void copy_coupling_state(t_state *statea, t_state *stateb,
gmx_ekindata_t *ekinda, gmx_ekindata_t *ekindb, t_grpopts* opts)
{
/* MRS note -- might be able to get rid of some of the arguments. Look over it when it's all debugged */
int i, j, nc;
/* Make sure we have enough space for x and v */
if (statea->nalloc > stateb->nalloc)
{
stateb->nalloc = statea->nalloc;
srenew(stateb->x, stateb->nalloc);
srenew(stateb->v, stateb->nalloc);
}
stateb->natoms = statea->natoms;
stateb->ngtc = statea->ngtc;
stateb->nnhpres = statea->nnhpres;
stateb->veta = statea->veta;
if (ekinda)
{
copy_mat(ekinda->ekin, ekindb->ekin);
for (i = 0; i < stateb->ngtc; i++)
{
ekindb->tcstat[i].T = ekinda->tcstat[i].T;
ekindb->tcstat[i].Th = ekinda->tcstat[i].Th;
copy_mat(ekinda->tcstat[i].ekinh, ekindb->tcstat[i].ekinh);
copy_mat(ekinda->tcstat[i].ekinf, ekindb->tcstat[i].ekinf);
ekindb->tcstat[i].ekinscalef_nhc = ekinda->tcstat[i].ekinscalef_nhc;
ekindb->tcstat[i].ekinscaleh_nhc = ekinda->tcstat[i].ekinscaleh_nhc;
ekindb->tcstat[i].vscale_nhc = ekinda->tcstat[i].vscale_nhc;
}
}
copy_rvecn(statea->x, stateb->x, 0, stateb->natoms);
copy_rvecn(statea->v, stateb->v, 0, stateb->natoms);
copy_mat(statea->box, stateb->box);
copy_mat(statea->box_rel, stateb->box_rel);
copy_mat(statea->boxv, stateb->boxv);
for (i = 0; i < stateb->ngtc; i++)
{
nc = i*opts->nhchainlength;
for (j = 0; j < opts->nhchainlength; j++)
{
stateb->nosehoover_xi[nc+j] = statea->nosehoover_xi[nc+j];
stateb->nosehoover_vxi[nc+j] = statea->nosehoover_vxi[nc+j];
}
}
if (stateb->nhpres_xi != NULL)
{
for (i = 0; i < stateb->nnhpres; i++)
{
nc = i*opts->nhchainlength;
for (j = 0; j < opts->nhchainlength; j++)
{
stateb->nhpres_xi[nc+j] = statea->nhpres_xi[nc+j];
stateb->nhpres_vxi[nc+j] = statea->nhpres_vxi[nc+j];
}
}
}
}
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);
}
}
