src/gromacs/fileio/trajectory_writing.c

   1 /*
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   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include "typedefs.h"
  40 #include "gromacs/utility/smalloc.h"
  41 #include "sysstuff.h"
  42 #include "vec.h"
  43 #include "sim_util.h"
  44 #include "mdrun.h"
  45 #include "confio.h"
  46 #include "trajectory_writing.h"
  47 #include "mdoutf.h"
  48
  49 #include "gromacs/timing/wallcycle.h"
  50
  51 void
  52 do_md_trajectory_writing(FILE           *fplog,
  53                          t_commrec      *cr,
  54                          int             nfile,
  55                          const t_filenm  fnm[],
  56                          gmx_int64_t     step,
  57                          gmx_int64_t     step_rel,
  58                          double          t,
  59                          t_inputrec     *ir,
  60                          t_state        *state,
  61                          t_state        *state_global,
  62                          gmx_mtop_t     *top_global,
  63                          t_forcerec     *fr,
  64                          gmx_mdoutf_t    outf,
  65                          t_mdebin       *mdebin,
  66                          gmx_ekindata_t *ekind,
  67                          rvec           *f,
  68                          rvec           *f_global,
  69                          int            *nchkpt,
  70                          gmx_bool        bCPT,
  71                          gmx_bool        bRerunMD,
  72                          gmx_bool        bLastStep,
  73                          gmx_bool        bDoConfOut,
  74                          gmx_bool        bSumEkinhOld
  75                          )
  76 {
  77     int   mdof_flags;
  78
  79     mdof_flags = 0;
  80     if (do_per_step(step, ir->nstxout))
  81     {
  82         mdof_flags |= MDOF_X;
  83     }
  84     if (do_per_step(step, ir->nstvout))
  85     {
  86         mdof_flags |= MDOF_V;
  87     }
  88     if (do_per_step(step, ir->nstfout))
  89     {
  90         mdof_flags |= MDOF_F;
  91     }
  92     if (do_per_step(step, ir->nstxout_compressed))
  93     {
  94         mdof_flags |= MDOF_X_COMPRESSED;
  95     }
  96     if (bCPT)
  97     {
  98         mdof_flags |= MDOF_CPT;
  99     }
 100     ;
 101
 102 #if defined(GMX_FAHCORE) || defined(GMX_WRITELASTSTEP)
 103     if (bLastStep)
 104     {
 105         /* Enforce writing positions and velocities at end of run */
 106         mdof_flags |= (MDOF_X | MDOF_V);
 107     }
 108 #endif
 109 #ifdef GMX_FAHCORE
 110     if (MASTER(cr))
 111     {
 112         fcReportProgress( ir->nsteps, step );
 113     }
 114
 115 #if defined(__native_client__)
 116     fcCheckin(MASTER(cr));
 117 #endif
 118
 119     /* sync bCPT and fc record-keeping */
 120     if (bCPT && MASTER(cr))
 121     {
 122         fcRequestCheckPoint();
 123     }
 124 #endif
 125
 126     if (mdof_flags != 0)
 127     {
 128         wallcycle_start(mdoutf_get_wcycle(outf), ewcTRAJ);
 129         if (bCPT)
 130         {
 131             if (MASTER(cr))
 132             {
 133                 if (bSumEkinhOld)
 134                 {
 135                     state_global->ekinstate.bUpToDate = FALSE;
 136                 }
 137                 else
 138                 {
 139                     update_ekinstate(&state_global->ekinstate, ekind);
 140                     state_global->ekinstate.bUpToDate = TRUE;
 141                 }
 142                 update_energyhistory(&state_global->enerhist, mdebin);
 143             }
 144         }
 145         mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global,
 146                                          step, t, state, state_global, f, f_global);
 147         if (bCPT)
 148         {
 149             (*nchkpt)++;
 150             bCPT = FALSE;
 151         }
 152         debug_gmx();
 153         if (bLastStep && step_rel == ir->nsteps &&
 154             bDoConfOut && MASTER(cr) &&
 155             !bRerunMD)
 156         {
 157             /* x and v have been collected in mdoutf_write_to_trajectory_files,
 158              * because a checkpoint file will always be written
 159              * at the last step.
 160              */
 161             fprintf(stderr, "\nWriting final coordinates.\n");
 162             if (fr->bMolPBC)
 163             {
 164                 /* Make molecules whole only for confout writing */
 165                 do_pbc_mtop(fplog, ir->ePBC, state->box, top_global, state_global->x);
 166             }
 167             write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm),
 168                                 *top_global->name, top_global,
 169                                 state_global->x, state_global->v,
 170                                 ir->ePBC, state->box);
 171             debug_gmx();
 172         }
 173         wallcycle_stop(mdoutf_get_wcycle(outf), ewcTRAJ);
 174     }
 175 }