src/gromacs/mdlib/trajectory_writing.cpp

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  35 #include "gmxpre.h"
  36
  37 #include "trajectory_writing.h"
  38
  39 #include "gromacs/commandline/filenm.h"
  40 #include "gromacs/fileio/confio.h"
  41 #include "gromacs/math/vec.h"
  42 #include "gromacs/mdlib/mdoutf.h"
  43 #include "gromacs/mdlib/mdrun.h"
  44 #include "gromacs/mdlib/sim_util.h"
  45 #include "gromacs/mdlib/update.h"
  46 #include "gromacs/mdtypes/commrec.h"
  47 #include "gromacs/mdtypes/inputrec.h"
  48 #include "gromacs/mdtypes/observableshistory.h"
  49 #include "gromacs/mdtypes/state.h"
  50 #include "gromacs/timing/wallcycle.h"
  51 #include "gromacs/topology/topology.h"
  52 #include "gromacs/utility/smalloc.h"
  53
  54 void
  55 do_md_trajectory_writing(FILE               *fplog,
  56                          t_commrec          *cr,
  57                          int                 nfile,
  58                          const t_filenm      fnm[],
  59                          gmx_int64_t         step,
  60                          gmx_int64_t         step_rel,
  61                          double              t,
  62                          t_inputrec         *ir,
  63                          t_state            *state,
  64                          t_state            *state_global,
  65                          ObservablesHistory *observablesHistory,
  66                          gmx_mtop_t         *top_global,
  67                          t_forcerec         *fr,
  68                          gmx_mdoutf_t        outf,
  69                          t_mdebin           *mdebin,
  70                          gmx_ekindata_t     *ekind,
  71                          PaddedRVecVector   *f,
  72                          int                *nchkpt,
  73                          gmx_bool            bCPT,
  74                          gmx_bool            bRerunMD,
  75                          gmx_bool            bLastStep,
  76                          gmx_bool            bDoConfOut,
  77                          gmx_bool            bSumEkinhOld
  78                          )
  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     ;
 105
 106 #if defined(GMX_FAHCORE)
 107     if (bLastStep)
 108     {
 109         /* Enforce writing positions and velocities at end of run */
 110         mdof_flags |= (MDOF_X | MDOF_V);
 111     }
 112     if (MASTER(cr))
 113     {
 114         fcReportProgress( ir->nsteps, step );
 115     }
 116
 117 #if defined(__native_client__)
 118     fcCheckin(MASTER(cr));
 119 #endif
 120
 121     /* sync bCPT and fc record-keeping */
 122     if (bCPT && MASTER(cr))
 123     {
 124         fcRequestCheckPoint();
 125     }
 126 #endif
 127
 128     if (mdof_flags != 0)
 129     {
 130         wallcycle_start(mdoutf_get_wcycle(outf), ewcTRAJ);
 131         if (bCPT)
 132         {
 133             if (MASTER(cr))
 134             {
 135                 if (bSumEkinhOld)
 136                 {
 137                     state_global->ekinstate.bUpToDate = FALSE;
 138                 }
 139                 else
 140                 {
 141                     update_ekinstate(&state_global->ekinstate, ekind);
 142                     state_global->ekinstate.bUpToDate = TRUE;
 143                 }
 144
 145                 update_energyhistory(observablesHistory->energyHistory.get(), mdebin);
 146             }
 147         }
 148         mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global,
 149                                          step, t, state, state_global, observablesHistory, f);
 150         if (bCPT)
 151         {
 152             (*nchkpt)++;
 153         }
 154         if (bLastStep && step_rel == ir->nsteps &&
 155             bDoConfOut && MASTER(cr) &&
 156             !bRerunMD)
 157         {
 158             if (fr->bMolPBC && state == state_global)
 159             {
 160                 /* This (single-rank) run needs to allocate a
 161                    temporary array of size natoms so that any
 162                    periodicity removal for mdrun -confout does not
 163                    perturb the update and thus the final .edr
 164                    output. This makes .cpt restarts look binary
 165                    identical, and makes .edr restarts binary
 166                    identical. */
 167                 snew(x_for_confout, state_global->natoms);
 168                 copy_rvecn(as_rvec_array(state_global->x.data()), x_for_confout, 0, state_global->natoms);
 169             }
 170             else
 171             {
 172                 /* With DD, or no bMolPBC, it doesn't matter if
 173                    we change as_rvec_array(state_global->x.data()) */
 174                 x_for_confout = as_rvec_array(state_global->x.data());
 175             }
 176
 177             /* x and v have been collected in mdoutf_write_to_trajectory_files,
 178              * because a checkpoint file will always be written
 179              * at the last step.
 180              */
 181             fprintf(stderr, "\nWriting final coordinates.\n");
 182             if (fr->bMolPBC)
 183             {
 184                 /* Make molecules whole only for confout writing */
 185                 do_pbc_mtop(fplog, ir->ePBC, state->box, top_global, x_for_confout);
 186             }
 187             write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm),
 188                                 *top_global->name, top_global,
 189                                 x_for_confout, as_rvec_array(state_global->v.data()),
 190                                 ir->ePBC, state->box);
 191             if (fr->bMolPBC && state == state_global)
 192             {
 193                 sfree(x_for_confout);
 194             }
 195         }
 196         wallcycle_stop(mdoutf_get_wcycle(outf), ewcTRAJ);
 197     }
 198 }