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/commrec.h"
  48 #include "gromacs/mdtypes/forcerec.h"
  49 #include "gromacs/mdtypes/inputrec.h"
  50 #include "gromacs/mdtypes/observableshistory.h"
  51 #include "gromacs/mdtypes/state.h"
  52 #include "gromacs/pbcutil/pbc.h"
  53 #include "gromacs/timing/wallcycle.h"
  54 #include "gromacs/topology/topology.h"
  55 #include "gromacs/utility/smalloc.h"
  56
  57 void do_md_trajectory_writing(FILE*                    fplog,
  58                               t_commrec*               cr,
  59                               int                      nfile,
  60                               const t_filenm           fnm[],
  61                               int64_t                  step,
  62                               int64_t                  step_rel,
  63                               double                   t,
  64                               t_inputrec*              ir,
  65                               t_state*                 state,
  66                               t_state*                 state_global,
  67                               ObservablesHistory*      observablesHistory,
  68                               const gmx_mtop_t*        top_global,
  69                               t_forcerec*              fr,
  70                               gmx_mdoutf_t             outf,
  71                               const gmx::EnergyOutput& energyOutput,
  72                               gmx_ekindata_t*          ekind,
  73                               gmx::ArrayRef<gmx::RVec> f,
  74                               gmx_bool                 bCPT,
  75                               gmx_bool                 bRerunMD,
  76                               gmx_bool                 bLastStep,
  77                               gmx_bool                 bDoConfOut,
  78                               gmx_bool                 bSumEkinhOld)
  79 {
  80     int   mdof_flags;
  81     rvec* x_for_confout = nullptr;
  82
  83     mdof_flags = 0;
  84     if (do_per_step(step, ir->nstxout))
  85     {
  86         mdof_flags |= MDOF_X;
  87     }
  88     if (do_per_step(step, ir->nstvout))
  89     {
  90         mdof_flags |= MDOF_V;
  91     }
  92     if (do_per_step(step, ir->nstfout))
  93     {
  94         mdof_flags |= MDOF_F;
  95     }
  96     if (do_per_step(step, ir->nstxout_compressed))
  97     {
  98         mdof_flags |= MDOF_X_COMPRESSED;
  99     }
 100     if (bCPT)
 101     {
 102         mdof_flags |= MDOF_CPT;
 103     }
 104     if (do_per_step(step, mdoutf_get_tng_box_output_interval(outf)))
 105     {
 106         mdof_flags |= MDOF_BOX;
 107     }
 108     if (do_per_step(step, mdoutf_get_tng_lambda_output_interval(outf)))
 109     {
 110         mdof_flags |= MDOF_LAMBDA;
 111     }
 112     if (do_per_step(step, mdoutf_get_tng_compressed_box_output_interval(outf)))
 113     {
 114         mdof_flags |= MDOF_BOX_COMPRESSED;
 115     }
 116     if (do_per_step(step, mdoutf_get_tng_compressed_lambda_output_interval(outf)))
 117     {
 118         mdof_flags |= MDOF_LAMBDA_COMPRESSED;
 119     }
 120
 121 #if GMX_FAHCORE
 122     if (bLastStep)
 123     {
 124         /* Enforce writing positions and velocities at end of run */
 125         mdof_flags |= (MDOF_X | MDOF_V);
 126     }
 127     if (MASTER(cr))
 128     {
 129         fcReportProgress(ir->nsteps, step);
 130     }
 131
 132 #    if defined(__native_client__)
 133     fcCheckin(MASTER(cr));
 134 #    endif
 135
 136     /* sync bCPT and fc record-keeping */
 137     if (bCPT && MASTER(cr))
 138     {
 139         fcRequestCheckPoint();
 140     }
 141 #endif
 142
 143     if (mdof_flags != 0)
 144     {
 145         wallcycle_start(mdoutf_get_wcycle(outf), ewcTRAJ);
 146         if (bCPT)
 147         {
 148             if (MASTER(cr))
 149             {
 150                 if (bSumEkinhOld)
 151                 {
 152                     state_global->ekinstate.bUpToDate = FALSE;
 153                 }
 154                 else
 155                 {
 156                     update_ekinstate(&state_global->ekinstate, ekind);
 157                     state_global->ekinstate.bUpToDate = TRUE;
 158                 }
 159
 160                 energyOutput.fillEnergyHistory(observablesHistory->energyHistory.get());
 161             }
 162         }
 163         // Note that part of the following code is duplicated in StatePropagatorData::trajectoryWriterTeardown.
 164         // This duplication is needed while both legacy and modular code paths are in use.
 165         // TODO: Remove duplication asap, make sure to keep in sync in the meantime.
 166         mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global->natoms, step, t,
 167                                          state, state_global, observablesHistory, f);
 168         if (bLastStep && step_rel == ir->nsteps && bDoConfOut && MASTER(cr) && !bRerunMD)
 169         {
 170             if (fr->bMolPBC && state == state_global)
 171             {
 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
 178                    identical. */
 179                 snew(x_for_confout, state_global->natoms);
 180                 copy_rvecn(state_global->x.rvec_array(), x_for_confout, 0, state_global->natoms);
 181             }
 182             else
 183             {
 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();
 187             }
 188
 189             /* x and v have been collected in mdoutf_write_to_trajectory_files,
 190              * because a checkpoint file will always be written
 191              * at the last step.
 192              */
 193             fprintf(stderr, "\nWriting final coordinates.\n");
 194             if (fr->bMolPBC && !ir->bPeriodicMols)
 195             {
 196                 /* Make molecules whole only for confout writing */
 197                 do_pbc_mtop(ir->pbcType, state->box, top_global, x_for_confout);
 198             }
 199             write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm), *top_global->name, top_global,
 200                                 x_for_confout, state_global->v.rvec_array(), ir->pbcType, state->box);
 201             if (fr->bMolPBC && state == state_global)
 202             {
 203                 sfree(x_for_confout);
 204             }
 205         }
 206         wallcycle_stop(mdoutf_get_wcycle(outf), ewcTRAJ);
 207     }
 208 }