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) 2018,2019,2020,2021, 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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  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     /* Always FAH checkpoint immediately after a GROMACS checkpoint.
 472      *
 473      * Note that it is critical that we save a FAH checkpoint directly
 474      * after writing a GROMACS checkpoint. If the program dies, either
 475      * by the machine powering off suddenly or the process being,
 476      * killed, FAH can recover files that have only appended data by
 477      * truncating them to the last recorded length. The GROMACS
 478      * checkpoint does not just append data, it is fully rewritten each
 479      * time so a crash between moving the new Gromacs checkpoint file in
 480      * to place and writing a FAH checkpoint is not recoverable. Thus
 481      * the time between these operations must be kept as short as
 482      * possible.
 483      */
 484     fcCheckpoint();
 485 #endif /* end GMX_FAHCORE block */
 486 }
 487
 488 void mdoutf_write_checkpoint(gmx_mdoutf_t                    of,
 489                              FILE*                           fplog,
 490                              const t_commrec*                cr,
 491                              int64_t                         step,
 492                              double                          t,
 493                              t_state*                        state_global,
 494                              ObservablesHistory*             observablesHistory,
 495                              gmx::WriteCheckpointDataHolder* modularSimulatorCheckpointData)
 496 {
 497     fflush_tng(of->tng);
 498     fflush_tng(of->tng_low_prec);
 499     /* Write the checkpoint file.
 500      * When simulations share the state, an MPI barrier is applied before
 501      * renaming old and new checkpoint files to minimize the risk of
 502      * checkpoint files getting out of sync.
 503      */
 504     ivec one_ivec = { 1, 1, 1 };
 505     write_checkpoint(of->fn_cpt, of->bKeepAndNumCPT, fplog, cr,
 506                      DOMAINDECOMP(cr) ? cr->dd->numCells : one_ivec,
 507                      DOMAINDECOMP(cr) ? cr->dd->nnodes : cr->nnodes, of->eIntegrator,
 508                      of->simulation_part, of->bExpanded, of->elamstats, step, t, state_global,
 509                      observablesHistory, *(of->mdModulesNotifier), modularSimulatorCheckpointData,
 510                      of->simulationsShareState, of->mastersComm);
 511 }
 512
 513 void mdoutf_write_to_trajectory_files(FILE*                           fplog,
 514                                       const t_commrec*                cr,
 515                                       gmx_mdoutf_t                    of,
 516                                       int                             mdof_flags,
 517                                       int                             natoms,
 518                                       int64_t                         step,
 519                                       double                          t,
 520                                       t_state*                        state_local,
 521                                       t_state*                        state_global,
 522                                       ObservablesHistory*             observablesHistory,
 523                                       gmx::ArrayRef<const gmx::RVec>  f_local,
 524                                       gmx::WriteCheckpointDataHolder* modularSimulatorCheckpointData)
 525 {
 526     const rvec* f_global;
 527
 528     if (DOMAINDECOMP(cr))
 529     {
 530         if (mdof_flags & MDOF_CPT)
 531         {
 532             dd_collect_state(cr->dd, state_local, state_global);
 533         }
 534         else
 535         {
 536             if (mdof_flags & (MDOF_X | MDOF_X_COMPRESSED))
 537             {
 538                 auto globalXRef = MASTER(cr) ? state_global->x : gmx::ArrayRef<gmx::RVec>();
 539                 dd_collect_vec(cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl,
 540                                state_local->cg_gl, state_local->x, globalXRef);
 541             }
 542             if (mdof_flags & MDOF_V)
 543             {
 544                 auto globalVRef = MASTER(cr) ? state_global->v : gmx::ArrayRef<gmx::RVec>();
 545                 dd_collect_vec(cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl,
 546                                state_local->cg_gl, state_local->v, globalVRef);
 547             }
 548         }
 549         f_global = of->f_global;
 550         if (mdof_flags & MDOF_F)
 551         {
 552             dd_collect_vec(
 553                     cr->dd, state_local->ddp_count, state_local->ddp_count_cg_gl, state_local->cg_gl, f_local,
 554                     gmx::arrayRefFromArray(reinterpret_cast<gmx::RVec*>(of->f_global), f_local.size()));
 555         }
 556     }
 557     else
 558     {
 559         /* We have the whole state locally: copy the local state pointer */
 560         state_global = state_local;
 561
 562         f_global = as_rvec_array(f_local.data());
 563     }
 564
 565     if (MASTER(cr))
 566     {
 567         if (mdof_flags & MDOF_CPT)
 568         {
 569             mdoutf_write_checkpoint(of, fplog, cr, step, t, state_global, observablesHistory,
 570                                     modularSimulatorCheckpointData);
 571         }
 572
 573         if (mdof_flags & (MDOF_X | MDOF_V | MDOF_F))
 574         {
 575             const rvec* x = (mdof_flags & MDOF_X) ? state_global->x.rvec_array() : nullptr;
 576             const rvec* v = (mdof_flags & MDOF_V) ? state_global->v.rvec_array() : nullptr;
 577             const rvec* f = (mdof_flags & MDOF_F) ? f_global : nullptr;
 578
 579             if (of->fp_trn)
 580             {
 581                 gmx_trr_write_frame(of->fp_trn, step, t, state_local->lambda[efptFEP],
 582                                     state_local->box, natoms, x, v, f);
 583                 if (gmx_fio_flush(of->fp_trn) != 0)
 584                 {
 585                     gmx_file("Cannot write trajectory; maybe you are out of disk space?");
 586                 }
 587             }
 588
 589             /* If a TNG file is open for uncompressed coordinate output also write
 590                velocities and forces to it. */
 591             else if (of->tng)
 592             {
 593                 gmx_fwrite_tng(of->tng, FALSE, step, t, state_local->lambda[efptFEP],
 594                                state_local->box, natoms, x, v, f);
 595             }
 596             /* If only a TNG file is open for compressed coordinate output (no uncompressed
 597                coordinate output) also write forces and velocities to it. */
 598             else if (of->tng_low_prec)
 599             {
 600                 gmx_fwrite_tng(of->tng_low_prec, FALSE, step, t, state_local->lambda[efptFEP],
 601                                state_local->box, natoms, x, v, f);
 602             }
 603         }
 604         if (mdof_flags & MDOF_X_COMPRESSED)
 605         {
 606             rvec* xxtc = nullptr;
 607
 608             if (of->natoms_x_compressed == of->natoms_global)
 609             {
 610                 /* We are writing the positions of all of the atoms to
 611                    the compressed output */
 612                 xxtc = state_global->x.rvec_array();
 613             }
 614             else
 615             {
 616                 /* We are writing the positions of only a subset of
 617                    the atoms to the compressed output, so we have to
 618                    make a copy of the subset of coordinates. */
 619                 int i, j;
 620
 621                 snew(xxtc, of->natoms_x_compressed);
 622                 auto x = makeArrayRef(state_global->x);
 623                 for (i = 0, j = 0; (i < of->natoms_global); i++)
 624                 {
 625                     if (getGroupType(*of->groups, SimulationAtomGroupType::CompressedPositionOutput, i) == 0)
 626                     {
 627                         copy_rvec(x[i], xxtc[j++]);
 628                     }
 629                 }
 630             }
 631             if (write_xtc(of->fp_xtc, of->natoms_x_compressed, step, t, state_local->box, xxtc,
 632                           of->x_compression_precision)
 633                 == 0)
 634             {
 635                 gmx_fatal(FARGS,
 636                           "XTC error. This indicates you are out of disk space, or a "
 637                           "simulation with major instabilities resulting in coordinates "
 638                           "that are NaN or too large to be represented in the XTC format.\n");
 639             }
 640             gmx_fwrite_tng(of->tng_low_prec, TRUE, step, t, state_local->lambda[efptFEP],
 641                            state_local->box, of->natoms_x_compressed, xxtc, nullptr, nullptr);
 642             if (of->natoms_x_compressed != of->natoms_global)
 643             {
 644                 sfree(xxtc);
 645             }
 646         }
 647         if (mdof_flags & (MDOF_BOX | MDOF_LAMBDA) && !(mdof_flags & (MDOF_X | MDOF_V | MDOF_F)))
 648         {
 649             if (of->tng)
 650             {
 651                 real  lambda = -1;
 652                 rvec* box    = nullptr;
 653                 if (mdof_flags & MDOF_BOX)
 654                 {
 655                     box = state_local->box;
 656                 }
 657                 if (mdof_flags & MDOF_LAMBDA)
 658                 {
 659                     lambda = state_local->lambda[efptFEP];
 660                 }
 661                 gmx_fwrite_tng(of->tng, FALSE, step, t, lambda, box, natoms, nullptr, nullptr, nullptr);
 662             }
 663         }
 664         if (mdof_flags & (MDOF_BOX_COMPRESSED | MDOF_LAMBDA_COMPRESSED)
 665             && !(mdof_flags & (MDOF_X_COMPRESSED)))
 666         {
 667             if (of->tng_low_prec)
 668             {
 669                 real  lambda = -1;
 670                 rvec* box    = nullptr;
 671                 if (mdof_flags & MDOF_BOX_COMPRESSED)
 672                 {
 673                     box = state_local->box;
 674                 }
 675                 if (mdof_flags & MDOF_LAMBDA_COMPRESSED)
 676                 {
 677                     lambda = state_local->lambda[efptFEP];
 678                 }
 679                 gmx_fwrite_tng(of->tng_low_prec, FALSE, step, t, lambda, box, natoms, nullptr,
 680                                nullptr, nullptr);
 681             }
 682         }
 683
 684 #if GMX_FAHCORE
 685         /* Write a FAH checkpoint after writing any other data.  We may end up
 686            checkpointing twice but it's fast so it's ok. */
 687         if ((mdof_flags & ~MDOF_CPT))
 688         {
 689             fcCheckpoint();
 690         }
 691 #endif
 692     }
 693 }
 694
 695 void mdoutf_tng_close(gmx_mdoutf_t of)
 696 {
 697     if (of->tng || of->tng_low_prec)
 698     {
 699         wallcycle_start(of->wcycle, ewcTRAJ);
 700         gmx_tng_close(&of->tng);
 701         gmx_tng_close(&of->tng_low_prec);
 702         wallcycle_stop(of->wcycle, ewcTRAJ);
 703     }
 704 }
 705
 706 void done_mdoutf(gmx_mdoutf_t of)
 707 {
 708     if (of->fp_ene != nullptr)
 709     {
 710         done_ener_file(of->fp_ene);
 711     }
 712     if (of->fp_xtc)
 713     {
 714         close_xtc(of->fp_xtc);
 715     }
 716     if (of->fp_trn)
 717     {
 718         gmx_trr_close(of->fp_trn);
 719     }
 720     if (of->fp_dhdl != nullptr)
 721     {
 722         gmx_fio_fclose(of->fp_dhdl);
 723     }
 724     of->outputProvider->finishOutput();
 725     if (of->f_global != nullptr)
 726     {
 727         sfree(of->f_global);
 728     }
 729
 730     gmx_tng_close(&of->tng);
 731     gmx_tng_close(&of->tng_low_prec);
 732
 733     sfree(of);
 734 }
 735
 736 int mdoutf_get_tng_box_output_interval(gmx_mdoutf_t of)
 737 {
 738     if (of->tng)
 739     {
 740         return gmx_tng_get_box_output_interval(of->tng);
 741     }
 742     return 0;
 743 }
 744
 745 int mdoutf_get_tng_lambda_output_interval(gmx_mdoutf_t of)
 746 {
 747     if (of->tng)
 748     {
 749         return gmx_tng_get_lambda_output_interval(of->tng);
 750     }
 751     return 0;
 752 }
 753
 754 int mdoutf_get_tng_compressed_box_output_interval(gmx_mdoutf_t of)
 755 {
 756     if (of->tng_low_prec)
 757     {
 758         return gmx_tng_get_box_output_interval(of->tng_low_prec);
 759     }
 760     return 0;
 761 }
 762
 763 int mdoutf_get_tng_compressed_lambda_output_interval(gmx_mdoutf_t of)
 764 {
 765     if (of->tng_low_prec)
 766     {
 767         return gmx_tng_get_lambda_output_interval(of->tng_low_prec);
 768     }
 769     return 0;
 770 }