* 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)
+ serializer->doInt(&pgrp->nat);
+ if (serializer->reading())
{
snew(pgrp->ind, pgrp->nat);
}
- gmx_fio_ndo_int(fio, pgrp->ind, pgrp->nat);
- gmx_fio_do_int(fio, pgrp->nweight);
- if (bRead)
+ serializer->doIntArray(pgrp->ind, pgrp->nat);
+ serializer->doInt(&pgrp->nweight);
+ if (serializer->reading())
{
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);
+ serializer->doRealArray(pgrp->weight, pgrp->nweight);
+ serializer->doInt(&pgrp->pbcatom);
+ serializer->doRvec(&pcrd->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)
+ serializer->doInt(&pgrp->nat);
+ if (serializer->reading())
{
snew(pgrp->ind, pgrp->nat);
}
- gmx_fio_ndo_int(fio, pgrp->ind, pgrp->nat);
- gmx_fio_do_int(fio, pgrp->nweight);
- if (bRead)
+ serializer->doIntArray(pgrp->ind, pgrp->nat);
+ serializer->doInt(&pgrp->nweight);
+ if (serializer->reading())
{
snew(pgrp->weight, pgrp->nweight);
}
- gmx_fio_ndo_real(fio, pgrp->weight, pgrp->nweight);
- gmx_fio_do_int(fio, pgrp->pbcatom);
+ serializer->doRealArray(pgrp->weight, pgrp->nweight);
+ serializer->doInt(&pgrp->pbcatom);
}
-static void do_pull_coord(t_fileio *fio, t_pull_coord *pcrd,
- gmx_bool bRead, int file_version,
+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)
{
- gmx_fio_do_int(fio, pcrd->eType);
+ serializer->doInt(&pcrd->eType);
if (file_version >= tpxv_PullExternalPotential)
{
if (pcrd->eType == epullEXTERNAL)
{
- if (bRead)
+ std::string buf;
+ if (serializer->reading())
{
- char buf[STRLEN];
-
- gmx_fio_do_string(fio, buf);
- pcrd->externalPotentialProvider = gmx_strdup(buf);
+ serializer->doString(&buf);
+ pcrd->externalPotentialProvider = gmx_strdup(buf.c_str());
}
else
{
- gmx_fio_do_string(fio, pcrd->externalPotentialProvider);
+ buf = pcrd->externalPotentialProvider;
+ serializer->doString(&buf);
}
}
else
}
else
{
- if (bRead)
+ if (serializer->reading())
{
pcrd->externalPotentialProvider = nullptr;
}
* 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->doInt(&pcrd->eGeom);
+ serializer->doInt(&pcrd->ngroup);
if (pcrd->ngroup <= c_pullCoordNgroupMax)
{
- gmx_fio_ndo_int(fio, pcrd->group, pcrd->ngroup);
+ serializer->doIntArray(pcrd->group, pcrd->ngroup);
}
else
{
*/
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);
}
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);
+ serializer->doInt(&pcrd->eType);
+ serializer->doInt(&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);
}
else
{
copy_ivec(dimOld, pcrd->dim);
}
}
- gmx_fio_do_rvec(fio, pcrd->origin);
- gmx_fio_do_rvec(fio, pcrd->vec);
+ serializer->doRvec(&pcrd->origin);
+ serializer->doRvec(&pcrd->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;
{
if (n_lambda > 0)
{
- if (bRead)
+ if (serializer->reading())
{
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);
+ serializer->doRealArray(expand->init_lambda_weights, n_lambda);
+ serializer->doBool(&expand->bInit_weights);
+ }
+
+ serializer->doInt(&expand->nstexpanded);
+ serializer->doInt(&expand->elmcmove);
+ serializer->doInt(&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->doInt(&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->doInt(&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);
}
- gmx_fio_ndo_real(fio, simtemp->temperatures, n_lambda);
+ serializer->doRealArray(simtemp->temperatures, 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;
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)
+ serializer->doInt(&fepvals->n_lambda);
+ if (serializer->reading())
{
snew(fepvals->all_lambda, efptNR);
}
{
if (fepvals->n_lambda > 0)
{
- if (bRead)
+ if (serializer->reading())
{
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);
+ serializer->doDoubleArray(fepvals->all_lambda[g], fepvals->n_lambda);
+ serializer->doBoolArray(fepvals->separate_dvdl, efptNR);
}
else if (fepvals->init_lambda >= 0)
{
}
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;
}
}
}
- gmx_fio_ndo_double(fio, fepvals->all_lambda[efptFEP],
- fepvals->n_lambda);
+ serializer->doDoubleArray(fepvals->all_lambda[efptFEP], fepvals->n_lambda);
if (fepvals->init_lambda >= 0)
{
int g, h;
fepvals->separate_dvdl[efptFEP] = TRUE;
- if (bRead)
+ if (serializer->reading())
{
/* copy the contents of the efptFEP lambda component to all
the other components */
fepvals->separate_dvdl[efptFEP] = 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)
+ 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->doInt(&fepvals->separate_dhdl_file);
+ serializer->doInt(&fepvals->dhdl_derivatives);
}
else
{
}
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->doInt(&fepvals->edHdLPrintEnergy);
}
else
{
/* handle lambda_neighbors */
if ((file_version >= 83 && file_version < 90) || file_version >= 92)
{
- gmx_fio_do_int(fio, fepvals->lambda_neighbors);
+ serializer->doInt(&fepvals->lambda_neighbors);
if ( (fepvals->lambda_neighbors >= 0) && (fepvals->init_fep_state >= 0) &&
(fepvals->init_lambda < 0) )
{
}
}
-static void do_awhBias(t_fileio *fio, gmx::AwhBiasParams *awhBiasParams, gmx_bool bRead,
+static void do_awhBias(gmx::ISerializer *serializer, gmx::AwhBiasParams *awhBiasParams,
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)
+ serializer->doInt(&awhBiasParams->eTarget);
+ serializer->doDouble(&awhBiasParams->targetBetaScaling);
+ serializer->doDouble(&awhBiasParams->targetCutoff);
+ serializer->doInt(&awhBiasParams->eGrowth);
+ serializer->doInt(&awhBiasParams->bUserData);
+ serializer->doDouble(&awhBiasParams->errorInitial);
+ serializer->doInt(&awhBiasParams->ndim);
+ serializer->doInt(&awhBiasParams->shareGroup);
+ serializer->doBool(&awhBiasParams->equilibrateHistogram);
+
+ if (serializer->reading())
{
snew(awhBiasParams->dimParams, awhBiasParams->ndim);
}
{
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);
+ serializer->doInt(&dimParams->eCoordProvider);
+ serializer->doInt(&dimParams->coordIndex);
+ serializer->doDouble(&dimParams->origin);
+ serializer->doDouble(&dimParams->end);
+ serializer->doDouble(&dimParams->period);
+ serializer->doDouble(&dimParams->forceConstant);
+ serializer->doDouble(&dimParams->diffusion);
+ serializer->doDouble(&dimParams->coordValueInit);
+ serializer->doDouble(&dimParams->coverDiameter);
}
}
-static void do_awh(t_fileio *fio, gmx::AwhParams *awhParams, gmx_bool bRead,
- int gmx_unused file_version)
+static void do_awh(gmx::ISerializer *serializer,
+ gmx::AwhParams *awhParams,
+ int gmx_unused file_version)
{
- 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);
+ serializer->doInt(&awhParams->numBias);
+ serializer->doInt(&awhParams->nstOut);
+ serializer->doInt64(&awhParams->seed);
+ serializer->doInt(&awhParams->nstSampleCoord);
+ serializer->doInt(&awhParams->numSamplesUpdateFreeEnergy);
+ serializer->doInt(&awhParams->ePotential);
+ serializer->doBool(&awhParams->shareBiasMultisim);
if (awhParams->numBias > 0)
{
- if (bRead)
+ if (serializer->reading())
{
snew(awhParams->awhBiasParams, awhParams->numBias);
}
for (int k = 0; k < awhParams->numBias; k++)
{
- do_awhBias(fio, &awhParams->awhBiasParams[k], bRead, file_version);
+ do_awhBias(serializer, &awhParams->awhBiasParams[k], file_version);
}
}
}
-static void do_pull(t_fileio *fio, pull_params_t *pull, gmx_bool bRead,
- 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;
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->doInt(&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)
+ if (serializer->reading())
{
snew(pull->group, pull->ngroup);
snew(pull->coord, pull->ncoord);
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;
{
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 (file_version >= tpxv_PullAverage)
gmx_bool v;
v = pull->bXOutAverage;
- gmx_fio_do_gmx_bool(fio, v);
+ 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->doInt(&rotg->eType);
+ serializer->doInt(&rotg->bMassW);
+ 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->doInt(&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, eCompNR);
}
-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 {
/* 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->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);
+ serializer->doInt(&swap->grp[3].nat);
+ serializer->doInt(&swap->grp[eGrpSolvent].nat);
+ serializer->doInt(&swap->grp[eGrpSplit0].nat);
+ serializer->doBool(&swap->massw_split[eChannel0]);
+ serializer->doInt(&swap->grp[eGrpSplit1].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
{
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" };
for (int j = 0; j < DIM; ++j)
{
int n, nt;
- gmx_fio_do_int(fio, n);
- gmx_fio_do_int(fio, nt);
+ serializer->doInt(&n);
+ serializer->doInt(&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->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)
}
-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;
gmx::KeyValueTreeObjectBuilder paramsObj = paramsBuilder.rootObject();
/* Basic inputrec stuff */
- gmx_fio_do_int(fio, ir->eI);
+ serializer->doInt(&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 >= 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->doInt(&ir->cutoff_scheme);
if (file_version < 94)
{
ir->cutoff_scheme = 1 - ir->cutoff_scheme;
{
ir->cutoff_scheme = ecutsGROUP;
}
- 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(&ir->ns_type);
+ 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->doInt(&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))
{
// 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->doInt(&ir->coulombtype);
if (file_version >= 81)
{
- gmx_fio_do_int(fio, ir->coulomb_modifier);
+ serializer->doInt(&ir->coulomb_modifier);
}
else
{
ir->coulomb_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
}
- 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->doInt(&ir->vdwtype);
if (file_version >= 81)
{
- gmx_fio_do_int(fio, ir->vdw_modifier);
+ serializer->doInt(&ir->vdw_modifier);
}
else
{
ir->vdw_modifier = (ir->cutoff_scheme == ecutsVERLET ? eintmodPOTSHIFT : eintmodNONE);
}
- 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->doInt(&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->doInt(&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->doInt(&ir->ljpme_combination_rule);
}
- gmx_fio_do_gmx_bool(fio, ir->bContinuation);
- gmx_fio_do_int(fio, ir->etc);
+ serializer->doBool(&ir->bContinuation);
+ serializer->doInt(&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->doInt(&ir->epc);
+ serializer->doInt(&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->doInt(&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->doInt(&ir->efep);
+ do_fepvals(serializer, ir->fepvals, 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);
+ do_simtempvals(serializer, ir->simtempvals, ir->fepvals->n_lambda, file_version);
}
if (file_version >= 79)
{
- gmx_fio_do_gmx_bool(fio, ir->bExpanded);
+ serializer->doBool(&ir->bExpanded);
if (ir->bExpanded)
{
ir->bExpanded = TRUE;
}
if (ir->bExpanded)
{
- do_expandedvals(fio, ir->expandedvals, ir->fepvals, bRead, file_version);
+ do_expandedvals(serializer, ir->expandedvals, ir->fepvals, 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->doInt(&ir->eDisre);
+ serializer->doInt(&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->doInt(&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());
}
}
}
if (file_version >= tpxv_PullCoordTypeGeom)
{
- gmx_fio_do_gmx_bool(fio, ir->bPull);
+ serializer->doBool(&ir->bPull);
}
else
{
- gmx_fio_do_int(fio, ePullOld);
+ serializer->doInt(&ePullOld);
ir->bPull = (ePullOld > 0);
/* We removed the first ePull=ePullNo for the enum */
ePullOld -= 1;
}
if (ir->bPull)
{
- if (bRead)
+ if (serializer->reading())
{
snew(ir->pull, 1);
}
- do_pull(fio, ir->pull, bRead, file_version, ePullOld);
+ do_pull(serializer, ir->pull, 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);
}
- do_awh(fio, ir->awhParams, bRead, file_version);
+ do_awh(serializer, ir->awhParams, 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);
+ 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);
}
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.acc, ir->opts.ngacc);
}
- 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->doIntArray(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->doInt(&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);
+ serializer->doInt(&ir->eSwapCoords);
if (ir->eSwapCoords != eswapNO)
{
- 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 */
{
- 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)
+ serializer->doBool(&ir->bQMMM);
+ serializer->doInt(&ir->QMMMscheme);
+ serializer->doReal(&ir->scalefactor);
+ serializer->doInt(&ir->opts.ngQM);
+ if (serializer->reading())
{
snew(ir->opts.QMmethod, ir->opts.ngQM);
snew(ir->opts.QMbasis, 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);
+ serializer->doIntArray(ir->opts.QMmethod, ir->opts.ngQM);
+ serializer->doIntArray(ir->opts.QMbasis, ir->opts.ngQM);
+ serializer->doIntArray(ir->opts.QMcharge, ir->opts.ngQM);
+ serializer->doIntArray(ir->opts.QMmult, ir->opts.ngQM);
+ serializer->doBoolArray(ir->opts.bSH, ir->opts.ngQM);
+ serializer->doIntArray(ir->opts.CASorbitals, ir->opts.ngQM);
+ serializer->doIntArray(ir->opts.CASelectrons, ir->opts.ngQM);
+ serializer->doRealArray(ir->opts.SAon, ir->opts.ngQM);
+ serializer->doRealArray(ir->opts.SAoff, ir->opts.ngQM);
+ serializer->doIntArray(ir->opts.SAsteps, ir->opts.ngQM);
/* We leave in dummy i/o for removed parameters to avoid
* changing the tpr format for every QMMM change.
*/
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);
+ serializer->doIntArray(dummy.data(), ir->opts.ngQM);
+ serializer->doIntArray(dummy.data(), ir->opts.ngQM);
}
/* end of QMMM stuff */
}
if (file_version >= tpxv_GenericParamsForElectricField)
{
- gmx::FileIOXdrSerializer serializer(fio);
- if (bRead)
+ if (serializer->reading())
{
paramsObj.mergeObject(
- gmx::deserializeKeyValueTree(&serializer));
+ 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());
}
}
-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;
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);
+ serializer->doReal(&iparams->cubic.b0);
+ serializer->doReal(&iparams->cubic.kb);
+ serializer->doReal(&iparams->cubic.kcub);
break;
case F_CONNBONDS:
break;
case F_POLARIZATION:
- gmx_fio_do_real(fio, iparams->polarize.alpha);
+ 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);
+ serializer->doReal(&iparams->thole.rfac);
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);
+ serializer->doInt(&iparams->fbposres.geom);
+ serializer->doRvec(&iparams->fbposres.pos0);
+ serializer->doReal(&iparams->fbposres.r);
+ serializer->doReal(&iparams->fbposres.k);
break;
case F_CBTDIHS:
- gmx_fio_ndo_real(fio, iparams->cbtdihs.cbtcA, NR_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);
+ serializer->doRealArray(iparams->rbdihs.rbcA, NR_RBDIHS);
+ serializer->doRealArray(iparams->rbdihs.rbcB, NR_RBDIHS);
break;
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_VSITE2:
- gmx_fio_do_real(fio, iparams->vsite.a);
+ 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",
}
}
-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++)
}
}
- do_iparams(fio, ffparams->functype[i], &ffparams->iparams[i], bRead,
+ do_iparams(serializer, ffparams->functype[i], &ffparams->iparams[i],
file_version);
}
}
}
}
-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");
{
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);
+ do_ilist(serializer, &ilist);
if (file_version < 78 && j == F_SETTLE && ilist.size() > 0)
{
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))
{
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 do_blocka(gmx::ISerializer *serializer, t_blocka *block)
{
- gmx_fio_do_int(fio, block->nr);
- gmx_fio_do_int(fio, block->nra);
- if (bRead)
+ serializer->doInt(&block->nr);
+ serializer->doInt(&block->nra);
+ if (serializer->reading())
{
block->nalloc_index = block->nr+1;
snew(block->index, block->nalloc_index);
block->nalloc_a = block->nra;
snew(block->a, block->nalloc_a);
}
- gmx_fio_ndo_int(fio, block->index, block->nr+1);
- gmx_fio_ndo_int(fio, block->a, block->nra);
+ serializer->doIntArray(block->index, block->nr+1);
+ serializer->doIntArray(block->a, block->nra);
}
/* This is a primitive routine to make it possible to translate atomic numbers
}
-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->doInt(&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)
{
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;
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;
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
}
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,
+static void do_atomtypes(gmx::ISerializer *serializer, t_atomtypes *atomtypes,
int file_version)
{
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];
- gmx_fio_do_int(fio, symtab->nr);
+ serializer->doInt(&symtab->nr);
nr = symtab->nr;
- if (bRead)
+ 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;
symbuf = symbuf->next;
}
}
-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 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);
+ do_block(serializer, &molt->cgs);
/* This used to be in the atoms struct */
- do_blocka(fio, &molt->excls, bRead);
+ do_blocka(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 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)
{
- 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)
{
- 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 (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;
/* XDR binary topology file */
precision = sizeof(real);
- if (bRead)
+ std::string buf;
+ std::string fileTag;
+ if (serializer->reading())
{
- gmx_fio_do_string(fio, buf);
- if (std::strncmp(buf, "VERSION", 7) != 0)
+ 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",
- gmx_fio_getname(fio));
+ filename);
}
- gmx_fio_do_int(fio, precision);
+ serializer->doInt(&precision);
bDouble = (precision == sizeof(double));
if ((precision != sizeof(float)) && !bDouble)
{
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));
+ filename, 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, buf.c_str(), bDouble ? "double" : "single");
}
else
{
- snprintf(buf, STRLEN, "VERSION %s", gmx_version());
- gmx_fio_write_string(fio, buf);
+ buf = gmx::formatString("VERSION %s", gmx_version());
+ serializer->doString(&buf);
bDouble = (precision == sizeof(double));
gmx_fio_setprecision(fio, bDouble);
- gmx_fio_do_int(fio, precision);
- sprintf(file_tag, "%s", tpx_tag);
+ serializer->doInt(&precision);
+ fileTag = gmx::formatString("%s", 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);
+ 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 (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,
+ filename, tpx->fileVersion, fileTag.c_str(),
tpx_version, tpx_tag);
}
}
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);
+ 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);
}
- 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);
+ 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->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)
+static int do_tpx_body(gmx::ISerializer *serializer,
+ TpxFileHeader *tpx,
+ t_inputrec *ir,
+ t_state *state,
+ rvec *x,
+ rvec *v,
+ gmx_mtop_t *mtop)
{
int ePBC;
gmx_bool bPeriodicMols;
- if (!bRead)
+ 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 x==NULL and v!=NULL is not supported");
}
- if (bRead)
+ if (serializer->reading())
{
state->flags = 0;
init_gtc_state(state, tpx->ngtc, 0, 0);
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))
+#define do_test(serializer, b, p) if ((serializer)->reading() && ((p) != nullptr) && !(b)) gmx_fatal(FARGS, "No %s in input file",#p)
- 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);
}
}
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);
+ do_test(serializer, tpx->bTop, mtop);
if (tpx->bTop)
{
if (mtop)
{
- do_mtop(fio, mtop, bRead, tpx->fileVersion);
+ do_mtop(serializer, mtop, tpx->fileVersion);
}
else
{
gmx_mtop_t dum_top;
- do_mtop(fio, &dum_top, bRead, tpx->fileVersion);
+ do_mtop(serializer, &dum_top, tpx->fileVersion);
}
}
- do_test(fio, tpx->bX, x);
+ do_test(serializer, tpx->bX, x);
if (tpx->bX)
{
- if (bRead)
+ if (serializer->reading())
{
state->flags |= (1<<estX);
}
- 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);
}
- gmx_fio_ndo_rvec(fio, v, tpx->natoms);
+ if (!v)
+ {
+ std::vector<gmx::RVec> dummyVelocities(tpx->natoms);
+ serializer->doRvecArray(as_rvec_array(dummyVelocities.data()), tpx->natoms);
+ }
+ else
+ {
+ serializer->doRvecArray(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);
}
/* Starting with tpx version 26, we have the inputrec
ePBC = -1;
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;
bPeriodicMols = ir->bPeriodicMols;
}
- gmx_fio_do_int(fio, ePBC);
- gmx_fio_do_gmx_bool(fio, bPeriodicMols);
+ serializer->doInt(&ePBC);
+ serializer->doBool(&bPeriodicMols);
}
if (tpx->fileGeneration <= tpx_generation && ir)
{
- do_inputrec(fio, ir, bRead, tpx->fileVersion);
+ do_inputrec(serializer, ir, tpx->fileVersion);
if (tpx->fileVersion < 51)
{
set_box_rel(ir, state);
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;
}
}
- if (bRead)
+ if (serializer->reading())
{
if (tpx->bIr && ir)
{
t_fileio *fio;
fio = open_tpx(fileName, "r");
- TpxFileHeader tpx;
- do_tpxheader(fio, &tpx, true, canReadTopologyOnly);
+ gmx::FileIOXdrSerializer serializer(fio);
+
+ TpxFileHeader tpx;
+ do_tpxheader(&serializer, &tpx, fileName, fio, canReadTopologyOnly);
close_tpx(fio);
return tpx;
}
TpxFileHeader tpx = populateTpxHeader(*state,
ir,
mtop);
- do_tpxheader(fio,
+
+ gmx::FileIOXdrSerializer serializer(fio);
+ do_tpxheader(&serializer,
&tpx,
- false,
+ fn,
+ fio,
ir == nullptr);
- do_tpx_body(fio,
+ do_tpx_body(&serializer,
&tpx,
- false,
const_cast<t_inputrec *>(ir),
const_cast<t_state *>(state), nullptr, nullptr,
const_cast<gmx_mtop_t *>(mtop));
void read_tpx_state(const char *fn,
t_inputrec *ir, t_state *state, gmx_mtop_t *mtop)
{
- t_fileio *fio;
+ t_fileio *fio;
- TpxFileHeader tpx;
+ TpxFileHeader tpx;
fio = open_tpx(fn, "r");
- do_tpxheader(fio,
+ gmx::FileIOXdrSerializer serializer(fio);
+ do_tpxheader(&serializer,
&tpx,
- true,
+ fn,
+ fio,
ir == nullptr);
- do_tpx_body(fio,
+ do_tpx_body(&serializer,
&tpx,
- true,
ir,
state,
nullptr,
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;
+ int ePBC;
- TpxFileHeader tpx;
+ TpxFileHeader tpx;
fio = open_tpx(fn, "r");
- do_tpxheader(fio,
+ gmx::FileIOXdrSerializer serializer(fio);
+ do_tpxheader(&serializer,
&tpx,
- true,
+ fn,
+ fio,
ir == nullptr);
- ePBC = do_tpx_body(fio,
+ ePBC = do_tpx_body(&serializer,
&tpx,
- true, ir, &state, x, v, mtop);
+ ir, &state, x, v, mtop);
close_tpx(fio);
if (mtop != nullptr && natoms != nullptr)
{
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff