src/gromacs/mdlib/trajectory_writing.cpp

   1 /*
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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/fileio/tngio.h"
  42 #include "gromacs/math/vec.h"
  43 #include "gromacs/mdlib/mdoutf.h"
  44 #include "gromacs/mdlib/mdrun.h"
  45 #include "gromacs/mdlib/sim_util.h"
  46 #include "gromacs/mdlib/update.h"
  47 #include "gromacs/mdtypes/commrec.h"
  48 #include "gromacs/mdtypes/inputrec.h"
  49 #include "gromacs/mdtypes/observableshistory.h"
  50 #include "gromacs/mdtypes/state.h"
  51 #include "gromacs/timing/wallcycle.h"
  52 #include "gromacs/topology/topology.h"
  53 #include "gromacs/utility/smalloc.h"
  54
  55 void
  56 do_md_trajectory_writing(FILE                    *fplog,
  57                          t_commrec               *cr,
  58                          int                      nfile,
  59                          const t_filenm           fnm[],
  60                          gmx_int64_t              step,
  61                          gmx_int64_t              step_rel,
  62                          double                   t,
  63                          t_inputrec              *ir,
  64                          t_state                 *state,
  65                          t_state                 *state_global,
  66                          ObservablesHistory      *observablesHistory,
  67                          gmx_mtop_t              *top_global,
  68                          t_forcerec              *fr,
  69                          gmx_mdoutf_t             outf,
  70                          t_mdebin                *mdebin,
  71                          gmx_ekindata_t          *ekind,
  72                          gmx::ArrayRef<gmx::RVec> f,
  73                          int                     *nchkpt,
  74                          gmx_bool                 bCPT,
  75                          gmx_bool                 bRerunMD,
  76                          gmx_bool                 bLastStep,
  77                          gmx_bool                 bDoConfOut,
  78                          gmx_bool                 bSumEkinhOld
  79                          )
  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 defined(GMX_FAHCORE)
 123     if (bLastStep)
 124     {
 125         /* Enforce writing positions and velocities at end of run */
 126         mdof_flags |= (MDOF_X | MDOF_V);
 127     }
 128     if (MASTER(cr))
 129     {
 130         fcReportProgress( ir->nsteps, step );
 131     }
 132
 133 #if defined(__native_client__)
 134     fcCheckin(MASTER(cr));
 135 #endif
 136
 137     /* sync bCPT and fc record-keeping */
 138     if (bCPT && MASTER(cr))
 139     {
 140         fcRequestCheckPoint();
 141     }
 142 #endif
 143
 144     if (mdof_flags != 0)
 145     {
 146         wallcycle_start(mdoutf_get_wcycle(outf), ewcTRAJ);
 147         if (bCPT)
 148         {
 149             if (MASTER(cr))
 150             {
 151                 if (bSumEkinhOld)
 152                 {
 153                     state_global->ekinstate.bUpToDate = FALSE;
 154                 }
 155                 else
 156                 {
 157                     update_ekinstate(&state_global->ekinstate, ekind);
 158                     state_global->ekinstate.bUpToDate = TRUE;
 159                 }
 160
 161                 update_energyhistory(observablesHistory->energyHistory.get(), mdebin);
 162             }
 163         }
 164         mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global,
 165                                          step, t, state, state_global, observablesHistory, f);
 166         if (bCPT)
 167         {
 168             (*nchkpt)++;
 169         }
 170         if (bLastStep && step_rel == ir->nsteps &&
 171             bDoConfOut && MASTER(cr) &&
 172             !bRerunMD)
 173         {
 174             if (fr->bMolPBC && state == state_global)
 175             {
 176                 /* This (single-rank) run needs to allocate a
 177                    temporary array of size natoms so that any
 178                    periodicity removal for mdrun -confout does not
 179                    perturb the update and thus the final .edr
 180                    output. This makes .cpt restarts look binary
 181                    identical, and makes .edr restarts binary
 182                    identical. */
 183                 snew(x_for_confout, state_global->natoms);
 184                 copy_rvecn(as_rvec_array(state_global->x.data()), x_for_confout, 0, state_global->natoms);
 185             }
 186             else
 187             {
 188                 /* With DD, or no bMolPBC, it doesn't matter if
 189                    we change as_rvec_array(state_global->x.data()) */
 190                 x_for_confout = as_rvec_array(state_global->x.data());
 191             }
 192
 193             /* x and v have been collected in mdoutf_write_to_trajectory_files,
 194              * because a checkpoint file will always be written
 195              * at the last step.
 196              */
 197             fprintf(stderr, "\nWriting final coordinates.\n");
 198             if (fr->bMolPBC && !ir->bPeriodicMols)
 199             {
 200                 /* Make molecules whole only for confout writing */
 201                 do_pbc_mtop(fplog, ir->ePBC, state->box, top_global, x_for_confout);
 202             }
 203             write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm),
 204                                 *top_global->name, top_global,
 205                                 x_for_confout, as_rvec_array(state_global->v.data()),
 206                                 ir->ePBC, state->box);
 207             if (fr->bMolPBC && state == state_global)
 208             {
 209                 sfree(x_for_confout);
 210             }
 211         }
 212         wallcycle_stop(mdoutf_get_wcycle(outf), ewcTRAJ);
 213     }
 214 }