#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 char* tpx_tag = TPX_TAG_RELEASE;
/*! \brief Enum of values that describe the contents of a tpr file
* whose format matches a version number
*/
enum tpxv
{
- tpxv_ComputationalElectrophysiology = 96, /**< support for ion/water position swaps (computational electrophysiology) */
- tpxv_Use64BitRandomSeed, /**< change ld_seed from int to int64_t */
+ tpxv_ComputationalElectrophysiology =
+ 96, /**< support for ion/water position swaps (computational electrophysiology) */
+ tpxv_Use64BitRandomSeed, /**< change ld_seed from int to int64_t */
tpxv_RestrictedBendingAndCombinedAngleTorsionPotentials, /**< potentials for supporting coarse-grained force fields */
- tpxv_InteractiveMolecularDynamics, /**< interactive molecular dynamics (IMD) */
- tpxv_RemoveObsoleteParameters1, /**< remove optimize_fft, dihre_fc, nstcheckpoint */
- tpxv_PullCoordTypeGeom, /**< add pull type and geometry per group and flat-bottom */
- tpxv_PullGeomDirRel, /**< add pull geometry direction-relative */
- tpxv_IntermolecularBondeds, /**< permit inter-molecular bonded interactions in the topology */
- tpxv_CompElWithSwapLayerOffset, /**< added parameters for improved CompEl setups */
- tpxv_CompElPolyatomicIonsAndMultipleIonTypes, /**< CompEl now can handle polyatomic ions and more than two types of ions */
- tpxv_RemoveAdress, /**< removed support for AdResS */
- tpxv_PullCoordNGroup, /**< add ngroup to pull coord */
- tpxv_RemoveTwinRange, /**< removed support for twin-range interactions */
- tpxv_ReplacePullPrintCOM12, /**< Replaced print-com-1, 2 with pull-print-com */
- tpxv_PullExternalPotential, /**< Added pull type external potential */
- tpxv_GenericParamsForElectricField, /**< Introduced KeyValueTree and moved electric field parameters */
- tpxv_AcceleratedWeightHistogram, /**< sampling with accelerated weight histogram method (AWH) */
- tpxv_RemoveImplicitSolvation, /**< removed support for implicit solvation */
- tpxv_PullPrevStepCOMAsReference, /**< Enabled using the COM of the pull group of the last frame as reference for PBC */
- tpxv_MimicQMMM, /**< Introduced support for MiMiC QM/MM interface */
- tpxv_PullAverage, /**< Added possibility to output average pull force and position */
- tpxv_GenericInternalParameters, /**< Added internal parameters for mdrun modules*/
- tpxv_VSite2FD, /**< Added 2FD type virtual site */
- tpxv_AddSizeField, /**< Added field with information about the size of the serialized tpr file in bytes, excluding the header */
- tpxv_Count /**< the total number of tpxv versions */
+ tpxv_InteractiveMolecularDynamics, /**< interactive molecular dynamics (IMD) */
+ tpxv_RemoveObsoleteParameters1, /**< remove optimize_fft, dihre_fc, nstcheckpoint */
+ tpxv_PullCoordTypeGeom, /**< add pull type and geometry per group and flat-bottom */
+ tpxv_PullGeomDirRel, /**< add pull geometry direction-relative */
+ tpxv_IntermolecularBondeds, /**< permit inter-molecular bonded interactions in the topology */
+ tpxv_CompElWithSwapLayerOffset, /**< added parameters for improved CompEl setups */
+ tpxv_CompElPolyatomicIonsAndMultipleIonTypes, /**< CompEl now can handle polyatomic ions and more than two types of ions */
+ tpxv_RemoveAdress, /**< removed support for AdResS */
+ tpxv_PullCoordNGroup, /**< add ngroup to pull coord */
+ tpxv_RemoveTwinRange, /**< removed support for twin-range interactions */
+ tpxv_ReplacePullPrintCOM12, /**< Replaced print-com-1, 2 with pull-print-com */
+ tpxv_PullExternalPotential, /**< Added pull type external potential */
+ tpxv_GenericParamsForElectricField, /**< Introduced KeyValueTree and moved electric field parameters */
+ tpxv_AcceleratedWeightHistogram, /**< sampling with accelerated weight histogram method (AWH) */
+ tpxv_RemoveImplicitSolvation, /**< removed support for implicit solvation */
+ tpxv_PullPrevStepCOMAsReference, /**< Enabled using the COM of the pull group of the last frame as reference for PBC */
+ tpxv_MimicQMMM, /**< Introduced support for MiMiC QM/MM interface */
+ tpxv_PullAverage, /**< Added possibility to output average pull force and position */
+ tpxv_GenericInternalParameters, /**< Added internal parameters for mdrun modules*/
+ tpxv_VSite2FD, /**< Added 2FD type virtual site */
+ tpxv_AddSizeField, /**< Added field with information about the size of the serialized tpr file in bytes, excluding the header */
+ tpxv_Count /**< the total number of tpxv versions */
};
/*! \brief Version number of the file format written to run input
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;
* them to make things clear.
*/
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 },
+ { 90, F_FBPOSRES },
+ { 69, F_VTEMP_NOLONGERUSED },
+ { 66, F_PDISPCORR },
+ { 76, F_ANHARM_POL },
+ { 79, F_DVDL_COUL },
+ {
+ 79,
+ F_DVDL_VDW,
+ },
+ {
+ 79,
+ F_DVDL_BONDED,
+ },
+ { 79, F_DVDL_RESTRAINT },
+ { 79, F_DVDL_TEMPERATURE },
{ tpxv_GenericInternalParameters, F_DENSITYFITTING },
{ tpxv_VSite2FD, F_VSITE2FD },
};
* Now the higer level routines that do io of the structures and arrays
*
**************************************************************/
-static void do_pullgrp_tpx_pre95(gmx::ISerializer *serializer,
- t_pull_group *pgrp,
- t_pull_coord *pcrd)
+static void do_pullgrp_tpx_pre95(gmx::ISerializer* serializer, t_pull_group* pgrp, t_pull_coord* pcrd)
{
rvec tmp;
serializer->doReal(&pcrd->kB);
}
-static void do_pull_group(gmx::ISerializer *serializer, t_pull_group *pgrp)
+static void do_pull_group(gmx::ISerializer* serializer, t_pull_group* pgrp)
{
serializer->doInt(&pgrp->nat);
if (serializer->reading())
serializer->doInt(&pgrp->pbcatom);
}
-static void do_pull_coord(gmx::ISerializer *serializer,
- t_pull_coord *pcrd,
- int file_version,
- int ePullOld, int eGeomOld, ivec dimOld)
+static void do_pull_coord(gmx::ISerializer* serializer,
+ t_pull_coord* pcrd,
+ int file_version,
+ int ePullOld,
+ int eGeomOld,
+ ivec dimOld)
{
if (file_version >= tpxv_PullCoordNGroup)
{
* use the groups for this coord (checks in the pull and WHAM code
* ensure this), we can ignore the groups and set ngroup=0.
*/
- int *dum;
+ int* dum;
snew(dum, pcrd->ngroup);
serializer->doIntArray(dum, pcrd->ngroup);
sfree(dum);
serializer->doReal(&pcrd->kB);
}
-static void do_expandedvals(gmx::ISerializer *serializer,
- t_expanded *expand,
- t_lambda *fepvals,
- int file_version)
+static void do_expandedvals(gmx::ISerializer* serializer, t_expanded* expand, t_lambda* fepvals, int file_version)
{
- int n_lambda = fepvals->n_lambda;
+ int n_lambda = fepvals->n_lambda;
/* reset the lambda calculation window */
fepvals->lambda_start_n = 0;
}
}
-static void do_simtempvals(gmx::ISerializer *serializer,
- t_simtemp *simtemp,
- int n_lambda,
- int file_version)
+static void do_simtempvals(gmx::ISerializer* serializer, t_simtemp* simtemp, int n_lambda, int file_version)
{
if (file_version >= 79)
{
}
}
-static void do_imd(gmx::ISerializer *serializer, t_IMD *imd)
+static void do_imd(gmx::ISerializer* serializer, t_IMD* imd)
{
serializer->doInt(&imd->nat);
if (serializer->reading())
serializer->doIntArray(imd->ind, imd->nat);
}
-static void do_fepvals(gmx::ISerializer *serializer,
- t_lambda *fepvals,
- int file_version)
+static void do_fepvals(gmx::ISerializer* serializer, t_lambda* fepvals, int file_version)
{
/* i is defined in the ndo_double macro; use g to iterate. */
- int g;
- real rdum;
+ int g;
+ real rdum;
/* free energy values */
{
if (g != efptFEP)
{
- fepvals->all_lambda[g][h] =
- fepvals->all_lambda[efptFEP][h];
+ fepvals->all_lambda[g][h] = fepvals->all_lambda[efptFEP][h];
}
}
}
}
else
{
- fepvals->n_lambda = 0;
- fepvals->all_lambda = nullptr;
+ fepvals->n_lambda = 0;
+ fepvals->all_lambda = nullptr;
if (fepvals->init_lambda >= 0)
{
fepvals->separate_dvdl[efptFEP] = TRUE;
if ((file_version >= 83 && file_version < 90) || file_version >= 92)
{
serializer->doInt(&fepvals->lambda_neighbors);
- if ( (fepvals->lambda_neighbors >= 0) && (fepvals->init_fep_state >= 0) &&
- (fepvals->init_lambda < 0) )
+ if ((fepvals->lambda_neighbors >= 0) && (fepvals->init_fep_state >= 0)
+ && (fepvals->init_lambda < 0))
{
- fepvals->lambda_start_n = (fepvals->init_fep_state -
- fepvals->lambda_neighbors);
- fepvals->lambda_stop_n = (fepvals->init_fep_state +
- fepvals->lambda_neighbors + 1);
+ fepvals->lambda_start_n = (fepvals->init_fep_state - fepvals->lambda_neighbors);
+ fepvals->lambda_stop_n = (fepvals->init_fep_state + fepvals->lambda_neighbors + 1);
if (fepvals->lambda_start_n < 0)
{
fepvals->lambda_start_n = 0;
}
}
-static void do_awhBias(gmx::ISerializer *serializer, gmx::AwhBiasParams *awhBiasParams,
- int gmx_unused file_version)
+static void do_awhBias(gmx::ISerializer* serializer, gmx::AwhBiasParams* awhBiasParams, int gmx_unused file_version)
{
serializer->doInt(&awhBiasParams->eTarget);
serializer->doDouble(&awhBiasParams->targetBetaScaling);
for (int d = 0; d < awhBiasParams->ndim; d++)
{
- gmx::AwhDimParams *dimParams = &awhBiasParams->dimParams[d];
+ gmx::AwhDimParams* dimParams = &awhBiasParams->dimParams[d];
serializer->doInt(&dimParams->eCoordProvider);
serializer->doInt(&dimParams->coordIndex);
}
}
-static void do_awh(gmx::ISerializer *serializer,
- gmx::AwhParams *awhParams,
- int gmx_unused file_version)
+static void do_awh(gmx::ISerializer* serializer, gmx::AwhParams* awhParams, int gmx_unused file_version)
{
serializer->doInt(&awhParams->numBias);
serializer->doInt(&awhParams->nstOut);
}
}
-static void do_pull(gmx::ISerializer *serializer,
- pull_params_t *pull,
- int file_version,
- int ePullOld)
+static void do_pull(gmx::ISerializer* serializer, pull_params_t* pull, int file_version, int ePullOld)
{
int eGeomOld = -1;
ivec dimOld;
for (g = 0; g < pull->ngroup; g++)
{
/* We read and ignore a pull coordinate for group 0 */
- do_pullgrp_tpx_pre95(serializer, &pull->group[g], &pull->coord[std::max(g-1, 0)]);
+ do_pullgrp_tpx_pre95(serializer, &pull->group[g], &pull->coord[std::max(g - 1, 0)]);
if (g > 0)
{
- pull->coord[g-1].group[0] = 0;
- pull->coord[g-1].group[1] = g;
+ pull->coord[g - 1].group[0] = 0;
+ pull->coord[g - 1].group[1] = g;
}
}
}
for (g = 0; g < pull->ncoord; g++)
{
- do_pull_coord(serializer, &pull->coord[g],
- file_version, ePullOld, eGeomOld, dimOld);
+ do_pull_coord(serializer, &pull->coord[g], file_version, ePullOld, eGeomOld, dimOld);
}
}
if (file_version >= tpxv_PullAverage)
{
gmx_bool v;
- v = pull->bXOutAverage;
+ v = pull->bXOutAverage;
serializer->doBool(&v);
pull->bXOutAverage = v;
v = pull->bFOutAverage;
}
-static void do_rotgrp(gmx::ISerializer *serializer,
- t_rotgrp *rotg)
+static void do_rotgrp(gmx::ISerializer* serializer, t_rotgrp* rotg)
{
serializer->doInt(&rotg->eType);
serializer->doInt(&rotg->bMassW);
serializer->doReal(&rotg->PotAngle_step);
}
-static void do_rot(gmx::ISerializer *serializer,
- t_rot *rot)
+static void do_rot(gmx::ISerializer* serializer, t_rot* rot)
{
int g;
}
-static void do_swapgroup(gmx::ISerializer *serializer,
- t_swapGroup *g)
+static void do_swapgroup(gmx::ISerializer* serializer, t_swapGroup* g)
{
/* Name of the group or molecule */
serializer->doIntArray(g->nmolReq, eCompNR);
}
-static void do_swapcoords_tpx(gmx::ISerializer *serializer,
- t_swapcoords *swap,
- int file_version)
+static void do_swapcoords_tpx(gmx::ISerializer* serializer, t_swapcoords* swap, int file_version)
{
/* Enums for better readability of the code */
- enum {
- eCompA = 0, eCompB
+ enum
+ {
+ eCompA = 0,
+ eCompB
};
- enum {
- eChannel0 = 0, eChannel1
+ enum
+ {
+ eChannel0 = 0,
+ eChannel1
};
swap->ngrp = 5;
snew(swap->grp, swap->ngrp);
- swap->grp[eGrpSplit0 ].molname = gmx_strdup("split0" ); // group 0: split0
- swap->grp[eGrpSplit1 ].molname = gmx_strdup("split1" ); // group 1: split1
- swap->grp[eGrpSolvent].molname = gmx_strdup("solvent"); // group 2: solvent
- swap->grp[3 ].molname = gmx_strdup("anions" ); // group 3: anions
- swap->grp[4 ].molname = gmx_strdup("cations"); // group 4: cations
+ swap->grp[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
serializer->doInt(&swap->grp[3].nat);
serializer->doInt(&swap->grp[eGrpSolvent].nat);
// 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, eGrpSolvent, eGrpSplit0, eGrpSplit1 };
for (int ig = 0; ig < 4; ig++)
{
serializer->doInt(&swap->grp[3].nmolReq[j]); // group 3 = anions
serializer->doInt(&swap->grp[4].nmolReq[j]); // group 4 = cations
}
- } /* End support reading older CompEl .tpr files */
+ } /* End support reading older CompEl .tpr files */
if (file_version >= tpxv_CompElWithSwapLayerOffset)
{
serializer->doReal(&swap->bulkOffset[eCompA]);
serializer->doReal(&swap->bulkOffset[eCompB]);
}
-
}
-static void do_legacy_efield(gmx::ISerializer *serializer, gmx::KeyValueTreeObjectBuilder *root)
+static void do_legacy_efield(gmx::ISerializer* serializer, gmx::KeyValueTreeObjectBuilder* root)
{
- const char *const dimName[] = { "x", "y", "z" };
+ const char* const dimName[] = { "x", "y", "z" };
- auto appliedForcesObj = root->addObject("applied-forces");
- auto efieldObj = appliedForcesObj.addObject("electric-field");
+ auto appliedForcesObj = root->addObject("applied-forces");
+ auto efieldObj = appliedForcesObj.addObject("electric-field");
// The content of the tpr file for this feature has
// been the same since gromacs 4.0 that was used for
// developing.
int n, nt;
serializer->doInt(&n);
serializer->doInt(&nt);
- std::vector<real> aa(n+1), phi(nt+1), at(nt+1), phit(nt+1);
- serializer->doRealArray(aa.data(), n);
+ std::vector<real> aa(n + 1), phi(nt + 1), at(nt + 1), phit(nt + 1);
+ serializer->doRealArray(aa.data(), n);
serializer->doRealArray(phi.data(), n);
- serializer->doRealArray(at.data(), nt);
+ serializer->doRealArray(at.data(), nt);
serializer->doRealArray(phit.data(), nt);
if (n > 0)
{
if (n > 1 || nt > 1)
{
- gmx_fatal(FARGS, "Can not handle tpr files with more than one electric field term per direction.");
+ gmx_fatal(FARGS,
+ "Can not handle tpr files with more than one electric field term per "
+ "direction.");
}
auto dimObj = efieldObj.addObject(dimName[j]);
dimObj.addValue<real>("E0", aa[0]);
}
-static void do_inputrec(gmx::ISerializer *serializer,
- t_inputrec *ir,
- int file_version)
+static void do_inputrec(gmx::ISerializer* serializer, t_inputrec* ir, int file_version)
{
int i, j, k, idum = 0;
real rdum;
if (file_version != tpx_version)
{
/* Give a warning about features that are not accessible */
- fprintf(stderr, "Note: file tpx version %d, software tpx version %d\n",
- file_version, tpx_version);
+ fprintf(stderr, "Note: file tpx version %d, software tpx version %d\n", file_version, tpx_version);
}
if (file_version == 0)
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.acc, ir->opts.ngacc);
+ snew(ir->opts.egp_flags, ir->opts.ngener * ir->opts.ngener);
}
if (ir->opts.ngtc > 0)
{
{
serializer->doRvecArray(ir->opts.acc, ir->opts.ngacc);
}
- serializer->doIntArray(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 */
serializer->doIntArray(ir->opts.annealing, ir->opts.ngtc);
serializer->doInt(&ir->opts.ngQM);
if (serializer->reading())
{
- snew(ir->opts.QMmethod, ir->opts.ngQM);
- snew(ir->opts.QMbasis, ir->opts.ngQM);
- snew(ir->opts.QMcharge, ir->opts.ngQM);
- snew(ir->opts.QMmult, ir->opts.ngQM);
- snew(ir->opts.bSH, ir->opts.ngQM);
+ snew(ir->opts.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);
+ snew(ir->opts.SAon, ir->opts.ngQM);
+ snew(ir->opts.SAoff, ir->opts.ngQM);
+ snew(ir->opts.SAsteps, ir->opts.ngQM);
}
if (ir->opts.ngQM > 0 && ir->bQMMM)
{
{
if (serializer->reading())
{
- paramsObj.mergeObject(
- gmx::deserializeKeyValueTree(serializer));
+ paramsObj.mergeObject(gmx::deserializeKeyValueTree(serializer));
}
else
{
{
if (serializer->reading())
{
- ir->internalParameters = std::make_unique<gmx::KeyValueTreeObject>(gmx::deserializeKeyValueTree(serializer));
+ ir->internalParameters =
+ std::make_unique<gmx::KeyValueTreeObject>(gmx::deserializeKeyValueTree(serializer));
}
else
{
}
-static void do_harm(gmx::ISerializer *serializer, t_iparams *iparams)
+static void do_harm(gmx::ISerializer* serializer, t_iparams* iparams)
{
serializer->doReal(&iparams->harmonic.rA);
serializer->doReal(&iparams->harmonic.krA);
serializer->doReal(&iparams->harmonic.krB);
}
-static void do_iparams(gmx::ISerializer *serializer,
- t_functype ftype,
- t_iparams *iparams,
- int file_version)
+static void do_iparams(gmx::ISerializer* serializer, t_functype ftype, t_iparams* iparams, int file_version)
{
- int idum;
- real rdum;
+ int idum;
+ real rdum;
switch (ftype)
{
serializer->doReal(&iparams->cubic.kb);
serializer->doReal(&iparams->cubic.kcub);
break;
- case F_CONNBONDS:
- break;
- case F_POLARIZATION:
- serializer->doReal(&iparams->polarize.alpha);
- break;
+ case F_CONNBONDS: break;
+ case F_POLARIZATION: serializer->doReal(&iparams->polarize.alpha); break;
case F_ANHARM_POL:
serializer->doReal(&iparams->anharm_polarize.alpha);
serializer->doReal(&iparams->anharm_polarize.drcut);
serializer->doReal(&iparams->fbposres.r);
serializer->doReal(&iparams->fbposres.k);
break;
- case F_CBTDIHS:
- serializer->doRealArray(iparams->cbtdihs.cbtcA, NR_CBTDIHS);
- break;
+ case F_CBTDIHS: serializer->doRealArray(iparams->cbtdihs.cbtcA, NR_CBTDIHS); break;
case F_RBDIHS:
serializer->doRealArray(iparams->rbdihs.rbcA, NR_RBDIHS);
serializer->doRealArray(iparams->rbdihs.rbcB, NR_RBDIHS);
serializer->doReal(&iparams->settle.dhh);
break;
case F_VSITE2:
- case F_VSITE2FD:
- serializer->doReal(&iparams->vsite.a);
- break;
+ case F_VSITE2FD: serializer->doReal(&iparams->vsite.a); break;
case F_VSITE3:
case F_VSITE3FD:
case F_VSITE3FAD:
serializer->doInt(&iparams->cmap.cmapB);
break;
default:
- gmx_fatal(FARGS, "unknown function type %d (%s) in %s line %d",
- ftype, interaction_function[ftype].name, __FILE__, __LINE__);
+ gmx_fatal(FARGS, "unknown function type %d (%s) in %s line %d", ftype,
+ interaction_function[ftype].name, __FILE__, __LINE__);
}
}
-static void do_ilist(gmx::ISerializer *serializer, InteractionList *ilist)
+static void do_ilist(gmx::ISerializer* serializer, InteractionList* ilist)
{
int nr = ilist->size();
serializer->doInt(&nr);
serializer->doIntArray(ilist->iatoms.data(), ilist->size());
}
-static void do_ffparams(gmx::ISerializer *serializer,
- gmx_ffparams_t *ffparams,
- int file_version)
+static void do_ffparams(gmx::ISerializer* serializer, gmx_ffparams_t* ffparams, int file_version)
{
serializer->doInt(&ffparams->atnr);
int numTypes = ffparams->numTypes();
for (int k = 0; k < NFTUPD; k++)
{
/* Compare the read file_version to the update table */
- if ((file_version < ftupd[k].fvnr) &&
- (ffparams->functype[i] >= ftupd[k].ftype))
+ if ((file_version < ftupd[k].fvnr) && (ffparams->functype[i] >= ftupd[k].ftype))
{
ffparams->functype[i] += 1;
}
}
}
- do_iparams(serializer, ffparams->functype[i], &ffparams->iparams[i],
- file_version);
+ do_iparams(serializer, ffparams->functype[i], &ffparams->iparams[i], file_version);
}
}
-static void add_settle_atoms(InteractionList *ilist)
+static void add_settle_atoms(InteractionList* ilist)
{
int i;
/* Settle used to only store the first atom: add the other two */
- ilist->iatoms.resize(2*ilist->size());
- for (i = ilist->size()/4 - 1; i >= 0; i--)
+ ilist->iatoms.resize(2 * ilist->size());
+ for (i = ilist->size() / 4 - 1; i >= 0; i--)
{
- ilist->iatoms[4*i+0] = ilist->iatoms[2*i+0];
- ilist->iatoms[4*i+1] = ilist->iatoms[2*i+1];
- ilist->iatoms[4*i+2] = ilist->iatoms[2*i+1] + 1;
- ilist->iatoms[4*i+3] = ilist->iatoms[2*i+1] + 2;
+ ilist->iatoms[4 * i + 0] = ilist->iatoms[2 * i + 0];
+ ilist->iatoms[4 * i + 1] = ilist->iatoms[2 * i + 1];
+ ilist->iatoms[4 * i + 2] = ilist->iatoms[2 * i + 1] + 1;
+ ilist->iatoms[4 * i + 3] = ilist->iatoms[2 * i + 1] + 2;
}
}
-static void do_ilists(gmx::ISerializer *serializer,
- InteractionLists *ilists,
- int file_version)
+static void do_ilists(gmx::ISerializer* serializer, InteractionLists* ilists, int file_version)
{
GMX_RELEASE_ASSERT(ilists, "Need a valid ilists object");
- GMX_RELEASE_ASSERT(ilists->size() == F_NRE, "The code needs to be in sync with InteractionLists");
+ GMX_RELEASE_ASSERT(ilists->size() == F_NRE,
+ "The code needs to be in sync with InteractionLists");
for (int j = 0; j < F_NRE; j++)
{
- InteractionList &ilist = (*ilists)[j];
+ InteractionList& ilist = (*ilists)[j];
gmx_bool bClear = FALSE;
if (serializer->reading())
{
}
}
-static void do_block(gmx::ISerializer *serializer, t_block *block)
+static void do_block(gmx::ISerializer* serializer, t_block* block)
{
serializer->doInt(&block->nr);
if (serializer->reading())
{
sfree(block->index);
}
- block->nalloc_index = block->nr+1;
+ block->nalloc_index = block->nr + 1;
snew(block->index, block->nalloc_index);
}
- serializer->doIntArray(block->index, block->nr+1);
+ serializer->doIntArray(block->index, block->nr + 1);
}
-static void do_blocka(gmx::ISerializer *serializer, t_blocka *block)
+static void do_blocka(gmx::ISerializer* serializer, t_blocka* block)
{
serializer->doInt(&block->nr);
serializer->doInt(&block->nra);
if (serializer->reading())
{
- block->nalloc_index = block->nr+1;
+ 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(block->index, block->nr+1);
+ serializer->doIntArray(block->index, block->nr + 1);
serializer->doIntArray(block->a, block->nra);
}
* to element names when reading TPR files, without making the Gromacs library
* directory a dependency on mdrun (which is the case if we need elements.dat).
*/
-static const char *
-atomicnumber_to_element(int atomicnumber)
+static const char* atomicnumber_to_element(int atomicnumber)
{
- const char * p;
+ const char* p;
/* This does not have to be complete, so we only include elements likely
* to occur in PDB files.
*/
switch (atomicnumber)
{
- case 1: p = "H"; break;
- case 5: p = "B"; break;
- case 6: p = "C"; break;
- case 7: p = "N"; break;
- case 8: p = "O"; break;
- case 9: p = "F"; break;
+ case 1: p = "H"; break;
+ case 5: p = "B"; break;
+ case 6: p = "C"; break;
+ case 7: p = "N"; break;
+ case 8: p = "O"; break;
+ case 9: p = "F"; break;
case 11: p = "Na"; break;
case 12: p = "Mg"; break;
- case 15: p = "P"; break;
- case 16: p = "S"; break;
+ case 15: p = "P"; break;
+ case 16: p = "S"; break;
case 17: p = "Cl"; break;
case 18: p = "Ar"; break;
- case 19: p = "K"; break;
+ case 19: p = "K"; break;
case 20: p = "Ca"; break;
case 25: p = "Mn"; break;
case 26: p = "Fe"; break;
case 30: p = "Zn"; break;
case 35: p = "Br"; break;
case 47: p = "Ag"; break;
- default: p = ""; break;
+ default: p = ""; break;
}
return p;
}
-static void do_atom(gmx::ISerializer *serializer, t_atom *atom)
+static void do_atom(gmx::ISerializer* serializer, t_atom* atom)
{
serializer->doReal(&atom->m);
serializer->doReal(&atom->q);
}
}
-static void do_grps(gmx::ISerializer *serializer,
- gmx::ArrayRef<AtomGroupIndices> grps)
+static void do_grps(gmx::ISerializer* serializer, gmx::ArrayRef<AtomGroupIndices> grps)
{
- for (auto &group : grps)
+ for (auto& group : grps)
{
int size = group.size();
serializer->doInt(&size);
}
}
-static void do_symstr(gmx::ISerializer *serializer, char ***nm, t_symtab *symtab)
+static void do_symstr(gmx::ISerializer* serializer, char*** nm, t_symtab* symtab)
{
int ls;
}
}
-static void do_strstr(gmx::ISerializer *serializer,
- int nstr,
- char ***nm,
- t_symtab *symtab)
+static void do_strstr(gmx::ISerializer* serializer, int nstr, char*** nm, t_symtab* symtab)
{
- int j;
+ int j;
for (j = 0; (j < nstr); j++)
{
}
}
-static void do_resinfo(gmx::ISerializer *serializer,
- int n,
- t_resinfo *ri,
- t_symtab *symtab,
- int file_version)
+static void do_resinfo(gmx::ISerializer* serializer, int n, t_resinfo* ri, t_symtab* symtab, int file_version)
{
- int j;
+ int j;
for (j = 0; (j < n); j++)
{
}
}
-static void do_atoms(gmx::ISerializer *serializer,
- t_atoms *atoms,
- t_symtab *symtab,
- int file_version)
+static void do_atoms(gmx::ISerializer* serializer, t_atoms* atoms, t_symtab* symtab, int file_version)
{
int i;
}
else
{
- GMX_RELEASE_ASSERT(atoms->haveMass && atoms->haveCharge && atoms->haveType && atoms->haveBState, "Mass, charge, atomtype and B-state parameters should be present in t_atoms when writing a tpr file");
+ GMX_RELEASE_ASSERT(atoms->haveMass && atoms->haveCharge && atoms->haveType && atoms->haveBState,
+ "Mass, charge, atomtype and B-state parameters should be present in "
+ "t_atoms when writing a tpr file");
}
for (i = 0; (i < atoms->nr); i++)
{
do_resinfo(serializer, atoms->nres, atoms->resinfo, symtab, file_version);
}
-static void do_groups(gmx::ISerializer *serializer,
- SimulationGroups *groups,
- t_symtab *symtab)
+static void do_groups(gmx::ISerializer* serializer, SimulationGroups* groups, t_symtab* symtab)
{
do_grps(serializer, groups->groups);
int numberOfGroupNames = groups->groupNames.size();
}
}
-static void do_atomtypes(gmx::ISerializer *serializer, t_atomtypes *atomtypes,
- int file_version)
+static void do_atomtypes(gmx::ISerializer* serializer, t_atomtypes* atomtypes, int file_version)
{
- int j;
+ int j;
serializer->doInt(&atomtypes->nr);
j = atomtypes->nr;
}
}
-static void do_symtab(gmx::ISerializer *serializer, t_symtab *symtab)
+static void do_symtab(gmx::ISerializer* serializer, t_symtab* symtab)
{
int i, nr;
- t_symbuf *symbuf;
+ t_symbuf* symbuf;
serializer->doInt(&symtab->nr);
- nr = symtab->nr;
+ nr = symtab->nr;
if (serializer->reading())
{
snew(symtab->symbuf, 1);
std::string buf = symbuf->buf[i];
serializer->doString(&buf);
}
- nr -= i;
+ nr -= i;
symbuf = symbuf->next;
}
if (nr != 0)
}
}
-static void do_cmap(gmx::ISerializer *serializer, gmx_cmap_t *cmap_grid)
+static void do_cmap(gmx::ISerializer* serializer, gmx_cmap_t* cmap_grid)
{
int ngrid = cmap_grid->cmapdata.size();
for (int i = 0; i < ngrid; i++)
{
- cmap_grid->cmapdata[i].cmap.resize(4*nelem);
+ cmap_grid->cmapdata[i].cmap.resize(4 * nelem);
}
}
{
for (int j = 0; j < nelem; j++)
{
- serializer->doReal(&cmap_grid->cmapdata[i].cmap[j*4]);
- serializer->doReal(&cmap_grid->cmapdata[i].cmap[j*4+1]);
- serializer->doReal(&cmap_grid->cmapdata[i].cmap[j*4+2]);
- serializer->doReal(&cmap_grid->cmapdata[i].cmap[j*4+3]);
+ serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4]);
+ serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4 + 1]);
+ serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4 + 2]);
+ serializer->doReal(&cmap_grid->cmapdata[i].cmap[j * 4 + 3]);
}
}
}
-static void do_moltype(gmx::ISerializer *serializer,
- gmx_moltype_t *molt,
- t_symtab *symtab,
- int file_version)
+static void do_moltype(gmx::ISerializer* serializer, gmx_moltype_t* molt, t_symtab* symtab, int file_version)
{
do_symstr(serializer, &(molt->name), symtab);
do_blocka(serializer, &molt->excls);
}
-static void do_molblock(gmx::ISerializer *serializer,
- gmx_molblock_t *molb,
- int numAtomsPerMolecule)
+static void do_molblock(gmx::ISerializer* serializer, gmx_molblock_t* molb, int numAtomsPerMolecule)
{
serializer->doInt(&molb->type);
serializer->doInt(&molb->nmol);
}
serializer->doRvecArray(as_rvec_array(molb->posres_xB.data()), numPosres_xB);
}
-
}
-static void set_disres_npair(gmx_mtop_t *mtop)
+static void set_disres_npair(gmx_mtop_t* mtop)
{
- gmx_mtop_ilistloop_t iloop;
- int nmol;
+ gmx_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))
+ iloop = gmx_mtop_ilistloop_init(mtop);
+ while (const InteractionLists* ilist = gmx_mtop_ilistloop_next(iloop, &nmol))
{
- const InteractionList &il = (*ilist)[F_DISRES];
+ const InteractionList& il = (*ilist)[F_DISRES];
if (il.size() > 0)
{
for (int i = 0; i < il.size(); i += 3)
{
npair++;
- if (i+3 == il.size() || ip[a[i]].disres.label != ip[a[i+3]].disres.label)
+ if (i + 3 == il.size() || ip[a[i]].disres.label != ip[a[i + 3]].disres.label)
{
ip[a[i]].disres.npair = npair;
npair = 0;
}
}
-static void do_mtop(gmx::ISerializer *serializer,
- gmx_mtop_t *mtop,
- int file_version)
+static void do_mtop(gmx::ISerializer* serializer, gmx_mtop_t* mtop, int file_version)
{
do_symtab(serializer, &(mtop->symtab));
{
mtop->moltype.resize(nmoltype);
}
- for (gmx_moltype_t &moltype : mtop->moltype)
+ for (gmx_moltype_t& moltype : mtop->moltype)
{
do_moltype(serializer, &moltype, &mtop->symtab, file_version);
}
{
mtop->molblock.resize(nmolblock);
}
- for (gmx_molblock_t &molblock : mtop->molblock)
+ for (gmx_molblock_t& molblock : mtop->molblock)
{
int numAtomsPerMolecule = (serializer->reading() ? 0 : mtop->moltype[molblock.type].atoms.nr);
do_molblock(serializer, &molblock, numAtomsPerMolecule);
mtop->bIntermolecularInteractions = FALSE;
}
- do_atomtypes (serializer, &(mtop->atomtypes), file_version);
+ do_atomtypes(serializer, &(mtop->atomtypes), file_version);
if (file_version >= 65)
{
* \param[in,out] fio File handle.
* \param[in] TopOnlyOK If not reading \p ir is fine or not.
*/
-static void do_tpxheader(gmx::FileIOXdrSerializer *serializer,
- TpxFileHeader *tpx,
- const char *filename,
- t_fileio *fio,
+static void do_tpxheader(gmx::FileIOXdrSerializer* serializer,
+ TpxFileHeader* tpx,
+ const char* filename,
+ t_fileio* fio,
bool TopOnlyOK)
{
- int precision;
- int idum = 0;
- real rdum = 0;
+ int precision;
+ int idum = 0;
+ real rdum = 0;
/* XDR binary topology file */
precision = sizeof(real);
serializer->doString(&buf);
if (std::strncmp(buf.c_str(), "VERSION", 7) != 0)
{
- gmx_fatal(FARGS, "Can not read file %s,\n"
- " this file is from a GROMACS version which is older than 2.0\n"
- " Make a new one with grompp or use a gro or pdb file, if possible",
- filename);
+ gmx_fatal(
+ FARGS,
+ "Can not read file %s,\n"
+ " this file is from a GROMACS version which is older than 2.0\n"
+ " Make a new one with grompp or use a gro or pdb file, if possible",
+ filename);
}
// We need to know the precision used to write the TPR file, to match it
// to the precision of the currently running binary. If the precisions match
tpx->isDouble = (precision == sizeof(double));
if ((precision != sizeof(float)) && !tpx->isDouble)
{
- gmx_fatal(FARGS, "Unknown precision in file %s: real is %d bytes "
+ gmx_fatal(FARGS,
+ "Unknown precision in file %s: real is %d bytes "
"instead of %zu or %zu",
filename, precision, sizeof(float), sizeof(double));
}
gmx_fio_setprecision(fio, tpx->isDouble);
- fprintf(stderr, "Reading file %s, %s (%s precision)\n",
- filename, buf.c_str(), tpx->isDouble ? "double" : "single");
+ fprintf(stderr, "Reading file %s, %s (%s precision)\n", filename, buf.c_str(),
+ tpx->isDouble ? "double" : "single");
}
else
{
serializer->doString(&buf);
gmx_fio_setprecision(fio, tpx->isDouble);
serializer->doInt(&precision);
- fileTag = gmx::formatString("%s", tpx_tag);
+ fileTag = gmx::formatString("%s", tpx_tag);
}
/* Check versions! */
if (fileTag != tpx_tag)
{
- fprintf(stderr, "Note: file tpx tag '%s', software tpx tag '%s'\n",
- fileTag.c_str(), tpx_tag);
+ fprintf(stderr, "Note: file tpx tag '%s', software tpx tag '%s'\n", fileTag.c_str(), tpx_tag);
/* We only support reading tpx files with the same tag as the code
* or tpx files with the release tag and with lower version number.
*/
if (fileTag != TPX_TAG_RELEASE && tpx->fileVersion < tpx_version)
{
- gmx_fatal(FARGS, "tpx tag/version mismatch: reading tpx file (%s) version %d, tag '%s' with program for tpx version %d, tag '%s'",
- filename, tpx->fileVersion, fileTag.c_str(),
- tpx_version, tpx_tag);
+ gmx_fatal(FARGS,
+ "tpx tag/version mismatch: reading tpx file (%s) version %d, tag '%s' "
+ "with program for tpx version %d, tag '%s'",
+ filename, tpx->fileVersion, fileTag.c_str(), tpx_version, tpx_tag);
}
}
}
- if ((tpx->fileVersion <= tpx_incompatible_version) ||
- ((tpx->fileVersion > tpx_version) && !TopOnlyOK) ||
- (tpx->fileGeneration > tpx_generation) ||
- tpx_version == 80) /*80 was used by both 5.0-dev and 4.6-dev*/
+ if ((tpx->fileVersion <= tpx_incompatible_version)
+ || ((tpx->fileVersion > tpx_version) && !TopOnlyOK) || (tpx->fileGeneration > tpx_generation)
+ || tpx_version == 80) /*80 was used by both 5.0-dev and 4.6-dev*/
{
- gmx_fatal(FARGS, "reading tpx file (%s) version %d with version %d program",
- filename, tpx->fileVersion, tpx_version);
+ gmx_fatal(FARGS, "reading tpx file (%s) version %d with version %d program", filename,
+ tpx->fileVersion, tpx_version);
}
serializer->doInt(&tpx->natoms);
{
if (!serializer->reading())
{
- GMX_RELEASE_ASSERT(tpx->sizeOfTprBody != 0, "Not possible to write new file with zero TPR body size");
+ GMX_RELEASE_ASSERT(tpx->sizeOfTprBody != 0,
+ "Not possible to write new file with zero TPR body size");
}
serializer->doInt64(&tpx->sizeOfTprBody);
}
}
}
-#define do_test(serializer, b, p) if ((serializer)->reading() && ((p) != nullptr) && !(b)) gmx_fatal(FARGS, "No %s in input file",#p)
+#define do_test(serializer, b, p) \
+ if ((serializer)->reading() && ((p) != nullptr) && !(b)) \
+ gmx_fatal(FARGS, "No %s in input file", #p)
/*! \brief
* Process the first part of the TPR into the state datastructure.
* \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)
+static void do_tpx_state_first(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_state* state)
{
if (serializer->reading())
{
if (state->ngtc > 0)
{
- real *dumv;
+ real* dumv;
snew(dumv, state->ngtc);
if (tpx->fileVersion < 69)
{
* \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)
+static void do_tpx_mtop(gmx::ISerializer* serializer, TpxFileHeader* tpx, gmx_mtop_t* mtop)
{
do_test(serializer, tpx->bTop, mtop);
if (tpx->bTop)
* \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)
+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");
+ 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");
+ GMX_RELEASE_ASSERT(!(x == nullptr && v != nullptr),
+ "Passing x==NULL and v!=NULL is not supported");
}
if (serializer->reading())
{
if (serializer->reading())
{
- state->flags |= (1<<estX);
+ state->flags |= (1 << estX);
}
serializer->doRvecArray(x, tpx->natoms);
}
{
if (serializer->reading())
{
- state->flags |= (1<<estV);
+ state->flags |= (1 << estV);
}
if (!v)
{
* \param[in] tpx The file header data.
* \param[in,out] ir Datastructure with simulation parameters.
*/
-static int do_tpx_ir(gmx::ISerializer *serializer,
- TpxFileHeader *tpx,
- t_inputrec *ir)
+static int do_tpx_ir(gmx::ISerializer* serializer, TpxFileHeader* tpx, t_inputrec* ir)
{
- int ePBC;
- gmx_bool bPeriodicMols;
+ int ePBC;
+ gmx_bool bPeriodicMols;
/* Starting with tpx version 26, we have the inputrec
* at the end of the file, so we can ignore it
* \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)
+static void do_tpx_finalize(TpxFileHeader* tpx, t_inputrec* ir, t_state* state, gmx_mtop_t* mtop)
{
if (tpx->fileVersion < 51 && state)
{
* \param[in,out] v Individual velocities for processing, deprecated.
* \param[in,out] mtop Global topology.
*/
-static int do_tpx_body(gmx::ISerializer *serializer,
- TpxFileHeader *tpx,
- t_inputrec *ir,
- t_state *state,
- rvec *x,
- rvec *v,
- gmx_mtop_t *mtop)
+static int do_tpx_body(gmx::ISerializer* serializer,
+ TpxFileHeader* tpx,
+ t_inputrec* ir,
+ t_state* state,
+ rvec* x,
+ rvec* v,
+ gmx_mtop_t* mtop)
{
if (state)
{
* \param[in,out] ir Datastructures with simulation parameters.
* \param[in,out] mtop Global topology.
*/
-static int do_tpx_body(gmx::ISerializer *serializer,
- TpxFileHeader *tpx,
- t_inputrec *ir,
- gmx_mtop_t *mtop)
+static int 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.bIr = ir != nullptr;
+ header.bTop = mtop != nullptr;
header.bX = (state.flags & (1 << estX)) != 0;
header.bV = (state.flags & (1 << estV)) != 0;
header.bF = false;
* 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)
+static void doTpxBodyBuffer(gmx::ISerializer* serializer, gmx::ArrayRef<char> buffer)
{
serializer->doCharArray(buffer.data(), buffer.size());
}
*
* \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)
+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)
doTpxBodyBuffer(serializer, partialDeserializedTpr.body);
partialDeserializedTpr.ePBC =
- completeTprDeserialization(&partialDeserializedTpr,
- ir,
- state,
- x, v,
- mtop);
+ completeTprDeserialization(&partialDeserializedTpr, ir, state, x, v, mtop);
}
else
{
- partialDeserializedTpr.ePBC =
- do_tpx_body(serializer,
- tpx,
- ir,
- state,
- x,
- v,
- mtop);
+ partialDeserializedTpr.ePBC = 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,
// in on master.
partialDeserializedTpr.header = populateTpxHeader(*state, ir, mtop);
gmx::InMemorySerializer tprBodySerializer;
- do_tpx_body(&tprBodySerializer,
- &partialDeserializedTpr.header,
- ir,
- mtop);
+ do_tpx_body(&tprBodySerializer, &partialDeserializedTpr.header, ir, mtop);
partialDeserializedTpr.body = tprBodySerializer.finishAndGetBuffer();
return partialDeserializedTpr;
*
************************************************************/
-TpxFileHeader readTpxHeader(const char *fileName, bool canReadTopologyOnly)
+TpxFileHeader readTpxHeader(const char* fileName, bool canReadTopologyOnly)
{
- t_fileio *fio;
+ t_fileio* fio;
fio = open_tpx(fileName, "r");
gmx::FileIOXdrSerializer serializer(fio);
- TpxFileHeader tpx;
+ TpxFileHeader tpx;
do_tpxheader(&serializer, &tpx, fileName, fio, canReadTopologyOnly);
close_tpx(fio);
return tpx;
}
-void write_tpx_state(const char *fn,
- const t_inputrec *ir, const t_state *state, const gmx_mtop_t *mtop)
+void write_tpx_state(const char* fn, const t_inputrec* ir, const t_state* state, const gmx_mtop_t* mtop)
{
/* To write a state, we first need to write the state information to a buffer before
* we append the raw bytes to the file. For this, the header information needs to be
* otherwise not available.
*/
- t_fileio *fio;
+ t_fileio* fio;
- TpxFileHeader tpx = populateTpxHeader(*state,
- ir,
- mtop);
+ TpxFileHeader tpx = populateTpxHeader(*state, ir, mtop);
gmx::InMemorySerializer tprBodySerializer;
- do_tpx_body(&tprBodySerializer,
- &tpx,
- const_cast<t_inputrec *>(ir),
- const_cast<t_state *>(state), nullptr, nullptr,
- const_cast<gmx_mtop_t *>(mtop));
+ do_tpx_body(&tprBodySerializer, &tpx, const_cast<t_inputrec*>(ir), const_cast<t_state*>(state),
+ nullptr, nullptr, const_cast<gmx_mtop_t*>(mtop));
std::vector<char> tprBody = tprBodySerializer.finishAndGetBuffer();
- tpx.sizeOfTprBody = tprBody.size();
+ tpx.sizeOfTprBody = tprBody.size();
fio = open_tpx(fn, "w");
gmx::FileIOXdrSerializer serializer(fio);
- do_tpxheader(&serializer,
- &tpx,
- fn,
- fio,
- ir == nullptr);
+ do_tpxheader(&serializer, &tpx, fn, fio, ir == nullptr);
doTpxBodyBuffer(&serializer, tprBody);
close_tpx(fio);
}
-int completeTprDeserialization(PartialDeserializedTprFile *partialDeserializedTpr,
- t_inputrec *ir,
- t_state *state,
- rvec *x,
- rvec *v,
- gmx_mtop_t *mtop)
+int completeTprDeserialization(PartialDeserializedTprFile* partialDeserializedTpr,
+ t_inputrec* ir,
+ t_state* state,
+ rvec* x,
+ rvec* v,
+ gmx_mtop_t* mtop)
{
gmx::InMemoryDeserializer tprBodyDeserializer(partialDeserializedTpr->body,
partialDeserializedTpr->header.isDouble);
- return do_tpx_body(&tprBodyDeserializer,
- &partialDeserializedTpr->header,
- ir,
- state,
- x,
- v,
- mtop);
+ return do_tpx_body(&tprBodyDeserializer, &partialDeserializedTpr->header, ir, state, x, v, mtop);
}
-int completeTprDeserialization(PartialDeserializedTprFile *partialDeserializedTpr,
- t_inputrec *ir,
- gmx_mtop_t *mtop)
+int 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)
+PartialDeserializedTprFile read_tpx_state(const char* fn, t_inputrec* ir, t_state* state, gmx_mtop_t* mtop)
{
- t_fileio *fio;
+ t_fileio* fio;
fio = open_tpx(fn, "r");
- 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);
+ 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)
+int 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;
+ t_fileio* fio;
+ t_state state;
- TpxFileHeader tpx;
- fio = open_tpx(fn, "r");
+ TpxFileHeader tpx;
+ fio = open_tpx(fn, "r");
gmx::FileIOXdrSerializer serializer(fio);
- do_tpxheader(&serializer,
- &tpx,
- fn,
- fio,
- ir == nullptr);
- PartialDeserializedTprFile partialDeserializedTpr
- = readTpxBody(&tpx, &serializer,
- ir, &state, x, v, mtop);
+ do_tpxheader(&serializer, &tpx, fn, fio, ir == nullptr);
+ PartialDeserializedTprFile partialDeserializedTpr =
+ readTpxBody(&tpx, &serializer, ir, &state, x, v, mtop);
close_tpx(fio);
if (mtop != nullptr && natoms != nullptr)
{
return partialDeserializedTpr.ePBC;
}
-int read_tpx_top(const char *fn,
- t_inputrec *ir, matrix box, int *natoms,
- rvec *x, rvec *v, t_topology *top)
+int 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;
+ int ePBC;
ePBC = read_tpx(fn, ir, box, natoms, x, v, &mtop);
return ePBC;
}
-gmx_bool fn2bTPX(const char *file)
+gmx_bool fn2bTPX(const char* file)
{
return (efTPR == fn2ftp(file));
}
-void pr_tpxheader(FILE *fp, int indent, const char *title, const TpxFileHeader *sh)
+void pr_tpxheader(FILE* fp, int indent, const char* title, const TpxFileHeader* sh)
{
if (available(fp, sh, indent, title))
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff