src/gromacs/tools/dump.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2013, The GROMACS development team.
   6  * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
   7  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   8  * and including many others, as listed in the AUTHORS file in the
   9  * top-level source directory and at http://www.gromacs.org.
  10  *
  11  * GROMACS is free software; you can redistribute it and/or
  12  * modify it under the terms of the GNU Lesser General Public License
  13  * as published by the Free Software Foundation; either version 2.1
  14  * of the License, or (at your option) any later version.
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  19  * Lesser General Public License for more details.
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  36  */
  37 /*! \internal \file
  38  * \brief Implements gmx dump utility.
  39  *
  40  * \ingroup module_tools
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "dump.h"
  45
  46 #include "config.h"
  47
  48 #include <cassert>
  49 #include <cmath>
  50 #include <cstdio>
  51 #include <cstring>
  52
  53 #include "gromacs/commandline/cmdlineoptionsmodule.h"
  54 #include "gromacs/fileio/checkpoint.h"
  55 #include "gromacs/fileio/enxio.h"
  56 #include "gromacs/fileio/filetypes.h"
  57 #include "gromacs/fileio/gmxfio.h"
  58 #include "gromacs/fileio/mtxio.h"
  59 #include "gromacs/fileio/tngio.h"
  60 #include "gromacs/fileio/tpxio.h"
  61 #include "gromacs/fileio/trrio.h"
  62 #include "gromacs/fileio/xtcio.h"
  63 #include "gromacs/gmxpreprocess/gmxcpp.h"
  64 #include "gromacs/math/vecdump.h"
  65 #include "gromacs/mdrun/mdmodules.h"
  66 #include "gromacs/mdtypes/forcerec.h"
  67 #include "gromacs/mdtypes/inputrec.h"
  68 #include "gromacs/mdtypes/md_enums.h"
  69 #include "gromacs/mdtypes/state.h"
  70 #include "gromacs/options/basicoptions.h"
  71 #include "gromacs/options/filenameoption.h"
  72 #include "gromacs/options/ioptionscontainer.h"
  73 #include "gromacs/topology/mtop_util.h"
  74 #include "gromacs/topology/topology.h"
  75 #include "gromacs/trajectory/energyframe.h"
  76 #include "gromacs/trajectory/trajectoryframe.h"
  77 #include "gromacs/utility/arraysize.h"
  78 #include "gromacs/utility/basedefinitions.h"
  79 #include "gromacs/utility/fatalerror.h"
  80 #include "gromacs/utility/futil.h"
  81 #include "gromacs/utility/smalloc.h"
  82 #include "gromacs/utility/txtdump.h"
  83
  84 namespace gmx
  85 {
  86
  87 namespace
  88 {
  89
  90 //! Dump a TPR file
  91 void list_tpr(const char *fn,
  92               gmx_bool    bShowNumbers,
  93               gmx_bool    bShowParameters,
  94               const char *mdpfn,
  95               gmx_bool    bSysTop,
  96               gmx_bool    bOriginalInputrec)
  97 {
  98     FILE         *gp;
  99     int           indent, atot;
 100     t_state       state;
 101     t_tpxheader   tpx;
 102     gmx_mtop_t    mtop;
 103     t_topology    top;
 104
 105     read_tpxheader(fn, &tpx, TRUE);
 106     t_inputrec     ir;
 107     read_tpx_state(fn,
 108                    tpx.bIr ? &ir : nullptr,
 109                    &state,
 110                    tpx.bTop ? &mtop : nullptr);
 111     if (tpx.bIr && !bOriginalInputrec)
 112     {
 113         MDModules().adjustInputrecBasedOnModules(&ir);
 114     }
 115
 116     if (mdpfn && tpx.bIr)
 117     {
 118         gp = gmx_fio_fopen(mdpfn, "w");
 119         pr_inputrec(gp, 0, nullptr, &ir, TRUE);
 120         gmx_fio_fclose(gp);
 121     }
 122
 123     if (!mdpfn)
 124     {
 125         if (bSysTop)
 126         {
 127             top = gmx_mtop_t_to_t_topology(&mtop, false);
 128         }
 129
 130         if (available(stdout, &tpx, 0, fn))
 131         {
 132             indent = 0;
 133             pr_title(stdout, indent, fn);
 134             pr_inputrec(stdout, 0, "inputrec", tpx.bIr ? &ir : nullptr, FALSE);
 135
 136             pr_tpxheader(stdout, indent, "header", &(tpx));
 137
 138             if (!bSysTop)
 139             {
 140                 pr_mtop(stdout, indent, "topology", &(mtop), bShowNumbers, bShowParameters);
 141             }
 142             else
 143             {
 144                 pr_top(stdout, indent, "topology", &(top), bShowNumbers, bShowParameters);
 145             }
 146
 147             pr_rvecs(stdout, indent, "box", tpx.bBox ? state.box : nullptr, DIM);
 148             pr_rvecs(stdout, indent, "box_rel", tpx.bBox ? state.box_rel : nullptr, DIM);
 149             pr_rvecs(stdout, indent, "boxv", tpx.bBox ? state.boxv : nullptr, DIM);
 150             pr_rvecs(stdout, indent, "pres_prev", tpx.bBox ? state.pres_prev : nullptr, DIM);
 151             pr_rvecs(stdout, indent, "svir_prev", tpx.bBox ? state.svir_prev : nullptr, DIM);
 152             pr_rvecs(stdout, indent, "fvir_prev", tpx.bBox ? state.fvir_prev : nullptr, DIM);
 153             /* leave nosehoover_xi in for now to match the tpr version */
 154             pr_doubles(stdout, indent, "nosehoover_xi", state.nosehoover_xi.data(), state.ngtc);
 155             /*pr_doubles(stdout,indent,"nosehoover_vxi",state.nosehoover_vxi,state.ngtc);*/
 156             /*pr_doubles(stdout,indent,"therm_integral",state.therm_integral,state.ngtc);*/
 157             pr_rvecs(stdout, indent, "x", tpx.bX ? state.x.rvec_array() : nullptr, state.natoms);
 158             pr_rvecs(stdout, indent, "v", tpx.bV ? state.v.rvec_array() : nullptr, state.natoms);
 159         }
 160
 161         const SimulationGroups &groups = mtop.groups;
 162
 163         gmx::EnumerationArray < SimulationAtomGroupType, std::vector < int>> gcount;
 164         for (auto group : keysOf(gcount))
 165         {
 166             gcount[group].resize(groups.groups[group].nr);
 167         }
 168
 169         for (int i = 0; (i < mtop.natoms); i++)
 170         {
 171             for (auto group : keysOf(gcount))
 172             {
 173                 gcount[group][getGroupType(groups, group, i)]++;
 174             }
 175         }
 176         printf("Group statistics\n");
 177         for (auto group : keysOf(gcount))
 178         {
 179             atot = 0;
 180             printf("%-12s: ", shortName(group));
 181             for (int j = 0; (j < groups.groups[group].nr); j++)
 182             {
 183                 printf("  %5d", gcount[group][j]);
 184                 atot += gcount[group][j];
 185             }
 186             printf("  (total %d atoms)\n", atot);
 187         }
 188     }
 189 }
 190
 191 //! Dump a topology file
 192 void list_top(const char *fn)
 193 {
 194     int       status, done;
 195     // Legacy string length macro
 196     char      buf[STRLEN];
 197     gmx_cpp_t handle;
 198     char     *cppopts[] = { nullptr };
 199
 200     status = cpp_open_file(fn, &handle, cppopts);
 201     if (status != 0)
 202     {
 203         gmx_fatal(FARGS, "%s", cpp_error(&handle, status));
 204     }
 205     do
 206     {
 207         status = cpp_read_line(&handle, STRLEN, buf);
 208         done   = static_cast<int>(status == eCPP_EOF);
 209         if (!done)
 210         {
 211             if (status != eCPP_OK)
 212             {
 213                 gmx_fatal(FARGS, "%s", cpp_error(&handle, status));
 214             }
 215             else
 216             {
 217                 printf("%s\n", buf);
 218             }
 219         }
 220     }
 221     while (done == 0);
 222     status = cpp_close_file(&handle);
 223     if (status != eCPP_OK)
 224     {
 225         gmx_fatal(FARGS, "%s", cpp_error(&handle, status));
 226     }
 227 }
 228
 229 //! Dump a TRR file
 230 void list_trr(const char *fn)
 231 {
 232     t_fileio         *fpread;
 233     int               nframe, indent;
 234     char              buf[256];
 235     rvec             *x, *v, *f;
 236     matrix            box;
 237     gmx_trr_header_t  trrheader;
 238     gmx_bool          bOK;
 239
 240     fpread  = gmx_trr_open(fn, "r");
 241
 242     nframe = 0;
 243     while (gmx_trr_read_frame_header(fpread, &trrheader, &bOK))
 244     {
 245         snew(x, trrheader.natoms);
 246         snew(v, trrheader.natoms);
 247         snew(f, trrheader.natoms);
 248         if (gmx_trr_read_frame_data(fpread, &trrheader,
 249                                     trrheader.box_size ? box : nullptr,
 250                                     trrheader.x_size   ? x : nullptr,
 251                                     trrheader.v_size   ? v : nullptr,
 252                                     trrheader.f_size   ? f : nullptr))
 253         {
 254             sprintf(buf, "%s frame %d", fn, nframe);
 255             indent = 0;
 256             indent = pr_title(stdout, indent, buf);
 257             pr_indent(stdout, indent);
 258             fprintf(stdout, "natoms=%10d  step=%10" PRId64 "  time=%12.7e  lambda=%10g\n",
 259                     trrheader.natoms, trrheader.step, trrheader.t, trrheader.lambda);
 260             if (trrheader.box_size)
 261             {
 262                 pr_rvecs(stdout, indent, "box", box, DIM);
 263             }
 264             if (trrheader.x_size)
 265             {
 266                 pr_rvecs(stdout, indent, "x", x, trrheader.natoms);
 267             }
 268             if (trrheader.v_size)
 269             {
 270                 pr_rvecs(stdout, indent, "v", v, trrheader.natoms);
 271             }
 272             if (trrheader.f_size)
 273             {
 274                 pr_rvecs(stdout, indent, "f", f, trrheader.natoms);
 275             }
 276         }
 277         else
 278         {
 279             fprintf(stderr, "\nWARNING: Incomplete frame: nr %d, t=%g\n",
 280                     nframe, trrheader.t);
 281         }
 282
 283         sfree(x);
 284         sfree(v);
 285         sfree(f);
 286         nframe++;
 287     }
 288     if (!bOK)
 289     {
 290         fprintf(stderr, "\nWARNING: Incomplete frame header: nr %d, t=%g\n",
 291                 nframe, trrheader.t);
 292     }
 293     gmx_trr_close(fpread);
 294 }
 295
 296 //! Dump an xtc file
 297 void list_xtc(const char *fn)
 298 {
 299     t_fileio   *xd;
 300     int         indent;
 301     char        buf[256];
 302     rvec       *x;
 303     matrix      box;
 304     int         nframe, natoms;
 305     int64_t     step;
 306     real        prec, time;
 307     gmx_bool    bOK;
 308
 309     xd = open_xtc(fn, "r");
 310     read_first_xtc(xd, &natoms, &step, &time, box, &x, &prec, &bOK);
 311
 312     nframe = 0;
 313     do
 314     {
 315         sprintf(buf, "%s frame %d", fn, nframe);
 316         indent = 0;
 317         indent = pr_title(stdout, indent, buf);
 318         pr_indent(stdout, indent);
 319         fprintf(stdout, "natoms=%10d  step=%10" PRId64 "  time=%12.7e  prec=%10g\n",
 320                 natoms, step, time, prec);
 321         pr_rvecs(stdout, indent, "box", box, DIM);
 322         pr_rvecs(stdout, indent, "x", x, natoms);
 323         nframe++;
 324     }
 325     while (read_next_xtc(xd, natoms, &step, &time, box, x, &prec, &bOK) != 0);
 326     if (!bOK)
 327     {
 328         fprintf(stderr, "\nWARNING: Incomplete frame at time %g\n", time);
 329     }
 330     sfree(x);
 331     close_xtc(xd);
 332 }
 333
 334 #if GMX_USE_TNG
 335
 336 /*! \brief Callback used by list_tng_for_gmx_dump. */
 337 void list_tng_inner(const char *fn,
 338                     gmx_bool    bFirstFrame,
 339                     real       *values,
 340                     int64_t     step,
 341                     double      frame_time,
 342                     int64_t     n_values_per_frame,
 343                     int64_t     n_atoms,
 344                     real        prec,
 345                     int64_t     nframe,
 346                     char       *block_name)
 347 {
 348     char                 buf[256];
 349     int                  indent = 0;
 350
 351     if (bFirstFrame)
 352     {
 353         sprintf(buf, "%s frame %" PRId64, fn, nframe);
 354         indent = 0;
 355         indent = pr_title(stdout, indent, buf);
 356         pr_indent(stdout, indent);
 357         fprintf(stdout, "natoms=%10" PRId64 "  step=%10" PRId64 "  time=%12.7e",
 358                 n_atoms, step, frame_time);
 359         if (prec > 0)
 360         {
 361             fprintf(stdout, "  prec=%10g", prec);
 362         }
 363         fprintf(stdout, "\n");
 364     }
 365     pr_reals_of_dim(stdout, indent, block_name, values, n_atoms, n_values_per_frame);
 366 }
 367
 368 #endif
 369
 370 //! Dump a TNG file
 371 void list_tng(const char *fn)
 372 {
 373 #if GMX_USE_TNG
 374     gmx_tng_trajectory_t tng;
 375     int64_t              nframe = 0;
 376     int64_t              i, *block_ids = nullptr, step, ndatablocks;
 377     gmx_bool             bOK;
 378     real                *values = nullptr;
 379
 380     gmx_tng_open(fn, 'r', &tng);
 381     gmx_print_tng_molecule_system(tng, stdout);
 382
 383     bOK    = gmx_get_tng_data_block_types_of_next_frame(tng, -1,
 384                                                         0,
 385                                                         nullptr,
 386                                                         &step, &ndatablocks,
 387                                                         &block_ids);
 388     do
 389     {
 390         for (i = 0; i < ndatablocks; i++)
 391         {
 392             double               frame_time;
 393             real                 prec;
 394             int64_t              n_values_per_frame, n_atoms;
 395             char                 block_name[STRLEN];
 396
 397             gmx_get_tng_data_next_frame_of_block_type(tng, block_ids[i], &values,
 398                                                       &step, &frame_time,
 399                                                       &n_values_per_frame, &n_atoms,
 400                                                       &prec,
 401                                                       block_name, STRLEN, &bOK);
 402             if (!bOK)
 403             {
 404                 /* Can't write any output because we don't know what
 405                    arrays are valid. */
 406                 fprintf(stderr, "\nWARNING: Incomplete frame at time %g, will not write output\n", frame_time);
 407             }
 408             else
 409             {
 410                 list_tng_inner(fn, (0 == i), values, step, frame_time,
 411                                n_values_per_frame, n_atoms, prec, nframe, block_name);
 412             }
 413         }
 414         nframe++;
 415     }
 416     while (gmx_get_tng_data_block_types_of_next_frame(tng, step,
 417                                                       0,
 418                                                       nullptr,
 419                                                       &step,
 420                                                       &ndatablocks,
 421                                                       &block_ids));
 422
 423     if (block_ids)
 424     {
 425         sfree(block_ids);
 426     }
 427     sfree(values);
 428     gmx_tng_close(&tng);
 429 #else
 430     GMX_UNUSED_VALUE(fn);
 431 #endif
 432 }
 433
 434 //! Dump a trajectory file
 435 void list_trx(const char *fn)
 436 {
 437     switch (fn2ftp(fn))
 438     {
 439         case efXTC:
 440             list_xtc(fn);
 441             break;
 442         case efTRR:
 443             list_trr(fn);
 444             break;
 445         case efTNG:
 446             list_tng(fn);
 447             break;
 448         default:
 449             fprintf(stderr, "File %s is of an unsupported type. Try using the command\n 'less %s'\n",
 450                     fn, fn);
 451     }
 452 }
 453
 454 //! Dump an energy file
 455 void list_ene(const char *fn)
 456 {
 457     ener_file_t    in;
 458     gmx_bool       bCont;
 459     gmx_enxnm_t   *enm = nullptr;
 460     t_enxframe    *fr;
 461     int            i, j, nre, b;
 462     char           buf[22];
 463
 464     printf("gmx dump: %s\n", fn);
 465     in = open_enx(fn, "r");
 466     do_enxnms(in, &nre, &enm);
 467     assert(enm);
 468
 469     printf("energy components:\n");
 470     for (i = 0; (i < nre); i++)
 471     {
 472         printf("%5d  %-24s (%s)\n", i, enm[i].name, enm[i].unit);
 473     }
 474
 475     snew(fr, 1);
 476     do
 477     {
 478         bCont = do_enx(in, fr);
 479
 480         if (bCont)
 481         {
 482             printf("\n%24s  %12.5e  %12s  %12s\n", "time:",
 483                    fr->t, "step:", gmx_step_str(fr->step, buf));
 484             printf("%24s  %12s  %12s  %12s\n",
 485                    "", "", "nsteps:", gmx_step_str(fr->nsteps, buf));
 486             printf("%24s  %12.5e  %12s  %12s\n",
 487                    "delta_t:", fr->dt, "sum steps:", gmx_step_str(fr->nsum, buf));
 488             if (fr->nre == nre)
 489             {
 490                 printf("%24s  %12s  %12s  %12s\n",
 491                        "Component", "Energy", "Av. Energy", "Sum Energy");
 492                 if (fr->nsum > 0)
 493                 {
 494                     for (i = 0; (i < nre); i++)
 495                     {
 496                         printf("%24s  %12.5e  %12.5e  %12.5e\n",
 497                                enm[i].name, fr->ener[i].e, fr->ener[i].eav,
 498                                fr->ener[i].esum);
 499                     }
 500                 }
 501                 else
 502                 {
 503                     for (i = 0; (i < nre); i++)
 504                     {
 505                         printf("%24s  %12.5e\n",
 506                                enm[i].name, fr->ener[i].e);
 507                     }
 508                 }
 509             }
 510             for (b = 0; b < fr->nblock; b++)
 511             {
 512                 const char *typestr = "";
 513
 514                 t_enxblock *eb = &(fr->block[b]);
 515                 printf("Block data %2d (%3d subblocks, id=%d)\n",
 516                        b, eb->nsub, eb->id);
 517
 518                 if (eb->id < enxNR)
 519                 {
 520                     typestr = enx_block_id_name[eb->id];
 521                 }
 522                 printf("  id='%s'\n", typestr);
 523                 for (i = 0; i < eb->nsub; i++)
 524                 {
 525                     t_enxsubblock *sb = &(eb->sub[i]);
 526                     printf("  Sub block %3d (%5d elems, type=%s) values:\n",
 527                            i, sb->nr, xdr_datatype_names[sb->type]);
 528
 529                     switch (sb->type)
 530                     {
 531                         case xdr_datatype_float:
 532                             for (j = 0; j < sb->nr; j++)
 533                             {
 534                                 printf("%14d   %8.4f\n", j, sb->fval[j]);
 535                             }
 536                             break;
 537                         case xdr_datatype_double:
 538                             for (j = 0; j < sb->nr; j++)
 539                             {
 540                                 printf("%14d   %10.6f\n", j, sb->dval[j]);
 541                             }
 542                             break;
 543                         case xdr_datatype_int:
 544                             for (j = 0; j < sb->nr; j++)
 545                             {
 546                                 printf("%14d %10d\n", j, sb->ival[j]);
 547                             }
 548                             break;
 549                         case xdr_datatype_int64:
 550                             for (j = 0; j < sb->nr; j++)
 551                             {
 552                                 printf("%14d %s\n",
 553                                        j, gmx_step_str(sb->lval[j], buf));
 554                             }
 555                             break;
 556                         case xdr_datatype_char:
 557                             for (j = 0; j < sb->nr; j++)
 558                             {
 559                                 printf("%14d %1c\n", j, sb->cval[j]);
 560                             }
 561                             break;
 562                         case xdr_datatype_string:
 563                             for (j = 0; j < sb->nr; j++)
 564                             {
 565                                 printf("%14d %80s\n", j, sb->sval[j]);
 566                             }
 567                             break;
 568                         default:
 569                             gmx_incons("Unknown subblock type");
 570                     }
 571                 }
 572             }
 573         }
 574     }
 575     while (bCont);
 576
 577     close_enx(in);
 578
 579     free_enxframe(fr);
 580     sfree(fr);
 581     sfree(enm);
 582 }
 583
 584 //! Dump a (Hessian) matrix file
 585 void list_mtx(const char *fn)
 586 {
 587     int                  nrow, ncol, i, j, k;
 588     real                *full   = nullptr, value;
 589     gmx_sparsematrix_t * sparse = nullptr;
 590
 591     gmx_mtxio_read(fn, &nrow, &ncol, &full, &sparse);
 592
 593     if (full == nullptr)
 594     {
 595         snew(full, nrow*ncol);
 596         for (i = 0; i < nrow*ncol; i++)
 597         {
 598             full[i] = 0;
 599         }
 600
 601         for (i = 0; i < sparse->nrow; i++)
 602         {
 603             for (j = 0; j < sparse->ndata[i]; j++)
 604             {
 605                 k              = sparse->data[i][j].col;
 606                 value          = sparse->data[i][j].value;
 607                 full[i*ncol+k] = value;
 608                 full[k*ncol+i] = value;
 609             }
 610         }
 611         gmx_sparsematrix_destroy(sparse);
 612     }
 613
 614     printf("%d %d\n", nrow, ncol);
 615     for (i = 0; i < nrow; i++)
 616     {
 617         for (j = 0; j < ncol; j++)
 618         {
 619             printf(" %g", full[i*ncol+j]);
 620         }
 621         printf("\n");
 622     }
 623
 624     sfree(full);
 625 }
 626
 627 class Dump : public ICommandLineOptionsModule
 628 {
 629     public:
 630         Dump()
 631         {}
 632
 633         // From ICommandLineOptionsModule
 634         void init(CommandLineModuleSettings * /*settings*/) override
 635         {
 636         }
 637
 638         void initOptions(IOptionsContainer                 *options,
 639                          ICommandLineOptionsModuleSettings *settings) override;
 640
 641         void optionsFinished() override;
 642
 643         int run() override;
 644
 645     private:
 646         //! Commandline options
 647         //! \{
 648         bool bShowNumbers_      = true;
 649         bool bShowParams_       = false;
 650         bool bSysTop_           = false;
 651         bool bOriginalInputrec_ = false;
 652         //! \}
 653         //! Commandline file options
 654         //! \{
 655         std::string inputTprFilename_;
 656         std::string inputTrajectoryFilename_;
 657         std::string inputEnergyFilename_;
 658         std::string inputCheckpointFilename_;
 659         std::string inputTopologyFilename_;
 660         std::string inputMatrixFilename_;
 661         std::string outputMdpFilename_;
 662         //! \}
 663 };
 664
 665 void Dump::initOptions(IOptionsContainer                 *options,
 666                        ICommandLineOptionsModuleSettings *settings)
 667 {
 668     const char *desc[] = {
 669         "[THISMODULE] reads a run input file ([REF].tpr[ref]),",
 670         "a trajectory ([REF].trr[ref]/[REF].xtc[ref]/[TT]tng[tt]), an energy",
 671         "file ([REF].edr[ref]), a checkpoint file ([REF].cpt[ref])",
 672         "or topology file ([REF].top[ref])",
 673         "and prints that to standard output in a readable format.",
 674         "This program is essential for checking your run input file in case of",
 675         "problems."
 676     };
 677     settings->setHelpText(desc);
 678     // TODO If this ancient note acknowledging a bug is still true,
 679     // fix it or block that run path:
 680     //   Position restraint output from -sys -s is broken
 681
 682     options->addOption(FileNameOption("s")
 683                            .filetype(eftRunInput).inputFile()
 684                            .store(&inputTprFilename_)
 685                            .description("Run input file to dump"));
 686     options->addOption(FileNameOption("f")
 687                            .filetype(eftTrajectory).inputFile()
 688                            .store(&inputTrajectoryFilename_)
 689                            .description("Trajectory file to dump"));
 690     options->addOption(FileNameOption("e")
 691                            .filetype(eftEnergy).inputFile()
 692                            .store(&inputEnergyFilename_)
 693                            .description("Energy file to dump"));
 694     options->addOption(FileNameOption("cp")
 695                            .legacyType(efCPT).inputFile()
 696                            .store(&inputCheckpointFilename_)
 697                            .description("Checkpoint file to dump"));
 698     options->addOption(FileNameOption("p")
 699                            .legacyType(efTOP).inputFile()
 700                            .store(&inputTopologyFilename_)
 701                            .description("Topology file to dump"));
 702     options->addOption(FileNameOption("mtx")
 703                            .legacyType(efMTX).inputFile()
 704                            .store(&inputMatrixFilename_)
 705                            .description("Hessian matrix to dump"));
 706     options->addOption(FileNameOption("om")
 707                            .legacyType(efMDP).outputFile()
 708                            .store(&outputMdpFilename_)
 709                            .description("grompp input file from run input file"));
 710
 711     options->addOption(BooleanOption("nr")
 712                            .store(&bShowNumbers_).defaultValue(true)
 713                            .description("Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)"));
 714     options->addOption(BooleanOption("param")
 715                            .store(&bShowParams_).defaultValue(false)
 716                            .description("Show parameters for each bonded interaction (for comparing dumps, it is useful to combine this with -nonr)"));
 717     options->addOption(BooleanOption("sys")
 718                            .store(&bShowParams_).defaultValue(false)
 719                            .description("List the atoms and bonded interactions for the whole system instead of for each molecule type"));
 720     options->addOption(BooleanOption("orgir")
 721                            .store(&bShowParams_).defaultValue(false)
 722                            .description("Show input parameters from tpr as they were written by the version that produced the file, instead of how the current version reads them"));
 723 }
 724
 725 void Dump::optionsFinished()
 726 {
 727     // TODO Currently gmx dump ignores user input that seeks to dump
 728     // multiple files. Here, we could enforce that the user only asks
 729     // to dump one file.
 730 }
 731
 732 int Dump::run()
 733 {
 734     if (!inputTprFilename_.empty())
 735     {
 736         list_tpr(inputTprFilename_.c_str(), bShowNumbers_, bShowParams_,
 737                  outputMdpFilename_.c_str(), bSysTop_, bOriginalInputrec_);
 738     }
 739     else if (!inputTrajectoryFilename_.empty())
 740     {
 741         list_trx(inputTrajectoryFilename_.c_str());
 742     }
 743     else if (!inputEnergyFilename_.empty())
 744     {
 745         list_ene(inputEnergyFilename_.c_str());
 746     }
 747     else if (!inputCheckpointFilename_.empty())
 748     {
 749         list_checkpoint(inputCheckpointFilename_.c_str(), stdout);
 750     }
 751     else if (!inputTopologyFilename_.empty())
 752     {
 753         list_top(inputTopologyFilename_.c_str());
 754     }
 755     else if (!inputMatrixFilename_.empty())
 756     {
 757         list_mtx(inputMatrixFilename_.c_str());
 758     }
 759
 760     return 0;
 761 }
 762
 763 }   // namespace
 764
 765 const char DumpInfo::name[]             = "dump";
 766 const char DumpInfo::shortDescription[] =
 767     "Make binary files human readable";
 768 ICommandLineOptionsModulePointer DumpInfo::create()
 769 {
 770     return std::make_unique<Dump>();
 771 }
 772
 773 }   // namespace gmx