src/gromacs/mdlib/mdoutf.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2013,2014,2015,2016,2017 The GROMACS development team.
   5  * Copyright (c) 2018,2019,2020, by the GROMACS development team, led by
   6  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   7  * and including many others, as listed in the AUTHORS file in the
   8  * top-level source directory and at http://www.gromacs.org.
   9  *
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  11  * modify it under the terms of the GNU Lesser General Public License
  12  * as published by the Free Software Foundation; either version 2.1
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  35  */
  36 #include "gmxpre.h"
  37
  38 #include "mdoutf.h"
  39
  40 #include "config.h"
  41
  42 #include "gromacs/commandline/filenm.h"
  43 #include "gromacs/domdec/collect.h"
  44 #include "gromacs/domdec/domdec_struct.h"
  45 #include "gromacs/fileio/checkpoint.h"
  46 #include "gromacs/fileio/gmxfio.h"
  47 #include "gromacs/fileio/tngio.h"
  48 #include "gromacs/fileio/trrio.h"
  49 #include "gromacs/fileio/xtcio.h"
  50 #include "gromacs/fileio/xvgr.h"
  51 #include "gromacs/math/vec.h"
  52 #include "gromacs/mdlib/trajectory_writing.h"
  53 #include "gromacs/mdrunutility/handlerestart.h"
  54 #include "gromacs/mdrunutility/multisim.h"
  55 #include "gromacs/mdtypes/awh_history.h"
  56 #include "gromacs/mdtypes/commrec.h"
  57 #include "gromacs/mdtypes/df_history.h"
  58 #include "gromacs/mdtypes/edsamhistory.h"
  59 #include "gromacs/mdtypes/energyhistory.h"
  60 #include "gromacs/mdtypes/imdoutputprovider.h"
  61 #include "gromacs/mdtypes/inputrec.h"
  62 #include "gromacs/mdtypes/md_enums.h"
  63 #include "gromacs/mdtypes/mdrunoptions.h"
  64 #include "gromacs/mdtypes/observableshistory.h"
  65 #include "gromacs/mdtypes/state.h"
  66 #include "gromacs/mdtypes/swaphistory.h"
  67 #include "gromacs/timing/wallcycle.h"
  68 #include "gromacs/topology/topology.h"
  69 #include "gromacs/utility/baseversion.h"
  70 #include "gromacs/utility/fatalerror.h"
  71 #include "gromacs/utility/pleasecite.h"
  72 #include "gromacs/utility/programcontext.h"
  73 #include "gromacs/utility/smalloc.h"
  74 #include "gromacs/utility/sysinfo.h"
  75
  76 struct gmx_mdoutf
  77 {
  78     t_fileio*                     fp_trn;
  79     t_fileio*                     fp_xtc;
  80     gmx_tng_trajectory_t          tng;
  81     gmx_tng_trajectory_t          tng_low_prec;
  82     int                           x_compression_precision; /* only used by XTC output */
  83     ener_file_t                   fp_ene;
  84     const char*                   fn_cpt;
  85     gmx_bool                      bKeepAndNumCPT;
  86     int                           eIntegrator;
  87     gmx_bool                      bExpanded;
  88     int                           elamstats;
  89     int                           simulation_part;
  90     FILE*                         fp_dhdl;
  91     int                           natoms_global;
  92     int                           natoms_x_compressed;
  93     const SimulationGroups*       groups; /* for compressed position writing */
  94     gmx_wallcycle_t               wcycle;
  95     rvec*                         f_global;
  96     gmx::IMDOutputProvider*       outputProvider;
  97     const gmx::MdModulesNotifier* mdModulesNotifier;
  98     bool                          simulationsShareState;
  99     MPI_Comm                      mastersComm;
 100 };
 101
 102
 103 gmx_mdoutf_t init_mdoutf(FILE*                         fplog,
 104                          int                           nfile,
 105                          const t_filenm                fnm[],
 106                          const gmx::MdrunOptions&      mdrunOptions,
 107                          const t_commrec*              cr,
 108                          gmx::IMDOutputProvider*       outputProvider,
 109                          const gmx::MdModulesNotifier& mdModulesNotifier,
 110                          const t_inputrec*             ir,
 111                          const gmx_mtop_t*             top_global,
 112                          const gmx_output_env_t*       oenv,
 113                          gmx_wallcycle_t               wcycle,
 114                          const gmx::StartingBehavior   startingBehavior,
 115                          bool                          simulationsShareState,
 116                          const gmx_multisim_t*         ms)
 117 {
 118     gmx_mdoutf_t of;
 119     const char * appendMode = "a+", *writeMode = "w+", *filemode;
 120     gmx_bool     bCiteTng = FALSE;
 121     int          i;
 122     bool restartWithAppending = (startingBehavior == gmx::StartingBehavior::RestartWithAppending);
 123
 124     snew(of, 1);
 125
 126     of->fp_trn       = nullptr;
 127     of->fp_ene       = nullptr;
 128     of->fp_xtc       = nullptr;
 129     of->tng          = nullptr;
 130     of->tng_low_prec = nullptr;
 131     of->fp_dhdl      = nullptr;
 132
 133     of->eIntegrator             = ir->eI;
 134     of->bExpanded               = ir->bExpanded;
 135     of->elamstats               = ir->expandedvals->elamstats;
 136     of->simulation_part         = ir->simulation_part;
 137     of->x_compression_precision = static_cast<int>(ir->x_compression_precision);
 138     of->wcycle                  = wcycle;
 139     of->f_global                = nullptr;
 140     of->outputProvider          = outputProvider;
 141
 142     GMX_RELEASE_ASSERT(!simulationsShareState || ms != nullptr,
 143                        "Need valid multisim object when simulations share state");
 144     of->simulationsShareState = simulationsShareState;
 145     if (of->simulationsShareState)
 146     {
 147         of->mastersComm = ms->mastersComm_;
 148     }
 149
 150     if (MASTER(cr))
 151     {
 152         of->bKeepAndNumCPT = mdrunOptions.checkpointOptions.keepAndNumberCheckpointFiles;
 153
 154         filemode = restartWithAppending ? appendMode : writeMode;
 155
 156         if (EI_DYNAMICS(ir->eI) && ir->nstxout_compressed > 0)
 157         {
 158             const char* filename;
 159             filename = ftp2fn(efCOMPRESSED, nfile, fnm);
 160             switch (fn2ftp(filename))
 161             {
 162                 case efXTC: of->fp_xtc = open_xtc(filename, filemode); break;
 163                 case efTNG:
 164                     gmx_tng_open(filename, filemode[0], &of->tng_low_prec);
 165                     if (filemode[0] == 'w')
 166                     {
 167                         gmx_tng_prepare_low_prec_writing(of->tng_low_prec, top_global, ir);
 168                     }
 169                     bCiteTng = TRUE;
 170                     break;
 171                 default: gmx_incons("Invalid reduced precision file format");
 172             }
 173         }
 174         if ((EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI))
 175             && (!GMX_FAHCORE
 176                 && !(EI_DYNAMICS(ir->eI) && ir->nstxout == 0 && ir->nstvout == 0 && ir->nstfout == 0)))
 177         {
 178             const char* filename;
 179             filename = ftp2fn(efTRN, nfile, fnm);
 180             switch (fn2ftp(filename))
 181             {
 182                 case efTRR:
 183                 case efTRN:
 184                     /* If there is no uncompressed coordinate output and
 185                        there is compressed TNG output write forces
 186                        and/or velocities to the TNG file instead. */
 187                     if (ir->nstxout != 0 || ir->nstxout_compressed == 0 || !of->tng_low_prec)
 188                     {
 189                         of->fp_trn = gmx_trr_open(filename, filemode);
 190                     }
 191                     break;
 192                 case efTNG:
 193                     gmx_tng_open(filename, filemode[0], &of->tng);
 194                     if (filemode[0] == 'w')
 195                     {
 196                         gmx_tng_prepare_md_writing(of->tng, top_global, ir);
 197                     }
 198                     bCiteTng = TRUE;
 199                     break;
 200                 default: gmx_incons("Invalid full precision file format");
 201             }
 202         }
 203         if (EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI))
 204         {
 205             of->fp_ene = open_enx(ftp2fn(efEDR, nfile, fnm), filemode);
 206         }
 207         of->fn_cpt = opt2fn("-cpo", nfile, fnm);
 208
 209         if ((ir->efep != efepNO || ir->bSimTemp) && ir->fepvals->nstdhdl > 0
 210             && (ir->fepvals->separate_dhdl_file == esepdhdlfileYES) && EI_DYNAMICS(ir->eI))
 211         {
 212             if (restartWithAppending)
 213             {
 214                 of->fp_dhdl = gmx_fio_fopen(opt2fn("-dhdl", nfile, fnm), filemode);
 215             }
 216             else
 217             {
 218                 of->fp_dhdl = open_dhdl(opt2fn("-dhdl", nfile, fnm), ir, oenv);
 219             }
 220         }
 221
 222         outputProvider->initOutput(fplog, nfile, fnm, restartWithAppending, oenv);
 223         of->mdModulesNotifier = &mdModulesNotifier;
 224
 225         /* Set up atom counts so they can be passed to actual
 226            trajectory-writing routines later. Also, XTC writing needs
 227            to know what (and how many) atoms might be in the XTC
 228            groups, and how to look up later which ones they are. */
 229         of->natoms_global       = top_global->natoms;
 230         of->groups              = &top_global->groups;
 231         of->natoms_x_compressed = 0;
 232         for (i = 0; (i < top_global->natoms); i++)
 233         {
 234             if (getGroupType(*of->groups, SimulationAtomGroupType::CompressedPositionOutput, i) == 0)
 235             {
 236                 of->natoms_x_compressed++;
 237             }
 238         }
 239
 240         if (ir->nstfout && DOMAINDECOMP(cr))
 241         {
 242             snew(of->f_global, top_global->natoms);
 243         }
 244     }
 245
 246     if (bCiteTng)
 247     {
 248         please_cite(fplog, "Lundborg2014");
 249     }
 250
 251     return of;
 252 }
 253
 254 ener_file_t mdoutf_get_fp_ene(gmx_mdoutf_t of)
 255 {
 256     return of->fp_ene;
 257 }
 258
 259 FILE* mdoutf_get_fp_dhdl(gmx_mdoutf_t of)
 260 {
 261     return of->fp_dhdl;
 262 }
 263
 264 gmx_wallcycle_t mdoutf_get_wcycle(gmx_mdoutf_t of)
 265 {
 266     return of->wcycle;
 267 }
 268
 269 static void mpiBarrierBeforeRename(const bool applyMpiBarrierBeforeRename, MPI_Comm mpiBarrierCommunicator)
 270 {
 271     if (applyMpiBarrierBeforeRename)
 272     {
 273 #if GMX_MPI
 274         MPI_Barrier(mpiBarrierCommunicator);
 275 #else
 276         GMX_RELEASE_ASSERT(false, "Should not request a barrier without MPI");
 277         GMX_UNUSED_VALUE(mpiBarrierCommunicator);
 278 #endif
 279     }
 280 }
 281 /*! \brief Write a checkpoint to the filename
 282  *
 283  * Appends the _step<step>.cpt with bNumberAndKeep, otherwise moves
 284  * the previous checkpoint filename with suffix _prev.cpt.
 285  */
 286 static void write_checkpoint(const char*                     fn,
 287                              gmx_bool                        bNumberAndKeep,
 288                              FILE*                           fplog,
 289                              const t_commrec*                cr,
 290                              ivec                            domdecCells,
 291                              int                             nppnodes,
 292                              int                             eIntegrator,
 293                              int                             simulation_part,
 294                              gmx_bool                        bExpanded,
 295                              int                             elamstats,
 296                              int64_t                         step,
 297                              double                          t,
 298                              t_state*                        state,
 299                              ObservablesHistory*             observablesHistory,
 300                              const gmx::MdModulesNotifier&   mdModulesNotifier,
 301                              gmx::WriteCheckpointDataHolder* modularSimulatorCheckpointData,
 302                              bool                            applyMpiBarrierBeforeRename,
 303                              MPI_Comm                        mpiBarrierCommunicator)
 304 {
 305     t_fileio* fp;
 306     char*     fntemp; /* the temporary checkpoint file name */
 307     int       npmenodes;
 308     char      buf[1024], suffix[5 + STEPSTRSIZE], sbuf[STEPSTRSIZE];
 309     t_fileio* ret;
 310
 311     if (DOMAINDECOMP(cr))
 312     {
 313         npmenodes = cr->npmenodes;
 314     }
 315     else
 316     {
 317         npmenodes = 0;
 318     }
 319
 320 #if !GMX_NO_RENAME
 321     /* make the new temporary filename */
 322     snew(fntemp, std::strlen(fn) + 5 + STEPSTRSIZE);
 323     std::strcpy(fntemp, fn);
 324     fntemp[std::strlen(fn) - std::strlen(ftp2ext(fn2ftp(fn))) - 1] = '\0';
 325     sprintf(suffix, "_%s%s", "step", gmx_step_str(step, sbuf));
 326     std::strcat(fntemp, suffix);
 327     std::strcat(fntemp, fn + std::strlen(fn) - std::strlen(ftp2ext(fn2ftp(fn))) - 1);
 328 #else
 329     /* if we can't rename, we just overwrite the cpt file.
 330      * dangerous if interrupted.
 331      */
 332     snew(fntemp, std::strlen(fn));
 333     std::strcpy(fntemp, fn);
 334 #endif
 335     std::string timebuf = gmx_format_current_time();
 336
 337     if (fplog)
 338     {
 339         fprintf(fplog, "Writing checkpoint, step %s at %s\n\n", gmx_step_str(step, buf), timebuf.c_str());
 340     }
 341
 342     /* Get offsets for open files */
 343     auto outputfiles = gmx_fio_get_output_file_positions();
 344
 345     fp = gmx_fio_open(fntemp, "w");
 346
 347     /* We can check many more things now (CPU, acceleration, etc), but
 348      * it is highly unlikely to have two separate builds with exactly
 349      * the same version, user, time, and build host!
 350      */
 351
 352     int nlambda = (state->dfhist ? state->dfhist->nlambda : 0);
 353
 354     edsamhistory_t* edsamhist = observablesHistory->edsamHistory.get();
 355     int             nED       = (edsamhist ? edsamhist->nED : 0);
 356
 357     swaphistory_t* swaphist    = observablesHistory->swapHistory.get();
 358     int            eSwapCoords = (swaphist ? swaphist->eSwapCoords : eswapNO);
 359
 360     CheckpointHeaderContents headerContents = { 0,
 361                                                 { 0 },
 362                                                 { 0 },
 363                                                 { 0 },
 364                                                 { 0 },
 365                                                 GMX_DOUBLE,
 366                                                 { 0 },
 367                                                 { 0 },
 368                                                 eIntegrator,
 369                                                 simulation_part,
 370                                                 step,
 371                                                 t,
 372                                                 nppnodes,
 373                                                 { 0 },
 374                                                 npmenodes,
 375                                                 state->natoms,
 376                                                 state->ngtc,
 377                                                 state->nnhpres,
 378                                                 state->nhchainlength,
 379                                                 nlambda,
 380                                                 state->flags,
 381                                                 0,
 382                                                 0,
 383                                                 0,
 384                                                 0,
 385                                                 0,
 386                                                 nED,
 387                                                 eSwapCoords,
 388                                                 false };
 389     std::strcpy(headerContents.version, gmx_version());
 390     std::strcpy(headerContents.fprog, gmx::getProgramContext().fullBinaryPath());
 391     std::strcpy(headerContents.ftime, timebuf.c_str());
 392     if (DOMAINDECOMP(cr))
 393     {
 394         copy_ivec(domdecCells, headerContents.dd_nc);
 395     }
 396
 397     write_checkpoint_data(fp, headerContents, bExpanded, elamstats, state, observablesHistory,
 398                           mdModulesNotifier, &outputfiles, modularSimulatorCheckpointData);
 399
 400     /* we really, REALLY, want to make sure to physically write the checkpoint,
 401        and all the files it depends on, out to disk. Because we've
 402        opened the checkpoint with gmx_fio_open(), it's in our list
 403        of open files.  */
 404     ret = gmx_fio_all_output_fsync();
 405
 406     if (ret)
 407     {
 408         char buf[STRLEN];
 409         sprintf(buf, "Cannot fsync '%s'; maybe you are out of disk space?", gmx_fio_getname(ret));
 410
 411         if (getenv(GMX_IGNORE_FSYNC_FAILURE_ENV) == nullptr)
 412         {
 413             gmx_file(buf);
 414         }
 415         else
 416         {
 417             gmx_warning("%s", buf);
 418         }
 419     }
 420
 421     if (gmx_fio_close(fp) != 0)
 422     {
 423         gmx_file("Cannot read/write checkpoint; corrupt file, or maybe you are out of disk space?");
 424     }
 425
 426     /* we don't move the checkpoint if the user specified they didn't want it,
 427        or if the fsyncs failed */
 428 #if !GMX_NO_RENAME
 429     if (!bNumberAndKeep && !ret)
 430     {
 431         if (gmx_fexist(fn))
 432         {
 433             /* Rename the previous checkpoint file */
 434             mpiBarrierBeforeRename(applyMpiBarrierBeforeRename, mpiBarrierCommunicator);
 435
 436             std::strcpy(buf, fn);
 437             buf[std::strlen(fn) - std::strlen(ftp2ext(fn2ftp(fn))) - 1] = '\0';
 438             std::strcat(buf, "_prev");
 439             std::strcat(buf, fn + std::strlen(fn) - std::strlen(ftp2ext(fn2ftp(fn))) - 1);
 440             if (!GMX_FAHCORE)
 441             {
 442                 /* we copy here so that if something goes wrong between now and
 443                  * the rename below, there's always a state.cpt.
 444                  * If renames are atomic (such as in POSIX systems),
 445                  * this copying should be unneccesary.
 446                  */
 447                 gmx_file_copy(fn, buf, FALSE);
 448                 /* We don't really care if this fails:
 449                  * there's already a new checkpoint.
 450                  */
 451             }
 452             else
 453             {
 454                 gmx_file_rename(fn, buf);
 455             }
 456         }
 457
 458         /* Rename the checkpoint file from the temporary to the final name */
 459         mpiBarrierBeforeRename(applyMpiBarrierBeforeRename, mpiBarrierCommunicator);
 460
 461         if (gmx_file_rename(fntemp, fn) != 0)
 462         {
 463             gmx_file("Cannot rename checkpoint file; maybe you are out of disk space?");
 464         }
 465     }
 466 #endif /* GMX_NO_RENAME */
 467
 468     sfree(fntemp);
 469
 470 #if GMX_FAHCORE
 471     /*code for alternate checkpointing scheme.  moved from top of loop over
 472        steps */
 473     fcRequestCheckPoint();
 474     if (fcCheckPointParallel(cr->nodeid, NULL, 0) == 0)
 475     {
 476         gmx_fatal(3, __FILE__, __LINE__, "Checkpoint error on step %d\n", step);
 477     }
 478 #endif /* end GMX_FAHCORE block */
 479 }
 480
 481 void mdoutf_write_checkpoint(gmx_mdoutf_t                    of,
 482                              FILE*                           fplog,
 483                              const t_commrec*                cr,
 484                              int64_t                         step,
 485                              double                          t,
 486                              t_state*                        state_global,
 487                              ObservablesHistory*             observablesHistory,
 488                              gmx::WriteCheckpointDataHolder* modularSimulatorCheckpointData)
 489 {
 490     fflush_tng(of->tng);
 491     fflush_tng(of->tng_low_prec);
 492     /* Write the checkpoint file.
 493      * When simulations share the state, an MPI barrier is applied before
 494      * renaming old and new checkpoint files to minimize the risk of
 495      * checkpoint files getting out of sync.
 496      */
 497     ivec one_ivec = { 1, 1, 1 };
 498     write_checkpoint(of->fn_cpt, of->bKeepAndNumCPT, fplog, cr,
 499                      DOMAINDECOMP(cr) ? cr->dd->numCells : one_ivec,
 500                      DOMAINDECOMP(cr) ? cr->dd->nnodes : cr->nnodes, of->eIntegrator,
 501                      of->simulation_part, of->bExpanded, of->elamstats, step, t, state_global,
 502                      observablesHistory, *(of->mdModulesNotifier), modularSimulatorCheckpointData,
 503                      of->simulationsShareState, of->mastersComm);
 504 }
 505
 506 void mdoutf_write_to_trajectory_files(FILE*                           fplog,
 507                                       const t_commrec*                cr,
 508                                       gmx_mdoutf_t                    of,
 509                                       int                             mdof_flags,
 510                                       int                             natoms,
 511                                       int64_t                         step,
 512                                       double                          t,
 513                                       t_state*                        state_local,
 514                                       t_state*                        state_global,
 515                                       ObservablesHistory*             observablesHistory,
 516                                       gmx::ArrayRef<const gmx::RVec>  f_local,
 517                                       gmx::WriteCheckpointDataHolder* modularSimulatorCheckpointData)
 518 {
 519     const rvec* f_global;
 520
 521     if (DOMAINDECOMP(cr))
 522     {
 523         if (mdof_flags & MDOF_CPT)
 524         {
 525             dd_collect_state(cr->dd, state_local, state_global);
 526         }
 527         else
 528         {
 529             if (mdof_flags & (MDOF_X | MDOF_X_COMPRESSED))
 530             {
 531                 auto globalXRef = MASTER(cr) ? state_global->x : gmx::ArrayRef<gmx::RVec>();
 532                 dd_collect_vec(cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl,
 533                                state_local->cg_gl, state_local->x, globalXRef);
 534             }
 535             if (mdof_flags & MDOF_V)
 536             {
 537                 auto globalVRef = MASTER(cr) ? state_global->v : gmx::ArrayRef<gmx::RVec>();
 538                 dd_collect_vec(cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl,
 539                                state_local->cg_gl, state_local->v, globalVRef);
 540             }
 541         }
 542         f_global = of->f_global;
 543         if (mdof_flags & MDOF_F)
 544         {
 545             dd_collect_vec(
 546                     cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl, state_local->cg_gl, f_local,
 547                     gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(of->f_global), f_local.size()));
 548         }
 549     }
 550     else
 551     {
 552         /* We have the whole state locally: copy the local state pointer */
 553         state_global = state_local;
 554
 555         f_global = as_rvec_array(f_local.data());
 556     }
 557
 558     if (MASTER(cr))
 559     {
 560         if (mdof_flags & MDOF_CPT)
 561         {
 562             mdoutf_write_checkpoint(of, fplog, cr, step, t, state_global, observablesHistory,
 563                                     modularSimulatorCheckpointData);
 564         }
 565
 566         if (mdof_flags & (MDOF_X | MDOF_V | MDOF_F))
 567         {
 568             const rvec* x = (mdof_flags & MDOF_X) ? state_global->x.rvec_array() : nullptr;
 569             const rvec* v = (mdof_flags & MDOF_V) ? state_global->v.rvec_array() : nullptr;
 570             const rvec* f = (mdof_flags & MDOF_F) ? f_global : nullptr;
 571
 572             if (of->fp_trn)
 573             {
 574                 gmx_trr_write_frame(of->fp_trn, step, t, state_local->lambda[efptFEP],
 575                                     state_local->box, natoms, x, v, f);
 576                 if (gmx_fio_flush(of->fp_trn) != 0)
 577                 {
 578                     gmx_file("Cannot write trajectory; maybe you are out of disk space?");
 579                 }
 580             }
 581
 582             /* If a TNG file is open for uncompressed coordinate output also write
 583                velocities and forces to it. */
 584             else if (of->tng)
 585             {
 586                 gmx_fwrite_tng(of->tng, FALSE, step, t, state_local->lambda[efptFEP],
 587                                state_local->box, natoms, x, v, f);
 588             }
 589             /* If only a TNG file is open for compressed coordinate output (no uncompressed
 590                coordinate output) also write forces and velocities to it. */
 591             else if (of->tng_low_prec)
 592             {
 593                 gmx_fwrite_tng(of->tng_low_prec, FALSE, step, t, state_local->lambda[efptFEP],
 594                                state_local->box, natoms, x, v, f);
 595             }
 596         }
 597         if (mdof_flags & MDOF_X_COMPRESSED)
 598         {
 599             rvec* xxtc = nullptr;
 600
 601             if (of->natoms_x_compressed == of->natoms_global)
 602             {
 603                 /* We are writing the positions of all of the atoms to
 604                    the compressed output */
 605                 xxtc = state_global->x.rvec_array();
 606             }
 607             else
 608             {
 609                 /* We are writing the positions of only a subset of
 610                    the atoms to the compressed output, so we have to
 611                    make a copy of the subset of coordinates. */
 612                 int i, j;
 613
 614                 snew(xxtc, of->natoms_x_compressed);
 615                 auto x = makeArrayRef(state_global->x);
 616                 for (i = 0, j = 0; (i < of->natoms_global); i++)
 617                 {
 618                     if (getGroupType(*of->groups, SimulationAtomGroupType::CompressedPositionOutput, i) == 0)
 619                     {
 620                         copy_rvec(x[i], xxtc[j++]);
 621                     }
 622                 }
 623             }
 624             if (write_xtc(of->fp_xtc, of->natoms_x_compressed, step, t, state_local->box, xxtc,
 625                           of->x_compression_precision)
 626                 == 0)
 627             {
 628                 gmx_fatal(FARGS,
 629                           "XTC error. This indicates you are out of disk space, or a "
 630                           "simulation with major instabilities resulting in coordinates "
 631                           "that are NaN or too large to be represented in the XTC format.\n");
 632             }
 633             gmx_fwrite_tng(of->tng_low_prec, TRUE, step, t, state_local->lambda[efptFEP],
 634                            state_local->box, of->natoms_x_compressed, xxtc, nullptr, nullptr);
 635             if (of->natoms_x_compressed != of->natoms_global)
 636             {
 637                 sfree(xxtc);
 638             }
 639         }
 640         if (mdof_flags & (MDOF_BOX | MDOF_LAMBDA) && !(mdof_flags & (MDOF_X | MDOF_V | MDOF_F)))
 641         {
 642             if (of->tng)
 643             {
 644                 real  lambda = -1;
 645                 rvec* box    = nullptr;
 646                 if (mdof_flags & MDOF_BOX)
 647                 {
 648                     box = state_local->box;
 649                 }
 650                 if (mdof_flags & MDOF_LAMBDA)
 651                 {
 652                     lambda = state_local->lambda[efptFEP];
 653                 }
 654                 gmx_fwrite_tng(of->tng, FALSE, step, t, lambda, box, natoms, nullptr, nullptr, nullptr);
 655             }
 656         }
 657         if (mdof_flags & (MDOF_BOX_COMPRESSED | MDOF_LAMBDA_COMPRESSED)
 658             && !(mdof_flags & (MDOF_X_COMPRESSED)))
 659         {
 660             if (of->tng_low_prec)
 661             {
 662                 real  lambda = -1;
 663                 rvec* box    = nullptr;
 664                 if (mdof_flags & MDOF_BOX_COMPRESSED)
 665                 {
 666                     box = state_local->box;
 667                 }
 668                 if (mdof_flags & MDOF_LAMBDA_COMPRESSED)
 669                 {
 670                     lambda = state_local->lambda[efptFEP];
 671                 }
 672                 gmx_fwrite_tng(of->tng_low_prec, FALSE, step, t, lambda, box, natoms, nullptr,
 673                                nullptr, nullptr);
 674             }
 675         }
 676     }
 677 }
 678
 679 void mdoutf_tng_close(gmx_mdoutf_t of)
 680 {
 681     if (of->tng || of->tng_low_prec)
 682     {
 683         wallcycle_start(of->wcycle, ewcTRAJ);
 684         gmx_tng_close(&of->tng);
 685         gmx_tng_close(&of->tng_low_prec);
 686         wallcycle_stop(of->wcycle, ewcTRAJ);
 687     }
 688 }
 689
 690 void done_mdoutf(gmx_mdoutf_t of)
 691 {
 692     if (of->fp_ene != nullptr)
 693     {
 694         done_ener_file(of->fp_ene);
 695     }
 696     if (of->fp_xtc)
 697     {
 698         close_xtc(of->fp_xtc);
 699     }
 700     if (of->fp_trn)
 701     {
 702         gmx_trr_close(of->fp_trn);
 703     }
 704     if (of->fp_dhdl != nullptr)
 705     {
 706         gmx_fio_fclose(of->fp_dhdl);
 707     }
 708     of->outputProvider->finishOutput();
 709     if (of->f_global != nullptr)
 710     {
 711         sfree(of->f_global);
 712     }
 713
 714     gmx_tng_close(&of->tng);
 715     gmx_tng_close(&of->tng_low_prec);
 716
 717     sfree(of);
 718 }
 719
 720 int mdoutf_get_tng_box_output_interval(gmx_mdoutf_t of)
 721 {
 722     if (of->tng)
 723     {
 724         return gmx_tng_get_box_output_interval(of->tng);
 725     }
 726     return 0;
 727 }
 728
 729 int mdoutf_get_tng_lambda_output_interval(gmx_mdoutf_t of)
 730 {
 731     if (of->tng)
 732     {
 733         return gmx_tng_get_lambda_output_interval(of->tng);
 734     }
 735     return 0;
 736 }
 737
 738 int mdoutf_get_tng_compressed_box_output_interval(gmx_mdoutf_t of)
 739 {
 740     if (of->tng_low_prec)
 741     {
 742         return gmx_tng_get_box_output_interval(of->tng_low_prec);
 743     }
 744     return 0;
 745 }
 746
 747 int mdoutf_get_tng_compressed_lambda_output_interval(gmx_mdoutf_t of)
 748 {
 749     if (of->tng_low_prec)
 750     {
 751         return gmx_tng_get_lambda_output_interval(of->tng_low_prec);
 752     }
 753     return 0;
 754 }