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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/trajectoryframe.h"
68 #include "gromacs/utility/arraysize.h"
69 #include "gromacs/utility/basedefinitions.h"
70 #include "gromacs/utility/fatalerror.h"
71 #include "gromacs/utility/futil.h"
72 #include "gromacs/utility/smalloc.h"
73 #include "gromacs/utility/txtdump.h"
75 static void list_tpx(const char *fn,
76 gmx_bool bShowNumbers,
77 gmx_bool bShowParameters,
80 gmx_bool bOriginalInputrec)
83 int indent, i, j, **gcount, atot;
90 read_tpxheader(fn, &tpx, TRUE);
93 tpx.bIr ? &ir : nullptr,
95 tpx.bTop ? &mtop : nullptr);
96 if (tpx.bIr && !bOriginalInputrec)
98 gmx::MDModules().adjustInputrecBasedOnModules(&ir);
101 if (mdpfn && tpx.bIr)
103 gp = gmx_fio_fopen(mdpfn, "w");
104 pr_inputrec(gp, 0, nullptr, &ir, TRUE);
112 top = gmx_mtop_t_to_t_topology(&mtop, false);
115 if (available(stdout, &tpx, 0, fn))
118 pr_title(stdout, indent, fn);
119 pr_inputrec(stdout, 0, "inputrec", tpx.bIr ? &ir : nullptr, FALSE);
121 pr_tpxheader(stdout, indent, "header", &(tpx));
125 pr_mtop(stdout, indent, "topology", &(mtop), bShowNumbers, bShowParameters);
129 pr_top(stdout, indent, "topology", &(top), bShowNumbers, bShowParameters);
132 pr_rvecs(stdout, indent, "box", tpx.bBox ? state.box : nullptr, DIM);
133 pr_rvecs(stdout, indent, "box_rel", tpx.bBox ? state.box_rel : nullptr, DIM);
134 pr_rvecs(stdout, indent, "boxv", tpx.bBox ? state.boxv : nullptr, DIM);
135 pr_rvecs(stdout, indent, "pres_prev", tpx.bBox ? state.pres_prev : nullptr, DIM);
136 pr_rvecs(stdout, indent, "svir_prev", tpx.bBox ? state.svir_prev : nullptr, DIM);
137 pr_rvecs(stdout, indent, "fvir_prev", tpx.bBox ? state.fvir_prev : nullptr, DIM);
138 /* leave nosehoover_xi in for now to match the tpr version */
139 pr_doubles(stdout, indent, "nosehoover_xi", state.nosehoover_xi.data(), state.ngtc);
140 /*pr_doubles(stdout,indent,"nosehoover_vxi",state.nosehoover_vxi,state.ngtc);*/
141 /*pr_doubles(stdout,indent,"therm_integral",state.therm_integral,state.ngtc);*/
142 pr_rvecs(stdout, indent, "x", tpx.bX ? as_rvec_array(state.x.data()) : nullptr, state.natoms);
143 pr_rvecs(stdout, indent, "v", tpx.bV ? as_rvec_array(state.v.data()) : nullptr, state.natoms);
146 groups = &mtop.groups;
149 for (i = 0; (i < egcNR); i++)
151 snew(gcount[i], groups->grps[i].nr);
154 for (i = 0; (i < mtop.natoms); i++)
156 for (j = 0; (j < egcNR); j++)
158 gcount[j][ggrpnr(groups, j, i)]++;
161 printf("Group statistics\n");
162 for (i = 0; (i < egcNR); i++)
165 printf("%-12s: ", gtypes[i]);
166 for (j = 0; (j < groups->grps[i].nr); j++)
168 printf(" %5d", gcount[i][j]);
169 atot += gcount[i][j];
171 printf(" (total %d atoms)\n", atot);
178 static void list_top(const char *fn)
184 char *cppopts[] = { nullptr };
186 status = cpp_open_file(fn, &handle, cppopts);
189 gmx_fatal(FARGS, cpp_error(&handle, status));
193 status = cpp_read_line(&handle, BUFLEN, buf);
194 done = (status == eCPP_EOF);
197 if (status != eCPP_OK)
199 gmx_fatal(FARGS, cpp_error(&handle, status));
208 status = cpp_close_file(&handle);
209 if (status != eCPP_OK)
211 gmx_fatal(FARGS, cpp_error(&handle, status));
215 static void list_trr(const char *fn)
222 gmx_trr_header_t trrheader;
225 fpread = gmx_trr_open(fn, "r");
228 while (gmx_trr_read_frame_header(fpread, &trrheader, &bOK))
230 snew(x, trrheader.natoms);
231 snew(v, trrheader.natoms);
232 snew(f, trrheader.natoms);
233 if (gmx_trr_read_frame_data(fpread, &trrheader,
234 trrheader.box_size ? box : nullptr,
235 trrheader.x_size ? x : nullptr,
236 trrheader.v_size ? v : nullptr,
237 trrheader.f_size ? f : nullptr))
239 sprintf(buf, "%s frame %d", fn, nframe);
241 indent = pr_title(stdout, indent, buf);
242 pr_indent(stdout, indent);
243 fprintf(stdout, "natoms=%10d step=%10" GMX_PRId64 " time=%12.7e lambda=%10g\n",
244 trrheader.natoms, trrheader.step, trrheader.t, trrheader.lambda);
245 if (trrheader.box_size)
247 pr_rvecs(stdout, indent, "box", box, DIM);
249 if (trrheader.x_size)
251 pr_rvecs(stdout, indent, "x", x, trrheader.natoms);
253 if (trrheader.v_size)
255 pr_rvecs(stdout, indent, "v", v, trrheader.natoms);
257 if (trrheader.f_size)
259 pr_rvecs(stdout, indent, "f", f, trrheader.natoms);
264 fprintf(stderr, "\nWARNING: Incomplete frame: nr %d, t=%g\n",
265 nframe, trrheader.t);
275 fprintf(stderr, "\nWARNING: Incomplete frame header: nr %d, t=%g\n",
276 nframe, trrheader.t);
278 gmx_trr_close(fpread);
281 static void list_xtc(const char *fn)
293 xd = open_xtc(fn, "r");
294 read_first_xtc(xd, &natoms, &step, &time, box, &x, &prec, &bOK);
299 sprintf(buf, "%s frame %d", fn, nframe);
301 indent = pr_title(stdout, indent, buf);
302 pr_indent(stdout, indent);
303 fprintf(stdout, "natoms=%10d step=%10" GMX_PRId64 " time=%12.7e prec=%10g\n",
304 natoms, step, time, prec);
305 pr_rvecs(stdout, indent, "box", box, DIM);
306 pr_rvecs(stdout, indent, "x", x, natoms);
309 while (read_next_xtc(xd, natoms, &step, &time, box, x, &prec, &bOK));
312 fprintf(stderr, "\nWARNING: Incomplete frame at time %g\n", time);
318 /*! \brief Callback used by list_tng_for_gmx_dump. */
319 static void list_tng_inner(const char *fn,
320 gmx_bool bFirstFrame,
324 gmx_int64_t n_values_per_frame,
335 sprintf(buf, "%s frame %" GMX_PRId64, fn, nframe);
337 indent = pr_title(stdout, indent, buf);
338 pr_indent(stdout, indent);
339 fprintf(stdout, "natoms=%10" GMX_PRId64 " step=%10" GMX_PRId64 " time=%12.7e",
340 n_atoms, step, frame_time);
343 fprintf(stdout, " prec=%10g", prec);
345 fprintf(stdout, "\n");
347 pr_reals_of_dim(stdout, indent, block_name, values, n_atoms, n_values_per_frame);
350 static void list_tng(const char gmx_unused *fn)
353 tng_trajectory_t tng;
354 gmx_int64_t nframe = 0;
355 gmx_int64_t i, *block_ids = nullptr, step, ndatablocks;
357 real *values = nullptr;
359 gmx_tng_open(fn, 'r', &tng);
360 gmx_print_tng_molecule_system(tng, stdout);
362 bOK = gmx_get_tng_data_block_types_of_next_frame(tng, -1,
369 for (i = 0; i < ndatablocks; i++)
373 gmx_int64_t n_values_per_frame, n_atoms;
374 char block_name[STRLEN];
376 gmx_get_tng_data_next_frame_of_block_type(tng, block_ids[i], &values,
378 &n_values_per_frame, &n_atoms,
380 block_name, STRLEN, &bOK);
383 /* Can't write any output because we don't know what
385 fprintf(stderr, "\nWARNING: Incomplete frame at time %g, will not write output\n", frame_time);
389 list_tng_inner(fn, (0 == i), values, step, frame_time,
390 n_values_per_frame, n_atoms, prec, nframe, block_name);
395 while (gmx_get_tng_data_block_types_of_next_frame(tng, step,
411 static void list_trx(const char *fn)
425 fprintf(stderr, "File %s is of an unsupported type. Try using the command\n 'less %s'\n",
430 static void list_ene(const char *fn)
434 gmx_enxnm_t *enm = nullptr;
439 printf("gmx dump: %s\n", fn);
440 in = open_enx(fn, "r");
441 do_enxnms(in, &nre, &enm);
444 printf("energy components:\n");
445 for (i = 0; (i < nre); i++)
447 printf("%5d %-24s (%s)\n", i, enm[i].name, enm[i].unit);
453 bCont = do_enx(in, fr);
457 printf("\n%24s %12.5e %12s %12s\n", "time:",
458 fr->t, "step:", gmx_step_str(fr->step, buf));
459 printf("%24s %12s %12s %12s\n",
460 "", "", "nsteps:", gmx_step_str(fr->nsteps, buf));
461 printf("%24s %12.5e %12s %12s\n",
462 "delta_t:", fr->dt, "sum steps:", gmx_step_str(fr->nsum, buf));
465 printf("%24s %12s %12s %12s\n",
466 "Component", "Energy", "Av. Energy", "Sum Energy");
469 for (i = 0; (i < nre); i++)
471 printf("%24s %12.5e %12.5e %12.5e\n",
472 enm[i].name, fr->ener[i].e, fr->ener[i].eav,
478 for (i = 0; (i < nre); i++)
480 printf("%24s %12.5e\n",
481 enm[i].name, fr->ener[i].e);
485 for (b = 0; b < fr->nblock; b++)
487 const char *typestr = "";
489 t_enxblock *eb = &(fr->block[b]);
490 printf("Block data %2d (%3d subblocks, id=%d)\n",
491 b, eb->nsub, eb->id);
495 typestr = enx_block_id_name[eb->id];
497 printf(" id='%s'\n", typestr);
498 for (i = 0; i < eb->nsub; i++)
500 t_enxsubblock *sb = &(eb->sub[i]);
501 printf(" Sub block %3d (%5d elems, type=%s) values:\n",
502 i, sb->nr, xdr_datatype_names[sb->type]);
506 case xdr_datatype_float:
507 for (j = 0; j < sb->nr; j++)
509 printf("%14d %8.4f\n", j, sb->fval[j]);
512 case xdr_datatype_double:
513 for (j = 0; j < sb->nr; j++)
515 printf("%14d %10.6f\n", j, sb->dval[j]);
518 case xdr_datatype_int:
519 for (j = 0; j < sb->nr; j++)
521 printf("%14d %10d\n", j, sb->ival[j]);
524 case xdr_datatype_int64:
525 for (j = 0; j < sb->nr; j++)
528 j, gmx_step_str(sb->lval[j], buf));
531 case xdr_datatype_char:
532 for (j = 0; j < sb->nr; j++)
534 printf("%14d %1c\n", j, sb->cval[j]);
537 case xdr_datatype_string:
538 for (j = 0; j < sb->nr; j++)
540 printf("%14d %80s\n", j, sb->sval[j]);
544 gmx_incons("Unknown subblock type");
559 static void list_mtx(const char *fn)
561 int nrow, ncol, i, j, k;
562 real *full = nullptr, value;
563 gmx_sparsematrix_t * sparse = nullptr;
565 gmx_mtxio_read(fn, &nrow, &ncol, &full, &sparse);
569 snew(full, nrow*ncol);
570 for (i = 0; i < nrow*ncol; i++)
575 for (i = 0; i < sparse->nrow; i++)
577 for (j = 0; j < sparse->ndata[i]; j++)
579 k = sparse->data[i][j].col;
580 value = sparse->data[i][j].value;
581 full[i*ncol+k] = value;
582 full[k*ncol+i] = value;
585 gmx_sparsematrix_destroy(sparse);
588 printf("%d %d\n", nrow, ncol);
589 for (i = 0; i < nrow; i++)
591 for (j = 0; j < ncol; j++)
593 printf(" %g", full[i*ncol+j]);
601 int gmx_dump(int argc, char *argv[])
603 const char *desc[] = {
604 "[THISMODULE] reads a run input file ([REF].tpr[ref]),",
605 "a trajectory ([REF].trr[ref]/[REF].xtc[ref]/[TT]/tng[tt]), an energy",
606 "file ([REF].edr[ref]) or a checkpoint file ([REF].cpt[ref])",
607 "and prints that to standard output in a readable format.",
608 "This program is essential for checking your run input file in case of",
610 "The program can also preprocess a topology to help finding problems.",
611 "Note that currently setting [TT]GMXLIB[tt] is the only way to customize",
612 "directories used for searching include files.",
614 const char *bugs[] = {
615 "Position restraint output from -sys -s is broken"
618 { efTPR, "-s", nullptr, ffOPTRD },
619 { efTRX, "-f", nullptr, ffOPTRD },
620 { efEDR, "-e", nullptr, ffOPTRD },
621 { efCPT, nullptr, nullptr, ffOPTRD },
622 { efTOP, "-p", nullptr, ffOPTRD },
623 { efMTX, "-mtx", "hessian", ffOPTRD },
624 { efMDP, "-om", nullptr, ffOPTWR }
626 #define NFILE asize(fnm)
628 gmx_output_env_t *oenv;
629 /* Command line options */
630 gmx_bool bShowNumbers = TRUE;
631 gmx_bool bShowParams = FALSE;
632 gmx_bool bSysTop = FALSE;
633 gmx_bool bOriginalInputrec = FALSE;
635 { "-nr", FALSE, etBOOL, {&bShowNumbers}, "Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)" },
636 { "-param", FALSE, etBOOL, {&bShowParams}, "Show parameters for each bonded interaction (for comparing dumps, it is useful to combine this with -nonr)" },
637 { "-sys", FALSE, etBOOL, {&bSysTop}, "List the atoms and bonded interactions for the whole system instead of for each molecule type" },
638 { "-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" }
641 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
642 asize(desc), desc, asize(bugs), bugs, &oenv))
648 if (ftp2bSet(efTPR, NFILE, fnm))
650 list_tpx(ftp2fn(efTPR, NFILE, fnm), bShowNumbers, bShowParams,
651 ftp2fn_null(efMDP, NFILE, fnm), bSysTop, bOriginalInputrec);
653 else if (ftp2bSet(efTRX, NFILE, fnm))
655 list_trx(ftp2fn(efTRX, NFILE, fnm));
657 else if (ftp2bSet(efEDR, NFILE, fnm))
659 list_ene(ftp2fn(efEDR, NFILE, fnm));
661 else if (ftp2bSet(efCPT, NFILE, fnm))
663 list_checkpoint(ftp2fn(efCPT, NFILE, fnm), stdout);
665 else if (ftp2bSet(efTOP, NFILE, fnm))
667 list_top(ftp2fn(efTOP, NFILE, fnm));
669 else if (ftp2bSet(efMTX, NFILE, fnm))
671 list_mtx(ftp2fn(efMTX, NFILE, fnm));