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/energyoutput.h"
  45 #include "gromacs/mdlib/mdoutf.h"
  46 #include "gromacs/mdlib/stat.h"
  47 #include "gromacs/mdlib/update.h"
  48 #include "gromacs/mdtypes/checkpointdata.h"
  49 #include "gromacs/mdtypes/commrec.h"
  50 #include "gromacs/mdtypes/forcerec.h"
  51 #include "gromacs/mdtypes/inputrec.h"
  52 #include "gromacs/mdtypes/observableshistory.h"
  53 #include "gromacs/mdtypes/state.h"
  54 #include "gromacs/pbcutil/pbc.h"
  55 #include "gromacs/timing/wallcycle.h"
  56 #include "gromacs/topology/topology.h"
  57 #include "gromacs/utility/smalloc.h"
  58
  59 void do_md_trajectory_writing(FILE*                          fplog,
  60                               t_commrec*                     cr,
  61                               int                            nfile,
  62                               const t_filenm                 fnm[],
  63                               int64_t                        step,
  64                               int64_t                        step_rel,
  65                               double                         t,
  66                               const t_inputrec*              ir,
  67                               t_state*                       state,
  68                               t_state*                       state_global,
  69                               ObservablesHistory*            observablesHistory,
  70                               const gmx_mtop_t&              top_global,
  71                               t_forcerec*                    fr,
  72                               gmx_mdoutf_t                   outf,
  73                               const gmx::EnergyOutput&       energyOutput,
  74                               gmx_ekindata_t*                ekind,
  75                               gmx::ArrayRef<const gmx::RVec> f,
  76                               gmx_bool                       bCPT,
  77                               gmx_bool                       bRerunMD,
  78                               gmx_bool                       bLastStep,
  79                               gmx_bool                       bDoConfOut,
  80                               gmx_bool                       bSumEkinhOld)
  81 {
  82     int   mdof_flags;
  83     rvec* x_for_confout = nullptr;
  84
  85     mdof_flags = 0;
  86     if (do_per_step(step, ir->nstxout))
  87     {
  88         mdof_flags |= MDOF_X;
  89     }
  90     if (do_per_step(step, ir->nstvout))
  91     {
  92         mdof_flags |= MDOF_V;
  93     }
  94     if (do_per_step(step, ir->nstfout))
  95     {
  96         mdof_flags |= MDOF_F;
  97     }
  98     if (do_per_step(step, ir->nstxout_compressed))
  99     {
 100         mdof_flags |= MDOF_X_COMPRESSED;
 101     }
 102     if (bCPT)
 103     {
 104         mdof_flags |= MDOF_CPT;
 105     }
 106     if (do_per_step(step, mdoutf_get_tng_box_output_interval(outf)))
 107     {
 108         mdof_flags |= MDOF_BOX;
 109     }
 110     if (do_per_step(step, mdoutf_get_tng_lambda_output_interval(outf)))
 111     {
 112         mdof_flags |= MDOF_LAMBDA;
 113     }
 114     if (do_per_step(step, mdoutf_get_tng_compressed_box_output_interval(outf)))
 115     {
 116         mdof_flags |= MDOF_BOX_COMPRESSED;
 117     }
 118     if (do_per_step(step, mdoutf_get_tng_compressed_lambda_output_interval(outf)))
 119     {
 120         mdof_flags |= MDOF_LAMBDA_COMPRESSED;
 121     }
 122
 123     if (mdof_flags != 0)
 124     {
 125         wallcycle_start(mdoutf_get_wcycle(outf), WallCycleCounter::Traj);
 126         if (bCPT)
 127         {
 128             if (MASTER(cr))
 129             {
 130                 if (bSumEkinhOld)
 131                 {
 132                     state_global->ekinstate.bUpToDate = FALSE;
 133                 }
 134                 else
 135                 {
 136                     update_ekinstate(&state_global->ekinstate, ekind);
 137                     state_global->ekinstate.bUpToDate = TRUE;
 138                 }
 139
 140                 energyOutput.fillEnergyHistory(observablesHistory->energyHistory.get());
 141             }
 142         }
 143         // The current function is only called by legacy code, while
 144         // mdoutf_write_to_trajectory_files is also called from modular simulator. Create a dummy
 145         // modular simulator checkpointing object for compatibility.
 146         gmx::WriteCheckpointDataHolder checkpointDataHolder;
 147         // Note that part of the following code is duplicated in StatePropagatorData::trajectoryWriterTeardown.
 148         // This duplication is needed while both legacy and modular code paths are in use.
 149         // TODO: Remove duplication asap, make sure to keep in sync in the meantime.
 150         mdoutf_write_to_trajectory_files(
 151                 fplog, cr, outf, mdof_flags, top_global.natoms, step, t, state, state_global, observablesHistory, f, &checkpointDataHolder);
 152         if (bLastStep && step_rel == ir->nsteps && bDoConfOut && MASTER(cr) && !bRerunMD)
 153         {
 154             if (fr->bMolPBC && state == state_global)
 155             {
 156                 /* This (single-rank) run needs to allocate a
 157                    temporary array of size natoms so that any
 158                    periodicity removal for mdrun -confout does not
 159                    perturb the update and thus the final .edr
 160                    output. This makes .cpt restarts look binary
 161                    identical, and makes .edr restarts binary
 162                    identical. */
 163                 snew(x_for_confout, state_global->natoms);
 164                 copy_rvecn(state_global->x.rvec_array(), x_for_confout, 0, state_global->natoms);
 165             }
 166             else
 167             {
 168                 /* With DD, or no bMolPBC, it doesn't matter if
 169                    we change state_global->x.rvec_array() */
 170                 x_for_confout = state_global->x.rvec_array();
 171             }
 172
 173             /* x and v have been collected in mdoutf_write_to_trajectory_files,
 174              * because a checkpoint file will always be written
 175              * at the last step.
 176              */
 177             fprintf(stderr, "\nWriting final coordinates.\n");
 178             if (fr->bMolPBC && !ir->bPeriodicMols)
 179             {
 180                 /* Make molecules whole only for confout writing */
 181                 do_pbc_mtop(ir->pbcType, state->box, &top_global, x_for_confout);
 182             }
 183             write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm),
 184                                 *top_global.name,
 185                                 top_global,
 186                                 x_for_confout,
 187                                 state_global->v.rvec_array(),
 188                                 ir->pbcType,
 189                                 state->box);
 190             if (fr->bMolPBC && state == state_global)
 191             {
 192                 sfree(x_for_confout);
 193             }
 194         }
 195         wallcycle_stop(mdoutf_get_wcycle(outf), WallCycleCounter::Traj);
 196     }
 197 #if GMX_FAHCORE
 198     if (MASTER(cr))
 199     {
 200         fcWriteVisFrame(ir->pbcType, state_global->box, top_global, state_global->x.rvec_array());
 201     }
 202 #endif
 203 }