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33 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
45 #include "gromacs/fileio/futil.h"
49 #include "gmx_fatal.h"
50 #include "gromacs/fileio/xtcio.h"
51 #include "gromacs/fileio/enxio.h"
54 #include "gromacs/fileio/gmxfio.h"
55 #include "gromacs/fileio/tpxio.h"
56 #include "gromacs/fileio/trnio.h"
59 #include "checkpoint.h"
60 #include "mtop_util.h"
62 #include "gromacs/linearalgebra/mtxio.h"
63 #include "gromacs/linearalgebra/sparsematrix.h"
66 static void list_tpx(const char *fn, gmx_bool bShowNumbers, const char *mdpfn,
70 int fp, indent, i, j, **gcount, atot;
79 read_tpxheader(fn, &tpx, TRUE, NULL, NULL);
83 &state, tpx.bF ? f : NULL,
84 tpx.bTop ? &mtop : NULL);
88 gp = gmx_fio_fopen(mdpfn, "w");
89 pr_inputrec(gp, 0, NULL, &(ir), TRUE);
97 top = gmx_mtop_t_to_t_topology(&mtop);
100 if (available(stdout, &tpx, 0, fn))
103 indent = pr_title(stdout, indent, fn);
104 pr_inputrec(stdout, 0, "inputrec", tpx.bIr ? &(ir) : NULL, FALSE);
107 pr_header(stdout, indent, "header", &(tpx));
111 pr_mtop(stdout, indent, "topology", &(mtop), bShowNumbers);
115 pr_top(stdout, indent, "topology", &(top), bShowNumbers);
118 pr_rvecs(stdout, indent, "box", tpx.bBox ? state.box : NULL, DIM);
119 pr_rvecs(stdout, indent, "box_rel", tpx.bBox ? state.box_rel : NULL, DIM);
120 pr_rvecs(stdout, indent, "boxv", tpx.bBox ? state.boxv : NULL, DIM);
121 pr_rvecs(stdout, indent, "pres_prev", tpx.bBox ? state.pres_prev : NULL, DIM);
122 pr_rvecs(stdout, indent, "svir_prev", tpx.bBox ? state.svir_prev : NULL, DIM);
123 pr_rvecs(stdout, indent, "fvir_prev", tpx.bBox ? state.fvir_prev : NULL, DIM);
124 /* leave nosehoover_xi in for now to match the tpr version */
125 pr_doubles(stdout, indent, "nosehoover_xi", state.nosehoover_xi, state.ngtc);
126 /*pr_doubles(stdout,indent,"nosehoover_vxi",state.nosehoover_vxi,state.ngtc);*/
127 /*pr_doubles(stdout,indent,"therm_integral",state.therm_integral,state.ngtc);*/
128 pr_rvecs(stdout, indent, "x", tpx.bX ? state.x : NULL, state.natoms);
129 pr_rvecs(stdout, indent, "v", tpx.bV ? state.v : NULL, state.natoms);
132 pr_rvecs(stdout, indent, "f", f, state.natoms);
136 groups = &mtop.groups;
139 for (i = 0; (i < egcNR); i++)
141 snew(gcount[i], groups->grps[i].nr);
144 for (i = 0; (i < mtop.natoms); i++)
146 for (j = 0; (j < egcNR); j++)
148 gcount[j][ggrpnr(groups, j, i)]++;
151 printf("Group statistics\n");
152 for (i = 0; (i < egcNR); i++)
155 printf("%-12s: ", gtypes[i]);
156 for (j = 0; (j < groups->grps[i].nr); j++)
158 printf(" %5d", gcount[i][j]);
159 atot += gcount[i][j];
161 printf(" (total %d atoms)\n", atot);
170 static void list_top(const char *fn)
176 char *cppopts[] = { NULL };
178 status = cpp_open_file(fn, &handle, cppopts);
181 gmx_fatal(FARGS, cpp_error(&handle, status));
185 status = cpp_read_line(&handle, BUFLEN, buf);
186 done = (status == eCPP_EOF);
189 if (status != eCPP_OK)
191 gmx_fatal(FARGS, cpp_error(&handle, status));
200 status = cpp_close_file(&handle);
201 if (status != eCPP_OK)
203 gmx_fatal(FARGS, cpp_error(&handle, status));
207 static void list_trn(const char *fn)
209 t_fileio *fpread, *fpwrite;
217 fpread = open_trn(fn, "r");
218 fpwrite = open_tpx(NULL, "w");
219 gmx_fio_setdebug(fpwrite, TRUE);
222 while (fread_trnheader(fpread, &trn, &bOK))
227 if (fread_htrn(fpread, &trn,
228 trn.box_size ? box : NULL,
229 trn.x_size ? x : NULL,
230 trn.v_size ? v : NULL,
231 trn.f_size ? f : NULL))
233 sprintf(buf, "%s frame %d", fn, nframe);
235 indent = pr_title(stdout, indent, buf);
236 pr_indent(stdout, indent);
237 fprintf(stdout, "natoms=%10d step=%10d time=%12.7e lambda=%10g\n",
238 trn.natoms, trn.step, trn.t, trn.lambda);
241 pr_rvecs(stdout, indent, "box", box, DIM);
245 pr_rvecs(stdout, indent, "x", x, trn.natoms);
249 pr_rvecs(stdout, indent, "v", v, trn.natoms);
253 pr_rvecs(stdout, indent, "f", f, trn.natoms);
258 fprintf(stderr, "\nWARNING: Incomplete frame: nr %d, t=%g\n",
269 fprintf(stderr, "\nWARNING: Incomplete frame header: nr %d, t=%g\n",
276 void list_xtc(const char *fn, gmx_bool bXVG)
283 int nframe, natoms, step;
287 xd = open_xtc(fn, "r");
288 read_first_xtc(xd, &natoms, &step, &time, box, &x, &prec, &bOK);
297 fprintf(stdout, "%g", time);
298 for (i = 0; i < natoms; i++)
300 for (d = 0; d < DIM; d++)
302 fprintf(stdout, " %g", x[i][d]);
305 fprintf(stdout, "\n");
309 sprintf(buf, "%s frame %d", fn, nframe);
311 indent = pr_title(stdout, indent, buf);
312 pr_indent(stdout, indent);
313 fprintf(stdout, "natoms=%10d step=%10d time=%12.7e prec=%10g\n",
314 natoms, step, time, prec);
315 pr_rvecs(stdout, indent, "box", box, DIM);
316 pr_rvecs(stdout, indent, "x", x, natoms);
320 while (read_next_xtc(xd, natoms, &step, &time, box, x, &prec, &bOK));
323 fprintf(stderr, "\nWARNING: Incomplete frame at time %g\n", time);
329 void list_trx(const char *fn, gmx_bool bXVG)
338 else if ((ftp == efTRR) || (ftp == efTRJ))
344 fprintf(stderr, "File %s is of an unsupported type. Try using the command\n 'less %s'\n",
349 void list_ene(const char *fn)
354 gmx_enxnm_t *enm = NULL;
360 printf("gmx dump: %s\n", fn);
361 in = open_enx(fn, "r");
362 do_enxnms(in, &nre, &enm);
365 printf("energy components:\n");
366 for (i = 0; (i < nre); i++)
368 printf("%5d %-24s (%s)\n", i, enm[i].name, enm[i].unit);
375 bCont = do_enx(in, fr);
379 printf("\n%24s %12.5e %12s %12s\n", "time:",
380 fr->t, "step:", gmx_step_str(fr->step, buf));
381 printf("%24s %12s %12s %12s\n",
382 "", "", "nsteps:", gmx_step_str(fr->nsteps, buf));
383 printf("%24s %12.5e %12s %12s\n",
384 "delta_t:", fr->dt, "sum steps:", gmx_step_str(fr->nsum, buf));
387 printf("%24s %12s %12s %12s\n",
388 "Component", "Energy", "Av. Energy", "Sum Energy");
391 for (i = 0; (i < nre); i++)
393 printf("%24s %12.5e %12.5e %12.5e\n",
394 enm[i].name, fr->ener[i].e, fr->ener[i].eav,
400 for (i = 0; (i < nre); i++)
402 printf("%24s %12.5e\n",
403 enm[i].name, fr->ener[i].e);
407 for (b = 0; b < fr->nblock; b++)
409 const char *typestr = "";
411 t_enxblock *eb = &(fr->block[b]);
412 printf("Block data %2d (%3d subblocks, id=%d)\n",
413 b, eb->nsub, eb->id);
417 typestr = enx_block_id_name[eb->id];
419 printf(" id='%s'\n", typestr);
420 for (i = 0; i < eb->nsub; i++)
422 t_enxsubblock *sb = &(eb->sub[i]);
423 printf(" Sub block %3d (%5d elems, type=%s) values:\n",
424 i, sb->nr, xdr_datatype_names[sb->type]);
428 case xdr_datatype_float:
429 for (j = 0; j < sb->nr; j++)
431 printf("%14d %8.4f\n", j, sb->fval[j]);
434 case xdr_datatype_double:
435 for (j = 0; j < sb->nr; j++)
437 printf("%14d %10.6f\n", j, sb->dval[j]);
440 case xdr_datatype_int:
441 for (j = 0; j < sb->nr; j++)
443 printf("%14d %10d\n", j, sb->ival[j]);
446 case xdr_datatype_large_int:
447 for (j = 0; j < sb->nr; j++)
450 j, gmx_step_str(sb->lval[j], buf));
453 case xdr_datatype_char:
454 for (j = 0; j < sb->nr; j++)
456 printf("%14d %1c\n", j, sb->cval[j]);
459 case xdr_datatype_string:
460 for (j = 0; j < sb->nr; j++)
462 printf("%14d %80s\n", j, sb->sval[j]);
466 gmx_incons("Unknown subblock type");
481 static void list_mtx(const char *fn)
483 int nrow, ncol, i, j, k;
484 real *full = NULL, value;
485 gmx_sparsematrix_t * sparse = NULL;
487 gmx_mtxio_read(fn, &nrow, &ncol, &full, &sparse);
491 snew(full, nrow*ncol);
492 for (i = 0; i < nrow*ncol; i++)
497 for (i = 0; i < sparse->nrow; i++)
499 for (j = 0; j < sparse->ndata[i]; j++)
501 k = sparse->data[i][j].col;
502 value = sparse->data[i][j].value;
503 full[i*ncol+k] = value;
504 full[k*ncol+i] = value;
507 gmx_sparsematrix_destroy(sparse);
510 printf("%d %d\n", nrow, ncol);
511 for (i = 0; i < nrow; i++)
513 for (j = 0; j < ncol; j++)
515 printf(" %g", full[i*ncol+j]);
523 int gmx_gmxdump(int argc, char *argv[])
525 const char *desc[] = {
526 "[THISMODULE] reads a run input file ([TT].tpa[tt]/[TT].tpr[tt]/[TT].tpb[tt]),",
527 "a trajectory ([TT].trj[tt]/[TT].trr[tt]/[TT].xtc[tt]), an energy",
528 "file ([TT].ene[tt]/[TT].edr[tt]), or a checkpoint file ([TT].cpt[tt])",
529 "and prints that to standard output in a readable format.",
530 "This program is essential for checking your run input file in case of",
532 "The program can also preprocess a topology to help finding problems.",
533 "Note that currently setting [TT]GMXLIB[tt] is the only way to customize",
534 "directories used for searching include files.",
536 const char *bugs[] = {
537 "Position restraint output from -sys -s is broken"
540 { efTPX, "-s", NULL, ffOPTRD },
541 { efTRX, "-f", NULL, ffOPTRD },
542 { efEDR, "-e", NULL, ffOPTRD },
543 { efCPT, NULL, NULL, ffOPTRD },
544 { efTOP, "-p", NULL, ffOPTRD },
545 { efMTX, "-mtx", "hessian", ffOPTRD },
546 { efMDP, "-om", NULL, ffOPTWR }
548 #define NFILE asize(fnm)
551 /* Command line options */
552 static gmx_bool bXVG = FALSE;
553 static gmx_bool bShowNumbers = TRUE;
554 static gmx_bool bSysTop = FALSE;
556 { "-xvg", FALSE, etBOOL, {&bXVG}, "HIDDENXVG layout for xtc" },
557 { "-nr", FALSE, etBOOL, {&bShowNumbers}, "Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)" },
558 { "-sys", FALSE, etBOOL, {&bSysTop}, "List the atoms and bonded interactions for the whole system instead of for each molecule type" }
561 if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
562 asize(desc), desc, asize(bugs), bugs, &oenv))
568 if (ftp2bSet(efTPX, NFILE, fnm))
570 list_tpx(ftp2fn(efTPX, NFILE, fnm), bShowNumbers,
571 ftp2fn_null(efMDP, NFILE, fnm), bSysTop);
573 else if (ftp2bSet(efTRX, NFILE, fnm))
575 list_trx(ftp2fn(efTRX, NFILE, fnm), bXVG);
577 else if (ftp2bSet(efEDR, NFILE, fnm))
579 list_ene(ftp2fn(efEDR, NFILE, fnm));
581 else if (ftp2bSet(efCPT, NFILE, fnm))
583 list_checkpoint(ftp2fn(efCPT, NFILE, fnm), stdout);
585 else if (ftp2bSet(efTOP, NFILE, fnm))
587 list_top(ftp2fn(efTOP, NFILE, fnm));
589 else if (ftp2bSet(efMTX, NFILE, fnm))
591 list_mtx(ftp2fn(efMTX, NFILE, fnm));