR_CBTDIHS); break;
case F_RBDIHS:
- serializer->doRealArray(iparams->rbdihs.rbcA, NR_RBDIHS);
- serializer->doRealArray(iparams->rbdihs.rbcB, NR_RBDIHS);
- break;
+ // Fall-through intended
case F_FOURDIHS:
/* Fourier dihedrals are internally represented
* as Ryckaert-Bellemans since those are faster to compute.
serializer->doReal(&iparams->settle.doh);
serializer->doReal(&iparams->settle.dhh);
break;
+ case F_VSITE1: break; // VSite1 has 0 parameters
case F_VSITE2:
- case F_VSITE2FD:
- serializer->doReal(&iparams->vsite.a);
- break;
+ case F_VSITE2FD: serializer->doReal(&iparams->vsite.a); break;
case F_VSITE3:
case F_VSITE3FD:
case F_VSITE3FAD:
serializer->doInt(&iparams->cmap.cmapB);
break;
default:
- gmx_fatal(FARGS, "unknown function type %d (%s) in %s line %d",
- ftype, interaction_function[ftype].name, __FILE__, __LINE__);
+ gmx_fatal(FARGS,
+ "unknown function type %d (%s) in %s line %d",
+ ftype,
+ interaction_function[ftype].name,
+ __FILE__,
+ __LINE__);
}
}
-static void do_ilist(gmx::ISerializer *serializer, InteractionList *ilist)
+static void do_ilist(gmx::ISerializer* serializer, InteractionList* ilist)
{
int nr = ilist->size();
serializer->doInt(&nr);
serializer->doIntArray(ilist->iatoms.data(), ilist->size());
}
-static void do_ffparams(gmx::ISerializer *serializer,
- gmx_ffparams_t *ffparams,
- int file_version)
+static void do_ffparams(gmx::ISerializer* serializer, gmx_ffparams_t* ffparams, int file_version)
{
serializer->doInt(&ffparams->atnr);
int numTypes = ffparams->numTypes();
for (int k = 0; k < NFTUPD; k++)
{
/* Compare the read file_version to the update table */
- if ((file_version < ftupd[k].fvnr) &&
- (ffparams->functype[i] >= ftupd[k].ftype))
+ if ((file_version < ftupd[k].fvnr) && (ffparams->functype[i] >= ftupd[k].ftype))
{
ffparams->functype[i] += 1;
}
}
}
- do_iparams(serializer, ffparams->functype[i], &ffparams->iparams[i],
- file_version);
+ do_iparams(serializer, ffparams->functype[i], &ffparams->iparams[i], file_version);
}
}
-static void add_settle_atoms(InteractionList *ilist)
+static void add_settle_atoms(InteractionList* ilist)
{
int i;
/* Settle used to only store the first atom: add the other two */
- ilist->iatoms.resize(2*ilist->size());
- for (i = ilist->size()/4 - 1; i >= 0; i--)
+ ilist->iatoms.resize(2 * ilist->size());
+ for (i = ilist->size() / 4 - 1; i >= 0; i--)
{
- ilist->iatoms[4*i+0] = ilist->iatoms[2*i+0];
- ilist->iatoms[4*i+1] = ilist->iatoms[2*i+1];
- ilist->iatoms[4*i+2] = ilist->iatoms[2*i+1] + 1;
- ilist->iatoms[4*i+3] = ilist->iatoms[2*i+1] + 2;
+ ilist->iatoms[4 * i + 0] = ilist->iatoms[2 * i + 0];
+ ilist->iatoms[4 * i + 1] = ilist->iatoms[2 * i + 1];
+ ilist->iatoms[4 * i + 2] = ilist->iatoms[2 * i + 1] + 1;
+ ilist->iatoms[4 * i + 3] = ilist->iatoms[2 * i + 1] + 2;
}
}
-static void do_ilists(gmx::ISerializer *serializer,
- InteractionLists *ilists,
- int file_version)
+static void do_ilists(gmx::ISerializer* serializer, InteractionLists* ilists, int file_version)
{
GMX_RELEASE_ASSERT(ilists, "Need a valid ilists object");
- GMX_RELEASE_ASSERT(ilists->size() == F_NRE, "The code needs to be in sync with InteractionLists");
+ GMX_RELEASE_ASSERT(ilists->size() == F_NRE,
+ "The code needs to be in sync with InteractionLists");
for (int j = 0; j < F_NRE; j++)
{
- InteractionList &ilist = (*ilists)[j];
+ InteractionList& ilist = (*ilists)[j];
gmx_bool bClear = FALSE;
if (serializer->reading())
{
else
{
do_ilist(serializer, &ilist);
- if (file_version < 78 && j == F_SETTLE && ilist.size() > 0)
+ if (file_version < 78 && j == F_SETTLE && !ilist.empty())
{
add_settle_atoms(&ilist);
}
}
}
-static void do_block(gmx::ISerializer *serializer, t_block *block)
+static void do_block(gmx::ISerializer* serializer, t_block* block)
{
serializer->doInt(&block->nr);
if (serializer->reading())
{
sfree(block->index);
}
- block->nalloc_index = block->nr+1;
+ block->nalloc_index = block->nr + 1;
snew(block->index, block->nalloc_index);
}
- serializer->doIntArray(block->index, block->nr+1);
+ serializer->doIntArray(block->index, block->nr + 1);
}
-static void do_blocka(gmx::ISerializer *serializer, t_blocka *block)
+static void doListOfLists(gmx::ISerializer* serializer, gmx::ListOfLists<int>* listOfLists)
{
- serializer->doInt(&block->nr);
- serializer->doInt(&block->nra);
+ int numLists = listOfLists->ssize();
+ serializer->doInt(&numLists);
+ int numElements = listOfLists->elementsView().ssize();
+ serializer->doInt(&numElements);
if (serializer->reading())
{
- block->nalloc_index = block->nr+1;
- snew(block->index, block->nalloc_index);
- block->nalloc_a = block->nra;
- snew(block->a, block->nalloc_a);
+ std::vector<int> listRanges(numLists + 1);
+ serializer->doIntArray(listRanges.data(), numLists + 1);
+ std::vector<int> elements(numElements);
+ serializer->doIntArray(elements.data(), numElements);
+ *listOfLists = gmx::ListOfLists<int>(std::move(listRanges), std::move(elements));
+ }
+ else
+ {
+ serializer->doIntArray(const_cast<int*>(listOfLists->listRangesView().data()), numLists + 1);
+ serializer->doIntArray(const_cast<int*>(listOfLists->elementsView().data()), numElements);
}
- serializer->doIntArray(block->index, block->nr+1);
- serializer->doIntArray(block->a, block->nra);
}
/* This is a primitive routine to make it possible to translate atomic numbers
* to element names when reading TPR files, without making the Gromacs library
* directory a dependency on mdrun (which is the case if we need elements.dat).
*/
-static const char *
-atomicnumber_to_element(int atomicnumber)
+static const char* atomicnumber_to_element(int atomicnumber)
{
- const char * p;
+ const char* p;
/* This does not have to be complete, so we only include elements likely
* to occur in PDB files.
*/
switch (atomicnumber)
{
- case 1: p = "H"; break;
- case 5: p = "B"; break;
- case 6: p = "C"; break;
- case 7: p = "N"; break;
- case 8: p = "O"; break;
- case 9: p = "F"; break;
+ case 1: p = "H"; break;
+ case 5: p = "B"; break;
+ case 6: p = "C"; break;
+ case 7: p = "N"; break;
+ case 8: p = "O"; break;
+ case 9: p = "F"; break;
case 11: p = "Na"; break;
case 12: p = "Mg"; break;
- case 15: p = "P"; break;
- case 16: p = "S"; break;
+ case 15: p = "P"; break;
+ case 16: p = "S"; break;
case 17: p = "Cl"; break;
case 18: p = "Ar"; break;
- case 19: p = "K"; break;
+ case 19: p = "K"; break;
case 20: p = "Ca"; break;
case 25: p = "Mn"; break;
case 26: p = "Fe"; break;
case 30: p = "Zn"; break;
case 35: p = "Br"; break;
case 47: p = "Ag"; break;
- default: p = ""; break;
+ default: p = ""; break;
}
return p;
}
-static void do_atom(gmx::ISerializer *serializer, t_atom *atom)
+static void do_atom(gmx::ISerializer* serializer, t_atom* atom)
{
serializer->doReal(&atom->m);
serializer->doReal(&atom->q);
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 do_grps(gmx::ISerializer *serializer,
- gmx::ArrayRef<AtomGroupIndices> grps)
+static void do_grps(gmx::ISerializer* serializer, gmx::ArrayRef<AtomGroupIndices> grps)
{
- for (auto &group : grps)
+ for (auto& group : grps)
{
int size = group.size();
serializer->doInt(&size);
}
}
-static void do_symstr(gmx::ISerializer *serializer, char ***nm, t_symtab *symtab)
+static void do_symstr(gmx::ISerializer* serializer, char*** nm, t_symtab* symtab)
{
int ls;
}
}
-static void do_strstr(gmx::ISerializer *serializer,
- int nstr,
- char ***nm,
- t_symtab *symtab)
+static void do_strstr(gmx::ISerializer* serializer, int nstr, char*** nm, t_symtab* symtab)
{
- int j;
+ int j;
for (j = 0; (j < nstr); j++)
{
}
}
-static void do_resinfo(gmx::ISerializer *serializer,
- int n,
- t_resinfo *ri,
- t_symtab *symtab,
- int file_version)
+static void do_resinfo(gmx::ISerializer* serializer, int n, t_resinfo* ri, t_symtab* symtab, int file_version)
{
- int j;
+ int j;
for (j = 0; (j < n); j++)
{
}
}
-static void do_atoms(gmx::ISerializer *serializer,
- t_atoms *atoms,
- t_symtab *symtab,
- int file_version)
+static void do_atoms(gmx::ISerializer* serializer, t_atoms* atoms, t_symtab* symtab, int file_version)
{
int i;
}
else
{
- GMX_RELEASE_ASSERT(atoms->haveMass && atoms->haveCharge && atoms->haveType && atoms->haveBState, "Mass, charge, atomtype and B-state parameters should be present in t_atoms when writing a tpr file");
+ GMX_RELEASE_ASSERT(atoms->haveMass && atoms->haveCharge && atoms->haveType && atoms->haveBState,
+ "Mass, charge, atomtype and B-state parameters should be present in "
+ "t_atoms when writing a tpr file");
}
for (i = 0; (i < atoms->nr); i++)
{
do_resinfo(serializer, atoms->nres, atoms->resinfo, symtab, file_version);
}
-static void do_groups(gmx::ISerializer *serializer,
- SimulationGroups *groups,
- t_symtab *symtab)
+static void do_groups(gmx::ISerializer* serializer, SimulationGroups* groups, t_symtab* symtab)
{
do_grps(serializer, groups->groups);
int numberOfGroupNames = groups->groupNames.size();
}
}
-static void do_atomtypes(gmx::ISerializer *serializer, t_atomtypes *atomtypes,
- int file_version)
+static void do_atomtypes(gmx::ISerializer* serializer, t_atomtypes* atomtypes, int file_version)
{
- int j;
+ int j;
serializer->doInt(&atomtypes->nr);
j = atomtypes->nr;
}
}
-static void do_symtab(gmx::ISerializer *serializer, t_symtab *symtab)
+static void do_symtab(gmx::ISerializer* serializer, t_symtab* symtab)
{
int i, nr;
- t_symbuf *symbuf;
+ t_symbuf* symbuf;
serializer->doInt(&symtab->nr);
- nr = symtab->nr;
+ nr = symtab->nr;
if (serializer->reading())
{
snew(symtab->symbuf, 1);
std::string buf = symbuf->buf[i];
serializer->doString(&buf);
}
- nr -= i;
+ nr -= i;
symbuf = symbuf->next;
}
if (nr != 0)
}
}
-static void do_cmap(gmx::ISerializer *serializer, gmx_cmap_t *cmap_grid)
+static void do_cmap(gmx::ISerializer* serializer, gmx_cmap_t* cmap_grid)
{
int ngrid = cmap_grid->cmapdata.size();
for (int i = 0; i < ngrid; i++)
{
- cmap_grid->cmapdata[i].cmap.resize(4*nelem);
+ cmap_grid->cmapdata[i].cmap.resize(4 * nelem);
}
}
{
for (int j = 0; j < nelem; j++)
{
- serializer->doReal(&cmap_grid->cmapdata[i].cmap[j*4]);
- serializer->doReal(&cmap_grid->cmapdata[i].cmap[j*4+1]);
- serializer->doReal(&cmap_grid->cmapdata[i].cmap[j*4+2]);
- serializer->doReal(&cmap_grid->cmapdata[i].cmap[j*4+3]);
+ serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4]);
+ serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4 + 1]);
+ serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4 + 2]);
+ serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4 + 3]);
}
}
}
-static void do_moltype(gmx::ISerializer *serializer,
- gmx_moltype_t *molt,
- t_symtab *symtab,
- int file_version)
+static void do_moltype(gmx::ISerializer* serializer, gmx_moltype_t* molt, t_symtab* symtab, int file_version)
{
do_symstr(serializer, &(molt->name), symtab);
do_ilists(serializer, &molt->ilist, file_version);
- do_block(serializer, &molt->cgs);
+ /* TODO: Remove the obsolete charge group index from the file */
+ t_block cgs;
+ cgs.nr = molt->atoms.nr;
+ cgs.nalloc_index = cgs.nr + 1;
+ snew(cgs.index, cgs.nalloc_index);
+ for (int i = 0; i < cgs.nr + 1; i++)
+ {
+ cgs.index[i] = i;
+ }
+ do_block(serializer, &cgs);
+ sfree(cgs.index);
/* This used to be in the atoms struct */
- do_blocka(serializer, &molt->excls);
+ doListOfLists(serializer, &molt->excls);
}
-static void do_molblock(gmx::ISerializer *serializer,
- gmx_molblock_t *molb,
- int numAtomsPerMolecule)
+static void do_molblock(gmx::ISerializer* serializer, gmx_molblock_t* molb, int numAtomsPerMolecule)
{
serializer->doInt(&molb->type);
serializer->doInt(&molb->nmol);
}
serializer->doRvecArray(as_rvec_array(molb->posres_xB.data()), numPosres_xB);
}
-
}
-static void set_disres_npair(gmx_mtop_t *mtop)
+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.size() > 0)
+ if (!il.empty())
{
gmx::ArrayRef<const int> a = il.iatoms;
int npair = 0;
for (int i = 0; i < il.size(); i += 3)
{
npair++;
- if (i+3 == il.size() || ip[a[i]].disres.label != ip[a[i+3]].disres.label)
+ if (i + 3 == il.size() || ip[a[i]].disres.label != ip[a[i + 3]].disres.label)
{
ip[a[i]].disres.npair = npair;
npair = 0;
}
}
-static void do_mtop(gmx::ISerializer *serializer,
- gmx_mtop_t *mtop,
- int file_version)
+static void do_mtop(gmx::ISerializer* serializer, gmx_mtop_t* mtop, int file_version)
{
do_symtab(serializer, &(mtop->symtab));
{
mtop->moltype.resize(nmoltype);
}
- for (gmx_moltype_t &moltype : mtop->moltype)
+ for (gmx_moltype_t& moltype : mtop->moltype)
{
do_moltype(serializer, &moltype, &mtop->symtab, file_version);
}
{
mtop->molblock.resize(nmolblock);
}
- for (gmx_molblock_t &molblock : mtop->molblock)
+ for (gmx_molblock_t& molblock : mtop->molblock)
{
int numAtomsPerMolecule = (serializer->reading() ? 0 : mtop->moltype[molblock.type].atoms.nr);
do_molblock(serializer, &molblock, numAtomsPerMolecule);
mtop->bIntermolecularInteractions = FALSE;
}
- do_atomtypes (serializer, &(mtop->atomtypes), file_version);
+ do_atomtypes(serializer, &(mtop->atomtypes), file_version);
if (file_version >= 65)
{
mtop->haveMoleculeIndices = true;
+ if (file_version >= tpxv_StoreNonBondedInteractionExclusionGroup)
+ {
+ std::int64_t intermolecularExclusionGroupSize = gmx::ssize(mtop->intermolecularExclusionGroup);
+ serializer->doInt64(&intermolecularExclusionGroupSize);
+ GMX_RELEASE_ASSERT(intermolecularExclusionGroupSize >= 0,
+ "Number of atoms with excluded intermolecular non-bonded interactions "
+ "is negative.");
+ mtop->intermolecularExclusionGroup.resize(intermolecularExclusionGroupSize); // no effect when writing
+ serializer->doIntArray(mtop->intermolecularExclusionGroup.data(),
+ mtop->intermolecularExclusionGroup.size());
+ }
+
if (serializer->reading())
{
close_symtab(&(mtop->symtab));
* \param[in,out] fio File handle.
* \param[in] TopOnlyOK If not reading \p ir is fine or not.
*/
-static void do_tpxheader(gmx::FileIOXdrSerializer *serializer,
- TpxFileHeader *tpx,
- const char *filename,
- t_fileio *fio,
+static void do_tpxheader(gmx::FileIOXdrSerializer* serializer,
+ TpxFileHeader* tpx,
+ const char* filename,
+ t_fileio* fio,
bool TopOnlyOK)
{
- gmx_bool bDouble;
- int precision;
- int idum = 0;
- real rdum = 0;
+ int precision;
+ int idum = 0;
+ real rdum = 0;
/* XDR binary topology file */
precision = sizeof(real);
serializer->doString(&buf);
if (std::strncmp(buf.c_str(), "VERSION", 7) != 0)
{
- gmx_fatal(FARGS, "Can not read file %s,\n"
- " this file is from a GROMACS version which is older than 2.0\n"
- " Make a new one with grompp or use a gro or pdb file, if possible",
- filename);
- }
+ gmx_fatal(
+ FARGS,
+ "Can not read file %s,\n"
+ " this file is from a GROMACS version which is older than 2.0\n"
+ " Make a new one with grompp or use a gro or pdb file, if possible",
+ filename);
+ }
+ // We need to know the precision used to write the TPR file, to match it
+ // to the precision of the currently running binary. If the precisions match
+ // there is no problem, but mismatching precision needs to be accounted for
+ // by reading into temporary variables of the correct precision instead
+ // of the desired target datastructures.
serializer->doInt(&precision);
- bDouble = (precision == sizeof(double));
- if ((precision != sizeof(float)) && !bDouble)
+ tpx->isDouble = (precision == sizeof(double));
+ if ((precision != sizeof(float)) && !tpx->isDouble)
{
- gmx_fatal(FARGS, "Unknown precision in file %s: real is %d bytes "
+ gmx_fatal(FARGS,
+ "Unknown precision in file %s: real is %d bytes "
"instead of %zu or %zu",
- filename, precision, sizeof(float), sizeof(double));
- }
- gmx_fio_setprecision(fio, bDouble);
- fprintf(stderr, "Reading file %s, %s (%s precision)\n",
- filename, buf.c_str(), bDouble ? "double" : "single");
+ filename,
+ precision,
+ sizeof(float),
+ sizeof(double));
+ }
+ gmx_fio_setprecision(fio, tpx->isDouble);
+ fprintf(stderr,
+ "Reading file %s, %s (%s precision)\n",
+ filename,
+ buf.c_str(),
+ tpx->isDouble ? "double" : "single");
}
else
{
buf = gmx::formatString("VERSION %s", gmx_version());
serializer->doString(&buf);
- bDouble = (precision == sizeof(double));
- gmx_fio_setprecision(fio, bDouble);
+ 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.
*/
if (fileTag != TPX_TAG_RELEASE && tpx->fileVersion < tpx_version)
{
- gmx_fatal(FARGS, "tpx tag/version mismatch: reading tpx file (%s) version %d, tag '%s' with program for tpx version %d, tag '%s'",
- filename, tpx->fileVersion, fileTag.c_str(),
- tpx_version, tpx_tag);
+ gmx_fatal(FARGS,
+ "tpx tag/version mismatch: reading tpx file (%s) version %d, tag '%s' "
+ "with program for tpx version %d, tag '%s'",
+ filename,
+ tpx->fileVersion,
+ fileTag.c_str(),
+ tpx_version,
+ tpx_tag.c_str());
}
}
}
- if ((tpx->fileVersion <= tpx_incompatible_version) ||
- ((tpx->fileVersion > tpx_version) && !TopOnlyOK) ||
- (tpx->fileGeneration > tpx_generation) ||
- tpx_version == 80) /*80 was used by both 5.0-dev and 4.6-dev*/
+ if ((tpx->fileVersion <= tpx_incompatible_version)
+ || ((tpx->fileVersion > tpx_version) && !TopOnlyOK) || (tpx->fileGeneration > tpx_generation)
+ || tpx_version == 80) /*80 was used by both 5.0-dev and 4.6-dev*/
{
- gmx_fatal(FARGS, "reading tpx file (%s) version %d with version %d program",
- filename, tpx->fileVersion, tpx_version);
+ gmx_fatal(FARGS,
+ "reading tpx file (%s) version %d with version %d program",
+ filename,
+ tpx->fileVersion,
+ tpx_version);
}
serializer->doInt(&tpx->natoms);
{
if (!serializer->reading())
{
- GMX_RELEASE_ASSERT(tpx->sizeOfTprBody != 0, "Not possible to write new file with zero TPR body size");
+ GMX_RELEASE_ASSERT(tpx->sizeOfTprBody != 0,
+ "Not possible to write new file with zero TPR body size");
}
serializer->doInt64(&tpx->sizeOfTprBody);
}
}
}
-static int do_tpx_body(gmx::ISerializer *serializer,
- TpxFileHeader *tpx,
- t_inputrec *ir,
- t_state *state,
- rvec *x,
- rvec *v,
- gmx_mtop_t *mtop)
-{
- int ePBC;
- gmx_bool bPeriodicMols;
-
- if (!serializer->reading())
- {
- GMX_RELEASE_ASSERT(x == nullptr && v == nullptr, "Passing separate x and v pointers to do_tpx() is not supported when writing");
- }
- else
- {
- GMX_RELEASE_ASSERT(!(x == nullptr && v != nullptr), "Passing x==NULL and v!=NULL is not supported");
- }
+#define do_test(serializer, b, p) \
+ if ((serializer)->reading() && ((p) != nullptr) && !(b)) \
+ gmx_fatal(FARGS, "No %s in input file", #p)
+/*! \brief
+ * Process the first part of the TPR into the state datastructure.
+ *
+ * Due to the structure of the legacy code, it is necessary
+ * to split up the state reading into two parts, with the
+ * box and legacy temperature coupling processed before the
+ * topology datastructures.
+ *
+ * See the documentation for do_tpx_body for the correct order of
+ * the operations for reading a tpr file.
+ *
+ * \param[in] serializer Abstract serializer used to read/write data.
+ * \param[in] tpx The file header data.
+ * \param[in, out] state Global state data.
+ */
+static void do_tpx_state_first(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_state* state)
+{
if (serializer->reading())
{
state->flags = 0;
init_gtc_state(state, tpx->ngtc, 0, 0);
- if (x == nullptr)
- {
- // v is also nullptr by the above assertion, so we may
- // need to make memory in state for storing the contents
- // of the tpx file.
- if (tpx->bX)
- {
- state->flags |= (1 << estX);
- }
- if (tpx->bV)
- {
- state->flags |= (1 << estV);
- }
- state_change_natoms(state, tpx->natoms);
- }
}
-
- if (x == nullptr)
- {
- x = state->x.rvec_array();
- v = state->v.rvec_array();
- }
-
-#define do_test(serializer, b, p) if ((serializer)->reading() && ((p) != nullptr) && !(b)) gmx_fatal(FARGS, "No %s in input file",#p)
-
do_test(serializer, tpx->bBox, state->box);
if (tpx->bBox)
{
if (state->ngtc > 0)
{
- real *dumv;
+ real* dumv;
snew(dumv, state->ngtc);
if (tpx->fileVersion < 69)
{
serializer->doRealArray(dumv, state->ngtc);
sfree(dumv);
}
+}
+/*! \brief
+ * Process global topology data.
+ *
+ * See the documentation for do_tpx_body for the correct order of
+ * the operations for reading a tpr file.
+ *
+ * \param[in] serializer Abstract serializer used to read/write data.
+ * \param[in] tpx The file header data.
+ * \param[in,out] mtop Global topology.
+ */
+static void do_tpx_mtop(gmx::ISerializer* serializer, TpxFileHeader* tpx, gmx_mtop_t* mtop)
+{
do_test(serializer, tpx->bTop, mtop);
if (tpx->bTop)
{
if (mtop)
{
do_mtop(serializer, mtop, tpx->fileVersion);
+ set_disres_npair(mtop);
+ mtop->finalize();
}
else
{
do_mtop(serializer, &dum_top, tpx->fileVersion);
}
}
+}
+/*! \brief
+ * Process coordinate vectors for state data.
+ *
+ * Main part of state gets processed here.
+ *
+ * See the documentation for do_tpx_body for the correct order of
+ * the operations for reading a tpr file.
+ *
+ * \param[in] serializer Abstract serializer used to read/write data.
+ * \param[in] tpx The file header data.
+ * \param[in,out] state Global state data.
+ * \param[in,out] x Individual coordinates for processing, deprecated.
+ * \param[in,out] v Individual velocities for processing, deprecated.
+ */
+static void do_tpx_state_second(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_state* state, rvec* x, rvec* v)
+{
+ if (!serializer->reading())
+ {
+ GMX_RELEASE_ASSERT(
+ x == nullptr && v == nullptr,
+ "Passing separate x and v pointers to do_tpx() is not supported when writing");
+ }
+ else
+ {
+ GMX_RELEASE_ASSERT(!(x == nullptr && v != nullptr),
+ "Passing x==NULL and v!=NULL is not supported");
+ }
+
+ if (serializer->reading())
+ {
+ if (x == nullptr)
+ {
+ // v is also nullptr by the above assertion, so we may
+ // need to make memory in state for storing the contents
+ // of the tpx file.
+ if (tpx->bX)
+ {
+ state->flags |= enumValueToBitMask(StateEntry::X);
+ }
+ if (tpx->bV)
+ {
+ state->flags |= enumValueToBitMask(StateEntry::V);
+ }
+ state_change_natoms(state, tpx->natoms);
+ }
+ }
+
+ if (x == nullptr)
+ {
+ x = state->x.rvec_array();
+ v = state->v.rvec_array();
+ }
do_test(serializer, tpx->bX, x);
if (tpx->bX)
{
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)
{
std::vector<gmx::RVec> dummyForces(state->natoms);
serializer->doRvecArray(as_rvec_array(dummyForces.data()), tpx->natoms);
}
+}
+/*! \brief
+ * Process simulation parameters.
+ *
+ * See the documentation for do_tpx_body for the correct order of
+ * the operations for reading a tpr file.
+ *
+ * \param[in] serializer Abstract serializer used to read/write data.
+ * \param[in] tpx The file header data.
+ * \param[in,out] ir Datastructure with simulation parameters.
+ */
+static PbcType do_tpx_ir(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_inputrec* ir)
+{
+ PbcType pbcType;
+ gmx_bool bPeriodicMols;
/* Starting with tpx version 26, we have the inputrec
* at the end of the file, so we can ignore it
*
*
*/
- ePBC = -1;
+ pbcType = PbcType::Unset;
bPeriodicMols = FALSE;
do_test(serializer, tpx->bIr, ir);
/* Removed the pbc info from do_inputrec, since we always want it */
if (!serializer->reading())
{
- ePBC = ir->ePBC;
+ pbcType = ir->pbcType;
bPeriodicMols = ir->bPeriodicMols;
}
- serializer->doInt(&ePBC);
+ serializer->doInt(reinterpret_cast<int*>(&pbcType));
serializer->doBool(&bPeriodicMols);
}
if (tpx->fileGeneration <= tpx_generation && ir)
{
do_inputrec(serializer, ir, tpx->fileVersion);
- if (tpx->fileVersion < 51)
- {
- set_box_rel(ir, state);
- }
if (tpx->fileVersion < 53)
{
- ePBC = ir->ePBC;
+ pbcType = ir->pbcType;
bPeriodicMols = ir->bPeriodicMols;
}
}
if (serializer->reading() && ir && tpx->fileVersion >= 53)
{
/* We need to do this after do_inputrec, since that initializes ir */
- ir->ePBC = ePBC;
+ ir->pbcType = pbcType;
ir->bPeriodicMols = bPeriodicMols;
}
}
+ return pbcType;
+}
- if (serializer->reading())
+/*! \brief
+ * Correct and finalize read information.
+ *
+ * If \p state is nullptr, skip the parts dependent on it.
+ *
+ * See the documentation for do_tpx_body for the correct order of
+ * the operations for reading a tpr file.
+ *
+ * \param[in] tpx The file header used to check version numbers.
+ * \param[out] ir Input rec that needs correction.
+ * \param[out] state State needing correction.
+ * \param[out] mtop Topology to finalize.
+ */
+static void do_tpx_finalize(TpxFileHeader* tpx, t_inputrec* ir, t_state* state, gmx_mtop_t* mtop)
+{
+ if (tpx->fileVersion < 51 && state)
+ {
+ set_box_rel(ir, state);
+ }
+ if (tpx->bIr && ir)
{
- if (tpx->bIr && ir)
+ if (state && state->ngtc == 0)
{
- if (state->ngtc == 0)
- {
- /* Reading old version without tcoupl state data: set it */
- init_gtc_state(state, ir->opts.ngtc, 0, ir->opts.nhchainlength);
- }
- if (tpx->bTop && mtop)
- {
- if (tpx->fileVersion < 57)
- {
- if (mtop->moltype[0].ilist[F_DISRES].size() > 0)
- {
- ir->eDisre = edrSimple;
- }
- else
- {
- ir->eDisre = edrNone;
- }
- }
- set_disres_npair(mtop);
- }
+ /* Reading old version without tcoupl state data: set it */
+ init_gtc_state(state, ir->opts.ngtc, 0, ir->opts.nhchainlength);
}
-
if (tpx->bTop && mtop)
{
- gmx_mtop_finalize(mtop);
+ if (tpx->fileVersion < 57)
+ {
+ ir->eDisre = !mtop->moltype[0].ilist[F_DISRES].empty()
+ ? DistanceRestraintRefinement::Simple
+ : DistanceRestraintRefinement::None;
+ }
}
}
+}
- return ePBC;
+/*! \brief
+ * Process TPR data for file reading/writing.
+ *
+ * The TPR file gets processed in in four stages due to the organization
+ * of the data within it.
+ *
+ * First, state data for the box is processed in do_tpx_state_first.
+ * This is followed by processing the topology in do_tpx_mtop.
+ * Coordinate and velocity vectors are handled next in do_tpx_state_second.
+ * The last file information processed is the collection of simulation parameters in do_tpx_ir.
+ * When reading, a final processing step is undertaken at the end.
+ *
+ * \param[in] serializer Abstract serializer used to read/write data.
+ * \param[in] tpx The file header data.
+ * \param[in,out] ir Datastructures with simulation parameters.
+ * \param[in,out] state Global state data.
+ * \param[in,out] x Individual coordinates for processing, deprecated.
+ * \param[in,out] v Individual velocities for processing, deprecated.
+ * \param[in,out] mtop Global topology.
+ */
+static PbcType do_tpx_body(gmx::ISerializer* serializer,
+ TpxFileHeader* tpx,
+ t_inputrec* ir,
+ t_state* state,
+ rvec* x,
+ rvec* v,
+ gmx_mtop_t* mtop)
+{
+ if (state)
+ {
+ do_tpx_state_first(serializer, tpx, state);
+ }
+ do_tpx_mtop(serializer, tpx, mtop);
+ if (state)
+ {
+ do_tpx_state_second(serializer, tpx, state, x, v);
+ }
+ PbcType pbcType = do_tpx_ir(serializer, tpx, ir);
+ if (serializer->reading())
+ {
+ do_tpx_finalize(tpx, ir, state, mtop);
+ }
+ return pbcType;
+}
+
+/*! \brief
+ * Overload for do_tpx_body that defaults to state vectors being nullptr.
+ *
+ * \param[in] serializer Abstract serializer used to read/write data.
+ * \param[in] tpx The file header data.
+ * \param[in,out] ir Datastructures with simulation parameters.
+ * \param[in,out] mtop Global topology.
+ */
+static PbcType do_tpx_body(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_inputrec* ir, gmx_mtop_t* mtop)
+{
+ return do_tpx_body(serializer, tpx, ir, nullptr, nullptr, nullptr, mtop);
}
-static t_fileio *open_tpx(const char *fn, const char *mode)
+static t_fileio* open_tpx(const char* fn, const char* mode)
{
return gmx_fio_open(fn, mode);
}
-static void close_tpx(t_fileio *fio)
+static void close_tpx(t_fileio* fio)
{
gmx_fio_close(fio);
}
* \param[in] mtop Global topology.
* \returns Fully populated header.
*/
-static TpxFileHeader populateTpxHeader(const t_state &state,
- const t_inputrec *ir,
- const gmx_mtop_t *mtop)
+static TpxFileHeader populateTpxHeader(const t_state& state, const t_inputrec* ir, const gmx_mtop_t* mtop)
{
TpxFileHeader header;
header.natoms = state.natoms;
header.ngtc = state.ngtc;
header.fep_state = state.fep_state;
- header.lambda = state.lambda[efptFEP];
- header.bIr = ir != nullptr;
- header.bTop = mtop != nullptr;
- header.bX = (state.flags & (1 << estX)) != 0;
- header.bV = (state.flags & (1 << estV)) != 0;
+ header.lambda = state.lambda[FreeEnergyPerturbationCouplingType::Fep];
+ header.bIr = ir != nullptr;
+ header.bTop = mtop != nullptr;
+ 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;
header.fileGeneration = tpx_generation;
+ header.isDouble = (sizeof(real) == sizeof(double));
return header;
}
-static void doTpxBodyBuffer(gmx::ISerializer *topologySerializer, gmx::ArrayRef<char> buffer)
+/*! \brief
+ * Process the body of a TPR file as an opaque data buffer.
+ *
+ * Reads/writes the information in \p buffer from/to the \p serializer
+ * provided to the function. Does not interact with the actual
+ * TPR datastructures but with an in memory representation of the
+ * data, so that this data can be efficiently read or written from/to
+ * an original source.
+ *
+ * \param[in] serializer The abstract serializer used for reading or writing
+ * the information in \p buffer.
+ * \param[in,out] buffer Information from TPR file as char buffer.
+ */
+static void doTpxBodyBuffer(gmx::ISerializer* serializer, gmx::ArrayRef<char> buffer)
{
- topologySerializer->doCharArray(buffer.data(), buffer.size());
+ serializer->doOpaque(buffer.data(), buffer.size());
+}
+
+/*! \brief
+ * Populates simulation datastructures.
+ *
+ * Here the information from the serialization interface \p serializer
+ * is used to first populate the datastructures containing the simulation
+ * information. Depending on the version found in the header \p tpx,
+ * this is done using the new reading of the data as one block from disk,
+ * followed by complete deserialization of the information read from there.
+ * Otherwise, the datastructures are populated as before one by one from disk.
+ * The second version is the default for the legacy tools that read the
+ * coordinates and velocities separate from the state.
+ *
+ * After reading in the data, a separate buffer is populated from them
+ * containing only \p ir and \p mtop that can be communicated directly
+ * to nodes needing the information to set up a simulation.
+ *
+ * \param[in] tpx The file header.
+ * \param[in] serializer The Serialization interface used to read the TPR.
+ * \param[out] ir Input rec to populate.
+ * \param[out] state State vectors to populate.
+ * \param[out] x Coordinates to populate if needed.
+ * \param[out] v Velocities to populate if needed.
+ * \param[out] mtop Global topology to populate.
+ *
+ * \returns Partial de-serialized TPR used for communication to nodes.
+ */
+static PartialDeserializedTprFile readTpxBody(TpxFileHeader* tpx,
+ gmx::ISerializer* serializer,
+ t_inputrec* ir,
+ t_state* state,
+ rvec* x,
+ rvec* v,
+ gmx_mtop_t* mtop)
+{
+ PartialDeserializedTprFile partialDeserializedTpr;
+ if (tpx->fileVersion >= tpxv_AddSizeField && tpx->fileGeneration >= 27)
+ {
+ partialDeserializedTpr.body.resize(tpx->sizeOfTprBody);
+ partialDeserializedTpr.header = *tpx;
+ doTpxBodyBuffer(serializer, partialDeserializedTpr.body);
+
+ partialDeserializedTpr.pbcType =
+ completeTprDeserialization(&partialDeserializedTpr, ir, state, x, v, mtop);
+ }
+ else
+ {
+ partialDeserializedTpr.pbcType = do_tpx_body(serializer, tpx, ir, state, x, v, mtop);
+ }
+ // Update header to system info for communication to nodes.
+ // As we only need to communicate the inputrec and mtop to other nodes,
+ // we prepare a new char buffer with the information we have already read
+ // in on master.
+ partialDeserializedTpr.header = 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
+ // if we swap the endian in the middle of the file, so we stick to big endian in the
+ // TPR file for now - and thus we ask the serializer to swap if this host is little endian.
+ gmx::InMemorySerializer tprBodySerializer(gmx::EndianSwapBehavior::SwapIfHostIsLittleEndian);
+ do_tpx_body(&tprBodySerializer, &partialDeserializedTpr.header, ir, mtop);
+ partialDeserializedTpr.body = tprBodySerializer.finishAndGetBuffer();
+
+ return partialDeserializedTpr;
}
/************************************************************
*
************************************************************/
-TpxFileHeader readTpxHeader(const char *fileName, bool canReadTopologyOnly)
+TpxFileHeader readTpxHeader(const char* fileName, bool canReadTopologyOnly)
{
- t_fileio *fio;
+ t_fileio* fio;
fio = open_tpx(fileName, "r");
gmx::FileIOXdrSerializer serializer(fio);
- TpxFileHeader tpx;
+ TpxFileHeader tpx;
do_tpxheader(&serializer, &tpx, fileName, fio, canReadTopologyOnly);
close_tpx(fio);
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
* otherwise not available.
*/
- t_fileio *fio;
+ t_fileio* fio;
- TpxFileHeader tpx = populateTpxHeader(*state,
- ir,
- mtop);
-
- gmx::InMemorySerializer tprBodySerializer;
+ 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
+ // if we swap the endian in the middle of the file, so we stick to big endian in the
+ // TPR file for now - and thus we ask the serializer to swap if this host is little endian.
+ gmx::InMemorySerializer tprBodySerializer(gmx::EndianSwapBehavior::SwapIfHostIsLittleEndian);
do_tpx_body(&tprBodySerializer,
&tpx,
- const_cast<t_inputrec *>(ir),
- const_cast<t_state *>(state), nullptr, nullptr,
- const_cast<gmx_mtop_t *>(mtop));
+ const_cast<t_inputrec*>(ir),
+ const_cast<t_state*>(state),
+ nullptr,
+ nullptr,
+ const_cast<gmx_mtop_t*>(&mtop));
std::vector<char> tprBody = tprBodySerializer.finishAndGetBuffer();
- tpx.sizeOfTprBody = tprBody.size();
+ tpx.sizeOfTprBody = tprBody.size();
fio = open_tpx(fn, "w");
gmx::FileIOXdrSerializer serializer(fio);
- do_tpxheader(&serializer,
- &tpx,
- fn,
- fio,
- ir == nullptr);
+ do_tpxheader(&serializer, &tpx, fn, fio, ir == nullptr);
doTpxBodyBuffer(&serializer, tprBody);
close_tpx(fio);
}
-/*! \brief
- * Wraps reading of header before and after introduction of size field.
- *
- * \param[in] tpx The file header.
- * \param[in] serializer The Serialization interface used to read the TPR.
- * \param[in] isDouble Whether the file is double or single precision.
- * \param[out] ir Input rec to populate.
- * \param[out] state State vectors to populate.
- * \param[out] x Coordinates to populate if needed.
- * \param[out] v Velocities to populate if needed.
- * \param[out] mtop Global topology to populate.
- *
- * \returns Flag for pbc.
- */
-static int do_tpx_body_dispatcher(TpxFileHeader *tpx,
- gmx::ISerializer *serializer,
- bool isDouble,
- t_inputrec *ir,
- t_state *state,
- rvec *x, rvec *v,
- gmx_mtop_t *mtop)
+PbcType completeTprDeserialization(PartialDeserializedTprFile* partialDeserializedTpr,
+ t_inputrec* ir,
+ t_state* state,
+ rvec* x,
+ rvec* v,
+ gmx_mtop_t* mtop)
{
- int ePBC;
- if (tpx->fileVersion >= tpxv_AddSizeField && tpx->fileGeneration >= 27)
- {
- std::vector<char> tprBody(tpx->sizeOfTprBody);
- doTpxBodyBuffer(serializer, tprBody);
- gmx::InMemoryDeserializer tprBodyDeserializer(tprBody, isDouble);
-
- ePBC = do_tpx_body(&tprBodyDeserializer,
- tpx,
- ir,
- state,
- x,
- v,
- mtop);
- }
- else
- {
- ePBC = do_tpx_body(serializer,
- tpx,
- ir,
- state,
- x,
- v,
- mtop);
- }
- return ePBC;
+ // 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
+ // if we swap the endian in the middle of the file, so we stick to big endian in the
+ // TPR file for now - and thus we ask the serializer to swap if this host is little endian.
+ gmx::InMemoryDeserializer tprBodyDeserializer(partialDeserializedTpr->body,
+ partialDeserializedTpr->header.isDouble,
+ gmx::EndianSwapBehavior::SwapIfHostIsLittleEndian);
+ return do_tpx_body(&tprBodyDeserializer, &partialDeserializedTpr->header, ir, state, x, v, mtop);
}
-
-void read_tpx_state(const char *fn,
- t_inputrec *ir, t_state *state, gmx_mtop_t *mtop)
+PbcType completeTprDeserialization(PartialDeserializedTprFile* partialDeserializedTpr,
+ t_inputrec* ir,
+ gmx_mtop_t* mtop)
{
- t_fileio *fio;
+ return completeTprDeserialization(partialDeserializedTpr, ir, nullptr, nullptr, nullptr, mtop);
+}
- TpxFileHeader tpx;
+PartialDeserializedTprFile read_tpx_state(const char* fn, t_inputrec* ir, t_state* state, gmx_mtop_t* mtop)
+{
+ t_fileio* fio;
fio = open_tpx(fn, "r");
- gmx::FileIOXdrSerializer serializer(fio);
- do_tpxheader(&serializer,
- &tpx,
- fn,
- fio,
- ir == nullptr);
- do_tpx_body_dispatcher(&tpx, &serializer, gmx_fio_is_double(fio),
- ir, state, nullptr, nullptr, mtop);
+ gmx::FileIOXdrSerializer serializer(fio);
+ PartialDeserializedTprFile partialDeserializedTpr;
+ do_tpxheader(&serializer, &partialDeserializedTpr.header, fn, fio, ir == nullptr);
+ partialDeserializedTpr =
+ readTpxBody(&partialDeserializedTpr.header, &serializer, ir, state, nullptr, nullptr, mtop);
close_tpx(fio);
+ return partialDeserializedTpr;
}
-int read_tpx(const char *fn,
- t_inputrec *ir, matrix box, int *natoms,
- rvec *x, rvec *v, gmx_mtop_t *mtop)
+PbcType read_tpx(const char* fn, t_inputrec* ir, matrix box, int* natoms, rvec* x, rvec* v, gmx_mtop_t* mtop)
{
- t_fileio *fio;
- t_state state;
- int ePBC;
+ t_fileio* fio;
+ t_state state;
- TpxFileHeader tpx;
- fio = open_tpx(fn, "r");
+ TpxFileHeader tpx;
+ fio = open_tpx(fn, "r");
gmx::FileIOXdrSerializer serializer(fio);
- do_tpxheader(&serializer,
- &tpx,
- fn,
- fio,
- ir == nullptr);
- ePBC = do_tpx_body_dispatcher(&tpx, &serializer, gmx_fio_is_double(fio),
- ir, &state, x, v, mtop);
+ do_tpxheader(&serializer, &tpx, fn, fio, ir == nullptr);
+ PartialDeserializedTprFile partialDeserializedTpr =
+ readTpxBody(&tpx, &serializer, ir, &state, x, v, mtop);
close_tpx(fio);
if (mtop != nullptr && natoms != nullptr)
{
{
copy_mat(state.box, box);
}
- return ePBC;
+ return partialDeserializedTpr.pbcType;
}
-int read_tpx_top(const char *fn,
- t_inputrec *ir, matrix box, int *natoms,
- rvec *x, rvec *v, t_topology *top)
+PbcType read_tpx_top(const char* fn, t_inputrec* ir, matrix box, int* natoms, rvec* x, rvec* v, t_topology* top)
{
- gmx_mtop_t mtop;
- int ePBC;
+ gmx_mtop_t mtop;
+ PbcType pbcType;
- ePBC = read_tpx(fn, ir, box, natoms, x, v, &mtop);
+ pbcType = read_tpx(fn, ir, box, natoms, x, v, &mtop);
*top = gmx_mtop_t_to_t_topology(&mtop, true);
- return ePBC;
+ return pbcType;
}
-gmx_bool fn2bTPX(const char *file)
+gmx_bool fn2bTPX(const char* file)
{
return (efTPR == fn2ftp(file));
}
-void pr_tpxheader(FILE *fp, int indent, const char *title, const TpxFileHeader *sh)
+void pr_tpxheader(FILE* fp, int indent, const char* title, const TpxFileHeader* sh)
{
if (available(fp, sh, indent, title))
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff