#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/smalloc.h"
-struct gmx_mdoutf {
- t_fileio *fp_trn;
- t_fileio *fp_xtc;
- gmx_tng_trajectory_t tng;
- gmx_tng_trajectory_t tng_low_prec;
- int x_compression_precision; /* only used by XTC output */
- ener_file_t fp_ene;
- const char *fn_cpt;
- gmx_bool bKeepAndNumCPT;
- int eIntegrator;
- gmx_bool bExpanded;
- int elamstats;
- int simulation_part;
- FILE *fp_dhdl;
- int natoms_global;
- int natoms_x_compressed;
- SimulationGroups *groups; /* for compressed position writing */
- gmx_wallcycle_t wcycle;
- rvec *f_global;
- gmx::IMDOutputProvider *outputProvider;
- const gmx::MdModulesNotifier *mdModulesNotifier;
+struct gmx_mdoutf
+{
+ t_fileio* fp_trn;
+ t_fileio* fp_xtc;
+ gmx_tng_trajectory_t tng;
+ gmx_tng_trajectory_t tng_low_prec;
+ int x_compression_precision; /* only used by XTC output */
+ ener_file_t fp_ene;
+ const char* fn_cpt;
+ gmx_bool bKeepAndNumCPT;
+ int eIntegrator;
+ gmx_bool bExpanded;
+ int elamstats;
+ int simulation_part;
+ FILE* fp_dhdl;
+ int natoms_global;
+ int natoms_x_compressed;
+ SimulationGroups* groups; /* for compressed position writing */
+ gmx_wallcycle_t wcycle;
+ rvec* f_global;
+ gmx::IMDOutputProvider* outputProvider;
+ const gmx::MdModulesNotifier* mdModulesNotifier;
};
-gmx_mdoutf_t init_mdoutf(FILE *fplog, int nfile, const t_filenm fnm[],
- const gmx::MdrunOptions &mdrunOptions,
- const t_commrec *cr,
- gmx::IMDOutputProvider *outputProvider,
- const gmx::MdModulesNotifier &mdModulesNotifier,
- const t_inputrec *ir, gmx_mtop_t *top_global,
- const gmx_output_env_t *oenv, gmx_wallcycle_t wcycle,
- const gmx::StartingBehavior startingBehavior)
+gmx_mdoutf_t init_mdoutf(FILE* fplog,
+ int nfile,
+ const t_filenm fnm[],
+ const gmx::MdrunOptions& mdrunOptions,
+ const t_commrec* cr,
+ gmx::IMDOutputProvider* outputProvider,
+ const gmx::MdModulesNotifier& mdModulesNotifier,
+ const t_inputrec* ir,
+ gmx_mtop_t* top_global,
+ const gmx_output_env_t* oenv,
+ gmx_wallcycle_t wcycle,
+ const gmx::StartingBehavior startingBehavior)
{
- gmx_mdoutf_t of;
- const char *appendMode = "a+", *writeMode = "w+", *filemode;
- gmx_bool bCiteTng = FALSE;
- int i;
- bool restartWithAppending = (startingBehavior == gmx::StartingBehavior::RestartWithAppending);
+ gmx_mdoutf_t of;
+ const char * appendMode = "a+", *writeMode = "w+", *filemode;
+ gmx_bool bCiteTng = FALSE;
+ int i;
+ bool restartWithAppending = (startingBehavior == gmx::StartingBehavior::RestartWithAppending);
snew(of, 1);
filemode = restartWithAppending ? appendMode : writeMode;
- if (EI_DYNAMICS(ir->eI) &&
- ir->nstxout_compressed > 0)
+ if (EI_DYNAMICS(ir->eI) && ir->nstxout_compressed > 0)
{
- const char *filename;
+ const char* filename;
filename = ftp2fn(efCOMPRESSED, nfile, fnm);
switch (fn2ftp(filename))
{
- case efXTC:
- of->fp_xtc = open_xtc(filename, filemode);
- break;
+ case efXTC: of->fp_xtc = open_xtc(filename, filemode); break;
case efTNG:
gmx_tng_open(filename, filemode[0], &of->tng_low_prec);
if (filemode[0] == 'w')
}
bCiteTng = TRUE;
break;
- default:
- gmx_incons("Invalid reduced precision file format");
+ default: gmx_incons("Invalid reduced precision file format");
}
}
- if ((EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI)) &&
- (!GMX_FAHCORE &&
- !(EI_DYNAMICS(ir->eI) &&
- ir->nstxout == 0 &&
- ir->nstvout == 0 &&
- ir->nstfout == 0)
- )
- )
+ if ((EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI))
+ && (!GMX_FAHCORE
+ && !(EI_DYNAMICS(ir->eI) && ir->nstxout == 0 && ir->nstvout == 0 && ir->nstfout == 0)))
{
- const char *filename;
+ const char* filename;
filename = ftp2fn(efTRN, nfile, fnm);
switch (fn2ftp(filename))
{
/* If there is no uncompressed coordinate output and
there is compressed TNG output write forces
and/or velocities to the TNG file instead. */
- if (ir->nstxout != 0 || ir->nstxout_compressed == 0 ||
- !of->tng_low_prec)
+ if (ir->nstxout != 0 || ir->nstxout_compressed == 0 || !of->tng_low_prec)
{
of->fp_trn = gmx_trr_open(filename, filemode);
}
}
bCiteTng = TRUE;
break;
- default:
- gmx_incons("Invalid full precision file format");
+ default: gmx_incons("Invalid full precision file format");
}
}
if (EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI))
}
of->fn_cpt = opt2fn("-cpo", nfile, fnm);
- if ((ir->efep != efepNO || ir->bSimTemp) && ir->fepvals->nstdhdl > 0 &&
- (ir->fepvals->separate_dhdl_file == esepdhdlfileYES ) &&
- EI_DYNAMICS(ir->eI))
+ if ((ir->efep != efepNO || ir->bSimTemp) && ir->fepvals->nstdhdl > 0
+ && (ir->fepvals->separate_dhdl_file == esepdhdlfileYES) && EI_DYNAMICS(ir->eI))
{
if (restartWithAppending)
{
return of->fp_ene;
}
-FILE *mdoutf_get_fp_dhdl(gmx_mdoutf_t of)
+FILE* mdoutf_get_fp_dhdl(gmx_mdoutf_t of)
{
return of->fp_dhdl;
}
return of->wcycle;
}
-void mdoutf_write_to_trajectory_files(FILE *fplog, const t_commrec *cr,
- gmx_mdoutf_t of,
- int mdof_flags,
- int natoms,
- int64_t step, double t,
- t_state *state_local, t_state *state_global,
- ObservablesHistory *observablesHistory,
+void mdoutf_write_to_trajectory_files(FILE* fplog,
+ const t_commrec* cr,
+ gmx_mdoutf_t of,
+ int mdof_flags,
+ int natoms,
+ int64_t step,
+ double t,
+ t_state* state_local,
+ t_state* state_global,
+ ObservablesHistory* observablesHistory,
gmx::ArrayRef<gmx::RVec> f_local)
{
- rvec *f_global;
+ rvec* f_global;
if (DOMAINDECOMP(cr))
{
f_global = of->f_global;
if (mdof_flags & MDOF_F)
{
- dd_collect_vec(cr->dd, state_local, f_local, gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec *>(f_global), f_local.size()));
+ dd_collect_vec(cr->dd, state_local, f_local,
+ gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(f_global), f_local.size()));
}
}
else
/* We have the whole state locally: copy the local state pointer */
state_global = state_local;
- f_global = as_rvec_array(f_local.data());
+ f_global = as_rvec_array(f_local.data());
}
if (MASTER(cr))
fflush_tng(of->tng);
fflush_tng(of->tng_low_prec);
ivec one_ivec = { 1, 1, 1 };
- write_checkpoint(of->fn_cpt, of->bKeepAndNumCPT,
- fplog, cr,
+ write_checkpoint(of->fn_cpt, of->bKeepAndNumCPT, fplog, cr,
DOMAINDECOMP(cr) ? cr->dd->nc : one_ivec,
- DOMAINDECOMP(cr) ? cr->dd->nnodes : cr->nnodes,
- of->eIntegrator, of->simulation_part,
- of->bExpanded, of->elamstats, step, t,
+ DOMAINDECOMP(cr) ? cr->dd->nnodes : cr->nnodes, of->eIntegrator,
+ of->simulation_part, of->bExpanded, of->elamstats, step, t,
state_global, observablesHistory, *(of->mdModulesNotifier));
}
if (mdof_flags & (MDOF_X | MDOF_V | MDOF_F))
{
- const rvec *x = (mdof_flags & MDOF_X) ? state_global->x.rvec_array() : nullptr;
- const rvec *v = (mdof_flags & MDOF_V) ? state_global->v.rvec_array() : nullptr;
- const rvec *f = (mdof_flags & MDOF_F) ? f_global : nullptr;
+ const rvec* x = (mdof_flags & MDOF_X) ? state_global->x.rvec_array() : nullptr;
+ const rvec* v = (mdof_flags & MDOF_V) ? state_global->v.rvec_array() : nullptr;
+ const rvec* f = (mdof_flags & MDOF_F) ? f_global : nullptr;
if (of->fp_trn)
{
gmx_trr_write_frame(of->fp_trn, step, t, state_local->lambda[efptFEP],
- state_local->box, natoms,
- x, v, f);
+ state_local->box, natoms, x, v, f);
if (gmx_fio_flush(of->fp_trn) != 0)
{
gmx_file("Cannot write trajectory; maybe you are out of disk space?");
else if (of->tng)
{
gmx_fwrite_tng(of->tng, FALSE, step, t, state_local->lambda[efptFEP],
- state_local->box,
- natoms,
- x, v, f);
+ state_local->box, natoms, x, v, f);
}
/* If only a TNG file is open for compressed coordinate output (no uncompressed
coordinate output) also write forces and velocities to it. */
else if (of->tng_low_prec)
{
gmx_fwrite_tng(of->tng_low_prec, FALSE, step, t, state_local->lambda[efptFEP],
- state_local->box,
- natoms,
- x, v, f);
+ state_local->box, natoms, x, v, f);
}
}
if (mdof_flags & MDOF_X_COMPRESSED)
{
- rvec *xxtc = nullptr;
+ rvec* xxtc = nullptr;
if (of->natoms_x_compressed == of->natoms_global)
{
}
}
}
- if (write_xtc(of->fp_xtc, of->natoms_x_compressed, step, t,
- state_local->box, xxtc, of->x_compression_precision) == 0)
+ if (write_xtc(of->fp_xtc, of->natoms_x_compressed, step, t, state_local->box, xxtc,
+ of->x_compression_precision)
+ == 0)
{
gmx_fatal(FARGS,
"XTC error. This indicates you are out of disk space, or a "
"simulation with major instabilities resulting in coordinates "
"that are NaN or too large to be represented in the XTC format.\n");
}
- gmx_fwrite_tng(of->tng_low_prec,
- TRUE,
- step,
- t,
- state_local->lambda[efptFEP],
- state_local->box,
- of->natoms_x_compressed,
- xxtc,
- nullptr,
- nullptr);
+ gmx_fwrite_tng(of->tng_low_prec, TRUE, step, t, state_local->lambda[efptFEP],
+ state_local->box, of->natoms_x_compressed, xxtc, nullptr, nullptr);
if (of->natoms_x_compressed != of->natoms_global)
{
sfree(xxtc);
}
}
- if (mdof_flags & (MDOF_BOX | MDOF_LAMBDA) && !(mdof_flags & (MDOF_X | MDOF_V | MDOF_F)) )
+ if (mdof_flags & (MDOF_BOX | MDOF_LAMBDA) && !(mdof_flags & (MDOF_X | MDOF_V | MDOF_F)))
{
if (of->tng)
{
real lambda = -1;
- rvec *box = nullptr;
+ rvec* box = nullptr;
if (mdof_flags & MDOF_BOX)
{
box = state_local->box;
{
lambda = state_local->lambda[efptFEP];
}
- gmx_fwrite_tng(of->tng, FALSE, step, t, lambda,
- box, natoms,
- nullptr, nullptr, nullptr);
+ gmx_fwrite_tng(of->tng, FALSE, step, t, lambda, box, natoms, nullptr, nullptr, nullptr);
}
}
- if (mdof_flags & (MDOF_BOX_COMPRESSED | MDOF_LAMBDA_COMPRESSED) && !(mdof_flags & (MDOF_X_COMPRESSED)) )
+ if (mdof_flags & (MDOF_BOX_COMPRESSED | MDOF_LAMBDA_COMPRESSED)
+ && !(mdof_flags & (MDOF_X_COMPRESSED)))
{
if (of->tng_low_prec)
{
real lambda = -1;
- rvec *box = nullptr;
+ rvec* box = nullptr;
if (mdof_flags & MDOF_BOX_COMPRESSED)
{
box = state_local->box;
{
lambda = state_local->lambda[efptFEP];
}
- gmx_fwrite_tng(of->tng_low_prec, FALSE, step, t, lambda,
- box, natoms,
- nullptr, nullptr, nullptr);
+ gmx_fwrite_tng(of->tng_low_prec, FALSE, step, t, lambda, box, natoms, nullptr,
+ nullptr, nullptr);
}
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff