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38 #include "trajectory_writing.h"
40 #include "gromacs/commandline/filenm.h"
41 #include "gromacs/fileio/confio.h"
42 #include "gromacs/fileio/tngio.h"
43 #include "gromacs/math/vec.h"
44 #include "gromacs/mdlib/mdoutf.h"
45 #include "gromacs/mdlib/stat.h"
46 #include "gromacs/mdlib/update.h"
47 #include "gromacs/mdtypes/checkpointdata.h"
48 #include "gromacs/mdtypes/commrec.h"
49 #include "gromacs/mdtypes/forcerec.h"
50 #include "gromacs/mdtypes/inputrec.h"
51 #include "gromacs/mdtypes/observableshistory.h"
52 #include "gromacs/mdtypes/state.h"
53 #include "gromacs/pbcutil/pbc.h"
54 #include "gromacs/timing/wallcycle.h"
55 #include "gromacs/topology/topology.h"
56 #include "gromacs/utility/smalloc.h"
58 void do_md_trajectory_writing(FILE* fplog
,
67 t_state
* state_global
,
68 ObservablesHistory
* observablesHistory
,
69 const gmx_mtop_t
* top_global
,
72 const gmx::EnergyOutput
& energyOutput
,
73 gmx_ekindata_t
* ekind
,
74 gmx::ArrayRef
<const gmx::RVec
> f
,
79 gmx_bool bSumEkinhOld
)
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
;
124 wallcycle_start(mdoutf_get_wcycle(outf
), ewcTRAJ
);
131 state_global
->ekinstate
.bUpToDate
= FALSE
;
135 update_ekinstate(&state_global
->ekinstate
, ekind
);
136 state_global
->ekinstate
.bUpToDate
= TRUE
;
139 energyOutput
.fillEnergyHistory(observablesHistory
->energyHistory
.get());
142 // The current function is only called by legacy code, while
143 // mdoutf_write_to_trajectory_files is also called from modular simulator. Create a dummy
144 // modular simulator checkpointing object for compatibility.
145 gmx::WriteCheckpointDataHolder checkpointDataHolder
;
146 // Note that part of the following code is duplicated in StatePropagatorData::trajectoryWriterTeardown.
147 // This duplication is needed while both legacy and modular code paths are in use.
148 // TODO: Remove duplication asap, make sure to keep in sync in the meantime.
149 mdoutf_write_to_trajectory_files(fplog
, cr
, outf
, mdof_flags
, top_global
->natoms
, step
, t
, state
,
150 state_global
, observablesHistory
, f
, &checkpointDataHolder
);
151 if (bLastStep
&& step_rel
== ir
->nsteps
&& bDoConfOut
&& MASTER(cr
) && !bRerunMD
)
153 if (fr
->bMolPBC
&& state
== state_global
)
155 /* This (single-rank) run needs to allocate a
156 temporary array of size natoms so that any
157 periodicity removal for mdrun -confout does not
158 perturb the update and thus the final .edr
159 output. This makes .cpt restarts look binary
160 identical, and makes .edr restarts binary
162 snew(x_for_confout
, state_global
->natoms
);
163 copy_rvecn(state_global
->x
.rvec_array(), x_for_confout
, 0, state_global
->natoms
);
167 /* With DD, or no bMolPBC, it doesn't matter if
168 we change state_global->x.rvec_array() */
169 x_for_confout
= state_global
->x
.rvec_array();
172 /* x and v have been collected in mdoutf_write_to_trajectory_files,
173 * because a checkpoint file will always be written
176 fprintf(stderr
, "\nWriting final coordinates.\n");
177 if (fr
->bMolPBC
&& !ir
->bPeriodicMols
)
179 /* Make molecules whole only for confout writing */
180 do_pbc_mtop(ir
->pbcType
, state
->box
, top_global
, x_for_confout
);
182 write_sto_conf_mtop(ftp2fn(efSTO
, nfile
, fnm
), *top_global
->name
, top_global
,
183 x_for_confout
, state_global
->v
.rvec_array(), ir
->pbcType
, state
->box
);
184 if (fr
->bMolPBC
&& state
== state_global
)
186 sfree(x_for_confout
);
189 wallcycle_stop(mdoutf_get_wcycle(outf
), ewcTRAJ
);
194 fcWriteVisFrame(ir
->ePBC
, state_global
->box
, top_global
, state_global
->x
.rvec_array());