*
* 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/fatalerror.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
* in this enumeration, and write code below that does the right thing
* according to the value of file_version.
*/
-enum tpxv {
- tpxv_ComputationalElectrophysiology = 96, /**< support for ion/water position swaps (computational electrophysiology) */
- tpxv_Use64BitRandomSeed, /**< change ld_seed from int to int64_t */
+enum tpxv
+{
+ 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, /**< Inroduced support for MiMiC QM/MM interface */
- tpxv_PullAverage, /**< Added possibility to output average pull force and position */
- 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.
*/
-static const int tpx_generation = 26;
+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 },
+ { 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(t_fileio *fio,
- t_pull_group *pgrp,
- t_pull_coord *pcrd,
- gmx_bool bRead)
+static void do_pullgrp_tpx_pre95(gmx::ISerializer* serializer, t_pull_group* pgrp, t_pull_coord* pcrd)
{
rvec tmp;
- gmx_fio_do_int(fio, pgrp->nat);
- if (bRead)
- {
- snew(pgrp->ind, pgrp->nat);
- }
- gmx_fio_ndo_int(fio, pgrp->ind, pgrp->nat);
- gmx_fio_do_int(fio, pgrp->nweight);
- if (bRead)
- {
- snew(pgrp->weight, pgrp->nweight);
- }
- gmx_fio_ndo_real(fio, pgrp->weight, pgrp->nweight);
- gmx_fio_do_int(fio, pgrp->pbcatom);
- gmx_fio_do_rvec(fio, pcrd->vec);
+ 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.as_vec());
clear_rvec(pcrd->origin);
- gmx_fio_do_rvec(fio, tmp);
+ serializer->doRvec(&tmp);
pcrd->init = tmp[0];
- gmx_fio_do_real(fio, pcrd->rate);
- gmx_fio_do_real(fio, pcrd->k);
- gmx_fio_do_real(fio, pcrd->kB);
+ serializer->doReal(&pcrd->rate);
+ serializer->doReal(&pcrd->k);
+ serializer->doReal(&pcrd->kB);
}
-static void do_pull_group(t_fileio *fio, t_pull_group *pgrp, gmx_bool bRead)
+static void do_pull_group(gmx::ISerializer* serializer, t_pull_group* pgrp)
{
- gmx_fio_do_int(fio, pgrp->nat);
- if (bRead)
- {
- snew(pgrp->ind, pgrp->nat);
- }
- gmx_fio_ndo_int(fio, pgrp->ind, pgrp->nat);
- gmx_fio_do_int(fio, pgrp->nweight);
- if (bRead)
- {
- snew(pgrp->weight, pgrp->nweight);
- }
- gmx_fio_ndo_real(fio, pgrp->weight, pgrp->nweight);
- gmx_fio_do_int(fio, pgrp->pbcatom);
+ 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(t_fileio *fio, t_pull_coord *pcrd,
- gmx_bool bRead, 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)
{
- gmx_fio_do_int(fio, pcrd->eType);
+ serializer->doEnumAsInt(&pcrd->eType);
if (file_version >= tpxv_PullExternalPotential)
{
- if (pcrd->eType == epullEXTERNAL)
+ if (pcrd->eType == PullingAlgorithm::External)
{
- if (bRead)
- {
- char buf[STRLEN];
-
- gmx_fio_do_string(fio, buf);
- pcrd->externalPotentialProvider = gmx_strdup(buf);
- }
- else
- {
- gmx_fio_do_string(fio, pcrd->externalPotentialProvider);
- }
+ serializer->doString(&pcrd->externalPotentialProvider);
}
else
{
- pcrd->externalPotentialProvider = nullptr;
+ pcrd->externalPotentialProvider.clear();
}
}
else
{
- if (bRead)
+ 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.
*/
- gmx_fio_do_int(fio, pcrd->eGeom);
- gmx_fio_do_int(fio, pcrd->ngroup);
+ serializer->doEnumAsInt(&pcrd->eGeom);
+ serializer->doInt(&pcrd->ngroup);
if (pcrd->ngroup <= c_pullCoordNgroupMax)
{
- gmx_fio_ndo_int(fio, 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);
- gmx_fio_ndo_int(fio, dum, pcrd->ngroup);
+ serializer->doIntArray(dum, pcrd->ngroup);
sfree(dum);
pcrd->ngroup = 0;
}
- gmx_fio_do_ivec(fio, 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
{
pcrd->ngroup = 2;
- gmx_fio_do_int(fio, pcrd->group[0]);
- gmx_fio_do_int(fio, pcrd->group[1]);
+ serializer->doInt(&pcrd->group[0]);
+ serializer->doInt(&pcrd->group[1]);
if (file_version >= tpxv_PullCoordTypeGeom)
{
- pcrd->ngroup = (pcrd->eGeom == epullgDIRRELATIVE ? 4 : 2);
- gmx_fio_do_int(fio, pcrd->eType);
- gmx_fio_do_int(fio, pcrd->eGeom);
+ pcrd->ngroup = (pcrd->eGeom == PullGroupGeometry::DirectionRelative ? 4 : 2);
+ serializer->doEnumAsInt(&pcrd->eType);
+ serializer->doEnumAsInt(&pcrd->eGeom);
if (pcrd->ngroup == 4)
{
- gmx_fio_do_int(fio, pcrd->group[2]);
- gmx_fio_do_int(fio, pcrd->group[3]);
+ serializer->doInt(&pcrd->group[2]);
+ serializer->doInt(&pcrd->group[3]);
}
- gmx_fio_do_ivec(fio, pcrd->dim);
+ serializer->doIvec(&pcrd->dim.as_vec());
}
else
{
copy_ivec(dimOld, pcrd->dim);
}
}
- gmx_fio_do_rvec(fio, pcrd->origin);
- gmx_fio_do_rvec(fio, pcrd->vec);
+ serializer->doRvec(&pcrd->origin.as_vec());
+ serializer->doRvec(&pcrd->vec.as_vec());
if (file_version >= tpxv_PullCoordTypeGeom)
{
- gmx_fio_do_gmx_bool(fio, pcrd->bStart);
+ serializer->doBool(&pcrd->bStart);
}
else
{
/* This parameter is only printed, but not actually used by mdrun */
pcrd->bStart = FALSE;
}
- gmx_fio_do_real(fio, pcrd->init);
- gmx_fio_do_real(fio, pcrd->rate);
- gmx_fio_do_real(fio, pcrd->k);
- gmx_fio_do_real(fio, pcrd->kB);
+ serializer->doReal(&pcrd->init);
+ serializer->doReal(&pcrd->rate);
+ serializer->doReal(&pcrd->k);
+ serializer->doReal(&pcrd->kB);
}
-static void do_expandedvals(t_fileio *fio, t_expanded *expand, t_lambda *fepvals, gmx_bool bRead, 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 (bRead)
- {
- snew(expand->init_lambda_weights, n_lambda);
- }
- gmx_fio_ndo_real(fio, expand->init_lambda_weights, n_lambda);
- gmx_fio_do_gmx_bool(fio, expand->bInit_weights);
- }
-
- gmx_fio_do_int(fio, expand->nstexpanded);
- gmx_fio_do_int(fio, expand->elmcmove);
- gmx_fio_do_int(fio, expand->elamstats);
- gmx_fio_do_int(fio, expand->lmc_repeats);
- gmx_fio_do_int(fio, expand->gibbsdeltalam);
- gmx_fio_do_int(fio, expand->lmc_forced_nstart);
- gmx_fio_do_int(fio, expand->lmc_seed);
- gmx_fio_do_real(fio, expand->mc_temp);
- gmx_fio_do_gmx_bool(fio, expand->bSymmetrizedTMatrix);
- gmx_fio_do_int(fio, expand->nstTij);
- gmx_fio_do_int(fio, expand->minvarmin);
- gmx_fio_do_int(fio, expand->c_range);
- gmx_fio_do_real(fio, expand->wl_scale);
- gmx_fio_do_real(fio, expand->wl_ratio);
- gmx_fio_do_real(fio, expand->init_wl_delta);
- gmx_fio_do_gmx_bool(fio, expand->bWLoneovert);
- gmx_fio_do_int(fio, expand->elmceq);
- gmx_fio_do_int(fio, expand->equil_steps);
- gmx_fio_do_int(fio, expand->equil_samples);
- gmx_fio_do_int(fio, expand->equil_n_at_lam);
- gmx_fio_do_real(fio, expand->equil_wl_delta);
- gmx_fio_do_real(fio, expand->equil_ratio);
+ 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->doEnumAsInt(&expand->elmcmove);
+ serializer->doEnumAsInt(&expand->elamstats);
+ serializer->doInt(&expand->lmc_repeats);
+ serializer->doInt(&expand->gibbsdeltalam);
+ serializer->doInt(&expand->lmc_forced_nstart);
+ serializer->doInt(&expand->lmc_seed);
+ serializer->doReal(&expand->mc_temp);
+ serializer->doBool(&expand->bSymmetrizedTMatrix);
+ serializer->doInt(&expand->nstTij);
+ serializer->doInt(&expand->minvarmin);
+ serializer->doInt(&expand->c_range);
+ serializer->doReal(&expand->wl_scale);
+ serializer->doReal(&expand->wl_ratio);
+ serializer->doReal(&expand->init_wl_delta);
+ serializer->doBool(&expand->bWLoneovert);
+ serializer->doEnumAsInt(&expand->elmceq);
+ serializer->doInt(&expand->equil_steps);
+ serializer->doInt(&expand->equil_samples);
+ serializer->doInt(&expand->equil_n_at_lam);
+ serializer->doReal(&expand->equil_wl_delta);
+ serializer->doReal(&expand->equil_ratio);
}
}
-static void do_simtempvals(t_fileio *fio, t_simtemp *simtemp, int n_lambda, gmx_bool bRead,
- int file_version)
+static void do_simtempvals(gmx::ISerializer* serializer, t_simtemp* simtemp, int n_lambda, int file_version)
{
if (file_version >= 79)
{
- gmx_fio_do_int(fio, simtemp->eSimTempScale);
- gmx_fio_do_real(fio, simtemp->simtemp_high);
- gmx_fio_do_real(fio, simtemp->simtemp_low);
+ serializer->doEnumAsInt(&simtemp->eSimTempScale);
+ serializer->doReal(&simtemp->simtemp_high);
+ serializer->doReal(&simtemp->simtemp_low);
if (n_lambda > 0)
{
- if (bRead)
+ if (serializer->reading())
{
- snew(simtemp->temperatures, n_lambda);
+ simtemp->temperatures.resize(n_lambda);
}
- gmx_fio_ndo_real(fio, simtemp->temperatures, n_lambda);
+ serializer->doRealArray(simtemp->temperatures.data(), n_lambda);
}
}
}
-static void do_imd(t_fileio *fio, t_IMD *imd, gmx_bool bRead)
+static void do_imd(gmx::ISerializer* serializer, t_IMD* imd)
{
- gmx_fio_do_int(fio, imd->nat);
- if (bRead)
+ serializer->doInt(&imd->nat);
+ if (serializer->reading())
{
snew(imd->ind, imd->nat);
}
- gmx_fio_ndo_int(fio, imd->ind, imd->nat);
+ serializer->doIntArray(imd->ind, imd->nat);
}
-static void do_fepvals(t_fileio *fio, t_lambda *fepvals, gmx_bool bRead, 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)
{
- gmx_fio_do_int(fio, fepvals->init_fep_state);
- gmx_fio_do_double(fio, fepvals->init_lambda);
- gmx_fio_do_double(fio, fepvals->delta_lambda);
+ serializer->doInt(&fepvals->init_fep_state);
+ serializer->doDouble(&fepvals->init_lambda);
+ serializer->doDouble(&fepvals->delta_lambda);
}
else if (file_version >= 59)
{
- gmx_fio_do_double(fio, fepvals->init_lambda);
- gmx_fio_do_double(fio, fepvals->delta_lambda);
+ serializer->doDouble(&fepvals->init_lambda);
+ serializer->doDouble(&fepvals->delta_lambda);
}
else
{
- gmx_fio_do_real(fio, rdum);
+ serializer->doReal(&rdum);
fepvals->init_lambda = rdum;
- gmx_fio_do_real(fio, rdum);
+ serializer->doReal(&rdum);
fepvals->delta_lambda = rdum;
}
if (file_version >= 79)
{
- gmx_fio_do_int(fio, fepvals->n_lambda);
- if (bRead)
- {
- snew(fepvals->all_lambda, efptNR);
- }
- for (g = 0; g < efptNR; g++)
+ serializer->doInt(&fepvals->n_lambda);
+ for (auto g : keysOf(fepvals->all_lambda))
{
if (fepvals->n_lambda > 0)
{
- if (bRead)
- {
- snew(fepvals->all_lambda[g], fepvals->n_lambda);
- }
- gmx_fio_ndo_double(fio, fepvals->all_lambda[g], fepvals->n_lambda);
- gmx_fio_ndo_gmx_bool(fio, 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;
}
}
}
else if (file_version >= 64)
{
- gmx_fio_do_int(fio, fepvals->n_lambda);
- if (bRead)
+ 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);
}
}
}
- gmx_fio_ndo_double(fio, 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 (bRead)
+ 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;
}
}
- gmx_fio_do_real(fio, fepvals->sc_alpha);
- gmx_fio_do_int(fio, fepvals->sc_power);
+ serializer->doReal(&fepvals->sc_alpha);
+ serializer->doInt(&fepvals->sc_power);
if (file_version >= 79)
{
- gmx_fio_do_real(fio, fepvals->sc_r_power);
+ serializer->doReal(&fepvals->sc_r_power);
}
else
{
fepvals->sc_r_power = 6.0;
}
- gmx_fio_do_real(fio, fepvals->sc_sigma);
- if (bRead)
+ 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 >= 71)
{
}
if (file_version >= 79)
{
- gmx_fio_do_gmx_bool(fio, fepvals->bScCoul);
+ serializer->doBool(&fepvals->bScCoul);
}
else
{
}
if (file_version >= 64)
{
- gmx_fio_do_int(fio, fepvals->nstdhdl);
+ serializer->doInt(&fepvals->nstdhdl);
}
else
{
if (file_version >= 73)
{
- gmx_fio_do_int(fio, fepvals->separate_dhdl_file);
- gmx_fio_do_int(fio, 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)
{
- gmx_fio_do_int(fio, fepvals->dh_hist_size);
- gmx_fio_do_double(fio, fepvals->dh_hist_spacing);
+ serializer->doInt(&fepvals->dh_hist_size);
+ serializer->doDouble(&fepvals->dh_hist_spacing);
}
else
{
}
if (file_version >= 79)
{
- gmx_fio_do_int(fio, fepvals->edHdLPrintEnergy);
+ serializer->doEnumAsInt(&fepvals->edHdLPrintEnergy);
+ }
+ else
+ {
+ 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->edHdLPrintEnergy = edHdLPrintEnergyNO;
+ 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)
{
- gmx_fio_do_int(fio, fepvals->lambda_neighbors);
- if ( (fepvals->lambda_neighbors >= 0) && (fepvals->init_fep_state >= 0) &&
- (fepvals->init_lambda < 0) )
+ serializer->doInt(&fepvals->lambda_neighbors);
+ 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;;
+ fepvals->lambda_start_n = 0;
}
if (fepvals->lambda_stop_n >= fepvals->n_lambda)
{
}
}
-static void do_awhBias(t_fileio *fio, gmx::AwhBiasParams *awhBiasParams, gmx_bool bRead,
- int gmx_unused file_version)
-{
- gmx_fio_do_int(fio, awhBiasParams->eTarget);
- gmx_fio_do_double(fio, awhBiasParams->targetBetaScaling);
- gmx_fio_do_double(fio, awhBiasParams->targetCutoff);
- gmx_fio_do_int(fio, awhBiasParams->eGrowth);
- gmx_fio_do_int(fio, awhBiasParams->bUserData);
- gmx_fio_do_double(fio, awhBiasParams->errorInitial);
- gmx_fio_do_int(fio, awhBiasParams->ndim);
- gmx_fio_do_int(fio, awhBiasParams->shareGroup);
- gmx_fio_do_gmx_bool(fio, awhBiasParams->equilibrateHistogram);
-
- if (bRead)
- {
- snew(awhBiasParams->dimParams, awhBiasParams->ndim);
- }
-
- for (int d = 0; d < awhBiasParams->ndim; d++)
- {
- gmx::AwhDimParams *dimParams = &awhBiasParams->dimParams[d];
-
- gmx_fio_do_int(fio, dimParams->eCoordProvider);
- gmx_fio_do_int(fio, dimParams->coordIndex);
- gmx_fio_do_double(fio, dimParams->origin);
- gmx_fio_do_double(fio, dimParams->end);
- gmx_fio_do_double(fio, dimParams->period);
- gmx_fio_do_double(fio, dimParams->forceConstant);
- gmx_fio_do_double(fio, dimParams->diffusion);
- gmx_fio_do_double(fio, dimParams->coordValueInit);
- gmx_fio_do_double(fio, dimParams->coverDiameter);
- }
-}
-
-static void do_awh(t_fileio *fio, gmx::AwhParams *awhParams, gmx_bool bRead,
- int gmx_unused file_version)
+static void do_pull(gmx::ISerializer* serializer, pull_params_t* pull, int file_version, PullingAlgorithm ePullOld)
{
- gmx_fio_do_int(fio, awhParams->numBias);
- gmx_fio_do_int(fio, awhParams->nstOut);
- gmx_fio_do_int64(fio, awhParams->seed);
- gmx_fio_do_int(fio, awhParams->nstSampleCoord);
- gmx_fio_do_int(fio, awhParams->numSamplesUpdateFreeEnergy);
- gmx_fio_do_int(fio, awhParams->ePotential);
- gmx_fio_do_gmx_bool(fio, awhParams->shareBiasMultisim);
-
- if (awhParams->numBias > 0)
- {
- if (bRead)
- {
- snew(awhParams->awhBiasParams, awhParams->numBias);
- }
-
- for (int k = 0; k < awhParams->numBias; k++)
- {
- do_awhBias(fio, &awhParams->awhBiasParams[k], bRead, file_version);
- }
- }
-}
-
-static void do_pull(t_fileio *fio, pull_params_t *pull, gmx_bool bRead,
- int file_version, int ePullOld)
-{
- int eGeomOld = -1;
- ivec dimOld;
- int g;
+ PullGroupGeometry eGeomOld = PullGroupGeometry::Count;
+ ivec dimOld;
+ int g;
if (file_version >= 95)
{
- gmx_fio_do_int(fio, pull->ngroup);
+ serializer->doInt(&pull->ngroup);
}
- gmx_fio_do_int(fio, pull->ncoord);
+ serializer->doInt(&pull->ncoord);
if (file_version < 95)
{
pull->ngroup = pull->ncoord + 1;
{
real dum;
- gmx_fio_do_int(fio, eGeomOld);
- gmx_fio_do_ivec(fio, dimOld);
+ serializer->doEnumAsInt(&eGeomOld);
+ serializer->doIvec(&dimOld);
/* The inner cylinder radius, now removed */
- gmx_fio_do_real(fio, dum);
+ serializer->doReal(&dum);
}
- gmx_fio_do_real(fio, pull->cylinder_r);
- gmx_fio_do_real(fio, pull->constr_tol);
+ serializer->doReal(&pull->cylinder_r);
+ serializer->doReal(&pull->constr_tol);
if (file_version >= 95)
{
- gmx_fio_do_gmx_bool(fio, pull->bPrintCOM);
+ serializer->doBool(&pull->bPrintCOM);
/* With file_version < 95 this value is set below */
}
if (file_version >= tpxv_ReplacePullPrintCOM12)
{
- gmx_fio_do_gmx_bool(fio, pull->bPrintRefValue);
- gmx_fio_do_gmx_bool(fio, pull->bPrintComp);
+ serializer->doBool(&pull->bPrintRefValue);
+ serializer->doBool(&pull->bPrintComp);
}
else if (file_version >= tpxv_PullCoordTypeGeom)
{
int idum;
- gmx_fio_do_int(fio, idum); /* used to be bPrintCOM2 */
- gmx_fio_do_gmx_bool(fio, pull->bPrintRefValue);
- gmx_fio_do_gmx_bool(fio, pull->bPrintComp);
+ serializer->doInt(&idum); /* used to be bPrintCOM2 */
+ serializer->doBool(&pull->bPrintRefValue);
+ serializer->doBool(&pull->bPrintComp);
}
else
{
pull->bPrintRefValue = FALSE;
pull->bPrintComp = TRUE;
}
- gmx_fio_do_int(fio, pull->nstxout);
- gmx_fio_do_int(fio, pull->nstfout);
+ serializer->doInt(&pull->nstxout);
+ serializer->doInt(&pull->nstfout);
if (file_version >= tpxv_PullPrevStepCOMAsReference)
{
- gmx_fio_do_gmx_bool(fio, pull->bSetPbcRefToPrevStepCOM);
+ serializer->doBool(&pull->bSetPbcRefToPrevStepCOM);
}
else
{
pull->bSetPbcRefToPrevStepCOM = FALSE;
}
- if (bRead)
- {
- 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(fio, &pull->group[g], &pull->coord[std::max(g-1, 0)],
- bRead);
+ 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->ngroup; g++)
{
- do_pull_group(fio, &pull->group[g], bRead);
+ do_pull_group(serializer, &pull->group[g]);
}
for (g = 0; g < pull->ncoord; g++)
{
- do_pull_coord(fio, &pull->coord[g],
- bRead, 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;
- gmx_fio_do_gmx_bool(fio, v);
+ v = pull->bXOutAverage;
+ serializer->doBool(&v);
pull->bXOutAverage = v;
v = pull->bFOutAverage;
- gmx_fio_do_gmx_bool(fio, v);
+ serializer->doBool(&v);
pull->bFOutAverage = v;
}
}
-static void do_rotgrp(t_fileio *fio, t_rotgrp *rotg, gmx_bool bRead)
+static void do_rotgrp(gmx::ISerializer* serializer, t_rotgrp* rotg)
{
- gmx_fio_do_int(fio, rotg->eType);
- gmx_fio_do_int(fio, rotg->bMassW);
- gmx_fio_do_int(fio, rotg->nat);
- if (bRead)
+ 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())
{
snew(rotg->ind, rotg->nat);
}
- gmx_fio_ndo_int(fio, rotg->ind, rotg->nat);
- if (bRead)
+ serializer->doIntArray(rotg->ind, rotg->nat);
+ if (serializer->reading())
{
snew(rotg->x_ref, rotg->nat);
}
- gmx_fio_ndo_rvec(fio, rotg->x_ref, rotg->nat);
- gmx_fio_do_rvec(fio, rotg->inputVec);
- gmx_fio_do_rvec(fio, rotg->pivot);
- gmx_fio_do_real(fio, rotg->rate);
- gmx_fio_do_real(fio, rotg->k);
- gmx_fio_do_real(fio, rotg->slab_dist);
- gmx_fio_do_real(fio, rotg->min_gaussian);
- gmx_fio_do_real(fio, rotg->eps);
- gmx_fio_do_int(fio, rotg->eFittype);
- gmx_fio_do_int(fio, rotg->PotAngle_nstep);
- gmx_fio_do_real(fio, rotg->PotAngle_step);
+ serializer->doRvecArray(rotg->x_ref, rotg->nat);
+ serializer->doRvec(&rotg->inputVec);
+ serializer->doRvec(&rotg->pivot);
+ serializer->doReal(&rotg->rate);
+ serializer->doReal(&rotg->k);
+ serializer->doReal(&rotg->slab_dist);
+ serializer->doReal(&rotg->min_gaussian);
+ serializer->doReal(&rotg->eps);
+ serializer->doEnumAsInt(&rotg->eFittype);
+ serializer->doInt(&rotg->PotAngle_nstep);
+ serializer->doReal(&rotg->PotAngle_step);
}
-static void do_rot(t_fileio *fio, t_rot *rot, gmx_bool bRead)
+static void do_rot(gmx::ISerializer* serializer, t_rot* rot)
{
int g;
- gmx_fio_do_int(fio, rot->ngrp);
- gmx_fio_do_int(fio, rot->nstrout);
- gmx_fio_do_int(fio, rot->nstsout);
- if (bRead)
+ serializer->doInt(&rot->ngrp);
+ serializer->doInt(&rot->nstrout);
+ serializer->doInt(&rot->nstsout);
+ if (serializer->reading())
{
snew(rot->grp, rot->ngrp);
}
for (g = 0; g < rot->ngrp; g++)
{
- do_rotgrp(fio, &rot->grp[g], bRead);
+ do_rotgrp(serializer, &rot->grp[g]);
}
}
-static void do_swapgroup(t_fileio *fio, t_swapGroup *g, gmx_bool bRead)
+static void do_swapgroup(gmx::ISerializer* serializer, t_swapGroup* g)
{
/* Name of the group or molecule */
- if (bRead)
+ std::string buf;
+ if (serializer->reading())
{
- char buf[STRLEN];
-
- gmx_fio_do_string(fio, buf);
- g->molname = gmx_strdup(buf);
+ serializer->doString(&buf);
+ g->molname = gmx_strdup(buf.c_str());
}
else
{
- gmx_fio_do_string(fio, g->molname);
+ buf = g->molname;
+ serializer->doString(&buf);
}
/* Number of atoms in the group */
- gmx_fio_do_int(fio, g->nat);
+ serializer->doInt(&g->nat);
/* The group's atom indices */
- if (bRead)
+ if (serializer->reading())
{
snew(g->ind, g->nat);
}
- gmx_fio_ndo_int(fio, g->ind, g->nat);
+ serializer->doIntArray(g->ind, g->nat);
/* Requested counts for compartments A and B */
- gmx_fio_ndo_int(fio, g->nmolReq, eCompNR);
+ serializer->doIntArray(g->nmolReq.data(), static_cast<int>(Compartment::Count));
}
-static void do_swapcoords_tpx(t_fileio *fio, t_swapcoords *swap, gmx_bool bRead, 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
};
/* The total number of swap groups is the sum of the fixed groups
* (split0, split1, solvent), and the user-defined groups (2+ types of ions)
*/
- gmx_fio_do_int(fio, swap->ngrp);
- if (bRead)
+ serializer->doInt(&swap->ngrp);
+ if (serializer->reading())
{
snew(swap->grp, swap->ngrp);
}
for (int ig = 0; ig < swap->ngrp; ig++)
{
- do_swapgroup(fio, &swap->grp[ig], bRead);
+ do_swapgroup(serializer, &swap->grp[ig]);
}
- gmx_fio_do_gmx_bool(fio, swap->massw_split[eChannel0]);
- gmx_fio_do_gmx_bool(fio, swap->massw_split[eChannel1]);
- gmx_fio_do_int(fio, swap->nstswap);
- gmx_fio_do_int(fio, swap->nAverage);
- gmx_fio_do_real(fio, swap->threshold);
- gmx_fio_do_real(fio, swap->cyl0r);
- gmx_fio_do_real(fio, swap->cyl0u);
- gmx_fio_do_real(fio, swap->cyl0l);
- gmx_fio_do_real(fio, swap->cyl1r);
- gmx_fio_do_real(fio, swap->cyl1u);
- gmx_fio_do_real(fio, swap->cyl1l);
+ serializer->doBool(&swap->massw_split[eChannel0]);
+ serializer->doBool(&swap->massw_split[eChannel1]);
+ serializer->doInt(&swap->nstswap);
+ serializer->doInt(&swap->nAverage);
+ serializer->doReal(&swap->threshold);
+ serializer->doReal(&swap->cyl0r);
+ serializer->doReal(&swap->cyl0u);
+ serializer->doReal(&swap->cyl0l);
+ serializer->doReal(&swap->cyl1r);
+ serializer->doReal(&swap->cyl1u);
+ serializer->doReal(&swap->cyl1l);
}
else
{
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
-
- gmx_fio_do_int(fio, swap->grp[3].nat);
- gmx_fio_do_int(fio, swap->grp[eGrpSolvent].nat);
- gmx_fio_do_int(fio, swap->grp[eGrpSplit0].nat);
- gmx_fio_do_gmx_bool(fio, swap->massw_split[eChannel0]);
- gmx_fio_do_int(fio, swap->grp[eGrpSplit1].nat);
- gmx_fio_do_gmx_bool(fio, swap->massw_split[eChannel1]);
- gmx_fio_do_int(fio, swap->nstswap);
- gmx_fio_do_int(fio, swap->nAverage);
- gmx_fio_do_real(fio, swap->threshold);
- gmx_fio_do_real(fio, swap->cyl0r);
- gmx_fio_do_real(fio, swap->cyl0u);
- gmx_fio_do_real(fio, swap->cyl0l);
- gmx_fio_do_real(fio, swap->cyl1r);
- gmx_fio_do_real(fio, swap->cyl1u);
- gmx_fio_do_real(fio, swap->cyl1l);
+ 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[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[static_cast<int>(SwapGroupSplittingType::Split1)].nat);
+ serializer->doBool(&swap->massw_split[eChannel1]);
+ serializer->doInt(&swap->nstswap);
+ serializer->doInt(&swap->nAverage);
+ serializer->doReal(&swap->threshold);
+ serializer->doReal(&swap->cyl0r);
+ serializer->doReal(&swap->cyl0u);
+ serializer->doReal(&swap->cyl0l);
+ serializer->doReal(&swap->cyl1r);
+ serializer->doReal(&swap->cyl1u);
+ serializer->doReal(&swap->cyl1l);
// 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++)
{
int g = order[ig];
snew(swap->grp[g].ind, swap->grp[g].nat);
- gmx_fio_ndo_int(fio, swap->grp[g].ind, swap->grp[g].nat);
+ serializer->doIntArray(swap->grp[g].ind, swap->grp[g].nat);
}
}
for (int j = eCompA; j <= eCompB; j++)
{
- gmx_fio_do_int(fio, swap->grp[3].nmolReq[j]); // group 3 = anions
- gmx_fio_do_int(fio, swap->grp[4].nmolReq[j]); // group 4 = cations
+ 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)
{
- gmx_fio_do_real(fio, swap->bulkOffset[eCompA]);
- gmx_fio_do_real(fio, swap->bulkOffset[eCompB]);
+ serializer->doReal(&swap->bulkOffset[eCompA]);
+ serializer->doReal(&swap->bulkOffset[eCompB]);
}
-
}
-static void do_legacy_efield(t_fileio *fio, 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.
for (int j = 0; j < DIM; ++j)
{
int n, nt;
- gmx_fio_do_int(fio, n);
- gmx_fio_do_int(fio, nt);
- std::vector<real> aa(n+1), phi(nt+1), at(nt+1), phit(nt+1);
- gmx_fio_ndo_real(fio, aa.data(), n);
- gmx_fio_ndo_real(fio, phi.data(), n);
- gmx_fio_ndo_real(fio, at.data(), nt);
- gmx_fio_ndo_real(fio, phit.data(), 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);
+ serializer->doRealArray(phi.data(), n);
+ 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(t_fileio *fio, t_inputrec *ir, gmx_bool bRead,
- 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 */
- gmx_fio_do_int(fio, ir->eI);
+ serializer->doEnumAsInt(&ir->eI);
if (file_version >= 62)
{
- gmx_fio_do_int64(fio, ir->nsteps);
+ serializer->doInt64(&ir->nsteps);
}
else
{
- gmx_fio_do_int(fio, idum);
+ serializer->doInt(&idum);
ir->nsteps = idum;
}
if (file_version >= 62)
{
- gmx_fio_do_int64(fio, ir->init_step);
+ serializer->doInt64(&ir->init_step);
}
else
{
- gmx_fio_do_int(fio, idum);
+ serializer->doInt(&idum);
ir->init_step = idum;
}
- gmx_fio_do_int(fio, ir->simulation_part);
+ 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)
{
- gmx_fio_do_int(fio, ir->nstcalcenergy);
+ serializer->doInt(&ir->nstcalcenergy);
}
else
{
}
if (file_version >= 81)
{
- gmx_fio_do_int(fio, 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;
}
- gmx_fio_do_int(fio, ir->ns_type);
- gmx_fio_do_int(fio, ir->nstlist);
- gmx_fio_do_int(fio, idum); /* used to be ndelta; not used anymore */
+ serializer->doInt(&idum); /* used to be ns_type; not used anymore */
+ serializer->doInt(&ir->nstlist);
+ serializer->doInt(&idum); /* used to be ndelta; not used anymore */
- gmx_fio_do_real(fio, ir->rtpi);
+ serializer->doReal(&ir->rtpi);
- gmx_fio_do_int(fio, ir->nstcomm);
- gmx_fio_do_int(fio, ir->comm_mode);
+ serializer->doInt(&ir->nstcomm);
+ serializer->doEnumAsInt(&ir->comm_mode);
/* ignore nstcheckpoint */
if (file_version < tpxv_RemoveObsoleteParameters1)
{
- gmx_fio_do_int(fio, idum);
+ serializer->doInt(&idum);
}
- gmx_fio_do_int(fio, ir->nstcgsteep);
+ serializer->doInt(&ir->nstcgsteep);
- gmx_fio_do_int(fio, ir->nbfgscorr);
+ serializer->doInt(&ir->nbfgscorr);
- gmx_fio_do_int(fio, ir->nstlog);
- gmx_fio_do_int(fio, ir->nstxout);
- gmx_fio_do_int(fio, ir->nstvout);
- gmx_fio_do_int(fio, ir->nstfout);
- gmx_fio_do_int(fio, ir->nstenergy);
- gmx_fio_do_int(fio, ir->nstxout_compressed);
+ serializer->doInt(&ir->nstlog);
+ serializer->doInt(&ir->nstxout);
+ serializer->doInt(&ir->nstvout);
+ serializer->doInt(&ir->nstfout);
+ serializer->doInt(&ir->nstenergy);
+ serializer->doInt(&ir->nstxout_compressed);
if (file_version >= 59)
{
- gmx_fio_do_double(fio, ir->init_t);
- gmx_fio_do_double(fio, ir->delta_t);
+ serializer->doDouble(&ir->init_t);
+ serializer->doDouble(&ir->delta_t);
}
else
{
- gmx_fio_do_real(fio, rdum);
+ serializer->doReal(&rdum);
ir->init_t = rdum;
- gmx_fio_do_real(fio, rdum);
+ serializer->doReal(&rdum);
ir->delta_t = rdum;
}
- gmx_fio_do_real(fio, ir->x_compression_precision);
+ serializer->doReal(&ir->x_compression_precision);
if (file_version >= 81)
{
- gmx_fio_do_real(fio, ir->verletbuf_tol);
+ serializer->doReal(&ir->verletbuf_tol);
}
else
{
ir->verletbuf_tol = 0;
}
- gmx_fio_do_real(fio, ir->rlist);
+ serializer->doReal(&ir->rlist);
if (file_version >= 67 && file_version < tpxv_RemoveTwinRange)
{
- if (bRead)
+ if (serializer->reading())
{
// Reading such a file version could invoke the twin-range
// scheme, about which mdrun should give a fatal error.
real dummy_rlistlong = -1;
- gmx_fio_do_real(fio, dummy_rlistlong);
+ 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
// support required the twin-range scheme, for which mdrun
// already emits a fatal error.
int dummy_nstcalclr = -1;
- gmx_fio_do_int(fio, dummy_nstcalclr);
+ serializer->doInt(&dummy_nstcalclr);
}
- gmx_fio_do_int(fio, ir->coulombtype);
+ serializer->doEnumAsInt(&ir->coulombtype);
if (file_version >= 81)
{
- gmx_fio_do_int(fio, 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);
}
- gmx_fio_do_real(fio, ir->rcoulomb_switch);
- gmx_fio_do_real(fio, ir->rcoulomb);
- gmx_fio_do_int(fio, ir->vdwtype);
+ serializer->doReal(&ir->rcoulomb_switch);
+ serializer->doReal(&ir->rcoulomb);
+ serializer->doEnumAsInt(&ir->vdwtype);
if (file_version >= 81)
{
- gmx_fio_do_int(fio, 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);
}
- gmx_fio_do_real(fio, ir->rvdw_switch);
- gmx_fio_do_real(fio, ir->rvdw);
- gmx_fio_do_int(fio, ir->eDispCorr);
- gmx_fio_do_real(fio, ir->epsilon_r);
- gmx_fio_do_real(fio, ir->epsilon_rf);
- gmx_fio_do_real(fio, ir->tabext);
+ serializer->doReal(&ir->rvdw_switch);
+ serializer->doReal(&ir->rvdw);
+ serializer->doEnumAsInt(&ir->eDispCorr);
+ serializer->doReal(&ir->epsilon_r);
+ serializer->doReal(&ir->epsilon_rf);
+ serializer->doReal(&ir->tabext);
// This permits reading a .tpr file that used implicit solvent,
// and later permitting mdrun to refuse to run it.
- if (bRead)
+ if (serializer->reading())
{
if (file_version < tpxv_RemoveImplicitSolvation)
{
- gmx_fio_do_int(fio, idum);
- gmx_fio_do_int(fio, idum);
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_int(fio, idum);
+ serializer->doInt(&idum);
+ serializer->doInt(&idum);
+ serializer->doReal(&rdum);
+ serializer->doReal(&rdum);
+ serializer->doInt(&idum);
ir->implicit_solvent = (idum > 0);
}
else
}
if (file_version < tpxv_RemoveImplicitSolvation)
{
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_real(fio, rdum);
+ serializer->doReal(&rdum);
+ serializer->doReal(&rdum);
+ serializer->doReal(&rdum);
+ serializer->doReal(&rdum);
if (file_version >= 60)
{
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_int(fio, idum);
+ serializer->doReal(&rdum);
+ serializer->doInt(&idum);
}
- gmx_fio_do_real(fio, rdum);
+ serializer->doReal(&rdum);
}
}
if (file_version >= 81)
{
- gmx_fio_do_real(fio, ir->fourier_spacing);
+ serializer->doReal(&ir->fourier_spacing);
}
else
{
ir->fourier_spacing = 0.0;
}
- gmx_fio_do_int(fio, ir->nkx);
- gmx_fio_do_int(fio, ir->nky);
- gmx_fio_do_int(fio, ir->nkz);
- gmx_fio_do_int(fio, ir->pme_order);
- gmx_fio_do_real(fio, ir->ewald_rtol);
+ serializer->doInt(&ir->nkx);
+ serializer->doInt(&ir->nky);
+ serializer->doInt(&ir->nkz);
+ serializer->doInt(&ir->pme_order);
+ serializer->doReal(&ir->ewald_rtol);
if (file_version >= 93)
{
- gmx_fio_do_real(fio, ir->ewald_rtol_lj);
+ serializer->doReal(&ir->ewald_rtol_lj);
}
else
{
ir->ewald_rtol_lj = ir->ewald_rtol;
}
- gmx_fio_do_int(fio, ir->ewald_geometry);
- gmx_fio_do_real(fio, ir->epsilon_surface);
+ serializer->doEnumAsInt(&ir->ewald_geometry);
+ serializer->doReal(&ir->epsilon_surface);
/* ignore bOptFFT */
if (file_version < tpxv_RemoveObsoleteParameters1)
{
- gmx_fio_do_gmx_bool(fio, bdum);
+ serializer->doBool(&bdum);
}
if (file_version >= 93)
{
- gmx_fio_do_int(fio, ir->ljpme_combination_rule);
+ serializer->doEnumAsInt(&ir->ljpme_combination_rule);
}
- gmx_fio_do_gmx_bool(fio, ir->bContinuation);
- gmx_fio_do_int(fio, ir->etc);
+ serializer->doBool(&ir->bContinuation);
+ 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.
*/
if (file_version >= 79)
{
- gmx_fio_do_gmx_bool(fio, ir->bPrintNHChains);
+ serializer->doBool(&ir->bPrintNHChains);
}
if (file_version >= 71)
{
- gmx_fio_do_int(fio, ir->nsttcouple);
+ serializer->doInt(&ir->nsttcouple);
}
else
{
ir->nsttcouple = ir->nstcalcenergy;
}
- gmx_fio_do_int(fio, ir->epc);
- gmx_fio_do_int(fio, ir->epct);
+ serializer->doEnumAsInt(&ir->epc);
+ serializer->doEnumAsInt(&ir->epct);
if (file_version >= 71)
{
- gmx_fio_do_int(fio, ir->nstpcouple);
+ serializer->doInt(&ir->nstpcouple);
}
else
{
ir->nstpcouple = ir->nstcalcenergy;
}
- gmx_fio_do_real(fio, ir->tau_p);
- gmx_fio_do_rvec(fio, ir->ref_p[XX]);
- gmx_fio_do_rvec(fio, ir->ref_p[YY]);
- gmx_fio_do_rvec(fio, ir->ref_p[ZZ]);
- gmx_fio_do_rvec(fio, ir->compress[XX]);
- gmx_fio_do_rvec(fio, ir->compress[YY]);
- gmx_fio_do_rvec(fio, ir->compress[ZZ]);
- gmx_fio_do_int(fio, ir->refcoord_scaling);
- gmx_fio_do_rvec(fio, ir->posres_com);
- gmx_fio_do_rvec(fio, ir->posres_comB);
+ serializer->doReal(&ir->tau_p);
+ serializer->doRvec(&ir->ref_p[XX]);
+ serializer->doRvec(&ir->ref_p[YY]);
+ serializer->doRvec(&ir->ref_p[ZZ]);
+ serializer->doRvec(&ir->compress[XX]);
+ serializer->doRvec(&ir->compress[YY]);
+ serializer->doRvec(&ir->compress[ZZ]);
+ serializer->doEnumAsInt(&ir->refcoord_scaling);
+ serializer->doRvec(&ir->posres_com);
+ serializer->doRvec(&ir->posres_comB);
if (file_version < 79)
{
- gmx_fio_do_int(fio, ir->andersen_seed);
+ serializer->doInt(&ir->andersen_seed);
}
else
{
ir->andersen_seed = 0;
}
- gmx_fio_do_real(fio, ir->shake_tol);
+ serializer->doReal(&ir->shake_tol);
- gmx_fio_do_int(fio, ir->efep);
- do_fepvals(fio, ir->fepvals, bRead, 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)
{
- gmx_fio_do_gmx_bool(fio, ir->bSimTemp);
+ serializer->doBool(&ir->bSimTemp);
if (ir->bSimTemp)
{
ir->bSimTemp = TRUE;
}
if (ir->bSimTemp)
{
- do_simtempvals(fio, ir->simtempvals, ir->fepvals->n_lambda, bRead, 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)
{
- gmx_fio_do_gmx_bool(fio, ir->bExpanded);
- if (ir->bExpanded)
- {
- ir->bExpanded = TRUE;
- }
- else
- {
- ir->bExpanded = FALSE;
- }
+ serializer->doBool(&ir->bExpanded);
}
if (ir->bExpanded)
{
- do_expandedvals(fio, ir->expandedvals, ir->fepvals, bRead, file_version);
+ if (serializer->reading())
+ {
+ ir->expandedvals = std::make_unique<t_expanded>();
+ }
+ do_expandedvals(serializer, ir->expandedvals.get(), ir->fepvals.get(), file_version);
}
- gmx_fio_do_int(fio, ir->eDisre);
- gmx_fio_do_int(fio, ir->eDisreWeighting);
- gmx_fio_do_gmx_bool(fio, ir->bDisreMixed);
- gmx_fio_do_real(fio, ir->dr_fc);
- gmx_fio_do_real(fio, ir->dr_tau);
- gmx_fio_do_int(fio, ir->nstdisreout);
- gmx_fio_do_real(fio, ir->orires_fc);
- gmx_fio_do_real(fio, ir->orires_tau);
- gmx_fio_do_int(fio, ir->nstorireout);
+ serializer->doEnumAsInt(&ir->eDisre);
+ serializer->doEnumAsInt(&ir->eDisreWeighting);
+ serializer->doBool(&ir->bDisreMixed);
+ serializer->doReal(&ir->dr_fc);
+ serializer->doReal(&ir->dr_tau);
+ serializer->doInt(&ir->nstdisreout);
+ serializer->doReal(&ir->orires_fc);
+ serializer->doReal(&ir->orires_tau);
+ serializer->doInt(&ir->nstorireout);
/* ignore dihre_fc */
if (file_version < 79)
{
- gmx_fio_do_real(fio, rdum);
+ serializer->doReal(&rdum);
}
- gmx_fio_do_real(fio, ir->em_stepsize);
- gmx_fio_do_real(fio, ir->em_tol);
- gmx_fio_do_gmx_bool(fio, ir->bShakeSOR);
- gmx_fio_do_int(fio, ir->niter);
- gmx_fio_do_real(fio, ir->fc_stepsize);
- gmx_fio_do_int(fio, ir->eConstrAlg);
- gmx_fio_do_int(fio, ir->nProjOrder);
- gmx_fio_do_real(fio, ir->LincsWarnAngle);
- gmx_fio_do_int(fio, ir->nLincsIter);
- gmx_fio_do_real(fio, ir->bd_fric);
+ serializer->doReal(&ir->em_stepsize);
+ serializer->doReal(&ir->em_tol);
+ serializer->doBool(&ir->bShakeSOR);
+ serializer->doInt(&ir->niter);
+ serializer->doReal(&ir->fc_stepsize);
+ serializer->doEnumAsInt(&ir->eConstrAlg);
+ serializer->doInt(&ir->nProjOrder);
+ serializer->doReal(&ir->LincsWarnAngle);
+ serializer->doInt(&ir->nLincsIter);
+ serializer->doReal(&ir->bd_fric);
if (file_version >= tpxv_Use64BitRandomSeed)
{
- gmx_fio_do_int64(fio, ir->ld_seed);
+ serializer->doInt64(&ir->ld_seed);
}
else
{
- gmx_fio_do_int(fio, idum);
+ serializer->doInt(&idum);
ir->ld_seed = idum;
}
for (i = 0; i < DIM; i++)
{
- gmx_fio_do_rvec(fio, ir->deform[i]);
+ serializer->doRvec(&ir->deform[i]);
}
- gmx_fio_do_real(fio, ir->cos_accel);
+ serializer->doReal(&ir->cos_accel);
- gmx_fio_do_int(fio, ir->userint1);
- gmx_fio_do_int(fio, ir->userint2);
- gmx_fio_do_int(fio, ir->userint3);
- gmx_fio_do_int(fio, ir->userint4);
- gmx_fio_do_real(fio, ir->userreal1);
- gmx_fio_do_real(fio, ir->userreal2);
- gmx_fio_do_real(fio, ir->userreal3);
- gmx_fio_do_real(fio, ir->userreal4);
+ serializer->doInt(&ir->userint1);
+ serializer->doInt(&ir->userint2);
+ serializer->doInt(&ir->userint3);
+ serializer->doInt(&ir->userint4);
+ serializer->doReal(&ir->userreal1);
+ serializer->doReal(&ir->userreal2);
+ serializer->doReal(&ir->userreal3);
+ serializer->doReal(&ir->userreal4);
/* AdResS is removed, but we need to be able to read old files,
and let mdrun refuse to run them */
if (file_version >= 77 && file_version < tpxv_RemoveAdress)
{
- gmx_fio_do_gmx_bool(fio, ir->bAdress);
+ serializer->doBool(&ir->bAdress);
if (ir->bAdress)
{
int idum, numThermoForceGroups, numEnergyGroups;
real rdum;
rvec rvecdum;
- gmx_fio_do_int(fio, idum);
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_int(fio, idum);
- gmx_fio_do_int(fio, idum);
- gmx_fio_do_rvec(fio, rvecdum);
- gmx_fio_do_int(fio, numThermoForceGroups);
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_int(fio, numEnergyGroups);
- gmx_fio_do_int(fio, idum);
+ serializer->doInt(&idum);
+ serializer->doReal(&rdum);
+ serializer->doReal(&rdum);
+ serializer->doReal(&rdum);
+ serializer->doInt(&idum);
+ serializer->doInt(&idum);
+ serializer->doRvec(&rvecdum);
+ serializer->doInt(&numThermoForceGroups);
+ serializer->doReal(&rdum);
+ serializer->doInt(&numEnergyGroups);
+ serializer->doInt(&idum);
if (numThermoForceGroups > 0)
{
std::vector<int> idumn(numThermoForceGroups);
- gmx_fio_ndo_int(fio, idumn.data(), idumn.size());
+ serializer->doIntArray(idumn.data(), idumn.size());
}
if (numEnergyGroups > 0)
{
std::vector<int> idumn(numEnergyGroups);
- gmx_fio_ndo_int(fio, idumn.data(), idumn.size());
+ serializer->doIntArray(idumn.data(), idumn.size());
}
}
}
/* pull stuff */
{
- int ePullOld = 0;
+ PullingAlgorithm ePullOld = PullingAlgorithm::Umbrella;
if (file_version >= tpxv_PullCoordTypeGeom)
{
- gmx_fio_do_gmx_bool(fio, ir->bPull);
+ serializer->doBool(&ir->bPull);
}
else
{
- gmx_fio_do_int(fio, 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 (bRead)
+ if (serializer->reading())
{
- snew(ir->pull, 1);
+ ir->pull = std::make_unique<pull_params_t>();
}
- do_pull(fio, ir->pull, bRead, file_version, ePullOld);
+ do_pull(serializer, ir->pull.get(), file_version, ePullOld);
}
}
if (file_version >= tpxv_AcceleratedWeightHistogram)
{
- gmx_fio_do_gmx_bool(fio, ir->bDoAwh);
+ serializer->doBool(&ir->bDoAwh);
if (ir->bDoAwh)
{
- if (bRead)
+ if (serializer->reading())
{
- snew(ir->awhParams, 1);
+ ir->awhParams = std::make_unique<gmx::AwhParams>(serializer);
+ }
+ else
+ {
+ ir->awhParams->serialize(serializer);
}
- do_awh(fio, ir->awhParams, bRead, file_version);
}
}
else
/* Enforced rotation */
if (file_version >= 74)
{
- gmx_fio_do_gmx_bool(fio, ir->bRot);
+ serializer->doBool(&ir->bRot);
if (ir->bRot)
{
- if (bRead)
+ if (serializer->reading())
{
snew(ir->rot, 1);
}
- do_rot(fio, ir->rot, bRead);
+ do_rot(serializer, ir->rot);
}
}
else
/* Interactive molecular dynamics */
if (file_version >= tpxv_InteractiveMolecularDynamics)
{
- gmx_fio_do_gmx_bool(fio, ir->bIMD);
+ serializer->doBool(&ir->bIMD);
if (ir->bIMD)
{
- if (bRead)
+ if (serializer->reading())
{
snew(ir->imd, 1);
}
- do_imd(fio, ir->imd, bRead);
+ do_imd(serializer, ir->imd);
}
}
else
}
/* grpopts stuff */
- gmx_fio_do_int(fio, ir->opts.ngtc);
+ serializer->doInt(&ir->opts.ngtc);
if (file_version >= 69)
{
- gmx_fio_do_int(fio, ir->opts.nhchainlength);
+ serializer->doInt(&ir->opts.nhchainlength);
}
else
{
ir->opts.nhchainlength = 1;
}
- gmx_fio_do_int(fio, ir->opts.ngacc);
- gmx_fio_do_int(fio, ir->opts.ngfrz);
- gmx_fio_do_int(fio, ir->opts.ngener);
+ 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 (bRead)
+ 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)
{
- gmx_fio_ndo_real(fio, ir->opts.nrdf, ir->opts.ngtc);
- gmx_fio_ndo_real(fio, ir->opts.ref_t, ir->opts.ngtc);
- gmx_fio_ndo_real(fio, ir->opts.tau_t, ir->opts.ngtc);
+ serializer->doRealArray(ir->opts.nrdf, ir->opts.ngtc);
+ serializer->doRealArray(ir->opts.ref_t, ir->opts.ngtc);
+ serializer->doRealArray(ir->opts.tau_t, ir->opts.ngtc);
}
if (ir->opts.ngfrz > 0)
{
- gmx_fio_ndo_ivec(fio, ir->opts.nFreeze, ir->opts.ngfrz);
+ serializer->doIvecArray(ir->opts.nFreeze, ir->opts.ngfrz);
}
if (ir->opts.ngacc > 0)
{
- gmx_fio_ndo_rvec(fio, ir->opts.acc, ir->opts.ngacc);
+ serializer->doRvecArray(ir->opts.acceleration, ir->opts.ngacc);
+ }
+ 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;
+ }
+ }
}
- gmx_fio_ndo_int(fio, ir->opts.egp_flags,
- ir->opts.ngener*ir->opts.ngener);
+ serializer->doIntArray(ir->opts.egp_flags, ir->opts.ngener * ir->opts.ngener);
/* First read the lists with annealing and npoints for each group */
- gmx_fio_ndo_int(fio, ir->opts.annealing, ir->opts.ngtc);
- gmx_fio_ndo_int(fio, ir->opts.anneal_npoints, 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++)
{
k = ir->opts.anneal_npoints[j];
- if (bRead)
+ if (serializer->reading())
{
snew(ir->opts.anneal_time[j], k);
snew(ir->opts.anneal_temp[j], k);
}
- gmx_fio_ndo_real(fio, ir->opts.anneal_time[j], k);
- gmx_fio_ndo_real(fio, ir->opts.anneal_temp[j], k);
+ serializer->doRealArray(ir->opts.anneal_time[j], k);
+ serializer->doRealArray(ir->opts.anneal_temp[j], k);
}
/* Walls */
{
- gmx_fio_do_int(fio, ir->nwall);
- gmx_fio_do_int(fio, ir->wall_type);
- gmx_fio_do_real(fio, ir->wall_r_linpot);
- gmx_fio_do_int(fio, ir->wall_atomtype[0]);
- gmx_fio_do_int(fio, ir->wall_atomtype[1]);
- gmx_fio_do_real(fio, ir->wall_density[0]);
- gmx_fio_do_real(fio, ir->wall_density[1]);
- gmx_fio_do_real(fio, ir->wall_ewald_zfac);
+ serializer->doInt(&ir->nwall);
+ serializer->doEnumAsInt(&ir->wall_type);
+ serializer->doReal(&ir->wall_r_linpot);
+ serializer->doInt(&ir->wall_atomtype[0]);
+ serializer->doInt(&ir->wall_atomtype[1]);
+ serializer->doReal(&ir->wall_density[0]);
+ serializer->doReal(&ir->wall_density[1]);
+ serializer->doReal(&ir->wall_ewald_zfac);
}
/* Cosine stuff for electric fields */
if (file_version < tpxv_GenericParamsForElectricField)
{
- do_legacy_efield(fio, ¶msObj);
+ do_legacy_efield(serializer, ¶msObj);
}
/* Swap ions */
if (file_version >= tpxv_ComputationalElectrophysiology)
{
- gmx_fio_do_int(fio, ir->eSwapCoords);
- if (ir->eSwapCoords != eswapNO)
+ serializer->doEnumAsInt(&ir->eSwapCoords);
+ if (ir->eSwapCoords != SwapType::No)
{
- if (bRead)
+ if (serializer->reading())
{
snew(ir->swap, 1);
}
- do_swapcoords_tpx(fio, ir->swap, bRead, file_version);
+ do_swapcoords_tpx(serializer, ir->swap, file_version);
}
}
- /* QMMM stuff */
+ /* QMMM reading - despite defunct we require reading for backwards
+ * compability and correct serialization
+ */
{
- gmx_fio_do_gmx_bool(fio, ir->bQMMM);
- gmx_fio_do_int(fio, ir->QMMMscheme);
- gmx_fio_do_real(fio, ir->scalefactor);
- gmx_fio_do_int(fio, ir->opts.ngQM);
- if (bRead)
- {
- 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);
- }
+ serializer->doBool(&ir->bQMMM);
+ int qmmmScheme;
+ serializer->doInt(&qmmmScheme);
+ real unusedScalefactor;
+ serializer->doReal(&unusedScalefactor);
+
+ // this is still used in Mimic
+ serializer->doInt(&ir->opts.ngQM);
if (ir->opts.ngQM > 0 && ir->bQMMM)
{
- gmx_fio_ndo_int(fio, ir->opts.QMmethod, ir->opts.ngQM);
- gmx_fio_ndo_int(fio, ir->opts.QMbasis, ir->opts.ngQM);
- gmx_fio_ndo_int(fio, ir->opts.QMcharge, ir->opts.ngQM);
- gmx_fio_ndo_int(fio, ir->opts.QMmult, ir->opts.ngQM);
- gmx_fio_ndo_gmx_bool(fio, ir->opts.bSH, ir->opts.ngQM);
- gmx_fio_ndo_int(fio, ir->opts.CASorbitals, ir->opts.ngQM);
- gmx_fio_ndo_int(fio, ir->opts.CASelectrons, ir->opts.ngQM);
- gmx_fio_ndo_real(fio, ir->opts.SAon, ir->opts.ngQM);
- gmx_fio_ndo_real(fio, ir->opts.SAoff, ir->opts.ngQM);
- gmx_fio_ndo_int(fio, 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);
- gmx_fio_ndo_int(fio, dummy.data(), ir->opts.ngQM);
- gmx_fio_ndo_int(fio, 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 (file_version >= tpxv_GenericParamsForElectricField)
{
- gmx::FileIOXdrSerializer serializer(fio);
- if (bRead)
+ if (serializer->reading())
{
- paramsObj.mergeObject(
- gmx::deserializeKeyValueTree(&serializer));
+ paramsObj.mergeObject(gmx::deserializeKeyValueTree(serializer));
}
else
{
GMX_RELEASE_ASSERT(ir->params != nullptr,
"Parameters should be present when writing inputrec");
- gmx::serializeKeyValueTree(*ir->params, &serializer);
+ gmx::serializeKeyValueTree(*ir->params, serializer);
}
}
- if (bRead)
+ if (serializer->reading())
{
ir->params = new gmx::KeyValueTreeObject(paramsBuilder.build());
+ // Initialize internal parameters to an empty kvt for all tpr versions
+ ir->internalParameters = std::make_unique<gmx::KeyValueTreeObject>();
+ }
+
+ if (file_version >= tpxv_GenericInternalParameters)
+ {
+ if (serializer->reading())
+ {
+ ir->internalParameters =
+ std::make_unique<gmx::KeyValueTreeObject>(gmx::deserializeKeyValueTree(serializer));
+ }
+ else
+ {
+ GMX_RELEASE_ASSERT(ir->internalParameters != nullptr,
+ "Parameters should be present when writing inputrec");
+ gmx::serializeKeyValueTree(*ir->internalParameters, serializer);
+ }
}
}
-static void do_harm(t_fileio *fio, t_iparams *iparams)
+static void do_harm(gmx::ISerializer* serializer, t_iparams* iparams)
{
- gmx_fio_do_real(fio, iparams->harmonic.rA);
- gmx_fio_do_real(fio, iparams->harmonic.krA);
- gmx_fio_do_real(fio, iparams->harmonic.rB);
- gmx_fio_do_real(fio, iparams->harmonic.krB);
+ serializer->doReal(&iparams->harmonic.rA);
+ serializer->doReal(&iparams->harmonic.krA);
+ serializer->doReal(&iparams->harmonic.rB);
+ serializer->doReal(&iparams->harmonic.krB);
}
-static void do_iparams(t_fileio *fio, t_functype ftype, t_iparams *iparams,
- gmx_bool bRead, 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)
{
case F_G96BONDS:
case F_HARMONIC:
case F_IDIHS:
- do_harm(fio, iparams);
- if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && bRead)
+ do_harm(serializer, iparams);
+ if ((ftype == F_ANGRES || ftype == F_ANGRESZ) && serializer->reading())
{
/* Correct incorrect storage of parameters */
iparams->pdihs.phiB = iparams->pdihs.phiA;
}
break;
case F_RESTRANGLES:
- gmx_fio_do_real(fio, iparams->harmonic.rA);
- gmx_fio_do_real(fio, iparams->harmonic.krA);
+ serializer->doReal(&iparams->harmonic.rA);
+ serializer->doReal(&iparams->harmonic.krA);
break;
case F_LINEAR_ANGLES:
- gmx_fio_do_real(fio, iparams->linangle.klinA);
- gmx_fio_do_real(fio, iparams->linangle.aA);
- gmx_fio_do_real(fio, iparams->linangle.klinB);
- gmx_fio_do_real(fio, iparams->linangle.aB);
+ serializer->doReal(&iparams->linangle.klinA);
+ serializer->doReal(&iparams->linangle.aA);
+ serializer->doReal(&iparams->linangle.klinB);
+ serializer->doReal(&iparams->linangle.aB);
break;
case F_FENEBONDS:
- gmx_fio_do_real(fio, iparams->fene.bm);
- gmx_fio_do_real(fio, iparams->fene.kb);
+ serializer->doReal(&iparams->fene.bm);
+ serializer->doReal(&iparams->fene.kb);
break;
case F_RESTRBONDS:
- gmx_fio_do_real(fio, iparams->restraint.lowA);
- gmx_fio_do_real(fio, iparams->restraint.up1A);
- gmx_fio_do_real(fio, iparams->restraint.up2A);
- gmx_fio_do_real(fio, iparams->restraint.kA);
- gmx_fio_do_real(fio, iparams->restraint.lowB);
- gmx_fio_do_real(fio, iparams->restraint.up1B);
- gmx_fio_do_real(fio, iparams->restraint.up2B);
- gmx_fio_do_real(fio, iparams->restraint.kB);
+ serializer->doReal(&iparams->restraint.lowA);
+ serializer->doReal(&iparams->restraint.up1A);
+ serializer->doReal(&iparams->restraint.up2A);
+ serializer->doReal(&iparams->restraint.kA);
+ serializer->doReal(&iparams->restraint.lowB);
+ serializer->doReal(&iparams->restraint.up1B);
+ serializer->doReal(&iparams->restraint.up2B);
+ serializer->doReal(&iparams->restraint.kB);
break;
case F_TABBONDS:
case F_TABBONDSNC:
case F_TABANGLES:
case F_TABDIHS:
- gmx_fio_do_real(fio, iparams->tab.kA);
- gmx_fio_do_int(fio, iparams->tab.table);
- gmx_fio_do_real(fio, iparams->tab.kB);
+ serializer->doReal(&iparams->tab.kA);
+ serializer->doInt(&iparams->tab.table);
+ serializer->doReal(&iparams->tab.kB);
break;
case F_CROSS_BOND_BONDS:
- gmx_fio_do_real(fio, iparams->cross_bb.r1e);
- gmx_fio_do_real(fio, iparams->cross_bb.r2e);
- gmx_fio_do_real(fio, iparams->cross_bb.krr);
+ serializer->doReal(&iparams->cross_bb.r1e);
+ serializer->doReal(&iparams->cross_bb.r2e);
+ serializer->doReal(&iparams->cross_bb.krr);
break;
case F_CROSS_BOND_ANGLES:
- gmx_fio_do_real(fio, iparams->cross_ba.r1e);
- gmx_fio_do_real(fio, iparams->cross_ba.r2e);
- gmx_fio_do_real(fio, iparams->cross_ba.r3e);
- gmx_fio_do_real(fio, iparams->cross_ba.krt);
+ serializer->doReal(&iparams->cross_ba.r1e);
+ serializer->doReal(&iparams->cross_ba.r2e);
+ serializer->doReal(&iparams->cross_ba.r3e);
+ serializer->doReal(&iparams->cross_ba.krt);
break;
case F_UREY_BRADLEY:
- gmx_fio_do_real(fio, iparams->u_b.thetaA);
- gmx_fio_do_real(fio, iparams->u_b.kthetaA);
- gmx_fio_do_real(fio, iparams->u_b.r13A);
- gmx_fio_do_real(fio, iparams->u_b.kUBA);
+ serializer->doReal(&iparams->u_b.thetaA);
+ serializer->doReal(&iparams->u_b.kthetaA);
+ serializer->doReal(&iparams->u_b.r13A);
+ serializer->doReal(&iparams->u_b.kUBA);
if (file_version >= 79)
{
- gmx_fio_do_real(fio, iparams->u_b.thetaB);
- gmx_fio_do_real(fio, iparams->u_b.kthetaB);
- gmx_fio_do_real(fio, iparams->u_b.r13B);
- gmx_fio_do_real(fio, iparams->u_b.kUBB);
+ serializer->doReal(&iparams->u_b.thetaB);
+ serializer->doReal(&iparams->u_b.kthetaB);
+ serializer->doReal(&iparams->u_b.r13B);
+ serializer->doReal(&iparams->u_b.kUBB);
}
else
{
}
break;
case F_QUARTIC_ANGLES:
- gmx_fio_do_real(fio, iparams->qangle.theta);
- gmx_fio_ndo_real(fio, iparams->qangle.c, 5);
+ serializer->doReal(&iparams->qangle.theta);
+ serializer->doRealArray(iparams->qangle.c, 5);
break;
case F_BHAM:
- gmx_fio_do_real(fio, iparams->bham.a);
- gmx_fio_do_real(fio, iparams->bham.b);
- gmx_fio_do_real(fio, iparams->bham.c);
+ serializer->doReal(&iparams->bham.a);
+ serializer->doReal(&iparams->bham.b);
+ serializer->doReal(&iparams->bham.c);
break;
case F_MORSE:
- gmx_fio_do_real(fio, iparams->morse.b0A);
- gmx_fio_do_real(fio, iparams->morse.cbA);
- gmx_fio_do_real(fio, iparams->morse.betaA);
+ serializer->doReal(&iparams->morse.b0A);
+ serializer->doReal(&iparams->morse.cbA);
+ serializer->doReal(&iparams->morse.betaA);
if (file_version >= 79)
{
- gmx_fio_do_real(fio, iparams->morse.b0B);
- gmx_fio_do_real(fio, iparams->morse.cbB);
- gmx_fio_do_real(fio, iparams->morse.betaB);
+ serializer->doReal(&iparams->morse.b0B);
+ serializer->doReal(&iparams->morse.cbB);
+ serializer->doReal(&iparams->morse.betaB);
}
else
{
}
break;
case F_CUBICBONDS:
- gmx_fio_do_real(fio, iparams->cubic.b0);
- gmx_fio_do_real(fio, iparams->cubic.kb);
- gmx_fio_do_real(fio, iparams->cubic.kcub);
- break;
- case F_CONNBONDS:
- break;
- case F_POLARIZATION:
- gmx_fio_do_real(fio, iparams->polarize.alpha);
+ serializer->doReal(&iparams->cubic.b0);
+ 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_ANHARM_POL:
- gmx_fio_do_real(fio, iparams->anharm_polarize.alpha);
- gmx_fio_do_real(fio, iparams->anharm_polarize.drcut);
- gmx_fio_do_real(fio, iparams->anharm_polarize.khyp);
+ serializer->doReal(&iparams->anharm_polarize.alpha);
+ serializer->doReal(&iparams->anharm_polarize.drcut);
+ serializer->doReal(&iparams->anharm_polarize.khyp);
break;
case F_WATER_POL:
- gmx_fio_do_real(fio, iparams->wpol.al_x);
- gmx_fio_do_real(fio, iparams->wpol.al_y);
- gmx_fio_do_real(fio, iparams->wpol.al_z);
- gmx_fio_do_real(fio, iparams->wpol.rOH);
- gmx_fio_do_real(fio, iparams->wpol.rHH);
- gmx_fio_do_real(fio, iparams->wpol.rOD);
+ serializer->doReal(&iparams->wpol.al_x);
+ serializer->doReal(&iparams->wpol.al_y);
+ serializer->doReal(&iparams->wpol.al_z);
+ serializer->doReal(&iparams->wpol.rOH);
+ serializer->doReal(&iparams->wpol.rHH);
+ serializer->doReal(&iparams->wpol.rOD);
break;
case F_THOLE_POL:
- gmx_fio_do_real(fio, iparams->thole.a);
- gmx_fio_do_real(fio, iparams->thole.alpha1);
- gmx_fio_do_real(fio, iparams->thole.alpha2);
- gmx_fio_do_real(fio, iparams->thole.rfac);
+ serializer->doReal(&iparams->thole.a);
+ serializer->doReal(&iparams->thole.alpha1);
+ serializer->doReal(&iparams->thole.alpha2);
+ if (file_version < tpxv_RemoveTholeRfac)
+ {
+ real noRfac = 0;
+ serializer->doReal(&noRfac);
+ }
+
break;
case F_LJ:
- gmx_fio_do_real(fio, iparams->lj.c6);
- gmx_fio_do_real(fio, iparams->lj.c12);
+ serializer->doReal(&iparams->lj.c6);
+ serializer->doReal(&iparams->lj.c12);
break;
case F_LJ14:
- gmx_fio_do_real(fio, iparams->lj14.c6A);
- gmx_fio_do_real(fio, iparams->lj14.c12A);
- gmx_fio_do_real(fio, iparams->lj14.c6B);
- gmx_fio_do_real(fio, iparams->lj14.c12B);
+ serializer->doReal(&iparams->lj14.c6A);
+ serializer->doReal(&iparams->lj14.c12A);
+ serializer->doReal(&iparams->lj14.c6B);
+ serializer->doReal(&iparams->lj14.c12B);
break;
case F_LJC14_Q:
- gmx_fio_do_real(fio, iparams->ljc14.fqq);
- gmx_fio_do_real(fio, iparams->ljc14.qi);
- gmx_fio_do_real(fio, iparams->ljc14.qj);
- gmx_fio_do_real(fio, iparams->ljc14.c6);
- gmx_fio_do_real(fio, iparams->ljc14.c12);
+ serializer->doReal(&iparams->ljc14.fqq);
+ serializer->doReal(&iparams->ljc14.qi);
+ serializer->doReal(&iparams->ljc14.qj);
+ serializer->doReal(&iparams->ljc14.c6);
+ serializer->doReal(&iparams->ljc14.c12);
break;
case F_LJC_PAIRS_NB:
- gmx_fio_do_real(fio, iparams->ljcnb.qi);
- gmx_fio_do_real(fio, iparams->ljcnb.qj);
- gmx_fio_do_real(fio, iparams->ljcnb.c6);
- gmx_fio_do_real(fio, iparams->ljcnb.c12);
+ serializer->doReal(&iparams->ljcnb.qi);
+ serializer->doReal(&iparams->ljcnb.qj);
+ serializer->doReal(&iparams->ljcnb.c6);
+ serializer->doReal(&iparams->ljcnb.c12);
break;
case F_PDIHS:
case F_PIDIHS:
case F_ANGRES:
case F_ANGRESZ:
- gmx_fio_do_real(fio, iparams->pdihs.phiA);
- gmx_fio_do_real(fio, iparams->pdihs.cpA);
- gmx_fio_do_real(fio, iparams->pdihs.phiB);
- gmx_fio_do_real(fio, iparams->pdihs.cpB);
- gmx_fio_do_int(fio, iparams->pdihs.mult);
+ serializer->doReal(&iparams->pdihs.phiA);
+ serializer->doReal(&iparams->pdihs.cpA);
+ serializer->doReal(&iparams->pdihs.phiB);
+ serializer->doReal(&iparams->pdihs.cpB);
+ serializer->doInt(&iparams->pdihs.mult);
break;
case F_RESTRDIHS:
- gmx_fio_do_real(fio, iparams->pdihs.phiA);
- gmx_fio_do_real(fio, iparams->pdihs.cpA);
+ serializer->doReal(&iparams->pdihs.phiA);
+ serializer->doReal(&iparams->pdihs.cpA);
break;
case F_DISRES:
- gmx_fio_do_int(fio, iparams->disres.label);
- gmx_fio_do_int(fio, iparams->disres.type);
- gmx_fio_do_real(fio, iparams->disres.low);
- gmx_fio_do_real(fio, iparams->disres.up1);
- gmx_fio_do_real(fio, iparams->disres.up2);
- gmx_fio_do_real(fio, iparams->disres.kfac);
+ serializer->doInt(&iparams->disres.label);
+ serializer->doInt(&iparams->disres.type);
+ serializer->doReal(&iparams->disres.low);
+ serializer->doReal(&iparams->disres.up1);
+ serializer->doReal(&iparams->disres.up2);
+ serializer->doReal(&iparams->disres.kfac);
break;
case F_ORIRES:
- gmx_fio_do_int(fio, iparams->orires.ex);
- gmx_fio_do_int(fio, iparams->orires.label);
- gmx_fio_do_int(fio, iparams->orires.power);
- gmx_fio_do_real(fio, iparams->orires.c);
- gmx_fio_do_real(fio, iparams->orires.obs);
- gmx_fio_do_real(fio, iparams->orires.kfac);
+ serializer->doInt(&iparams->orires.ex);
+ serializer->doInt(&iparams->orires.label);
+ serializer->doInt(&iparams->orires.power);
+ serializer->doReal(&iparams->orires.c);
+ serializer->doReal(&iparams->orires.obs);
+ serializer->doReal(&iparams->orires.kfac);
break;
case F_DIHRES:
if (file_version < 82)
{
- gmx_fio_do_int(fio, idum);
- gmx_fio_do_int(fio, idum);
+ serializer->doInt(&idum);
+ serializer->doInt(&idum);
}
- gmx_fio_do_real(fio, iparams->dihres.phiA);
- gmx_fio_do_real(fio, iparams->dihres.dphiA);
- gmx_fio_do_real(fio, iparams->dihres.kfacA);
+ serializer->doReal(&iparams->dihres.phiA);
+ serializer->doReal(&iparams->dihres.dphiA);
+ serializer->doReal(&iparams->dihres.kfacA);
if (file_version >= 82)
{
- gmx_fio_do_real(fio, iparams->dihres.phiB);
- gmx_fio_do_real(fio, iparams->dihres.dphiB);
- gmx_fio_do_real(fio, iparams->dihres.kfacB);
+ serializer->doReal(&iparams->dihres.phiB);
+ serializer->doReal(&iparams->dihres.dphiB);
+ serializer->doReal(&iparams->dihres.kfacB);
}
else
{
}
break;
case F_POSRES:
- gmx_fio_do_rvec(fio, iparams->posres.pos0A);
- gmx_fio_do_rvec(fio, iparams->posres.fcA);
- gmx_fio_do_rvec(fio, iparams->posres.pos0B);
- gmx_fio_do_rvec(fio, iparams->posres.fcB);
+ serializer->doRvec(&iparams->posres.pos0A);
+ serializer->doRvec(&iparams->posres.fcA);
+ serializer->doRvec(&iparams->posres.pos0B);
+ serializer->doRvec(&iparams->posres.fcB);
break;
case F_FBPOSRES:
- gmx_fio_do_int(fio, iparams->fbposres.geom);
- gmx_fio_do_rvec(fio, iparams->fbposres.pos0);
- gmx_fio_do_real(fio, iparams->fbposres.r);
- gmx_fio_do_real(fio, iparams->fbposres.k);
- break;
- case F_CBTDIHS:
- gmx_fio_ndo_real(fio, iparams->cbtdihs.cbtcA, NR_CBTDIHS);
+ serializer->doInt(&iparams->fbposres.geom);
+ serializer->doRvec(&iparams->fbposres.pos0);
+ serializer->doReal(&iparams->fbposres.r);
+ serializer->doReal(&iparams->fbposres.k);
break;
+ case F_CBTDIHS: serializer->doRealArray(iparams->cbtdihs.cbtcA, NR_CBTDIHS); break;
case F_RBDIHS:
- gmx_fio_ndo_real(fio, iparams->rbdihs.rbcA, NR_RBDIHS);
- gmx_fio_ndo_real(fio, 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.
*/
- gmx_fio_ndo_real(fio, iparams->rbdihs.rbcA, NR_RBDIHS);
- gmx_fio_ndo_real(fio, iparams->rbdihs.rbcB, NR_RBDIHS);
+ serializer->doRealArray(iparams->rbdihs.rbcA, NR_RBDIHS);
+ serializer->doRealArray(iparams->rbdihs.rbcB, NR_RBDIHS);
break;
case F_CONSTR:
case F_CONSTRNC:
- gmx_fio_do_real(fio, iparams->constr.dA);
- gmx_fio_do_real(fio, iparams->constr.dB);
+ serializer->doReal(&iparams->constr.dA);
+ serializer->doReal(&iparams->constr.dB);
break;
case F_SETTLE:
- gmx_fio_do_real(fio, iparams->settle.doh);
- gmx_fio_do_real(fio, iparams->settle.dhh);
+ serializer->doReal(&iparams->settle.doh);
+ serializer->doReal(&iparams->settle.dhh);
break;
+ case F_VSITE1: break; // VSite1 has 0 parameters
case F_VSITE2:
- gmx_fio_do_real(fio, iparams->vsite.a);
- break;
+ case F_VSITE2FD: serializer->doReal(&iparams->vsite.a); break;
case F_VSITE3:
case F_VSITE3FD:
case F_VSITE3FAD:
- gmx_fio_do_real(fio, iparams->vsite.a);
- gmx_fio_do_real(fio, iparams->vsite.b);
+ serializer->doReal(&iparams->vsite.a);
+ serializer->doReal(&iparams->vsite.b);
break;
case F_VSITE3OUT:
case F_VSITE4FD:
case F_VSITE4FDN:
- gmx_fio_do_real(fio, iparams->vsite.a);
- gmx_fio_do_real(fio, iparams->vsite.b);
- gmx_fio_do_real(fio, iparams->vsite.c);
+ serializer->doReal(&iparams->vsite.a);
+ serializer->doReal(&iparams->vsite.b);
+ serializer->doReal(&iparams->vsite.c);
break;
case F_VSITEN:
- gmx_fio_do_int(fio, iparams->vsiten.n);
- gmx_fio_do_real(fio, iparams->vsiten.a);
+ serializer->doInt(&iparams->vsiten.n);
+ serializer->doReal(&iparams->vsiten.a);
break;
case F_GB12_NOLONGERUSED:
case F_GB13_NOLONGERUSED:
case F_GB14_NOLONGERUSED:
// Implicit solvent parameters can still be read, but never used
- if (bRead)
+ if (serializer->reading())
{
if (file_version < 68)
{
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_real(fio, rdum);
+ serializer->doReal(&rdum);
+ serializer->doReal(&rdum);
+ serializer->doReal(&rdum);
+ serializer->doReal(&rdum);
}
if (file_version < tpxv_RemoveImplicitSolvation)
{
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_real(fio, rdum);
- gmx_fio_do_real(fio, rdum);
+ serializer->doReal(&rdum);
+ serializer->doReal(&rdum);
+ serializer->doReal(&rdum);
+ serializer->doReal(&rdum);
+ serializer->doReal(&rdum);
}
}
break;
case F_CMAP:
- gmx_fio_do_int(fio, iparams->cmap.cmapA);
- gmx_fio_do_int(fio, iparams->cmap.cmapB);
+ serializer->doInt(&iparams->cmap.cmapA);
+ 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(t_fileio *fio, InteractionList *ilist, gmx_bool bRead)
+static void do_ilist(gmx::ISerializer* serializer, InteractionList* ilist)
{
int nr = ilist->size();
- gmx_fio_do_int(fio, nr);
- if (bRead)
+ serializer->doInt(&nr);
+ if (serializer->reading())
{
ilist->iatoms.resize(nr);
}
- gmx_fio_ndo_int(fio, ilist->iatoms.data(), ilist->size());
+ serializer->doIntArray(ilist->iatoms.data(), ilist->size());
}
-static void do_ffparams(t_fileio *fio, gmx_ffparams_t *ffparams,
- gmx_bool bRead, int file_version)
+static void do_ffparams(gmx::ISerializer* serializer, gmx_ffparams_t* ffparams, int file_version)
{
- gmx_fio_do_int(fio, ffparams->atnr);
+ serializer->doInt(&ffparams->atnr);
int numTypes = ffparams->numTypes();
- gmx_fio_do_int(fio, numTypes);
- if (bRead)
+ serializer->doInt(&numTypes);
+ if (serializer->reading())
{
ffparams->functype.resize(numTypes);
ffparams->iparams.resize(numTypes);
}
/* Read/write all the function types */
- gmx_fio_ndo_int(fio, ffparams->functype.data(), ffparams->functype.size());
+ serializer->doIntArray(ffparams->functype.data(), ffparams->functype.size());
if (file_version >= 66)
{
- gmx_fio_do_double(fio, ffparams->reppow);
+ serializer->doDouble(&ffparams->reppow);
}
else
{
ffparams->reppow = 12.0;
}
- gmx_fio_do_real(fio, ffparams->fudgeQQ);
+ serializer->doReal(&ffparams->fudgeQQ);
/* Check whether all these function types are supported by the code.
* In practice the code is backwards compatible, which means that the
*/
for (int i = 0; i < ffparams->numTypes(); i++)
{
- if (bRead)
+ if (serializer->reading())
{
/* Loop over file versions */
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(fio, ffparams->functype[i], &ffparams->iparams[i], bRead,
- 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(t_fileio *fio, InteractionLists *ilists, gmx_bool bRead,
- 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 (bRead)
+ if (serializer->reading())
{
for (int k = 0; k < NFTUPD; k++)
{
}
else
{
- do_ilist(fio, &ilist, bRead);
- if (file_version < 78 && j == F_SETTLE && ilist.size() > 0)
+ do_ilist(serializer, &ilist);
+ if (file_version < 78 && j == F_SETTLE && !ilist.empty())
{
add_settle_atoms(&ilist);
}
}
}
-static void do_block(t_fileio *fio, t_block *block, gmx_bool bRead)
+static void do_block(gmx::ISerializer* serializer, t_block* block)
{
- gmx_fio_do_int(fio, block->nr);
- if (bRead)
+ serializer->doInt(&block->nr);
+ if (serializer->reading())
{
if ((block->nalloc_index > 0) && (nullptr != block->index))
{
sfree(block->index);
}
- block->nalloc_index = block->nr+1;
+ block->nalloc_index = block->nr + 1;
snew(block->index, block->nalloc_index);
}
- gmx_fio_ndo_int(fio, block->index, block->nr+1);
+ serializer->doIntArray(block->index, block->nr + 1);
}
-static void do_blocka(t_fileio *fio, t_blocka *block, gmx_bool bRead)
+static void doListOfLists(gmx::ISerializer* serializer, gmx::ListOfLists<int>* listOfLists)
{
- gmx_fio_do_int(fio, block->nr);
- gmx_fio_do_int(fio, block->nra);
- if (bRead)
+ int numLists = listOfLists->ssize();
+ serializer->doInt(&numLists);
+ int numElements = listOfLists->elementsView().ssize();
+ serializer->doInt(&numElements);
+ if (serializer->reading())
+ {
+ 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
{
- block->nalloc_index = block->nr+1;
- snew(block->index, block->nalloc_index);
- block->nalloc_a = block->nra;
- snew(block->a, block->nalloc_a);
+ serializer->doIntArray(const_cast<int*>(listOfLists->listRangesView().data()), numLists + 1);
+ serializer->doIntArray(const_cast<int*>(listOfLists->elementsView().data()), numElements);
}
- gmx_fio_ndo_int(fio, block->index, block->nr+1);
- gmx_fio_ndo_int(fio, 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(t_fileio *fio, t_atom *atom, gmx_bool bRead)
+static void do_atom(gmx::ISerializer* serializer, t_atom* atom)
{
- gmx_fio_do_real(fio, atom->m);
- gmx_fio_do_real(fio, atom->q);
- gmx_fio_do_real(fio, atom->mB);
- gmx_fio_do_real(fio, atom->qB);
- gmx_fio_do_ushort(fio, atom->type);
- gmx_fio_do_ushort(fio, atom->typeB);
- gmx_fio_do_int(fio, atom->ptype);
- gmx_fio_do_int(fio, atom->resind);
- gmx_fio_do_int(fio, atom->atomnumber);
- if (bRead)
+ serializer->doReal(&atom->m);
+ serializer->doReal(&atom->q);
+ serializer->doReal(&atom->mB);
+ serializer->doReal(&atom->qB);
+ serializer->doUShort(&atom->type);
+ serializer->doUShort(&atom->typeB);
+ serializer->doEnumAsInt(&atom->ptype);
+ serializer->doInt(&atom->resind);
+ serializer->doInt(&atom->atomnumber);
+ if (serializer->reading())
{
/* Set element string from atomic number if present.
* This routine returns an empty string if the name is not found.
}
}
-static void do_grps(t_fileio *fio,
- gmx::ArrayRef<AtomGroupIndices> grps,
- gmx_bool bRead)
+static void do_grps(gmx::ISerializer* serializer, gmx::ArrayRef<AtomGroupIndices> grps)
{
- for (auto &group : grps)
+ for (auto& group : grps)
{
int size = group.size();
- gmx_fio_do_int(fio, size);
- if (bRead)
+ serializer->doInt(&size);
+ if (serializer->reading())
{
group.resize(size);
}
- gmx_fio_ndo_int(fio, group.data(), size);
+ serializer->doIntArray(group.data(), size);
}
}
-static void do_symstr(t_fileio *fio, char ***nm, gmx_bool bRead, t_symtab *symtab)
+static void do_symstr(gmx::ISerializer* serializer, char*** nm, t_symtab* symtab)
{
int ls;
- if (bRead)
+ if (serializer->reading())
{
- gmx_fio_do_int(fio, ls);
+ serializer->doInt(&ls);
*nm = get_symtab_handle(symtab, ls);
}
else
{
ls = lookup_symtab(symtab, *nm);
- gmx_fio_do_int(fio, ls);
+ serializer->doInt(&ls);
}
}
-static void do_strstr(t_fileio *fio, int nstr, char ***nm, gmx_bool bRead,
- 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++)
{
- do_symstr(fio, &(nm[j]), bRead, symtab);
+ do_symstr(serializer, &(nm[j]), symtab);
}
}
-static void do_resinfo(t_fileio *fio, int n, t_resinfo *ri, gmx_bool bRead,
- 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++)
{
- do_symstr(fio, &(ri[j].name), bRead, symtab);
+ do_symstr(serializer, &(ri[j].name), symtab);
if (file_version >= 63)
{
- gmx_fio_do_int(fio, ri[j].nr);
- gmx_fio_do_uchar(fio, ri[j].ic);
+ serializer->doInt(&ri[j].nr);
+ serializer->doUChar(&ri[j].ic);
}
else
{
}
}
-static void do_atoms(t_fileio *fio, t_atoms *atoms, gmx_bool bRead, t_symtab *symtab,
- int file_version)
+static void do_atoms(gmx::ISerializer* serializer, t_atoms* atoms, t_symtab* symtab, int file_version)
{
int i;
- gmx_fio_do_int(fio, atoms->nr);
- gmx_fio_do_int(fio, atoms->nres);
- if (bRead)
+ serializer->doInt(&atoms->nr);
+ serializer->doInt(&atoms->nres);
+ if (serializer->reading())
{
/* Since we have always written all t_atom properties in the tpr file
* (at least for all backward compatible versions), we don't store
}
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_atom(fio, &atoms->atom[i], bRead);
+ do_atom(serializer, &atoms->atom[i]);
}
- do_strstr(fio, atoms->nr, atoms->atomname, bRead, symtab);
- do_strstr(fio, atoms->nr, atoms->atomtype, bRead, symtab);
- do_strstr(fio, atoms->nr, atoms->atomtypeB, bRead, symtab);
+ do_strstr(serializer, atoms->nr, atoms->atomname, symtab);
+ do_strstr(serializer, atoms->nr, atoms->atomtype, symtab);
+ do_strstr(serializer, atoms->nr, atoms->atomtypeB, symtab);
- do_resinfo(fio, atoms->nres, atoms->resinfo, bRead, symtab, file_version);
+ do_resinfo(serializer, atoms->nres, atoms->resinfo, symtab, file_version);
}
-static void do_groups(t_fileio *fio, SimulationGroups *groups,
- gmx_bool bRead, t_symtab *symtab)
+static void do_groups(gmx::ISerializer* serializer, SimulationGroups* groups, t_symtab* symtab)
{
- do_grps(fio, groups->groups, bRead);
+ do_grps(serializer, groups->groups);
int numberOfGroupNames = groups->groupNames.size();
- gmx_fio_do_int(fio, numberOfGroupNames);
- if (bRead)
+ serializer->doInt(&numberOfGroupNames);
+ if (serializer->reading())
{
groups->groupNames.resize(numberOfGroupNames);
}
- do_strstr(fio, numberOfGroupNames, groups->groupNames.data(), bRead, symtab);
+ do_strstr(serializer, numberOfGroupNames, groups->groupNames.data(), symtab);
for (auto group : gmx::keysOf(groups->groupNumbers))
{
int numberOfGroupNumbers = groups->numberOfGroupNumbers(group);
- gmx_fio_do_int(fio, numberOfGroupNumbers);
+ serializer->doInt(&numberOfGroupNumbers);
if (numberOfGroupNumbers != 0)
{
- if (bRead)
+ if (serializer->reading())
{
groups->groupNumbers[group].resize(numberOfGroupNumbers);
}
- gmx_fio_ndo_uchar(fio, groups->groupNumbers[group].data(), numberOfGroupNumbers);
+ serializer->doUCharArray(groups->groupNumbers[group].data(), numberOfGroupNumbers);
}
}
}
-static void do_atomtypes(t_fileio *fio, t_atomtypes *atomtypes, gmx_bool bRead,
- int file_version)
+static void do_atomtypes(gmx::ISerializer* serializer, t_atomtypes* atomtypes, int file_version)
{
- int j;
+ int j;
- gmx_fio_do_int(fio, atomtypes->nr);
+ serializer->doInt(&atomtypes->nr);
j = atomtypes->nr;
- if (bRead)
+ if (serializer->reading())
{
snew(atomtypes->atomnumber, j);
}
- if (bRead && file_version < tpxv_RemoveImplicitSolvation)
+ if (serializer->reading() && file_version < tpxv_RemoveImplicitSolvation)
{
std::vector<real> dummy(atomtypes->nr, 0);
- gmx_fio_ndo_real(fio, dummy.data(), dummy.size());
- gmx_fio_ndo_real(fio, dummy.data(), dummy.size());
- gmx_fio_ndo_real(fio, dummy.data(), dummy.size());
+ serializer->doRealArray(dummy.data(), dummy.size());
+ serializer->doRealArray(dummy.data(), dummy.size());
+ serializer->doRealArray(dummy.data(), dummy.size());
}
- gmx_fio_ndo_int(fio, atomtypes->atomnumber, j);
+ serializer->doIntArray(atomtypes->atomnumber, j);
- if (bRead && file_version >= 60 && file_version < tpxv_RemoveImplicitSolvation)
+ if (serializer->reading() && file_version >= 60 && file_version < tpxv_RemoveImplicitSolvation)
{
std::vector<real> dummy(atomtypes->nr, 0);
- gmx_fio_ndo_real(fio, dummy.data(), dummy.size());
- gmx_fio_ndo_real(fio, dummy.data(), dummy.size());
+ serializer->doRealArray(dummy.data(), dummy.size());
+ serializer->doRealArray(dummy.data(), dummy.size());
}
}
-static void do_symtab(t_fileio *fio, t_symtab *symtab, gmx_bool bRead)
+static void do_symtab(gmx::ISerializer* serializer, t_symtab* symtab)
{
int i, nr;
- t_symbuf *symbuf;
- char buf[STRLEN];
+ t_symbuf* symbuf;
- gmx_fio_do_int(fio, symtab->nr);
- nr = symtab->nr;
- if (bRead)
+ serializer->doInt(&symtab->nr);
+ nr = symtab->nr;
+ if (serializer->reading())
{
snew(symtab->symbuf, 1);
symbuf = symtab->symbuf;
snew(symbuf->buf, nr);
for (i = 0; (i < nr); i++)
{
- gmx_fio_do_string(fio, buf);
- symbuf->buf[i] = gmx_strdup(buf);
+ std::string buf;
+ serializer->doString(&buf);
+ symbuf->buf[i] = gmx_strdup(buf.c_str());
}
}
else
{
for (i = 0; (i < symbuf->bufsize) && (i < nr); i++)
{
- gmx_fio_do_string(fio, symbuf->buf[i]);
+ std::string buf = symbuf->buf[i];
+ serializer->doString(&buf);
}
- nr -= i;
+ nr -= i;
symbuf = symbuf->next;
}
if (nr != 0)
}
}
-static void do_cmap(t_fileio *fio, gmx_cmap_t *cmap_grid, gmx_bool bRead)
+static void do_cmap(gmx::ISerializer* serializer, gmx_cmap_t* cmap_grid)
{
int ngrid = cmap_grid->cmapdata.size();
- gmx_fio_do_int(fio, ngrid);
- gmx_fio_do_int(fio, cmap_grid->grid_spacing);
+ serializer->doInt(&ngrid);
+ serializer->doInt(&cmap_grid->grid_spacing);
int gs = cmap_grid->grid_spacing;
int nelem = gs * gs;
- if (bRead)
+ if (serializer->reading())
{
cmap_grid->cmapdata.resize(ngrid);
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++)
{
- gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4]);
- gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4+1]);
- gmx_fio_do_real(fio, cmap_grid->cmapdata[i].cmap[j*4+2]);
- gmx_fio_do_real(fio, 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(t_fileio *fio, gmx_moltype_t *molt, gmx_bool bRead,
- 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(fio, &(molt->name), bRead, symtab);
+ do_symstr(serializer, &(molt->name), symtab);
- do_atoms(fio, &molt->atoms, bRead, symtab, file_version);
+ do_atoms(serializer, &molt->atoms, symtab, file_version);
- do_ilists(fio, &molt->ilist, bRead, file_version);
+ do_ilists(serializer, &molt->ilist, file_version);
- do_block(fio, &molt->cgs, bRead);
+ /* 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(fio, &molt->excls, bRead);
+ doListOfLists(serializer, &molt->excls);
}
-static void do_molblock(t_fileio *fio, gmx_molblock_t *molb,
- int numAtomsPerMolecule,
- gmx_bool bRead)
+static void do_molblock(gmx::ISerializer* serializer, gmx_molblock_t* molb, int numAtomsPerMolecule)
{
- gmx_fio_do_int(fio, molb->type);
- gmx_fio_do_int(fio, molb->nmol);
+ serializer->doInt(&molb->type);
+ serializer->doInt(&molb->nmol);
/* To maintain forward topology reading compatibility, we store #atoms.
* TODO: Change this to conditional reading of a dummy int when we
* increase tpx_generation.
*/
- gmx_fio_do_int(fio, numAtomsPerMolecule);
+ serializer->doInt(&numAtomsPerMolecule);
/* Position restraint coordinates */
int numPosres_xA = molb->posres_xA.size();
- gmx_fio_do_int(fio, numPosres_xA);
+ serializer->doInt(&numPosres_xA);
if (numPosres_xA > 0)
{
- if (bRead)
+ if (serializer->reading())
{
molb->posres_xA.resize(numPosres_xA);
}
- gmx_fio_ndo_rvec(fio, as_rvec_array(molb->posres_xA.data()), numPosres_xA);
+ serializer->doRvecArray(as_rvec_array(molb->posres_xA.data()), numPosres_xA);
}
int numPosres_xB = molb->posres_xB.size();
- gmx_fio_do_int(fio, numPosres_xB);
+ serializer->doInt(&numPosres_xB);
if (numPosres_xB > 0)
{
- if (bRead)
+ if (serializer->reading())
{
molb->posres_xB.resize(numPosres_xB);
}
- gmx_fio_ndo_rvec(fio, as_rvec_array(molb->posres_xB.data()), numPosres_xB);
+ 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(t_fileio *fio, gmx_mtop_t *mtop, gmx_bool bRead,
- int file_version)
+static void do_mtop(gmx::ISerializer* serializer, gmx_mtop_t* mtop, int file_version)
{
- do_symtab(fio, &(mtop->symtab), bRead);
+ do_symtab(serializer, &(mtop->symtab));
- do_symstr(fio, &(mtop->name), bRead, &(mtop->symtab));
+ do_symstr(serializer, &(mtop->name), &(mtop->symtab));
- do_ffparams(fio, &mtop->ffparams, bRead, file_version);
+ do_ffparams(serializer, &mtop->ffparams, file_version);
int nmoltype = mtop->moltype.size();
- gmx_fio_do_int(fio, nmoltype);
- if (bRead)
+ serializer->doInt(&nmoltype);
+ if (serializer->reading())
{
mtop->moltype.resize(nmoltype);
}
- for (gmx_moltype_t &moltype : mtop->moltype)
+ for (gmx_moltype_t& moltype : mtop->moltype)
{
- do_moltype(fio, &moltype, bRead, &mtop->symtab, file_version);
+ do_moltype(serializer, &moltype, &mtop->symtab, file_version);
}
int nmolblock = mtop->molblock.size();
- gmx_fio_do_int(fio, nmolblock);
- if (bRead)
+ serializer->doInt(&nmolblock);
+ if (serializer->reading())
{
mtop->molblock.resize(nmolblock);
}
- for (gmx_molblock_t &molblock : mtop->molblock)
+ for (gmx_molblock_t& molblock : mtop->molblock)
{
- int numAtomsPerMolecule = (bRead ? 0 : mtop->moltype[molblock.type].atoms.nr);
- do_molblock(fio, &molblock, numAtomsPerMolecule, bRead);
+ int numAtomsPerMolecule = (serializer->reading() ? 0 : mtop->moltype[molblock.type].atoms.nr);
+ do_molblock(serializer, &molblock, numAtomsPerMolecule);
}
- gmx_fio_do_int(fio, mtop->natoms);
+ serializer->doInt(&mtop->natoms);
if (file_version >= tpxv_IntermolecularBondeds)
{
- gmx_fio_do_gmx_bool(fio, mtop->bIntermolecularInteractions);
+ serializer->doBool(&mtop->bIntermolecularInteractions);
if (mtop->bIntermolecularInteractions)
{
- if (bRead)
+ if (serializer->reading())
{
mtop->intermolecular_ilist = std::make_unique<InteractionLists>();
}
- do_ilists(fio, mtop->intermolecular_ilist.get(), bRead, file_version);
+ do_ilists(serializer, mtop->intermolecular_ilist.get(), file_version);
}
}
else
mtop->bIntermolecularInteractions = FALSE;
}
- do_atomtypes (fio, &(mtop->atomtypes), bRead, file_version);
+ do_atomtypes(serializer, &(mtop->atomtypes), file_version);
if (file_version >= 65)
{
- do_cmap(fio, &mtop->ffparams.cmap_grid, bRead);
+ do_cmap(serializer, &mtop->ffparams.cmap_grid);
}
else
{
mtop->ffparams.cmap_grid.cmapdata.clear();
}
- do_groups(fio, &mtop->groups, bRead, &(mtop->symtab));
+ do_groups(serializer, &mtop->groups, &(mtop->symtab));
mtop->haveMoleculeIndices = true;
- if (bRead)
+ 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));
}
*
* If possible, we will read the \p ir even when \p TopOnlyOK is true.
*
- * \param[in,out] fio Fileio datastructure.
+ * \param[in,out] serializer The serializer used to handle header processing.
* \param[in,out] tpx File header datastructure.
- * \param[in] bRead If we are reading or writing.
+ * \param[in] filename The name of the file being read/written
+ * \param[in,out] fio File handle.
* \param[in] TopOnlyOK If not reading \p ir is fine or not.
*/
-static void do_tpxheader(t_fileio *fio, TpxFileHeader *tpx, bool bRead,
- bool TopOnlyOK)
+static void do_tpxheader(gmx::FileIOXdrSerializer* serializer,
+ TpxFileHeader* tpx,
+ const char* filename,
+ t_fileio* fio,
+ bool TopOnlyOK)
{
- char buf[STRLEN];
- char file_tag[STRLEN];
- 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);
- if (bRead)
- {
- gmx_fio_do_string(fio, buf);
- if (std::strncmp(buf, "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",
- gmx_fio_getname(fio));
- }
- gmx_fio_do_int(fio, precision);
- bDouble = (precision == sizeof(double));
- if ((precision != sizeof(float)) && !bDouble)
- {
- gmx_fatal(FARGS, "Unknown precision in file %s: real is %d bytes "
+ std::string buf;
+ std::string fileTag;
+ if (serializer->reading())
+ {
+ 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);
+ }
+ // 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);
+ tpx->isDouble = (precision == sizeof(double));
+ if ((precision != sizeof(float)) && !tpx->isDouble)
+ {
+ gmx_fatal(FARGS,
+ "Unknown precision in file %s: real is %d bytes "
"instead of %zu or %zu",
- gmx_fio_getname(fio), precision, sizeof(float), sizeof(double));
- }
- gmx_fio_setprecision(fio, bDouble);
- fprintf(stderr, "Reading file %s, %s (%s precision)\n",
- gmx_fio_getname(fio), buf, 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
{
- snprintf(buf, STRLEN, "VERSION %s", gmx_version());
- gmx_fio_write_string(fio, buf);
- bDouble = (precision == sizeof(double));
- gmx_fio_setprecision(fio, bDouble);
- gmx_fio_do_int(fio, precision);
- sprintf(file_tag, "%s", tpx_tag);
+ buf = gmx::formatString("VERSION %s", gmx_version());
+ serializer->doString(&buf);
+ gmx_fio_setprecision(fio, tpx->isDouble);
+ serializer->doInt(&precision);
+ fileTag = tpx_tag;
}
/* Check versions! */
- gmx_fio_do_int(fio, tpx->fileVersion);
+ serializer->doInt(&tpx->fileVersion);
/* This is for backward compatibility with development versions 77-79
* where the tag was, mistakenly, placed before the generation,
*/
if (tpx->fileVersion >= 77 && tpx->fileVersion <= 79)
{
- gmx_fio_do_string(fio, file_tag);
+ serializer->doString(&fileTag);
}
- gmx_fio_do_int(fio, tpx->fileGeneration);
+ serializer->doInt(&tpx->fileGeneration);
if (tpx->fileVersion >= 81)
{
- gmx_fio_do_string(fio, file_tag);
+ serializer->doString(&fileTag);
}
- if (bRead)
+ if (serializer->reading())
{
if (tpx->fileVersion < 77)
{
/* Versions before 77 don't have the tag, set it to release */
- sprintf(file_tag, "%s", TPX_TAG_RELEASE);
+ fileTag = gmx::formatString("%s", TPX_TAG_RELEASE);
}
- if (std::strcmp(file_tag, tpx_tag) != 0)
+ if (fileTag != tpx_tag)
{
- fprintf(stderr, "Note: file tpx tag '%s', software tpx tag '%s'\n",
- file_tag, 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 (std::strcmp(file_tag, TPX_TAG_RELEASE) != 0 && tpx->fileVersion < tpx_version)
+ 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'",
- gmx_fio_getname(fio), tpx->fileVersion, file_tag,
- 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",
- gmx_fio_getname(fio), tpx->fileVersion, tpx_version);
+ gmx_fatal(FARGS,
+ "reading tpx file (%s) version %d with version %d program",
+ filename,
+ tpx->fileVersion,
+ tpx_version);
}
- gmx_fio_do_int(fio, tpx->natoms);
- gmx_fio_do_int(fio, tpx->ngtc);
+ serializer->doInt(&tpx->natoms);
+ serializer->doInt(&tpx->ngtc);
if (tpx->fileVersion < 62)
{
- gmx_fio_do_int(fio, idum);
- gmx_fio_do_real(fio, rdum);
+ serializer->doInt(&idum);
+ serializer->doReal(&rdum);
}
if (tpx->fileVersion >= 79)
{
- gmx_fio_do_int(fio, tpx->fep_state);
+ serializer->doInt(&tpx->fep_state);
+ }
+ serializer->doReal(&tpx->lambda);
+ serializer->doBool(&tpx->bIr);
+ serializer->doBool(&tpx->bTop);
+ serializer->doBool(&tpx->bX);
+ serializer->doBool(&tpx->bV);
+ serializer->doBool(&tpx->bF);
+ serializer->doBool(&tpx->bBox);
+
+ if (tpx->fileVersion >= tpxv_AddSizeField && tpx->fileGeneration >= 27)
+ {
+ if (!serializer->reading())
+ {
+ GMX_RELEASE_ASSERT(tpx->sizeOfTprBody != 0,
+ "Not possible to write new file with zero TPR body size");
+ }
+ serializer->doInt64(&tpx->sizeOfTprBody);
}
- gmx_fio_do_real(fio, tpx->lambda);
- gmx_fio_do_gmx_bool(fio, tpx->bIr);
- gmx_fio_do_gmx_bool(fio, tpx->bTop);
- gmx_fio_do_gmx_bool(fio, tpx->bX);
- gmx_fio_do_gmx_bool(fio, tpx->bV);
- gmx_fio_do_gmx_bool(fio, tpx->bF);
- gmx_fio_do_gmx_bool(fio, tpx->bBox);
if ((tpx->fileGeneration > tpx_generation))
{
}
}
-static int do_tpx_body(t_fileio *fio,
- TpxFileHeader *tpx,
- bool bRead,
- t_inputrec *ir,
- t_state *state,
- rvec *x,
- rvec *v,
- gmx_mtop_t *mtop)
-{
- int ePBC;
- gmx_bool bPeriodicMols;
+#define do_test(serializer, b, p) \
+ if ((serializer)->reading() && ((p) != nullptr) && !(b)) \
+ gmx_fatal(FARGS, "No %s in input file", #p)
- if (!bRead)
- {
- 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 (bRead)
+/*! \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(fio, b, p) if (bRead && ((p) != NULL) && !(b)) gmx_fatal(FARGS, "No %s in %s",#p, gmx_fio_getname(fio))
-
- do_test(fio, tpx->bBox, state->box);
+ do_test(serializer, tpx->bBox, state->box);
if (tpx->bBox)
{
- gmx_fio_ndo_rvec(fio, state->box, DIM);
+ serializer->doRvecArray(state->box, DIM);
if (tpx->fileVersion >= 51)
{
- gmx_fio_ndo_rvec(fio, state->box_rel, DIM);
+ serializer->doRvecArray(state->box_rel, DIM);
}
else
{
/* We initialize box_rel after reading the inputrec */
clear_mat(state->box_rel);
}
- gmx_fio_ndo_rvec(fio, state->boxv, DIM);
+ serializer->doRvecArray(state->boxv, DIM);
if (tpx->fileVersion < 56)
{
matrix mdum;
- gmx_fio_ndo_rvec(fio, mdum, DIM);
+ serializer->doRvecArray(mdum, DIM);
}
}
if (state->ngtc > 0)
{
- real *dumv;
+ real* dumv;
snew(dumv, state->ngtc);
if (tpx->fileVersion < 69)
{
- gmx_fio_ndo_real(fio, dumv, state->ngtc);
+ serializer->doRealArray(dumv, state->ngtc);
}
/* These used to be the Berendsen tcoupl_lambda's */
- gmx_fio_ndo_real(fio, dumv, state->ngtc);
+ serializer->doRealArray(dumv, state->ngtc);
sfree(dumv);
}
+}
- do_test(fio, tpx->bTop, mtop);
+/*! \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(fio, mtop, bRead, tpx->fileVersion);
+ do_mtop(serializer, mtop, tpx->fileVersion);
+ set_disres_npair(mtop);
+ mtop->finalize();
}
else
{
gmx_mtop_t dum_top;
- do_mtop(fio, &dum_top, bRead, tpx->fileVersion);
+ 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);
}
}
- do_test(fio, tpx->bX, x);
+
+ if (x == nullptr)
+ {
+ x = state->x.rvec_array();
+ v = state->v.rvec_array();
+ }
+ do_test(serializer, tpx->bX, x);
if (tpx->bX)
{
- if (bRead)
+ if (serializer->reading())
{
- state->flags |= (1<<estX);
+ state->flags |= enumValueToBitMask(StateEntry::X);
}
- gmx_fio_ndo_rvec(fio, x, tpx->natoms);
+ serializer->doRvecArray(x, tpx->natoms);
}
- do_test(fio, tpx->bV, v);
+ do_test(serializer, tpx->bV, v);
if (tpx->bV)
{
- if (bRead)
+ if (serializer->reading())
{
- state->flags |= (1<<estV);
+ state->flags |= enumValueToBitMask(StateEntry::V);
+ }
+ if (!v)
+ {
+ std::vector<gmx::RVec> dummyVelocities(tpx->natoms);
+ serializer->doRvecArray(as_rvec_array(dummyVelocities.data()), tpx->natoms);
+ }
+ else
+ {
+ serializer->doRvecArray(v, tpx->natoms);
}
- gmx_fio_ndo_rvec(fio, v, tpx->natoms);
}
// No need to run do_test when the last argument is NULL
if (tpx->bF)
{
- rvec *dummyForces;
- snew(dummyForces, state->natoms);
- gmx_fio_ndo_rvec(fio, dummyForces, tpx->natoms);
- sfree(dummyForces);
+ 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(fio, tpx->bIr, ir);
+ do_test(serializer, tpx->bIr, ir);
if (tpx->bIr)
{
if (tpx->fileVersion >= 53)
{
/* Removed the pbc info from do_inputrec, since we always want it */
- if (!bRead)
+ if (!serializer->reading())
{
- ePBC = ir->ePBC;
+ pbcType = ir->pbcType;
bPeriodicMols = ir->bPeriodicMols;
}
- gmx_fio_do_int(fio, ePBC);
- gmx_fio_do_gmx_bool(fio, bPeriodicMols);
+ serializer->doInt(reinterpret_cast<int*>(&pbcType));
+ serializer->doBool(&bPeriodicMols);
}
if (tpx->fileGeneration <= tpx_generation && ir)
{
- do_inputrec(fio, ir, bRead, tpx->fileVersion);
- if (tpx->fileVersion < 51)
- {
- set_box_rel(ir, state);
- }
+ do_inputrec(serializer, ir, tpx->fileVersion);
if (tpx->fileVersion < 53)
{
- ePBC = ir->ePBC;
+ pbcType = ir->pbcType;
bPeriodicMols = ir->bPeriodicMols;
}
}
- if (bRead && ir && tpx->fileVersion >= 53)
+ 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 (bRead)
+/*! \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;
}
+/*! \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)
+{
+ 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;
+}
+
/************************************************************
*
* The following routines are the exported ones
*
************************************************************/
-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;
- do_tpxheader(fio, &tpx, true, canReadTopologyOnly);
+ 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)
{
- t_fileio *fio;
+ /* 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
+ * populated before we write the main body because it has some information that is
+ * otherwise not available.
+ */
- fio = open_tpx(fn, "w");
+ t_fileio* fio;
+
+ 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);
- TpxFileHeader tpx = populateTpxHeader(*state,
- ir,
- mtop);
- do_tpxheader(fio,
- &tpx,
- false,
- ir == nullptr);
- do_tpx_body(fio,
+ do_tpx_body(&tprBodySerializer,
&tpx,
- false,
- 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();
+
+ fio = open_tpx(fn, "w");
+ gmx::FileIOXdrSerializer serializer(fio);
+ do_tpxheader(&serializer, &tpx, fn, fio, ir == nullptr);
+ doTpxBodyBuffer(&serializer, tprBody);
+
close_tpx(fio);
}
-void read_tpx_state(const char *fn,
- t_inputrec *ir, t_state *state, gmx_mtop_t *mtop)
+PbcType completeTprDeserialization(PartialDeserializedTprFile* partialDeserializedTpr,
+ t_inputrec* ir,
+ t_state* state,
+ rvec* x,
+ rvec* v,
+ gmx_mtop_t* mtop)
{
- t_fileio *fio;
+ // 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);
+}
- TpxFileHeader tpx;
+PbcType completeTprDeserialization(PartialDeserializedTprFile* partialDeserializedTpr,
+ t_inputrec* ir,
+ gmx_mtop_t* mtop)
+{
+ return completeTprDeserialization(partialDeserializedTpr, ir, nullptr, nullptr, nullptr, mtop);
+}
+
+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");
- do_tpxheader(fio,
- &tpx,
- true,
- ir == nullptr);
- do_tpx_body(fio,
- &tpx,
- true,
- 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");
- do_tpxheader(fio,
- &tpx,
- true,
- ir == nullptr);
- ePBC = do_tpx_body(fio,
- &tpx,
- true, ir, &state, x, v, mtop);
+ fio = open_tpx(fn, "r");
+ gmx::FileIOXdrSerializer serializer(fio);
+ 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))
{
fprintf(fp, "natoms = %d\n", sh->natoms);
pr_indent(fp, indent);
fprintf(fp, "lambda = %e\n", sh->lambda);
+ pr_indent(fp, indent);
+ fprintf(fp, "buffer size = %" PRId64 "\n", sh->sizeOfTprBody);
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff