* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+#include "gmxpre.h"
+
#include "mdoutf.h"
-#include "gromacs/legacyheaders/xvgr.h"
+#include "gromacs/fileio/tngio.h"
+#include "gromacs/fileio/trajectory_writing.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/xtcio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/domdec.h"
#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/smalloc.h"
#include "gromacs/legacyheaders/mvdata.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "trnio.h"
-#include "xtcio.h"
-#include "tngio.h"
-#include "trajectory_writing.h"
-#include "checkpoint.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
struct gmx_mdoutf {
t_fileio *fp_trn;
int natoms_global;
int natoms_x_compressed;
gmx_groups_t *groups; /* for compressed position writing */
+ gmx_wallcycle_t wcycle;
};
-gmx_mdoutf_t init_mdoutf(int nfile, const t_filenm fnm[], int mdrun_flags,
- const t_commrec *cr, const t_inputrec *ir,
- gmx_mtop_t *top_global,
- const output_env_t oenv)
+gmx_mdoutf_t init_mdoutf(FILE *fplog, int nfile, const t_filenm fnm[],
+ int mdrun_flags, const t_commrec *cr,
+ const t_inputrec *ir, gmx_mtop_t *top_global,
+ const output_env_t oenv, gmx_wallcycle_t wcycle)
{
gmx_mdoutf_t of;
char filemode[3];
- gmx_bool bAppendFiles;
+ gmx_bool bAppendFiles, bCiteTng = FALSE;
int i;
snew(of, 1);
of->fp_dhdl = NULL;
of->fp_field = NULL;
- of->eIntegrator = ir->eI;
- of->bExpanded = ir->bExpanded;
- of->elamstats = ir->expandedvals->elamstats;
- of->simulation_part = ir->simulation_part;
+ of->eIntegrator = ir->eI;
+ of->bExpanded = ir->bExpanded;
+ of->elamstats = ir->expandedvals->elamstats;
+ of->simulation_part = ir->simulation_part;
of->x_compression_precision = ir->x_compression_precision;
+ of->wcycle = wcycle;
if (MASTER(cr))
{
{
gmx_tng_prepare_md_writing(of->tng, top_global, ir);
}
+ bCiteTng = TRUE;
break;
default:
gmx_incons("Invalid full precision file format");
{
gmx_tng_prepare_low_prec_writing(of->tng_low_prec, top_global, ir);
}
+ bCiteTng = TRUE;
break;
default:
gmx_incons("Invalid reduced precision file format");
trajectory-writing routines later. Also, XTC writing needs
to know what (and how many) atoms might be in the XTC
groups, and how to look up later which ones they are. */
- of->natoms_global = top_global->natoms;
- of->groups = &top_global->groups;
+ of->natoms_global = top_global->natoms;
+ of->groups = &top_global->groups;
of->natoms_x_compressed = 0;
for (i = 0; (i < top_global->natoms); i++)
{
}
}
+ if (bCiteTng)
+ {
+ please_cite(fplog, "Lundborg2014");
+ }
+
return of;
}
return of->fp_dhdl;
}
-static void moveit(t_commrec *cr, rvec xx[])
+gmx_wallcycle_t mdoutf_get_wcycle(gmx_mdoutf_t of)
{
- if (!xx)
- {
- return;
- }
-
- move_rvecs(cr, FALSE, FALSE, xx, NULL, (cr->nnodes-cr->npmenodes)-1, NULL);
+ return of->wcycle;
}
void mdoutf_write_to_trajectory_files(FILE *fplog, t_commrec *cr,
rvec *local_v;
rvec *global_v;
-#define MX(xvf) moveit(cr, xvf)
-
/* MRS -- defining these variables is to manage the difference
* between half step and full step velocities, but there must be a better way . . . */
copy_mat(state_local->fvir_prev, state_global->fvir_prev);
copy_mat(state_local->pres_prev, state_global->pres_prev);
}
- if (cr->nnodes > 1)
- {
- /* Particle decomposition, collect the data on the master node */
- if (mdof_flags & MDOF_CPT)
- {
- if (state_local->flags & (1<<estX))
- {
- MX(state_global->x);
- }
- if (state_local->flags & (1<<estV))
- {
- MX(state_global->v);
- }
- if (state_local->flags & (1<<estSDX))
- {
- MX(state_global->sd_X);
- }
- if (state_global->nrngi > 1)
- {
- if (state_local->flags & (1<<estLD_RNG))
- {
-#ifdef GMX_MPI
- MPI_Gather(state_local->ld_rng,
- state_local->nrng*sizeof(state_local->ld_rng[0]), MPI_BYTE,
- state_global->ld_rng,
- state_local->nrng*sizeof(state_local->ld_rng[0]), MPI_BYTE,
- MASTERRANK(cr), cr->mpi_comm_mygroup);
-#endif
- }
- if (state_local->flags & (1<<estLD_RNGI))
- {
-#ifdef GMX_MPI
- MPI_Gather(state_local->ld_rngi,
- sizeof(state_local->ld_rngi[0]), MPI_BYTE,
- state_global->ld_rngi,
- sizeof(state_local->ld_rngi[0]), MPI_BYTE,
- MASTERRANK(cr), cr->mpi_comm_mygroup);
-#endif
- }
- }
- }
- else
- {
- if (mdof_flags & (MDOF_X | MDOF_X_COMPRESSED))
- {
- MX(state_global->x);
- }
- if (mdof_flags & MDOF_V)
- {
- MX(global_v);
- }
- }
- if (mdof_flags & MDOF_F)
- {
- MX(f_global);
- }
- }
}
if (MASTER(cr))
int i, j;
snew(xxtc, of->natoms_x_compressed);
- for (i = 0, j = 0; (i < of->natoms_x_compressed); i++)
+ for (i = 0, j = 0; (i < of->natoms_global); i++)
{
if (ggrpnr(of->groups, egcCompressedX, i) == 0)
{
}
}
+void mdoutf_tng_close(gmx_mdoutf_t of)
+{
+ if (of->tng || of->tng_low_prec)
+ {
+ wallcycle_start(of->wcycle, ewcTRAJ);
+ gmx_tng_close(&of->tng);
+ gmx_tng_close(&of->tng_low_prec);
+ wallcycle_stop(of->wcycle, ewcTRAJ);
+ }
+}
+
void done_mdoutf(gmx_mdoutf_t of)
{
if (of->fp_ene != NULL)
{
gmx_fio_fclose(of->fp_field);
}
+
gmx_tng_close(&of->tng);
gmx_tng_close(&of->tng_low_prec);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff