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46 #include "gromacs/commandline/pargs.h"
47 #include "gromacs/fileio/checkpoint.h"
48 #include "gromacs/fileio/enxio.h"
49 #include "gromacs/fileio/gmxfio.h"
50 #include "gromacs/fileio/mtxio.h"
51 #include "gromacs/fileio/tngio.h"
52 #include "gromacs/fileio/tngio_for_tools.h"
53 #include "gromacs/fileio/tpxio.h"
54 #include "gromacs/fileio/trrio.h"
55 #include "gromacs/fileio/xtcio.h"
56 #include "gromacs/gmxpreprocess/gmxcpp.h"
57 #include "gromacs/linearalgebra/sparsematrix.h"
58 #include "gromacs/math/vecdump.h"
59 #include "gromacs/mdrunutility/mdmodules.h"
60 #include "gromacs/mdtypes/forcerec.h"
61 #include "gromacs/mdtypes/inputrec.h"
62 #include "gromacs/mdtypes/md_enums.h"
63 #include "gromacs/mdtypes/state.h"
64 #include "gromacs/topology/mtop_util.h"
65 #include "gromacs/topology/topology.h"
66 #include "gromacs/trajectory/trajectoryframe.h"
67 #include "gromacs/utility/arraysize.h"
68 #include "gromacs/utility/basedefinitions.h"
69 #include "gromacs/utility/fatalerror.h"
70 #include "gromacs/utility/futil.h"
71 #include "gromacs/utility/smalloc.h"
72 #include "gromacs/utility/txtdump.h"
74 static void list_tpx(const char *fn,
75 gmx_bool bShowNumbers,
76 gmx_bool bShowParameters,
81 int indent, i, j, **gcount, atot;
83 t_inputrec *ir = nullptr;
89 read_tpxheader(fn, &tpx, TRUE);
90 gmx::MDModules mdModules;
93 ir = mdModules.inputrec();
98 tpx.bTop ? &mtop : NULL);
100 if (mdpfn && tpx.bIr)
102 gp = gmx_fio_fopen(mdpfn, "w");
103 pr_inputrec(gp, 0, NULL, ir, TRUE);
111 top = gmx_mtop_t_to_t_topology(&mtop, false);
114 if (available(stdout, &tpx, 0, fn))
117 pr_title(stdout, indent, fn);
118 pr_inputrec(stdout, 0, "inputrec", ir, FALSE);
120 pr_tpxheader(stdout, indent, "header", &(tpx));
124 pr_mtop(stdout, indent, "topology", &(mtop), bShowNumbers, bShowParameters);
128 pr_top(stdout, indent, "topology", &(top), bShowNumbers, bShowParameters);
131 pr_rvecs(stdout, indent, "box", tpx.bBox ? state.box : NULL, DIM);
132 pr_rvecs(stdout, indent, "box_rel", tpx.bBox ? state.box_rel : NULL, DIM);
133 pr_rvecs(stdout, indent, "boxv", tpx.bBox ? state.boxv : NULL, DIM);
134 pr_rvecs(stdout, indent, "pres_prev", tpx.bBox ? state.pres_prev : NULL, DIM);
135 pr_rvecs(stdout, indent, "svir_prev", tpx.bBox ? state.svir_prev : NULL, DIM);
136 pr_rvecs(stdout, indent, "fvir_prev", tpx.bBox ? state.fvir_prev : NULL, DIM);
137 /* leave nosehoover_xi in for now to match the tpr version */
138 pr_doubles(stdout, indent, "nosehoover_xi", state.nosehoover_xi.data(), state.ngtc);
139 /*pr_doubles(stdout,indent,"nosehoover_vxi",state.nosehoover_vxi,state.ngtc);*/
140 /*pr_doubles(stdout,indent,"therm_integral",state.therm_integral,state.ngtc);*/
141 pr_rvecs(stdout, indent, "x", tpx.bX ? as_rvec_array(state.x.data()) : NULL, state.natoms);
142 pr_rvecs(stdout, indent, "v", tpx.bV ? as_rvec_array(state.v.data()) : NULL, state.natoms);
145 groups = &mtop.groups;
148 for (i = 0; (i < egcNR); i++)
150 snew(gcount[i], groups->grps[i].nr);
153 for (i = 0; (i < mtop.natoms); i++)
155 for (j = 0; (j < egcNR); j++)
157 gcount[j][ggrpnr(groups, j, i)]++;
160 printf("Group statistics\n");
161 for (i = 0; (i < egcNR); i++)
164 printf("%-12s: ", gtypes[i]);
165 for (j = 0; (j < groups->grps[i].nr); j++)
167 printf(" %5d", gcount[i][j]);
168 atot += gcount[i][j];
170 printf(" (total %d atoms)\n", atot);
177 static void list_top(const char *fn)
183 char *cppopts[] = { NULL };
185 status = cpp_open_file(fn, &handle, cppopts);
188 gmx_fatal(FARGS, cpp_error(&handle, status));
192 status = cpp_read_line(&handle, BUFLEN, buf);
193 done = (status == eCPP_EOF);
196 if (status != eCPP_OK)
198 gmx_fatal(FARGS, cpp_error(&handle, status));
207 status = cpp_close_file(&handle);
208 if (status != eCPP_OK)
210 gmx_fatal(FARGS, cpp_error(&handle, status));
214 static void list_trr(const char *fn)
221 gmx_trr_header_t trrheader;
224 fpread = gmx_trr_open(fn, "r");
227 while (gmx_trr_read_frame_header(fpread, &trrheader, &bOK))
229 snew(x, trrheader.natoms);
230 snew(v, trrheader.natoms);
231 snew(f, trrheader.natoms);
232 if (gmx_trr_read_frame_data(fpread, &trrheader,
233 trrheader.box_size ? box : NULL,
234 trrheader.x_size ? x : NULL,
235 trrheader.v_size ? v : NULL,
236 trrheader.f_size ? f : NULL))
238 sprintf(buf, "%s frame %d", fn, nframe);
240 indent = pr_title(stdout, indent, buf);
241 pr_indent(stdout, indent);
242 fprintf(stdout, "natoms=%10d step=%10" GMX_PRId64 " time=%12.7e lambda=%10g\n",
243 trrheader.natoms, trrheader.step, trrheader.t, trrheader.lambda);
244 if (trrheader.box_size)
246 pr_rvecs(stdout, indent, "box", box, DIM);
248 if (trrheader.x_size)
250 pr_rvecs(stdout, indent, "x", x, trrheader.natoms);
252 if (trrheader.v_size)
254 pr_rvecs(stdout, indent, "v", v, trrheader.natoms);
256 if (trrheader.f_size)
258 pr_rvecs(stdout, indent, "f", f, trrheader.natoms);
263 fprintf(stderr, "\nWARNING: Incomplete frame: nr %d, t=%g\n",
264 nframe, trrheader.t);
274 fprintf(stderr, "\nWARNING: Incomplete frame header: nr %d, t=%g\n",
275 nframe, trrheader.t);
277 gmx_trr_close(fpread);
280 void list_xtc(const char *fn)
292 xd = open_xtc(fn, "r");
293 read_first_xtc(xd, &natoms, &step, &time, box, &x, &prec, &bOK);
298 sprintf(buf, "%s frame %d", fn, nframe);
300 indent = pr_title(stdout, indent, buf);
301 pr_indent(stdout, indent);
302 fprintf(stdout, "natoms=%10d step=%10" GMX_PRId64 " time=%12.7e prec=%10g\n",
303 natoms, step, time, prec);
304 pr_rvecs(stdout, indent, "box", box, DIM);
305 pr_rvecs(stdout, indent, "x", x, natoms);
308 while (read_next_xtc(xd, natoms, &step, &time, box, x, &prec, &bOK));
311 fprintf(stderr, "\nWARNING: Incomplete frame at time %g\n", time);
317 /*! \brief Callback used by list_tng_for_gmx_dump. */
318 static void list_tng_inner(const char *fn,
319 gmx_bool bFirstFrame,
323 gmx_int64_t n_values_per_frame,
334 sprintf(buf, "%s frame %" GMX_PRId64, fn, nframe);
336 indent = pr_title(stdout, indent, buf);
337 pr_indent(stdout, indent);
338 fprintf(stdout, "natoms=%10" GMX_PRId64 " step=%10" GMX_PRId64 " time=%12.7e",
339 n_atoms, step, frame_time);
342 fprintf(stdout, " prec=%10g", prec);
344 fprintf(stdout, "\n");
346 pr_reals_of_dim(stdout, indent, block_name, values, n_atoms, n_values_per_frame);
349 static void list_tng(const char gmx_unused *fn)
352 tng_trajectory_t tng;
353 gmx_int64_t nframe = 0;
354 gmx_int64_t i, *block_ids = NULL, step, ndatablocks;
357 gmx_tng_open(fn, 'r', &tng);
358 gmx_print_tng_molecule_system(tng, stdout);
360 bOK = gmx_get_tng_data_block_types_of_next_frame(tng, -1,
367 for (i = 0; i < ndatablocks; i++)
370 real prec, *values = NULL;
371 gmx_int64_t n_values_per_frame, n_atoms;
372 char block_name[STRLEN];
374 gmx_get_tng_data_next_frame_of_block_type(tng, block_ids[i], &values,
376 &n_values_per_frame, &n_atoms,
378 block_name, STRLEN, &bOK);
381 /* Can't write any output because we don't know what
383 fprintf(stderr, "\nWARNING: Incomplete frame at time %g, will not write output\n", frame_time);
387 list_tng_inner(fn, (0 == i), values, step, frame_time,
388 n_values_per_frame, n_atoms, prec, nframe, block_name);
393 while (gmx_get_tng_data_block_types_of_next_frame(tng, step,
409 void list_trx(const char *fn)
423 fprintf(stderr, "File %s is of an unsupported type. Try using the command\n 'less %s'\n",
428 void list_ene(const char *fn)
432 gmx_enxnm_t *enm = NULL;
437 printf("gmx dump: %s\n", fn);
438 in = open_enx(fn, "r");
439 do_enxnms(in, &nre, &enm);
442 printf("energy components:\n");
443 for (i = 0; (i < nre); i++)
445 printf("%5d %-24s (%s)\n", i, enm[i].name, enm[i].unit);
451 bCont = do_enx(in, fr);
455 printf("\n%24s %12.5e %12s %12s\n", "time:",
456 fr->t, "step:", gmx_step_str(fr->step, buf));
457 printf("%24s %12s %12s %12s\n",
458 "", "", "nsteps:", gmx_step_str(fr->nsteps, buf));
459 printf("%24s %12.5e %12s %12s\n",
460 "delta_t:", fr->dt, "sum steps:", gmx_step_str(fr->nsum, buf));
463 printf("%24s %12s %12s %12s\n",
464 "Component", "Energy", "Av. Energy", "Sum Energy");
467 for (i = 0; (i < nre); i++)
469 printf("%24s %12.5e %12.5e %12.5e\n",
470 enm[i].name, fr->ener[i].e, fr->ener[i].eav,
476 for (i = 0; (i < nre); i++)
478 printf("%24s %12.5e\n",
479 enm[i].name, fr->ener[i].e);
483 for (b = 0; b < fr->nblock; b++)
485 const char *typestr = "";
487 t_enxblock *eb = &(fr->block[b]);
488 printf("Block data %2d (%3d subblocks, id=%d)\n",
489 b, eb->nsub, eb->id);
493 typestr = enx_block_id_name[eb->id];
495 printf(" id='%s'\n", typestr);
496 for (i = 0; i < eb->nsub; i++)
498 t_enxsubblock *sb = &(eb->sub[i]);
499 printf(" Sub block %3d (%5d elems, type=%s) values:\n",
500 i, sb->nr, xdr_datatype_names[sb->type]);
504 case xdr_datatype_float:
505 for (j = 0; j < sb->nr; j++)
507 printf("%14d %8.4f\n", j, sb->fval[j]);
510 case xdr_datatype_double:
511 for (j = 0; j < sb->nr; j++)
513 printf("%14d %10.6f\n", j, sb->dval[j]);
516 case xdr_datatype_int:
517 for (j = 0; j < sb->nr; j++)
519 printf("%14d %10d\n", j, sb->ival[j]);
522 case xdr_datatype_int64:
523 for (j = 0; j < sb->nr; j++)
526 j, gmx_step_str(sb->lval[j], buf));
529 case xdr_datatype_char:
530 for (j = 0; j < sb->nr; j++)
532 printf("%14d %1c\n", j, sb->cval[j]);
535 case xdr_datatype_string:
536 for (j = 0; j < sb->nr; j++)
538 printf("%14d %80s\n", j, sb->sval[j]);
542 gmx_incons("Unknown subblock type");
557 static void list_mtx(const char *fn)
559 int nrow, ncol, i, j, k;
560 real *full = NULL, value;
561 gmx_sparsematrix_t * sparse = NULL;
563 gmx_mtxio_read(fn, &nrow, &ncol, &full, &sparse);
567 snew(full, nrow*ncol);
568 for (i = 0; i < nrow*ncol; i++)
573 for (i = 0; i < sparse->nrow; i++)
575 for (j = 0; j < sparse->ndata[i]; j++)
577 k = sparse->data[i][j].col;
578 value = sparse->data[i][j].value;
579 full[i*ncol+k] = value;
580 full[k*ncol+i] = value;
583 gmx_sparsematrix_destroy(sparse);
586 printf("%d %d\n", nrow, ncol);
587 for (i = 0; i < nrow; i++)
589 for (j = 0; j < ncol; j++)
591 printf(" %g", full[i*ncol+j]);
599 int gmx_dump(int argc, char *argv[])
601 const char *desc[] = {
602 "[THISMODULE] reads a run input file ([REF].tpr[ref]),",
603 "a trajectory ([REF].trr[ref]/[REF].xtc[ref]/[TT]/tng[tt]), an energy",
604 "file ([REF].edr[ref]) or a checkpoint file ([REF].cpt[ref])",
605 "and prints that to standard output in a readable format.",
606 "This program is essential for checking your run input file in case of",
608 "The program can also preprocess a topology to help finding problems.",
609 "Note that currently setting [TT]GMXLIB[tt] is the only way to customize",
610 "directories used for searching include files.",
612 const char *bugs[] = {
613 "Position restraint output from -sys -s is broken"
616 { efTPR, "-s", NULL, ffOPTRD },
617 { efTRX, "-f", NULL, ffOPTRD },
618 { efEDR, "-e", NULL, ffOPTRD },
619 { efCPT, NULL, NULL, ffOPTRD },
620 { efTOP, "-p", NULL, ffOPTRD },
621 { efMTX, "-mtx", "hessian", ffOPTRD },
622 { efMDP, "-om", NULL, ffOPTWR }
624 #define NFILE asize(fnm)
626 gmx_output_env_t *oenv;
627 /* Command line options */
628 static gmx_bool bShowNumbers = TRUE;
629 static gmx_bool bShowParams = FALSE;
630 static gmx_bool bSysTop = FALSE;
632 { "-nr", FALSE, etBOOL, {&bShowNumbers}, "Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)" },
633 { "-param", FALSE, etBOOL, {&bShowParams}, "Show parameters for each bonded interaction (for comparing dumps, it is useful to combine this with -nonr)" },
634 { "-sys", FALSE, etBOOL, {&bSysTop}, "List the atoms and bonded interactions for the whole system instead of for each molecule type" }
637 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
638 asize(desc), desc, asize(bugs), bugs, &oenv))
644 if (ftp2bSet(efTPR, NFILE, fnm))
646 list_tpx(ftp2fn(efTPR, NFILE, fnm), bShowNumbers, bShowParams,
647 ftp2fn_null(efMDP, NFILE, fnm), bSysTop);
649 else if (ftp2bSet(efTRX, NFILE, fnm))
651 list_trx(ftp2fn(efTRX, NFILE, fnm));
653 else if (ftp2bSet(efEDR, NFILE, fnm))
655 list_ene(ftp2fn(efEDR, NFILE, fnm));
657 else if (ftp2bSet(efCPT, NFILE, fnm))
659 list_checkpoint(ftp2fn(efCPT, NFILE, fnm), stdout);
661 else if (ftp2bSet(efTOP, NFILE, fnm))
663 list_top(ftp2fn(efTOP, NFILE, fnm));
665 else if (ftp2bSet(efMTX, NFILE, fnm))
667 list_mtx(ftp2fn(efMTX, NFILE, fnm));