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37 #include "trajectory_writing.h"
39 #include "gromacs/commandline/filenm.h"
40 #include "gromacs/fileio/confio.h"
41 #include "gromacs/fileio/tngio.h"
42 #include "gromacs/math/vec.h"
43 #include "gromacs/mdlib/mdoutf.h"
44 #include "gromacs/mdlib/sim_util.h"
45 #include "gromacs/mdlib/update.h"
46 #include "gromacs/mdtypes/commrec.h"
47 #include "gromacs/mdtypes/forcerec.h"
48 #include "gromacs/mdtypes/inputrec.h"
49 #include "gromacs/mdtypes/observableshistory.h"
50 #include "gromacs/mdtypes/state.h"
51 #include "gromacs/pbcutil/pbc.h"
52 #include "gromacs/timing/wallcycle.h"
53 #include "gromacs/topology/topology.h"
54 #include "gromacs/utility/smalloc.h"
57 do_md_trajectory_writing(FILE *fplog,
66 t_state *state_global,
67 ObservablesHistory *observablesHistory,
68 gmx_mtop_t *top_global,
71 const gmx::EnergyOutput &energyOutput,
72 gmx_ekindata_t *ekind,
73 gmx::ArrayRef<gmx::RVec> f,
82 rvec *x_for_confout = nullptr;
85 if (do_per_step(step, ir->nstxout))
89 if (do_per_step(step, ir->nstvout))
93 if (do_per_step(step, ir->nstfout))
97 if (do_per_step(step, ir->nstxout_compressed))
99 mdof_flags |= MDOF_X_COMPRESSED;
103 mdof_flags |= MDOF_CPT;
105 if (do_per_step(step, mdoutf_get_tng_box_output_interval(outf)))
107 mdof_flags |= MDOF_BOX;
109 if (do_per_step(step, mdoutf_get_tng_lambda_output_interval(outf)))
111 mdof_flags |= MDOF_LAMBDA;
113 if (do_per_step(step, mdoutf_get_tng_compressed_box_output_interval(outf)))
115 mdof_flags |= MDOF_BOX_COMPRESSED;
117 if (do_per_step(step, mdoutf_get_tng_compressed_lambda_output_interval(outf)))
119 mdof_flags |= MDOF_LAMBDA_COMPRESSED;
125 /* Enforce writing positions and velocities at end of run */
126 mdof_flags |= (MDOF_X | MDOF_V);
130 fcReportProgress( ir->nsteps, step );
133 #if defined(__native_client__)
134 fcCheckin(MASTER(cr));
137 /* sync bCPT and fc record-keeping */
138 if (bCPT && MASTER(cr))
140 fcRequestCheckPoint();
146 wallcycle_start(mdoutf_get_wcycle(outf), ewcTRAJ);
153 state_global->ekinstate.bUpToDate = FALSE;
157 update_ekinstate(&state_global->ekinstate, ekind);
158 state_global->ekinstate.bUpToDate = TRUE;
161 energyOutput.fillEnergyHistory(observablesHistory->energyHistory.get());
164 mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global,
165 step, t, state, state_global, observablesHistory, f);
166 if (bLastStep && step_rel == ir->nsteps &&
167 bDoConfOut && MASTER(cr) &&
170 if (fr->bMolPBC && state == state_global)
172 /* This (single-rank) run needs to allocate a
173 temporary array of size natoms so that any
174 periodicity removal for mdrun -confout does not
175 perturb the update and thus the final .edr
176 output. This makes .cpt restarts look binary
177 identical, and makes .edr restarts binary
179 snew(x_for_confout, state_global->natoms);
180 copy_rvecn(state_global->x.rvec_array(), x_for_confout, 0, state_global->natoms);
184 /* With DD, or no bMolPBC, it doesn't matter if
185 we change state_global->x.rvec_array() */
186 x_for_confout = state_global->x.rvec_array();
189 /* x and v have been collected in mdoutf_write_to_trajectory_files,
190 * because a checkpoint file will always be written
193 fprintf(stderr, "\nWriting final coordinates.\n");
194 if (fr->bMolPBC && !ir->bPeriodicMols)
196 /* Make molecules whole only for confout writing */
197 do_pbc_mtop(ir->ePBC, state->box, top_global, x_for_confout);
199 write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm),
200 *top_global->name, top_global,
201 x_for_confout, state_global->v.rvec_array(),
202 ir->ePBC, state->box);
203 if (fr->bMolPBC && state == state_global)
205 sfree(x_for_confout);
208 wallcycle_stop(mdoutf_get_wcycle(outf), ewcTRAJ);