src/gromacs/mdlib/trajectory_writing.cpp

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  36 #include "gmxpre.h"
  37
  38 #include "trajectory_writing.h"
  39
  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"
  57
  58 void do_md_trajectory_writing(FILE*                          fplog,
  59                               t_commrec*                     cr,
  60                               int                            nfile,
  61                               const t_filenm                 fnm[],
  62                               int64_t                        step,
  63                               int64_t                        step_rel,
  64                               double                         t,
  65                               const t_inputrec*              ir,
  66                               t_state*                       state,
  67                               t_state*                       state_global,
  68                               ObservablesHistory*            observablesHistory,
  69                               const gmx_mtop_t&              top_global,
  70                               t_forcerec*                    fr,
  71                               gmx_mdoutf_t                   outf,
  72                               const gmx::EnergyOutput&       energyOutput,
  73                               gmx_ekindata_t*                ekind,
  74                               gmx::ArrayRef<const gmx::RVec> f,
  75                               gmx_bool                       bCPT,
  76                               gmx_bool                       bRerunMD,
  77                               gmx_bool                       bLastStep,
  78                               gmx_bool                       bDoConfOut,
  79                               gmx_bool                       bSumEkinhOld)
  80 {
  81     int   mdof_flags;
  82     rvec* x_for_confout = nullptr;
  83
  84     mdof_flags = 0;
  85     if (do_per_step(step, ir->nstxout))
  86     {
  87         mdof_flags |= MDOF_X;
  88     }
  89     if (do_per_step(step, ir->nstvout))
  90     {
  91         mdof_flags |= MDOF_V;
  92     }
  93     if (do_per_step(step, ir->nstfout))
  94     {
  95         mdof_flags |= MDOF_F;
  96     }
  97     if (do_per_step(step, ir->nstxout_compressed))
  98     {
  99         mdof_flags |= MDOF_X_COMPRESSED;
 100     }
 101     if (bCPT)
 102     {
 103         mdof_flags |= MDOF_CPT;
 104     }
 105     if (do_per_step(step, mdoutf_get_tng_box_output_interval(outf)))
 106     {
 107         mdof_flags |= MDOF_BOX;
 108     }
 109     if (do_per_step(step, mdoutf_get_tng_lambda_output_interval(outf)))
 110     {
 111         mdof_flags |= MDOF_LAMBDA;
 112     }
 113     if (do_per_step(step, mdoutf_get_tng_compressed_box_output_interval(outf)))
 114     {
 115         mdof_flags |= MDOF_BOX_COMPRESSED;
 116     }
 117     if (do_per_step(step, mdoutf_get_tng_compressed_lambda_output_interval(outf)))
 118     {
 119         mdof_flags |= MDOF_LAMBDA_COMPRESSED;
 120     }
 121
 122     if (mdof_flags != 0)
 123     {
 124         wallcycle_start(mdoutf_get_wcycle(outf), WallCycleCounter::Traj);
 125         if (bCPT)
 126         {
 127             if (MASTER(cr))
 128             {
 129                 if (bSumEkinhOld)
 130                 {
 131                     state_global->ekinstate.bUpToDate = FALSE;
 132                 }
 133                 else
 134                 {
 135                     update_ekinstate(&state_global->ekinstate, ekind);
 136                     state_global->ekinstate.bUpToDate = TRUE;
 137                 }
 138
 139                 energyOutput.fillEnergyHistory(observablesHistory->energyHistory.get());
 140             }
 141         }
 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(
 150                 fplog, cr, outf, mdof_flags, top_global.natoms, step, t, state, state_global, observablesHistory, f, &checkpointDataHolder);
 151         if (bLastStep && step_rel == ir->nsteps && bDoConfOut && MASTER(cr) && !bRerunMD)
 152         {
 153             if (fr->bMolPBC && state == state_global)
 154             {
 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
 161                    identical. */
 162                 snew(x_for_confout, state_global->natoms);
 163                 copy_rvecn(state_global->x.rvec_array(), x_for_confout, 0, state_global->natoms);
 164             }
 165             else
 166             {
 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();
 170             }
 171
 172             /* x and v have been collected in mdoutf_write_to_trajectory_files,
 173              * because a checkpoint file will always be written
 174              * at the last step.
 175              */
 176             fprintf(stderr, "\nWriting final coordinates.\n");
 177             if (fr->bMolPBC && !ir->bPeriodicMols)
 178             {
 179                 /* Make molecules whole only for confout writing */
 180                 do_pbc_mtop(ir->pbcType, state->box, &top_global, x_for_confout);
 181             }
 182             write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm),
 183                                 *top_global.name,
 184                                 top_global,
 185                                 x_for_confout,
 186                                 state_global->v.rvec_array(),
 187                                 ir->pbcType,
 188                                 state->box);
 189             if (fr->bMolPBC && state == state_global)
 190             {
 191                 sfree(x_for_confout);
 192             }
 193         }
 194         wallcycle_stop(mdoutf_get_wcycle(outf), WallCycleCounter::Traj);
 195     }
 196 #if GMX_FAHCORE
 197     if (MASTER(cr))
 198     {
 199         fcWriteVisFrame(ir->pbcType, state_global->box, top_global, state_global->x.rvec_array());
 200     }
 201 #endif
 202 }