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37 #include "gromacs/legacyheaders/typedefs.h"
38 #include "gromacs/utility/smalloc.h"
39 #include "gromacs/math/vec.h"
40 #include "gromacs/legacyheaders/sim_util.h"
41 #include "gromacs/legacyheaders/mdrun.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,
78 if (do_per_step(step, ir->nstxout))
82 if (do_per_step(step, ir->nstvout))
86 if (do_per_step(step, ir->nstfout))
90 if (do_per_step(step, ir->nstxout_compressed))
92 mdof_flags |= MDOF_X_COMPRESSED;
96 mdof_flags |= MDOF_CPT;
100 #if defined(GMX_FAHCORE) || defined(GMX_WRITELASTSTEP)
103 /* Enforce writing positions and velocities at end of run */
104 mdof_flags |= (MDOF_X | MDOF_V);
110 fcReportProgress( ir->nsteps, step );
113 #if defined(__native_client__)
114 fcCheckin(MASTER(cr));
117 /* sync bCPT and fc record-keeping */
118 if (bCPT && MASTER(cr))
120 fcRequestCheckPoint();
126 wallcycle_start(mdoutf_get_wcycle(outf), ewcTRAJ);
133 state_global->ekinstate.bUpToDate = FALSE;
137 update_ekinstate(&state_global->ekinstate, ekind);
138 state_global->ekinstate.bUpToDate = TRUE;
140 update_energyhistory(&state_global->enerhist, mdebin);
143 mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global,
144 step, t, state, state_global, f, f_global);
150 if (bLastStep && step_rel == ir->nsteps &&
151 bDoConfOut && MASTER(cr) &&
154 /* x and v have been collected in mdoutf_write_to_trajectory_files,
155 * because a checkpoint file will always be written
158 fprintf(stderr, "\nWriting final coordinates.\n");
161 /* Make molecules whole only for confout writing */
162 do_pbc_mtop(fplog, ir->ePBC, state->box, top_global, state_global->x);
164 write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm),
165 *top_global->name, top_global,
166 state_global->x, state_global->v,
167 ir->ePBC, state->box);
170 wallcycle_stop(mdoutf_get_wcycle(outf), ewcTRAJ);