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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/stat.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"
56 void do_md_trajectory_writing(FILE* fplog,
65 t_state* state_global,
66 ObservablesHistory* observablesHistory,
67 const gmx_mtop_t* top_global,
70 const gmx::EnergyOutput& energyOutput,
71 gmx_ekindata_t* ekind,
72 gmx::ArrayRef<gmx::RVec> f,
77 gmx_bool bSumEkinhOld)
80 rvec* x_for_confout = nullptr;
83 if (do_per_step(step, ir->nstxout))
87 if (do_per_step(step, ir->nstvout))
91 if (do_per_step(step, ir->nstfout))
95 if (do_per_step(step, ir->nstxout_compressed))
97 mdof_flags |= MDOF_X_COMPRESSED;
101 mdof_flags |= MDOF_CPT;
103 if (do_per_step(step, mdoutf_get_tng_box_output_interval(outf)))
105 mdof_flags |= MDOF_BOX;
107 if (do_per_step(step, mdoutf_get_tng_lambda_output_interval(outf)))
109 mdof_flags |= MDOF_LAMBDA;
111 if (do_per_step(step, mdoutf_get_tng_compressed_box_output_interval(outf)))
113 mdof_flags |= MDOF_BOX_COMPRESSED;
115 if (do_per_step(step, mdoutf_get_tng_compressed_lambda_output_interval(outf)))
117 mdof_flags |= MDOF_LAMBDA_COMPRESSED;
122 wallcycle_start(mdoutf_get_wcycle(outf), ewcTRAJ);
129 state_global->ekinstate.bUpToDate = FALSE;
133 update_ekinstate(&state_global->ekinstate, ekind);
134 state_global->ekinstate.bUpToDate = TRUE;
137 energyOutput.fillEnergyHistory(observablesHistory->energyHistory.get());
140 // Note that part of the following code is duplicated in StatePropagatorData::trajectoryWriterTeardown.
141 // This duplication is needed while both legacy and modular code paths are in use.
142 // TODO: Remove duplication asap, make sure to keep in sync in the meantime.
143 mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step, t,
144 state, state_global, observablesHistory, f);
145 if (bLastStep && step_rel == ir->nsteps && bDoConfOut && MASTER(cr) && !bRerunMD)
147 if (fr->bMolPBC && state == state_global)
149 /* This (single-rank) run needs to allocate a
150 temporary array of size natoms so that any
151 periodicity removal for mdrun -confout does not
152 perturb the update and thus the final .edr
153 output. This makes .cpt restarts look binary
154 identical, and makes .edr restarts binary
156 snew(x_for_confout, state_global->natoms);
157 copy_rvecn(state_global->x.rvec_array(), x_for_confout, 0, state_global->natoms);
161 /* With DD, or no bMolPBC, it doesn't matter if
162 we change state_global->x.rvec_array() */
163 x_for_confout = state_global->x.rvec_array();
166 /* x and v have been collected in mdoutf_write_to_trajectory_files,
167 * because a checkpoint file will always be written
170 fprintf(stderr, "\nWriting final coordinates.\n");
171 if (fr->bMolPBC && !ir->bPeriodicMols)
173 /* Make molecules whole only for confout writing */
174 do_pbc_mtop(ir->ePBC, state->box, top_global, x_for_confout);
176 write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm), *top_global->name, top_global,
177 x_for_confout, state_global->v.rvec_array(), ir->ePBC, state->box);
178 if (fr->bMolPBC && state == state_global)
180 sfree(x_for_confout);
183 wallcycle_stop(mdoutf_get_wcycle(outf), ewcTRAJ);
188 fcWriteVisFrame(ir->ePBC, state_global->box, top_global, state_global->x.rvec_array());