/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* 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 "trnio.h"
-#include "xtcio.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/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;
+ t_fileio *fp_xtc;
+ tng_trajectory_t tng;
+ 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;
+ FILE *fp_field;
+ 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,
- 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;
+ gmx_mdoutf_t of;
char filemode[3];
- gmx_bool bAppendFiles;
+ gmx_bool bAppendFiles, bCiteTng = FALSE;
+ int i;
snew(of, 1);
- of->fp_trn = NULL;
- of->fp_ene = NULL;
- of->fp_xtc = NULL;
- of->fp_dhdl = NULL;
- of->fp_field = NULL;
+ of->fp_trn = NULL;
+ of->fp_ene = NULL;
+ of->fp_xtc = NULL;
+ of->tng = NULL;
+ of->tng_low_prec = NULL;
+ 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))
{
#endif
)
{
- of->fp_trn = open_trn(ftp2fn(efTRN, nfile, fnm), filemode);
+ const char *filename;
+ filename = ftp2fn(efTRN, nfile, fnm);
+ switch (fn2ftp(filename))
+ {
+ case efTRR:
+ case efTRN:
+ of->fp_trn = open_trn(filename, filemode);
+ break;
+ case efTNG:
+ gmx_tng_open(filename, filemode[0], &of->tng);
+ if (filemode[0] == 'w')
+ {
+ gmx_tng_prepare_md_writing(of->tng, top_global, ir);
+ }
+ bCiteTng = TRUE;
+ break;
+ default:
+ gmx_incons("Invalid full precision file format");
+ }
}
if (EI_DYNAMICS(ir->eI) &&
- ir->nstxtcout > 0)
+ ir->nstxout_compressed > 0)
{
- of->fp_xtc = open_xtc(ftp2fn(efXTC, nfile, fnm), filemode);
- of->xtc_prec = ir->xtcprec;
+ const char *filename;
+ filename = ftp2fn(efCOMPRESSED, nfile, fnm);
+ switch (fn2ftp(filename))
+ {
+ 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')
+ {
+ gmx_tng_prepare_low_prec_writing(of->tng_low_prec, top_global, ir);
+ }
+ bCiteTng = TRUE;
+ break;
+ default:
+ gmx_incons("Invalid reduced precision file format");
+ }
}
if (EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI))
{
"E (V/nm)", oenv);
}
}
+
+ /* Set up atom counts so they can be passed to actual
+ 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_x_compressed = 0;
+ for (i = 0; (i < top_global->natoms); i++)
+ {
+ if (ggrpnr(of->groups, egcCompressedX, i) == 0)
+ {
+ of->natoms_x_compressed++;
+ }
+ }
+ }
+
+ if (bCiteTng)
+ {
+ please_cite(fplog, "Lundborg2014");
}
return of;
}
-void done_mdoutf(gmx_mdoutf_t *of)
+FILE *mdoutf_get_fp_field(gmx_mdoutf_t of)
+{
+ return of->fp_field;
+}
+
+ener_file_t mdoutf_get_fp_ene(gmx_mdoutf_t of)
+{
+ return of->fp_ene;
+}
+
+FILE *mdoutf_get_fp_dhdl(gmx_mdoutf_t of)
+{
+ return of->fp_dhdl;
+}
+
+gmx_wallcycle_t mdoutf_get_wcycle(gmx_mdoutf_t of)
+{
+ return of->wcycle;
+}
+
+void mdoutf_write_to_trajectory_files(FILE *fplog, t_commrec *cr,
+ gmx_mdoutf_t of,
+ int mdof_flags,
+ gmx_mtop_t *top_global,
+ gmx_int64_t step, double t,
+ t_state *state_local, t_state *state_global,
+ rvec *f_local, rvec *f_global)
+{
+ rvec *local_v;
+ rvec *global_v;
+
+ /* MRS -- defining these variables is to manage the difference
+ * between half step and full step velocities, but there must be a better way . . . */
+
+ local_v = state_local->v;
+ global_v = state_global->v;
+
+ if (DOMAINDECOMP(cr))
+ {
+ if (mdof_flags & MDOF_CPT)
+ {
+ dd_collect_state(cr->dd, state_local, state_global);
+ }
+ else
+ {
+ if (mdof_flags & (MDOF_X | MDOF_X_COMPRESSED))
+ {
+ dd_collect_vec(cr->dd, state_local, state_local->x,
+ state_global->x);
+ }
+ if (mdof_flags & MDOF_V)
+ {
+ dd_collect_vec(cr->dd, state_local, local_v,
+ global_v);
+ }
+ }
+ if (mdof_flags & MDOF_F)
+ {
+ dd_collect_vec(cr->dd, state_local, f_local, f_global);
+ }
+ }
+ else
+ {
+ if (mdof_flags & MDOF_CPT)
+ {
+ /* All pointers in state_local are equal to state_global,
+ * but we need to copy the non-pointer entries.
+ */
+ state_global->lambda = state_local->lambda;
+ state_global->veta = state_local->veta;
+ state_global->vol0 = state_local->vol0;
+ copy_mat(state_local->box, state_global->box);
+ copy_mat(state_local->boxv, state_global->boxv);
+ copy_mat(state_local->svir_prev, state_global->svir_prev);
+ copy_mat(state_local->fvir_prev, state_global->fvir_prev);
+ copy_mat(state_local->pres_prev, state_global->pres_prev);
+ }
+ }
+
+ if (MASTER(cr))
+ {
+ if (mdof_flags & MDOF_CPT)
+ {
+ fflush_tng(of->tng);
+ fflush_tng(of->tng_low_prec);
+ write_checkpoint(of->fn_cpt, of->bKeepAndNumCPT,
+ fplog, cr, of->eIntegrator, of->simulation_part,
+ of->bExpanded, of->elamstats, step, t, state_global);
+ }
+
+ if (mdof_flags & (MDOF_X | MDOF_V | MDOF_F))
+ {
+ if (of->fp_trn)
+ {
+ fwrite_trn(of->fp_trn, step, t, state_local->lambda[efptFEP],
+ state_local->box, top_global->natoms,
+ (mdof_flags & MDOF_X) ? state_global->x : NULL,
+ (mdof_flags & MDOF_V) ? global_v : NULL,
+ (mdof_flags & MDOF_F) ? f_global : NULL);
+ if (gmx_fio_flush(of->fp_trn) != 0)
+ {
+ gmx_file("Cannot write trajectory; maybe you are out of disk space?");
+ }
+ }
+
+ gmx_fwrite_tng(of->tng, FALSE, step, t, state_local->lambda[efptFEP],
+ (const rvec *) state_local->box,
+ top_global->natoms,
+ (mdof_flags & MDOF_X) ? (const rvec *) state_global->x : NULL,
+ (mdof_flags & MDOF_V) ? (const rvec *) global_v : NULL,
+ (mdof_flags & MDOF_F) ? (const rvec *) f_global : NULL);
+ }
+ if (mdof_flags & MDOF_X_COMPRESSED)
+ {
+ rvec *xxtc = NULL;
+
+ if (of->natoms_x_compressed == of->natoms_global)
+ {
+ /* We are writing the positions of all of the atoms to
+ the compressed output */
+ xxtc = state_global->x;
+ }
+ else
+ {
+ /* We are writing the positions of only a subset of
+ the atoms to the compressed output, so we have to
+ make a copy of the subset of coordinates. */
+ int i, j;
+
+ snew(xxtc, of->natoms_x_compressed);
+ for (i = 0, j = 0; (i < of->natoms_global); i++)
+ {
+ if (ggrpnr(of->groups, egcCompressedX, i) == 0)
+ {
+ copy_rvec(state_global->x[i], xxtc[j++]);
+ }
+ }
+ }
+ 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 - maybe you are out of disk space?");
+ }
+ gmx_fwrite_tng(of->tng_low_prec,
+ TRUE,
+ step,
+ t,
+ state_local->lambda[efptFEP],
+ (const rvec *) state_local->box,
+ of->natoms_x_compressed,
+ (const rvec *) xxtc,
+ NULL,
+ NULL);
+ if (of->natoms_x_compressed != of->natoms_global)
+ {
+ sfree(xxtc);
+ }
+ }
+ }
+}
+
+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);
+
sfree(of);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff