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38 #include "gromacs/utility/smalloc.h"
39 #include "gromacs/math/vec.h"
43 #include "trajectory_writing.h"
46 #include "gromacs/legacyheaders/types/commrec.h"
47 #include "gromacs/timing/wallcycle.h"
50 do_md_trajectory_writing(FILE *fplog,
59 t_state *state_global,
60 gmx_mtop_t *top_global,
64 gmx_ekindata_t *ekind,
67 gmx_wallcycle_t wcycle,
79 if (do_per_step(step, ir->nstxout))
83 if (do_per_step(step, ir->nstvout))
87 if (do_per_step(step, ir->nstfout))
91 if (do_per_step(step, ir->nstxout_compressed))
93 mdof_flags |= MDOF_X_COMPRESSED;
97 mdof_flags |= MDOF_CPT;
101 #if defined(GMX_FAHCORE) || defined(GMX_WRITELASTSTEP)
104 /* Enforce writing positions and velocities at end of run */
105 mdof_flags |= (MDOF_X | MDOF_V);
111 fcReportProgress( ir->nsteps, step );
114 #if defined(__native_client__)
115 fcCheckin(MASTER(cr));
118 /* sync bCPT and fc record-keeping */
119 if (bCPT && MASTER(cr))
121 fcRequestCheckPoint();
127 wallcycle_start(wcycle, ewcTRAJ);
134 state_global->ekinstate.bUpToDate = FALSE;
138 update_ekinstate(&state_global->ekinstate, ekind);
139 state_global->ekinstate.bUpToDate = TRUE;
141 update_energyhistory(&state_global->enerhist, mdebin);
144 mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global,
145 step, t, state, state_global, f, f_global);
151 if (bLastStep && step_rel == ir->nsteps &&
152 bDoConfOut && MASTER(cr) &&
155 /* x and v have been collected in mdoutf_write_to_trajectory_files,
156 * because a checkpoint file will always be written
159 fprintf(stderr, "\nWriting final coordinates.\n");
162 /* Make molecules whole only for confout writing */
163 do_pbc_mtop(fplog, ir->ePBC, state->box, top_global, state_global->x);
165 write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm),
166 *top_global->name, top_global,
167 state_global->x, state_global->v,
168 ir->ePBC, state->box);
171 wallcycle_stop(wcycle, ewcTRAJ);