-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
- *
+/*
*
* This source code is part of
*
gmx_bool bDoDHDL = FALSE, bDoFEP = FALSE, bDoExpanded = FALSE;
gmx_bool do_ene, do_log, do_verbose, bRerunWarnNoV = TRUE,
bForceUpdate = FALSE, bCPT;
- int mdof_flags;
gmx_bool bMasterState;
int force_flags, cglo_flags;
tensor force_vir, shake_vir, total_vir, tmp_vir, pres;
df_history_t df_history;
t_state *state = NULL;
rvec *f_global = NULL;
- int n_xtc = -1;
- rvec *x_xtc = NULL;
gmx_enerdata_t *enerd;
rvec *f = NULL;
gmx_global_stat_t gstat;
lamnew = ExpandedEnsembleDynamics(fplog, ir, enerd, state, &MassQ, &df_history, step, mcrng, state->v, mdatoms);
}
- /* ################## START TRAJECTORY OUTPUT ################# */
/* Now we have the energies and forces corresponding to the
* coordinates at time t. We must output all of this before
* the update.
- * for RerunMD t is read from input trajectory
*/
- mdof_flags = 0;
- if (do_per_step(step, ir->nstxout))
- {
- mdof_flags |= MDOF_X;
- }
- if (do_per_step(step, ir->nstvout))
- {
- mdof_flags |= MDOF_V;
- }
- if (do_per_step(step, ir->nstfout))
- {
- mdof_flags |= MDOF_F;
- }
- if (do_per_step(step, ir->nstxtcout))
- {
- mdof_flags |= MDOF_XTC;
- }
- if (bCPT)
- {
- mdof_flags |= MDOF_CPT;
- }
- ;
-
-#if defined(GMX_FAHCORE) || defined(GMX_WRITELASTSTEP)
- if (bLastStep)
- {
- /* Enforce writing positions and velocities at end of run */
- mdof_flags |= (MDOF_X | MDOF_V);
- }
-#endif
-#ifdef GMX_FAHCORE
- if (MASTER(cr))
- {
- fcReportProgress( ir->nsteps, step );
- }
-
- /* sync bCPT and fc record-keeping */
- if (bCPT && MASTER(cr))
- {
- fcRequestCheckPoint();
- }
-#endif
-
- if (mdof_flags != 0)
- {
- wallcycle_start(wcycle, ewcTRAJ);
- if (bCPT)
- {
- if (state->flags & (1<<estLD_RNG))
- {
- get_stochd_state(upd, state);
- }
- if (state->flags & (1<<estMC_RNG))
- {
- get_mc_state(mcrng, state);
- }
- if (MASTER(cr))
- {
- if (bSumEkinhOld)
- {
- state_global->ekinstate.bUpToDate = FALSE;
- }
- else
- {
- update_ekinstate(&state_global->ekinstate, ekind);
- state_global->ekinstate.bUpToDate = TRUE;
- }
- update_energyhistory(&state_global->enerhist, mdebin);
- if (ir->efep != efepNO || ir->bSimTemp)
- {
- state_global->fep_state = state->fep_state; /* MRS: seems kludgy. The code should be
- structured so this isn't necessary.
- Note this reassignment is only necessary
- for single threads.*/
- copy_df_history(&state_global->dfhist, &df_history);
- }
- }
- }
- write_traj(fplog, cr, outf, mdof_flags, top_global,
- step, t, state, state_global, f, f_global, &n_xtc, &x_xtc);
- if (bCPT)
- {
- nchkpt++;
- bCPT = FALSE;
- }
- debug_gmx();
- if (bLastStep && step_rel == ir->nsteps &&
- (Flags & MD_CONFOUT) && MASTER(cr) &&
- !bRerunMD)
- {
- /* x and v have been collected in write_traj,
- * because a checkpoint file will always be written
- * at the last step.
- */
- fprintf(stderr, "\nWriting final coordinates.\n");
- if (fr->bMolPBC)
- {
- /* Make molecules whole only for confout writing */
- do_pbc_mtop(fplog, ir->ePBC, state->box, top_global, state_global->x);
- }
- write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm),
- *top_global->name, top_global,
- state_global->x, state_global->v,
- ir->ePBC, state->box);
- debug_gmx();
- }
- wallcycle_stop(wcycle, ewcTRAJ);
- }
+ do_trajectory_writing(fplog, cr, nfile, fnm, step, step_rel, t,
+ ir, state, state_global, top_global, fr, upd,
+ outf, mdebin, ekind, df_history, f, f_global,
+ wcycle, mcrng, &nchkpt,
+ bCPT, bRerunMD, bLastStep, (Flags & MD_CONFOUT),
+ bSumEkinhOld);
/* kludge -- virial is lost with restart for NPT control. Must restart */
if (bStartingFromCpt && bVV)
copy_mat(state->svir_prev, shake_vir);
copy_mat(state->fvir_prev, force_vir);
}
- /* ################## END TRAJECTORY OUTPUT ################ */
/* Determine the wallclock run time up till now */
run_time = gmx_gettime() - (double)runtime->real;
--- /dev/null
+/*
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * VERSION 3.2.0
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2004, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+#ifdef HAVE_CONFIG_H
+#include <config.h>
+#endif
+
+#include "typedefs.h"
+#include "smalloc.h"
+#include "sysstuff.h"
+#include "vec.h"
+#include "sim_util.h"
+#include "gmx_wallcycle.h"
+#include "mdrun.h"
+#include "confio.h"
+
+void
+do_trajectory_writing(FILE *fplog,
+ t_commrec *cr,
+ int nfile,
+ const t_filenm fnm[],
+ gmx_large_int_t step,
+ gmx_large_int_t step_rel,
+ double t,
+ t_inputrec *ir,
+ t_state *state,
+ t_state *state_global,
+ gmx_mtop_t *top_global,
+ t_forcerec *fr,
+ gmx_update_t upd,
+ gmx_mdoutf_t *outf,
+ t_mdebin *mdebin,
+ gmx_ekindata_t *ekind,
+ df_history_t df_history,
+ rvec *f,
+ rvec *f_global,
+ gmx_wallcycle_t wcycle,
+ gmx_rng_t mcrng,
+ int *nchkpt,
+ gmx_bool bCPT,
+ gmx_bool bRerunMD,
+ gmx_bool bLastStep,
+ gmx_bool bDoConfOut,
+ gmx_bool bSumEkinhOld
+ )
+{
+ int mdof_flags;
+ int n_xtc = -1;
+ rvec *x_xtc = NULL;
+
+ mdof_flags = 0;
+ if (do_per_step(step, ir->nstxout))
+ {
+ mdof_flags |= MDOF_X;
+ }
+ if (do_per_step(step, ir->nstvout))
+ {
+ mdof_flags |= MDOF_V;
+ }
+ if (do_per_step(step, ir->nstfout))
+ {
+ mdof_flags |= MDOF_F;
+ }
+ if (do_per_step(step, ir->nstxtcout))
+ {
+ mdof_flags |= MDOF_XTC;
+ }
+ if (bCPT)
+ {
+ mdof_flags |= MDOF_CPT;
+ }
+ ;
+
+#if defined(GMX_FAHCORE) || defined(GMX_WRITELASTSTEP)
+ if (bLastStep)
+ {
+ /* Enforce writing positions and velocities at end of run */
+ mdof_flags |= (MDOF_X | MDOF_V);
+ }
+#endif
+#ifdef GMX_FAHCORE
+ if (MASTER(cr))
+ {
+ fcReportProgress( ir->nsteps, step );
+ }
+
+ /* sync bCPT and fc record-keeping */
+ if (bCPT && MASTER(cr))
+ {
+ fcRequestCheckPoint();
+ }
+#endif
+
+ if (mdof_flags != 0)
+ {
+ wallcycle_start(wcycle, ewcTRAJ);
+ if (bCPT)
+ {
+ if (state->flags & (1<<estLD_RNG))
+ {
+ get_stochd_state(upd, state);
+ }
+ if (state->flags & (1<<estMC_RNG))
+ {
+ get_mc_state(mcrng, state);
+ }
+ if (MASTER(cr))
+ {
+ if (bSumEkinhOld)
+ {
+ state_global->ekinstate.bUpToDate = FALSE;
+ }
+ else
+ {
+ update_ekinstate(&state_global->ekinstate, ekind);
+ state_global->ekinstate.bUpToDate = TRUE;
+ }
+ update_energyhistory(&state_global->enerhist, mdebin);
+ if (ir->efep != efepNO || ir->bSimTemp)
+ {
+ state_global->fep_state = state->fep_state; /* MRS: seems kludgy. The code should be
+ structured so this isn't necessary.
+ Note this reassignment is only necessary
+ for single threads.*/
+ copy_df_history(&state_global->dfhist, &df_history);
+ }
+ }
+ }
+ write_traj(fplog, cr, outf, mdof_flags, top_global,
+ step, t, state, state_global, f, f_global, &n_xtc, &x_xtc);
+ if (bCPT)
+ {
+ (*nchkpt)++;
+ bCPT = FALSE;
+ }
+ debug_gmx();
+ if (bLastStep && step_rel == ir->nsteps &&
+ bDoConfOut && MASTER(cr) &&
+ !bRerunMD)
+ {
+ /* x and v have been collected in write_traj,
+ * because a checkpoint file will always be written
+ * at the last step.
+ */
+ fprintf(stderr, "\nWriting final coordinates.\n");
+ if (fr->bMolPBC)
+ {
+ /* Make molecules whole only for confout writing */
+ do_pbc_mtop(fplog, ir->ePBC, state->box, top_global, state_global->x);
+ }
+ write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm),
+ *top_global->name, top_global,
+ state_global->x, state_global->v,
+ ir->ePBC, state->box);
+ debug_gmx();
+ }
+ wallcycle_stop(wcycle, ewcTRAJ);
+ }
+}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff