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48 #include "gromacs/commandline/pargs.h"
49 #include "gromacs/fileio/checkpoint.h"
50 #include "gromacs/fileio/enxio.h"
51 #include "gromacs/fileio/gmxfio.h"
52 #include "gromacs/fileio/mtxio.h"
53 #include "gromacs/fileio/tngio.h"
54 #include "gromacs/fileio/tpxio.h"
55 #include "gromacs/fileio/trrio.h"
56 #include "gromacs/fileio/xtcio.h"
57 #include "gromacs/gmxpreprocess/gmxcpp.h"
58 #include "gromacs/linearalgebra/sparsematrix.h"
59 #include "gromacs/math/vecdump.h"
60 #include "gromacs/mdrunutility/mdmodules.h"
61 #include "gromacs/mdtypes/forcerec.h"
62 #include "gromacs/mdtypes/inputrec.h"
63 #include "gromacs/mdtypes/md_enums.h"
64 #include "gromacs/mdtypes/state.h"
65 #include "gromacs/topology/mtop_util.h"
66 #include "gromacs/topology/topology.h"
67 #include "gromacs/trajectory/energyframe.h"
68 #include "gromacs/trajectory/trajectoryframe.h"
69 #include "gromacs/utility/arraysize.h"
70 #include "gromacs/utility/basedefinitions.h"
71 #include "gromacs/utility/fatalerror.h"
72 #include "gromacs/utility/futil.h"
73 #include "gromacs/utility/smalloc.h"
74 #include "gromacs/utility/txtdump.h"
76 static void list_tpx(const char *fn,
77 gmx_bool bShowNumbers,
78 gmx_bool bShowParameters,
81 gmx_bool bOriginalInputrec)
84 int indent, i, j, **gcount, atot;
91 read_tpxheader(fn, &tpx, TRUE);
94 tpx.bIr ? &ir : nullptr,
96 tpx.bTop ? &mtop : nullptr);
97 if (tpx.bIr && !bOriginalInputrec)
99 gmx::MDModules().adjustInputrecBasedOnModules(&ir);
102 if (mdpfn && tpx.bIr)
104 gp = gmx_fio_fopen(mdpfn, "w");
105 pr_inputrec(gp, 0, nullptr, &ir, TRUE);
113 top = gmx_mtop_t_to_t_topology(&mtop, false);
116 if (available(stdout, &tpx, 0, fn))
119 pr_title(stdout, indent, fn);
120 pr_inputrec(stdout, 0, "inputrec", tpx.bIr ? &ir : nullptr, FALSE);
122 pr_tpxheader(stdout, indent, "header", &(tpx));
126 pr_mtop(stdout, indent, "topology", &(mtop), bShowNumbers, bShowParameters);
130 pr_top(stdout, indent, "topology", &(top), bShowNumbers, bShowParameters);
133 pr_rvecs(stdout, indent, "box", tpx.bBox ? state.box : nullptr, DIM);
134 pr_rvecs(stdout, indent, "box_rel", tpx.bBox ? state.box_rel : nullptr, DIM);
135 pr_rvecs(stdout, indent, "boxv", tpx.bBox ? state.boxv : nullptr, DIM);
136 pr_rvecs(stdout, indent, "pres_prev", tpx.bBox ? state.pres_prev : nullptr, DIM);
137 pr_rvecs(stdout, indent, "svir_prev", tpx.bBox ? state.svir_prev : nullptr, DIM);
138 pr_rvecs(stdout, indent, "fvir_prev", tpx.bBox ? state.fvir_prev : nullptr, DIM);
139 /* leave nosehoover_xi in for now to match the tpr version */
140 pr_doubles(stdout, indent, "nosehoover_xi", state.nosehoover_xi.data(), state.ngtc);
141 /*pr_doubles(stdout,indent,"nosehoover_vxi",state.nosehoover_vxi,state.ngtc);*/
142 /*pr_doubles(stdout,indent,"therm_integral",state.therm_integral,state.ngtc);*/
143 pr_rvecs(stdout, indent, "x", tpx.bX ? state.x.rvec_array() : nullptr, state.natoms);
144 pr_rvecs(stdout, indent, "v", tpx.bV ? state.v.rvec_array() : nullptr, state.natoms);
147 groups = &mtop.groups;
150 for (i = 0; (i < egcNR); i++)
152 snew(gcount[i], groups->grps[i].nr);
155 for (i = 0; (i < mtop.natoms); i++)
157 for (j = 0; (j < egcNR); j++)
159 gcount[j][getGroupType(groups, j, i)]++;
162 printf("Group statistics\n");
163 for (i = 0; (i < egcNR); i++)
166 printf("%-12s: ", gtypes[i]);
167 for (j = 0; (j < groups->grps[i].nr); j++)
169 printf(" %5d", gcount[i][j]);
170 atot += gcount[i][j];
172 printf(" (total %d atoms)\n", atot);
179 static void list_top(const char *fn)
185 char *cppopts[] = { nullptr };
187 status = cpp_open_file(fn, &handle, cppopts);
190 gmx_fatal(FARGS, "%s", cpp_error(&handle, status));
194 status = cpp_read_line(&handle, BUFLEN, buf);
195 done = static_cast<int>(status == eCPP_EOF);
198 if (status != eCPP_OK)
200 gmx_fatal(FARGS, "%s", cpp_error(&handle, status));
209 status = cpp_close_file(&handle);
210 if (status != eCPP_OK)
212 gmx_fatal(FARGS, "%s", cpp_error(&handle, status));
216 static void list_trr(const char *fn)
223 gmx_trr_header_t trrheader;
226 fpread = gmx_trr_open(fn, "r");
229 while (gmx_trr_read_frame_header(fpread, &trrheader, &bOK))
231 snew(x, trrheader.natoms);
232 snew(v, trrheader.natoms);
233 snew(f, trrheader.natoms);
234 if (gmx_trr_read_frame_data(fpread, &trrheader,
235 trrheader.box_size ? box : nullptr,
236 trrheader.x_size ? x : nullptr,
237 trrheader.v_size ? v : nullptr,
238 trrheader.f_size ? f : nullptr))
240 sprintf(buf, "%s frame %d", fn, nframe);
242 indent = pr_title(stdout, indent, buf);
243 pr_indent(stdout, indent);
244 fprintf(stdout, "natoms=%10d step=%10" PRId64 " time=%12.7e lambda=%10g\n",
245 trrheader.natoms, trrheader.step, trrheader.t, trrheader.lambda);
246 if (trrheader.box_size)
248 pr_rvecs(stdout, indent, "box", box, DIM);
250 if (trrheader.x_size)
252 pr_rvecs(stdout, indent, "x", x, trrheader.natoms);
254 if (trrheader.v_size)
256 pr_rvecs(stdout, indent, "v", v, trrheader.natoms);
258 if (trrheader.f_size)
260 pr_rvecs(stdout, indent, "f", f, trrheader.natoms);
265 fprintf(stderr, "\nWARNING: Incomplete frame: nr %d, t=%g\n",
266 nframe, trrheader.t);
276 fprintf(stderr, "\nWARNING: Incomplete frame header: nr %d, t=%g\n",
277 nframe, trrheader.t);
279 gmx_trr_close(fpread);
282 static void list_xtc(const char *fn)
294 xd = open_xtc(fn, "r");
295 read_first_xtc(xd, &natoms, &step, &time, box, &x, &prec, &bOK);
300 sprintf(buf, "%s frame %d", fn, nframe);
302 indent = pr_title(stdout, indent, buf);
303 pr_indent(stdout, indent);
304 fprintf(stdout, "natoms=%10d step=%10" PRId64 " time=%12.7e prec=%10g\n",
305 natoms, step, time, prec);
306 pr_rvecs(stdout, indent, "box", box, DIM);
307 pr_rvecs(stdout, indent, "x", x, natoms);
310 while (read_next_xtc(xd, natoms, &step, &time, box, x, &prec, &bOK) != 0);
313 fprintf(stderr, "\nWARNING: Incomplete frame at time %g\n", time);
321 /*! \brief Callback used by list_tng_for_gmx_dump. */
322 static void list_tng_inner(const char *fn,
323 gmx_bool bFirstFrame,
327 int64_t n_values_per_frame,
338 sprintf(buf, "%s frame %" PRId64, fn, nframe);
340 indent = pr_title(stdout, indent, buf);
341 pr_indent(stdout, indent);
342 fprintf(stdout, "natoms=%10" PRId64 " step=%10" PRId64 " time=%12.7e",
343 n_atoms, step, frame_time);
346 fprintf(stdout, " prec=%10g", prec);
348 fprintf(stdout, "\n");
350 pr_reals_of_dim(stdout, indent, block_name, values, n_atoms, n_values_per_frame);
355 static void list_tng(const char gmx_unused *fn)
358 gmx_tng_trajectory_t tng;
360 int64_t i, *block_ids = nullptr, step, ndatablocks;
362 real *values = nullptr;
364 gmx_tng_open(fn, 'r', &tng);
365 gmx_print_tng_molecule_system(tng, stdout);
367 bOK = gmx_get_tng_data_block_types_of_next_frame(tng, -1,
374 for (i = 0; i < ndatablocks; i++)
378 int64_t n_values_per_frame, n_atoms;
379 char block_name[STRLEN];
381 gmx_get_tng_data_next_frame_of_block_type(tng, block_ids[i], &values,
383 &n_values_per_frame, &n_atoms,
385 block_name, STRLEN, &bOK);
388 /* Can't write any output because we don't know what
390 fprintf(stderr, "\nWARNING: Incomplete frame at time %g, will not write output\n", frame_time);
394 list_tng_inner(fn, (0 == i), values, step, frame_time,
395 n_values_per_frame, n_atoms, prec, nframe, block_name);
400 while (gmx_get_tng_data_block_types_of_next_frame(tng, step,
416 static void list_trx(const char *fn)
430 fprintf(stderr, "File %s is of an unsupported type. Try using the command\n 'less %s'\n",
435 static void list_ene(const char *fn)
439 gmx_enxnm_t *enm = nullptr;
444 printf("gmx dump: %s\n", fn);
445 in = open_enx(fn, "r");
446 do_enxnms(in, &nre, &enm);
449 printf("energy components:\n");
450 for (i = 0; (i < nre); i++)
452 printf("%5d %-24s (%s)\n", i, enm[i].name, enm[i].unit);
458 bCont = do_enx(in, fr);
462 printf("\n%24s %12.5e %12s %12s\n", "time:",
463 fr->t, "step:", gmx_step_str(fr->step, buf));
464 printf("%24s %12s %12s %12s\n",
465 "", "", "nsteps:", gmx_step_str(fr->nsteps, buf));
466 printf("%24s %12.5e %12s %12s\n",
467 "delta_t:", fr->dt, "sum steps:", gmx_step_str(fr->nsum, buf));
470 printf("%24s %12s %12s %12s\n",
471 "Component", "Energy", "Av. Energy", "Sum Energy");
474 for (i = 0; (i < nre); i++)
476 printf("%24s %12.5e %12.5e %12.5e\n",
477 enm[i].name, fr->ener[i].e, fr->ener[i].eav,
483 for (i = 0; (i < nre); i++)
485 printf("%24s %12.5e\n",
486 enm[i].name, fr->ener[i].e);
490 for (b = 0; b < fr->nblock; b++)
492 const char *typestr = "";
494 t_enxblock *eb = &(fr->block[b]);
495 printf("Block data %2d (%3d subblocks, id=%d)\n",
496 b, eb->nsub, eb->id);
500 typestr = enx_block_id_name[eb->id];
502 printf(" id='%s'\n", typestr);
503 for (i = 0; i < eb->nsub; i++)
505 t_enxsubblock *sb = &(eb->sub[i]);
506 printf(" Sub block %3d (%5d elems, type=%s) values:\n",
507 i, sb->nr, xdr_datatype_names[sb->type]);
511 case xdr_datatype_float:
512 for (j = 0; j < sb->nr; j++)
514 printf("%14d %8.4f\n", j, sb->fval[j]);
517 case xdr_datatype_double:
518 for (j = 0; j < sb->nr; j++)
520 printf("%14d %10.6f\n", j, sb->dval[j]);
523 case xdr_datatype_int:
524 for (j = 0; j < sb->nr; j++)
526 printf("%14d %10d\n", j, sb->ival[j]);
529 case xdr_datatype_int64:
530 for (j = 0; j < sb->nr; j++)
533 j, gmx_step_str(sb->lval[j], buf));
536 case xdr_datatype_char:
537 for (j = 0; j < sb->nr; j++)
539 printf("%14d %1c\n", j, sb->cval[j]);
542 case xdr_datatype_string:
543 for (j = 0; j < sb->nr; j++)
545 printf("%14d %80s\n", j, sb->sval[j]);
549 gmx_incons("Unknown subblock type");
564 static void list_mtx(const char *fn)
566 int nrow, ncol, i, j, k;
567 real *full = nullptr, value;
568 gmx_sparsematrix_t * sparse = nullptr;
570 gmx_mtxio_read(fn, &nrow, &ncol, &full, &sparse);
574 snew(full, nrow*ncol);
575 for (i = 0; i < nrow*ncol; i++)
580 for (i = 0; i < sparse->nrow; i++)
582 for (j = 0; j < sparse->ndata[i]; j++)
584 k = sparse->data[i][j].col;
585 value = sparse->data[i][j].value;
586 full[i*ncol+k] = value;
587 full[k*ncol+i] = value;
590 gmx_sparsematrix_destroy(sparse);
593 printf("%d %d\n", nrow, ncol);
594 for (i = 0; i < nrow; i++)
596 for (j = 0; j < ncol; j++)
598 printf(" %g", full[i*ncol+j]);
606 int gmx_dump(int argc, char *argv[])
608 const char *desc[] = {
609 "[THISMODULE] reads a run input file ([REF].tpr[ref]),",
610 "a trajectory ([REF].trr[ref]/[REF].xtc[ref]/[TT]/tng[tt]), an energy",
611 "file ([REF].edr[ref]) or a checkpoint file ([REF].cpt[ref])",
612 "and prints that to standard output in a readable format.",
613 "This program is essential for checking your run input file in case of",
615 "The program can also preprocess a topology to help finding problems.",
616 "Note that currently setting [TT]GMXLIB[tt] is the only way to customize",
617 "directories used for searching include files.",
619 const char *bugs[] = {
620 "Position restraint output from -sys -s is broken"
623 { efTPR, "-s", nullptr, ffOPTRD },
624 { efTRX, "-f", nullptr, ffOPTRD },
625 { efEDR, "-e", nullptr, ffOPTRD },
626 { efCPT, nullptr, nullptr, ffOPTRD },
627 { efTOP, "-p", nullptr, ffOPTRD },
628 { efMTX, "-mtx", "hessian", ffOPTRD },
629 { efMDP, "-om", nullptr, ffOPTWR }
631 #define NFILE asize(fnm)
633 gmx_output_env_t *oenv;
634 /* Command line options */
635 gmx_bool bShowNumbers = TRUE;
636 gmx_bool bShowParams = FALSE;
637 gmx_bool bSysTop = FALSE;
638 gmx_bool bOriginalInputrec = FALSE;
640 { "-nr", FALSE, etBOOL, {&bShowNumbers}, "Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)" },
641 { "-param", FALSE, etBOOL, {&bShowParams}, "Show parameters for each bonded interaction (for comparing dumps, it is useful to combine this with -nonr)" },
642 { "-sys", FALSE, etBOOL, {&bSysTop}, "List the atoms and bonded interactions for the whole system instead of for each molecule type" },
643 { "-orgir", FALSE, etBOOL, {&bOriginalInputrec}, "Show input parameters from tpr as they were written by the version that produced the file, instead of how the current version reads them" }
646 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
647 asize(desc), desc, asize(bugs), bugs, &oenv))
653 if (ftp2bSet(efTPR, NFILE, fnm))
655 list_tpx(ftp2fn(efTPR, NFILE, fnm), bShowNumbers, bShowParams,
656 ftp2fn_null(efMDP, NFILE, fnm), bSysTop, bOriginalInputrec);
658 else if (ftp2bSet(efTRX, NFILE, fnm))
660 list_trx(ftp2fn(efTRX, NFILE, fnm));
662 else if (ftp2bSet(efEDR, NFILE, fnm))
664 list_ene(ftp2fn(efEDR, NFILE, fnm));
666 else if (ftp2bSet(efCPT, NFILE, fnm))
668 list_checkpoint(ftp2fn(efCPT, NFILE, fnm), stdout);
670 else if (ftp2bSet(efTOP, NFILE, fnm))
672 list_top(ftp2fn(efTOP, NFILE, fnm));
674 else if (ftp2bSet(efMTX, NFILE, fnm))
676 list_mtx(ftp2fn(efMTX, NFILE, fnm));