void
do_md_trajectory_writing(FILE *fplog,
t_commrec *cr,
int nfile,
const t_filenm fnm[],
gmx_int64_t step,
gmx_int64_t step_rel,
double t,
t_inputrec *ir,
t_state *state,
t_state *state_global,
gmx_mtop_t *top_global,
t_forcerec *fr,
gmx_mdoutf_t outf,
t_mdebin *mdebin,
gmx_ekindata_t *ekind,
rvec *f,
rvec *f_global,
int *nchkpt,
gmx_bool bCPT,
gmx_bool bRerunMD,
gmx_bool bLastStep,
gmx_bool bDoConfOut,
gmx_bool bSumEkinhOld
)
{
int mdof_flags;
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->nstxout_compressed))
{
mdof_flags |= MDOF_X_COMPRESSED;
}
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 );
}
#if defined(__native_client__)
fcCheckin(MASTER(cr));
#endif
/* sync bCPT and fc record-keeping */
if (bCPT && MASTER(cr))
{
fcRequestCheckPoint();
}
#endif
if (mdof_flags != 0)
{
wallcycle_start(mdoutf_get_wcycle(outf), ewcTRAJ);
if (bCPT)
{
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);
}
}
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global,
step, t, state, state_global, f, f_global);
if (bCPT)
{
(*nchkpt)++;
}
debug_gmx();
if (bLastStep && step_rel == ir->nsteps &&
bDoConfOut && MASTER(cr) &&
!bRerunMD)
{
/* x and v have been collected in mdoutf_write_to_trajectory_files,
* 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(mdoutf_get_wcycle(outf), ewcTRAJ);
}
}
void
do_md_trajectory_writing(FILE *fplog,
t_commrec *cr,
int nfile,
const t_filenm fnm[],
gmx_int64_t step,
gmx_int64_t step_rel,
double t,
t_inputrec *ir,
t_state *state,
t_state *state_global,
gmx_mtop_t *top_global,
t_forcerec *fr,
gmx_mdoutf_t outf,
t_mdebin *mdebin,
gmx_ekindata_t *ekind,
rvec *f,
rvec *f_global,
int *nchkpt,
gmx_bool bCPT,
gmx_bool bRerunMD,
gmx_bool bLastStep,
gmx_bool bDoConfOut,
gmx_bool bSumEkinhOld
)
{
int mdof_flags;
rvec *x_for_confout = 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->nstxout_compressed))
{
mdof_flags |= MDOF_X_COMPRESSED;
}
if (bCPT)
{
mdof_flags |= MDOF_CPT;
}
;
#if defined(GMX_FAHCORE)
if (bLastStep)
{
/* Enforce writing positions and velocities at end of run */
mdof_flags |= (MDOF_X | MDOF_V);
}
if (MASTER(cr))
{
fcReportProgress( ir->nsteps, step );
}
#if defined(__native_client__)
fcCheckin(MASTER(cr));
#endif
/* sync bCPT and fc record-keeping */
if (bCPT && MASTER(cr))
{
fcRequestCheckPoint();
}
#endif
if (mdof_flags != 0)
{
wallcycle_start(mdoutf_get_wcycle(outf), ewcTRAJ);
if (bCPT)
{
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);
}
}
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global,
step, t, state, state_global, f, f_global);
if (bCPT)
{
(*nchkpt)++;
}
debug_gmx();
if (bLastStep && step_rel == ir->nsteps &&
bDoConfOut && MASTER(cr) &&
!bRerunMD)
{
if (fr->bMolPBC && state->x == state_global->x)
{
/* This (single-rank) run needs to allocate a
temporary array of size natoms so that any
periodicity removal for mdrun -confout does not
perturb the update and thus the final .edr
output. This makes .cpt restarts look binary
identical, and makes .edr restarts binary
identical. */
snew(x_for_confout, state_global->natoms);
copy_rvecn(state_global->x, x_for_confout, 0, state_global->natoms);
}
else
{
/* With DD, or no bMolPBC, it doesn't matter if
we change state_global->x */
x_for_confout = state_global->x;
}
/* x and v have been collected in mdoutf_write_to_trajectory_files,
* 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, x_for_confout);
}
write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm),
*top_global->name, top_global,
x_for_confout, state_global->v,
ir->ePBC, state->box);
if (fr->bMolPBC && state->x == state_global->x)
{
sfree(x_for_confout);
}
debug_gmx();
}
wallcycle_stop(mdoutf_get_wcycle(outf), ewcTRAJ);
}
}
