src/gmxlib/filenm.c

   1 /*
   2  *
   3  *                This source code is part of
   4  *
   5  *                 G   R   O   M   A   C   S
   6  *
   7  *          GROningen MAchine for Chemical Simulations
   8  *
   9  *                        VERSION 3.2.0
  10  * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
  11  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  12  * Copyright (c) 2001-2004, The GROMACS development team,
  13  * check out http://www.gromacs.org for more information.
  14
  15  * This program is free software; you can redistribute it and/or
  16  * modify it under the terms of the GNU General Public License
  17  * as published by the Free Software Foundation; either version 2
  18  * of the License, or (at your option) any later version.
  19  *
  20  * If you want to redistribute modifications, please consider that
  21  * scientific software is very special. Version control is crucial -
  22  * bugs must be traceable. We will be happy to consider code for
  23  * inclusion in the official distribution, but derived work must not
  24  * be called official GROMACS. Details are found in the README & COPYING
  25  * files - if they are missing, get the official version at www.gromacs.org.
  26  *
  27  * To help us fund GROMACS development, we humbly ask that you cite
  28  * the papers on the package - you can find them in the top README file.
  29  *
  30  * For more info, check our website at http://www.gromacs.org
  31  *
  32  * And Hey:
  33  * GROningen Mixture of Alchemy and Childrens' Stories
  34  */
  35 #ifdef HAVE_CONFIG_H
  36 #include <config.h>
  37 #endif
  38
  39 #include <string.h>
  40 #include "sysstuff.h"
  41 #include "typedefs.h"
  42 #include "smalloc.h"
  43 #include "string2.h"
  44 #include "gmx_fatal.h"
  45 #include "filenm.h"
  46 #include "futil.h"
  47 #include "wman.h"
  48 #include "xdrf.h"
  49 #include "macros.h"
  50
  51 #ifdef GMX_THREAD_MPI
  52 #include "thread_mpi.h"
  53 #endif
  54
  55 /* NOTE: this was a cesspool of thread-unsafe code, has now been
  56  properly proteced by mutexes (hopefully). */
  57
  58 /* XDR should be available on all platforms now,
  59  * but we keep the possibility of turning it off...
  60  */
  61 #define USE_XDR
  62
  63 /* Use bitflag ... */
  64 #define IS_SET(fn) ((fn.flag & ffSET) != 0)
  65 #define IS_OPT(fn) ((fn.flag & ffOPT) != 0)
  66 #define IS_MULT(fn) ((fn.flag & ffMULT) != 0)
  67 #define UN_SET(fn) (fn.flag = (fn.flag & ~ffSET))
  68 #define DO_SET(fn) (fn.flag = (fn.flag |  ffSET))
  69
  70 enum
  71 {
  72     eftASC, eftBIN, eftXDR, eftGEN, eftNR
  73 };
  74
  75 /* To support multiple file types with one general (eg TRX) we have
  76  * these arrays.
  77  */
  78 static const int trxs[] =
  79     {
  80 #ifdef USE_XDR
  81         efXTC, efTRR, efCPT,
  82 #endif
  83         efTRJ, efGRO, efG96, efPDB, efG87 };
  84 #define NTRXS asize(trxs)
  85
  86 static const int tros[] =
  87     {
  88 #ifdef USE_XDR
  89         efXTC, efTRR,
  90 #endif
  91         efTRJ, efGRO, efG96, efPDB, efG87 };
  92 #define NTROS asize(tros)
  93
  94 static const int trns[] =
  95     {
  96 #ifdef USE_XDR
  97         efTRR, efCPT,
  98 #endif
  99         efTRJ };
 100 #define NTRNS asize(trns)
 101
 102 static const int stos[] =
 103     { efGRO, efG96, efPDB, efBRK, efENT, efESP, efXYZ };
 104 #define NSTOS asize(stos)
 105
 106 static const int stxs[] =
 107     { efGRO, efG96, efPDB, efBRK, efENT, efESP, efXYZ,
 108 #ifdef USE_XDR
 109         efTPR,
 110 #endif
 111         efTPB, efTPA };
 112 #define NSTXS asize(stxs)
 113
 114 static const int tpxs[] =
 115     {
 116 #ifdef USE_XDR
 117         efTPR,
 118 #endif
 119         efTPB, efTPA };
 120 #define NTPXS asize(tpxs)
 121
 122 static const int tpss[] =
 123     {
 124 #ifdef USE_XDR
 125         efTPR,
 126 #endif
 127         efTPB, efTPA, efGRO, efG96, efPDB, efBRK, efENT };
 128 #define NTPSS asize(tpss)
 129
 130 typedef struct
 131 {
 132     int ftype;
 133     const char *ext;
 134     const char *defnm;
 135     const char *defopt;
 136     const char *descr;
 137     int ntps;
 138     const int *tps;
 139 } t_deffile;
 140
 141 /* this array should correspond to the enum in include/types/filenm.h */
 142 static const t_deffile
 143     deffile[efNR] =
 144 {
 145     { eftASC, ".mdp", "grompp", "-f", "grompp input file with MD parameters" },
 146     { eftASC, ".gct", "gct",    "-f", "General coupling stuff"},
 147     { eftGEN, ".???", "traj", "-f",
 148       "Trajectory: xtc trr trj gro g96 pdb cpt", NTRXS, trxs },
 149     { eftGEN, ".???", "trajout", "-f",
 150       "Trajectory: xtc trr trj gro g96 pdb", NTROS, tros },
 151     { eftGEN, ".???", "traj", NULL,
 152       "Full precision trajectory: trr trj cpt", NTRNS, trns },
 153     { eftXDR, ".trr", "traj", NULL, "Trajectory in portable xdr format" },
 154     { eftBIN, ".trj", "traj", NULL, "Trajectory file (architecture specific)" },
 155     { eftXDR, ".xtc", "traj", NULL,
 156       "Compressed trajectory (portable xdr format)" },
 157     { eftASC, ".g87", "gtraj", NULL, "Gromos-87 ASCII trajectory format" },
 158     { eftXDR, ".edr", "ener",   NULL, "Energy file"},
 159     { eftGEN, ".???", "conf", "-c", "Structure file: gro g96 pdb tpr etc.",
 160       NSTXS, stxs },
 161     { eftGEN, ".???", "out", "-o", "Structure file: gro g96 pdb etc.",
 162       NSTOS, stos },
 163     { eftASC, ".gro", "conf", "-c", "Coordinate file in Gromos-87 format" },
 164     { eftASC, ".g96", "conf", "-c", "Coordinate file in Gromos-96 format" },
 165     { eftASC, ".pdb", "eiwit",  "-f", "Protein data bank file"},
 166     { eftASC, ".brk", "eiwit",  "-f", "Brookhaven data bank file"},
 167     { eftASC, ".ent", "eiwit", "-f", "Entry in the protein date bank" },
 168     { eftASC, ".esp", "conf", "-f", "Coordinate file in Espresso format" },
 169     { eftASC, ".pqr", "state",  "-o", "Coordinate file for MEAD"},
 170     { eftASC, ".xyz", "conf", "-o", "Coordinate file for some other programs" },
 171     { eftXDR, ".cpt", "state",  "-cp","Checkpoint file"},
 172     { eftASC, ".log", "run",    "-l", "Log file"},
 173     { eftASC, ".xvg", "graph",  "-o", "xvgr/xmgr file"},
 174     { eftASC, ".out", "hello",  "-o", "Generic output file"},
 175     { eftASC, ".ndx", "index",  "-n", "Index file",},
 176     { eftASC, ".top", "topol",  "-p", "Topology file"},
 177     { eftASC, ".itp", "topinc", NULL, "Include file for topology"},
 178     { eftGEN, ".???", "topol", "-s", "Run input file: tpr tpb tpa",
 179       NTPXS, tpxs },
 180     { eftGEN, ".???", "topol", "-s",
 181       "Structure+mass(db): tpr tpb tpa gro g96 pdb", NTPSS, tpss },
 182     { eftXDR, ".tpr", "topol",  "-s", "Portable xdr run input file"},
 183     { eftASC, ".tpa", "topol",  "-s", "Ascii run input file"},
 184     { eftBIN, ".tpb", "topol",  "-s", "Binary run input file"},
 185     { eftASC, ".tex", "doc",    "-o", "LaTeX file"},
 186     { eftASC, ".rtp", "residue", NULL, "Residue Type file used by pdb2gmx" },
 187     { eftASC, ".atp", "atomtp", NULL, "Atomtype file used by pdb2gmx" },
 188     { eftASC, ".hdb", "polar",  NULL, "Hydrogen data base"},
 189     { eftASC, ".dat", "nnnice", NULL, "Generic data file"},
 190     { eftASC, ".dlg", "user",   NULL, "Dialog Box data for ngmx"},
 191     { eftASC, ".map", "ss", NULL, "File that maps matrix data to colors" },
 192     { eftASC, ".eps", "plot", NULL, "Encapsulated PostScript (tm) file" },
 193     { eftASC, ".mat", "ss",     NULL, "Matrix Data file"},
 194     { eftASC, ".m2p", "ps",     NULL, "Input file for mat2ps"},
 195     { eftXDR, ".mtx", "hessian","-m", "Hessian matrix"},
 196     { eftASC, ".edi", "sam",    NULL, "ED sampling input"},
 197     { eftASC, ".edo", "sam",    NULL, "ED sampling output"},
 198     { eftASC, ".hat", "gk", NULL, "Fourier transform of spread function" },
 199     { eftASC, ".cub", "pot",  NULL, "Gaussian cube file" },
 200     { eftASC, ".xpm", "root", NULL, "X PixMap compatible matrix file" },
 201     { eftASC, "", "rundir", NULL, "Run directory" }
 202 };
 203
 204 static char *default_file_name = NULL;
 205
 206 #ifdef GMX_THREAD_MPI
 207 static tMPI_Thread_mutex_t filenm_mutex=TMPI_THREAD_MUTEX_INITIALIZER;
 208 #endif
 209
 210 #define NZEXT 2
 211 const char *z_ext[NZEXT] =
 212     { ".gz", ".Z" };
 213
 214 void set_default_file_name(const char *name)
 215 {
 216     int i;
 217 #ifdef GMX_THREAD_MPI
 218     tMPI_Thread_mutex_lock(&filenm_mutex);
 219 #endif
 220     default_file_name = strdup(name);
 221 #ifdef GMX_THREAD_MPI
 222     tMPI_Thread_mutex_unlock(&filenm_mutex);
 223 #endif
 224
 225 #if 0
 226     for(i=0; i<efNR; i++)
 227     deffile[i].defnm = default_file_name;
 228 #endif
 229 }
 230
 231 const char *ftp2ext(int ftp)
 232 {
 233     if ((0 <= ftp) && (ftp < efNR))
 234         return deffile[ftp].ext + 1;
 235     else
 236         return "unknown";
 237 }
 238
 239 const char *ftp2ext_generic(int ftp)
 240 {
 241     if ((0 <= ftp) && (ftp < efNR))
 242     {
 243         switch (ftp)
 244         {
 245         case efTRX:
 246             return "trx";
 247         case efTRN:
 248             return "trn";
 249         case efSTO:
 250             return "sto";
 251         case efSTX:
 252             return "stx";
 253         case efTPX:
 254             return "tpx";
 255         case efTPS:
 256             return "tps";
 257         default:
 258             return ftp2ext(ftp);
 259         }
 260     }
 261     else
 262         return "unknown";
 263 }
 264
 265 const char *ftp2desc(int ftp)
 266 {
 267     if ((0 <= ftp) && (ftp < efNR))
 268         return deffile[ftp].descr;
 269     else
 270         return "unknown filetype";
 271 }
 272
 273 const char *ftp2ftype(int ftp)
 274 {
 275     if ((ftp >= 0) && (ftp < efNR))
 276     {
 277         switch (deffile[ftp].ftype)
 278         {
 279         case eftASC:
 280             return "ASCII";
 281         case eftBIN:
 282             return "Binary";
 283         case eftXDR:
 284             return "XDR portable";
 285         case eftGEN:
 286             return "";
 287         default:
 288             gmx_fatal(FARGS, "Unknown filetype %d in ftp2ftype",deffile[ftp].ftype);
 289             break;
 290         }
 291     }
 292     return "unknown";
 293 }
 294
 295 const char *ftp2defnm(int ftp)
 296 {
 297     const char *buf = NULL;
 298
 299 #ifdef GMX_THREAD_MPI
 300     tMPI_Thread_mutex_lock(&filenm_mutex);
 301 #endif
 302
 303     if (default_file_name)
 304     {
 305         buf = default_file_name;
 306     }
 307     else
 308     {
 309         if ((0 <= ftp) && (ftp < efNR))
 310         {
 311             buf = deffile[ftp].defnm;
 312         }
 313     }
 314 #ifdef GMX_THREAD_MPI
 315     tMPI_Thread_mutex_unlock(&filenm_mutex);
 316 #endif
 317
 318     return buf;
 319 }
 320
 321 void pr_def(FILE *fp, int ftp)
 322 {
 323     const t_deffile *df;
 324     const char *s = NULL;
 325     char *flst, *tmp, *desc;
 326     const char *ext;
 327     const char *defnm;
 328
 329     df = &(deffile[ftp]);
 330     defnm = ftp2defnm(ftp);
 331     /* find default file extension and \tt-ify description */
 332     /* FIXME: The constness should not be cast away */
 333     flst = (char *) "";
 334     desc = strdup(df->descr);
 335
 336     if (df->ntps)
 337     {
 338         ext = deffile[df->tps[0]].ext;
 339         tmp = strstr(desc, ": ") + 1;
 340         if (tmp)
 341         {
 342             tmp[0] = '\0';
 343             tmp++;
 344             snew(flst,strlen(tmp)+6);
 345             strcpy(flst, " \\tt ");
 346             strcat(flst, tmp);
 347         }
 348     }
 349     else
 350     {
 351         ext = df->ext;
 352     }
 353     /* now skip dot */
 354     if (ext[0])
 355         ext++;
 356     else
 357         ext = "";
 358     /* set file contents type */
 359     switch (df->ftype)
 360     {
 361     case eftASC:
 362         s = "Asc";
 363         break;
 364     case eftBIN:
 365         s = "Bin";
 366         break;
 367     case eftXDR:
 368         s = "xdr";
 369         break;
 370     case eftGEN:
 371         s = "";
 372         break;
 373     default:
 374         gmx_fatal(FARGS, "Unimplemented filetype %d %d",ftp,
 375         df->ftype);
 376     }
 377     fprintf(fp,"\\tt %8s & \\tt %3s & %3s & \\tt %2s & %s%s \\\\[-0.1ex]\n",
 378         defnm, ext, s, df->defopt ? df->defopt : "",
 379         check_tex(desc),check_tex(flst));
 380     free(desc);
 381 }
 382
 383 void pr_fns(FILE *fp, int nf, const t_filenm tfn[])
 384 {
 385     int i, f;
 386     size_t j;
 387     char buf[256], *wbuf, opt_buf[32];
 388 #define OPTLEN 4
 389 #define NAMELEN 14
 390     fprintf(fp, "%6s %12s  %-12s %s\n", "Option", "Filename", "Type",
 391             "Description");
 392     fprintf(fp,
 393             "------------------------------------------------------------\n");
 394     for (i = 0; (i < nf); i++)
 395     {
 396         for (f = 0; (f < tfn[i].nfiles); f++)
 397         {
 398             sprintf(buf, "%4s %14s  %-12s ", (f == 0) ? tfn[i].opt : "",
 399                     tfn[i].fns[f], (f == 0) ? fileopt(tfn[i].flag, opt_buf, 32)
 400                         : "");
 401             if (f < tfn[i].nfiles - 1)
 402                 fprintf(fp, "%s\n", buf);
 403         }
 404         if (tfn[i].nfiles > 0)
 405         {
 406             strcat(buf, deffile[tfn[i].ftp].descr);
 407             if ((strlen(tfn[i].opt) > OPTLEN)
 408                 && (strlen(tfn[i].opt) <= ((OPTLEN + NAMELEN)
 409                     - strlen(tfn[i].fns[tfn[i].nfiles - 1]))))
 410             {
 411                 for (j = strlen(tfn[i].opt); j < strlen(buf)
 412                     - (strlen(tfn[i].opt) - OPTLEN) + 1; j++)
 413                     buf[j] = buf[j + strlen(tfn[i].opt) - OPTLEN];
 414             }
 415             wbuf = wrap_lines(buf, 78, 35, FALSE);
 416             fprintf(fp, "%s\n", wbuf);
 417             sfree(wbuf);
 418         }
 419     }
 420     fprintf(fp, "\n");
 421     fflush(fp);
 422 }
 423
 424 void pr_fopts(FILE *fp, int nf, const t_filenm tfn[], int shell)
 425 {
 426     int i, j;
 427
 428     switch (shell)
 429     {
 430     case eshellCSH:
 431         for (i = 0; (i < nf); i++)
 432         {
 433             fprintf(fp, " \"n/%s/f:*.", tfn[i].opt);
 434             if (deffile[tfn[i].ftp].ntps)
 435             {
 436                 fprintf(fp, "{");
 437                 for (j = 0; j < deffile[tfn[i].ftp].ntps; j++)
 438                 {
 439                     if (j > 0)
 440                         fprintf(fp, ",");
 441                     fprintf(fp, "%s", deffile[deffile[tfn[i].ftp].tps[j]].ext
 442                             + 1);
 443                 }
 444                 fprintf(fp, "}");
 445             }
 446             else
 447                 fprintf(fp, "%s", deffile[tfn[i].ftp].ext + 1);
 448             fprintf(fp, "{");
 449             for (j = 0; j < NZEXT; j++)
 450                 fprintf(fp, ",%s", z_ext[j]);
 451             fprintf(fp, "}/\"");
 452         }
 453         break;
 454     case eshellBASH:
 455         for (i = 0; (i < nf); i++)
 456         {
 457             fprintf(fp, "%s) COMPREPLY=( $(compgen -X '!*.", tfn[i].opt);
 458             if (deffile[tfn[i].ftp].ntps)
 459             {
 460                 fprintf(fp, "+(");
 461                 for (j = 0; j < deffile[tfn[i].ftp].ntps; j++)
 462                 {
 463                     if (j > 0)
 464                         fprintf(fp, "|");
 465                     fprintf(fp, "%s", deffile[deffile[tfn[i].ftp].tps[j]].ext
 466                             + 1);
 467                 }
 468                 fprintf(fp, ")");
 469             }
 470             else
 471                 fprintf(fp, "%s", deffile[tfn[i].ftp].ext + 1);
 472             fprintf(fp, "*(");
 473             for (j = 0; j < NZEXT; j++)
 474             {
 475                 if (j > 0)
 476                     fprintf(fp, "|");
 477                 fprintf(fp, "%s", z_ext[j]);
 478             }
 479             fprintf(fp, ")' -f $c ; compgen -S '/' -X '.*' -d $c ));;\n");
 480         }
 481         break;
 482     case eshellZSH:
 483         for (i = 0; (i < nf); i++)
 484         {
 485             fprintf(fp, "- 'c[-1,%s]' -g '*.", tfn[i].opt);
 486             if (deffile[tfn[i].ftp].ntps)
 487             {
 488                 fprintf(fp, "(");
 489                 for (j = 0; j < deffile[tfn[i].ftp].ntps; j++)
 490                 {
 491                     if (j > 0)
 492                         fprintf(fp, "|");
 493                     fprintf(fp, "%s", deffile[deffile[tfn[i].ftp].tps[j]].ext
 494                             + 1);
 495                 }
 496                 fprintf(fp, ")");
 497             }
 498             else
 499                 fprintf(fp, "%s", deffile[tfn[i].ftp].ext + 1);
 500             fprintf(fp, "(");
 501             for (j = 0; j < NZEXT; j++)
 502                 fprintf(fp, "|%s", z_ext[j]);
 503             fprintf(fp, ") *(/)' ");
 504         }
 505         break;
 506     }
 507 }
 508
 509 static void check_opts(int nf, t_filenm fnm[])
 510 {
 511     int i;
 512     const t_deffile *df;
 513
 514     for (i = 0; (i < nf); i++)
 515     {
 516         df = &(deffile[fnm[i].ftp]);
 517         if (fnm[i].opt == NULL)
 518         {
 519             if (df->defopt == NULL)
 520             {
 521                 gmx_fatal(FARGS, "No default cmd-line option for %s (type %d)\n",
 522                           deffile[fnm[i].ftp].ext,fnm[i].ftp);
 523             }
 524             else
 525             {
 526                 fnm[i].opt=df->defopt;
 527             }
 528         }
 529     }
 530 }
 531
 532 int fn2ftp(const char *fn)
 533 {
 534     int i, len;
 535     const char *feptr;
 536     const char *eptr;
 537
 538     if (!fn)
 539         return efNR;
 540
 541     len = strlen(fn);
 542     if ((len >= 4) && (fn[len - 4] == '.'))
 543         feptr = &(fn[len - 4]);
 544     else
 545         return efNR;
 546
 547     for (i = 0; (i < efNR); i++)
 548         if ((eptr = deffile[i].ext) != NULL)
 549             if (gmx_strcasecmp(feptr, eptr) == 0)
 550                 break;
 551
 552     return i;
 553 }
 554
 555 static void set_extension(char *buf, int ftp)
 556 {
 557     int len, extlen;
 558     const t_deffile *df;
 559
 560     /* check if extension is already at end of filename */
 561     df = &(deffile[ftp]);
 562     len = strlen(buf);
 563     extlen = strlen(df->ext);
 564     if ((len <= extlen) || (gmx_strcasecmp(&(buf[len - extlen]), df->ext) != 0))
 565         strcat(buf, df->ext);
 566 }
 567
 568 static void add_filenm(t_filenm *fnm, const char *filenm)
 569 {
 570     srenew(fnm->fns, fnm->nfiles+1);
 571     fnm->fns[fnm->nfiles] = strdup(filenm);
 572     fnm->nfiles++;
 573 }
 574
 575 static void set_grpfnm(t_filenm *fnm, const char *name, gmx_bool bCanNotOverride)
 576 {
 577     char buf[256], buf2[256];
 578     int i, type;
 579     gmx_bool bValidExt;
 580     int nopts;
 581     const int *ftps;
 582
 583     nopts = deffile[fnm->ftp].ntps;
 584     ftps = deffile[fnm->ftp].tps;
 585     if ((nopts == 0) || (ftps == NULL))
 586         gmx_fatal(FARGS, "nopts == 0 || ftps == NULL");
 587
 588     bValidExt = FALSE;
 589     if (name && (bCanNotOverride || (default_file_name == NULL)))
 590     {
 591         strcpy(buf,name);
 592         /* First check whether we have a valid filename already */
 593         type = fn2ftp(name);
 594         if ((fnm->flag & ffREAD) && (fnm->ftp == efTRX))
 595         {
 596             /*if file exist don't add an extension for trajectory reading*/
 597             bValidExt = gmx_fexist(name);
 598         }
 599         for(i=0; (i<nopts) && !bValidExt; i++)
 600         {
 601             if (type == ftps[i])
 602             {
 603                 bValidExt = TRUE;
 604             }
 605         }
 606     }
 607     else
 608         /* No name given, set the default name */
 609         strcpy(buf,ftp2defnm(fnm->ftp));
 610
 611     if (!bValidExt && (fnm->flag & ffREAD))
 612     {
 613         /* for input-files only: search for filenames in the directory */
 614         for(i=0; (i<nopts) && !bValidExt; i++)
 615         {
 616             type = ftps[i];
 617             strcpy(buf2,buf);
 618             set_extension(buf2,type);
 619             if (gmx_fexist(buf2))
 620             {
 621                 bValidExt = TRUE;
 622                 strcpy(buf,buf2);
 623             }
 624         }
 625     }
 626
 627     if (!bValidExt)
 628     {
 629         /* Use the first extension type */
 630         set_extension(buf,ftps[0]);
 631     }
 632
 633     add_filenm(fnm, buf);
 634 }
 635
 636 static void set_filenm(t_filenm *fnm, const char *name, gmx_bool bCanNotOverride,
 637                        gmx_bool bReadNode)
 638 {
 639     /* Set the default filename, extension and option for those fields that
 640      * are not already set. An extension is added if not present, if fn = NULL
 641      * or empty, the default filename is given.
 642      */
 643     char buf[256];
 644     int i, len, extlen;
 645
 646     if ((fnm->flag & ffREAD) && !bReadNode)
 647     {
 648         return;
 649     }
 650
 651     if ((fnm->ftp < 0) || (fnm->ftp >= efNR))
 652         gmx_fatal(FARGS, "file type out of range (%d)",fnm->ftp);
 653
 654     if (name)
 655         strcpy(buf, name);
 656     if ((fnm->flag & ffREAD) && name && gmx_fexist(name))
 657     {
 658         /* check if filename ends in .gz or .Z, if so remove that: */
 659         len = strlen(name);
 660         for (i=0; i<NZEXT; i++)
 661         {
 662             extlen = strlen(z_ext[i]);
 663             if (len > extlen)
 664             {
 665                 if (gmx_strcasecmp(name+len-extlen,z_ext[i]) == 0)
 666                 {
 667                     buf[len-extlen]='\0';
 668                     break;
 669                 }
 670             }
 671         }
 672     }
 673
 674     if (deffile[fnm->ftp].ntps)
 675     {
 676         set_grpfnm(fnm,name ? buf : NULL,bCanNotOverride);
 677     }
 678     else
 679     {
 680         if ((name == NULL) || !(bCanNotOverride || (default_file_name ==NULL)))
 681         {
 682             const char *defnm=ftp2defnm(fnm->ftp);
 683             strcpy(buf,defnm);
 684         }
 685         set_extension(buf,fnm->ftp);
 686
 687         add_filenm(fnm, buf);
 688     }
 689 }
 690
 691 static void set_filenms(int nf, t_filenm fnm[], gmx_bool bReadNode)
 692 {
 693     int i;
 694
 695     for (i = 0; (i < nf); i++)
 696         if (!IS_SET(fnm[i]))
 697             set_filenm(&(fnm[i]), fnm[i].fn, FALSE, bReadNode);
 698 }
 699
 700 void parse_file_args(int *argc, char *argv[], int nf, t_filenm fnm[],
 701                      gmx_bool bKeep, gmx_bool bReadNode)
 702 {
 703     int i, j;
 704     gmx_bool *bRemove;
 705
 706     check_opts(nf, fnm);
 707
 708     for (i = 0; (i < nf); i++)
 709         UN_SET(fnm[i]);
 710
 711     if (*argc > 1)
 712     {
 713         snew(bRemove,(*argc)+1);
 714         i = 1;
 715         do
 716         {
 717             for (j = 0; (j < nf); j++)
 718             {
 719                 if (strcmp(argv[i], fnm[j].opt) == 0)
 720                 {
 721                     DO_SET(fnm[j]);
 722                     bRemove[i] = TRUE;
 723                     i++;
 724                     /* check if we are out of arguments for this option */
 725                     if ((i >= *argc) || (argv[i][0] == '-'))
 726                         set_filenm(&fnm[j], fnm[j].fn, FALSE, bReadNode);
 727                     /* sweep up all file arguments for this option */
 728                     while ((i < *argc) && (argv[i][0] != '-'))
 729                     {
 730                         set_filenm(&fnm[j], argv[i], TRUE, bReadNode);
 731                         bRemove[i] = TRUE;
 732                         i++;
 733                         /* only repeat for 'multiple' file options: */
 734                         if (!IS_MULT(fnm[j]))
 735                             break;
 736                     }
 737
 738                     break; /* jump out of 'j' loop */
 739                 }
 740             }
 741             /* No file found corresponding to option argv[i] */
 742             if (j == nf)
 743                 i++;
 744         } while (i < *argc);
 745
 746         if (!bKeep)
 747         {
 748             /* Remove used entries */
 749             for (i = j = 0; (i <= *argc); i++)
 750             {
 751                 if (!bRemove[i])
 752                     argv[j++] = argv[i];
 753             }
 754             (*argc) = j - 1;
 755         }
 756         sfree(bRemove);
 757     }
 758
 759     set_filenms(nf, fnm, bReadNode);
 760
 761 }
 762
 763 const char *opt2fn(const char *opt, int nfile, const t_filenm fnm[])
 764 {
 765     int i;
 766
 767     for (i = 0; (i < nfile); i++)
 768         if (strcmp(opt, fnm[i].opt) == 0)
 769         {
 770             return fnm[i].fns[0];
 771         }
 772
 773     fprintf(stderr, "No option %s\n", opt);
 774
 775     return NULL;
 776 }
 777
 778 const char *opt2fn_master(const char *opt, int nfile, const t_filenm fnm[],
 779                           t_commrec *cr)
 780 {
 781     return SIMMASTER(cr) ? opt2fn(opt, nfile, fnm) : NULL;
 782 }
 783
 784 int opt2fns(char **fns[], const char *opt, int nfile, const t_filenm fnm[])
 785 {
 786     int i;
 787
 788     for (i = 0; (i < nfile); i++)
 789         if (strcmp(opt, fnm[i].opt) == 0)
 790         {
 791             *fns = fnm[i].fns;
 792             return fnm[i].nfiles;
 793         }
 794
 795     fprintf(stderr, "No option %s\n", opt);
 796     return 0;
 797 }
 798
 799 const char *ftp2fn(int ftp, int nfile, const t_filenm fnm[])
 800 {
 801     int i;
 802
 803     for (i = 0; (i < nfile); i++)
 804         if (ftp == fnm[i].ftp)
 805             return fnm[i].fns[0];
 806
 807     fprintf(stderr, "ftp2fn: No filetype %s\n", deffile[ftp].ext);
 808     return NULL;
 809 }
 810
 811 int ftp2fns(char **fns[], int ftp, int nfile, const t_filenm fnm[])
 812 {
 813     int i;
 814
 815     for (i = 0; (i < nfile); i++)
 816         if (ftp == fnm[i].ftp)
 817         {
 818             *fns = fnm[i].fns;
 819             return fnm[i].nfiles;
 820         }
 821
 822     fprintf(stderr, "ftp2fn: No filetype %s\n", deffile[ftp].ext);
 823     return 0;
 824 }
 825
 826 gmx_bool ftp2bSet(int ftp, int nfile, const t_filenm fnm[])
 827 {
 828     int i;
 829
 830     for (i = 0; (i < nfile); i++)
 831         if (ftp == fnm[i].ftp)
 832             return (gmx_bool) IS_SET(fnm[i]);
 833
 834     fprintf(stderr, "ftp2bSet: No filetype %s\n", deffile[ftp].ext);
 835
 836     return FALSE;
 837 }
 838
 839 gmx_bool opt2bSet(const char *opt, int nfile, const t_filenm fnm[])
 840 {
 841     int i;
 842
 843     for (i = 0; (i < nfile); i++)
 844         if (strcmp(opt, fnm[i].opt) == 0)
 845             return (gmx_bool) IS_SET(fnm[i]);
 846
 847     fprintf(stderr, "No option %s\n", opt);
 848
 849     return FALSE;
 850 }
 851
 852 const char *opt2fn_null(const char *opt, int nfile, const t_filenm fnm[])
 853 {
 854     int i;
 855
 856     for (i = 0; (i < nfile); i++)
 857         if (strcmp(opt, fnm[i].opt) == 0)
 858         {
 859             if (IS_OPT(fnm[i]) && !IS_SET(fnm[i]))
 860                 return NULL;
 861             else
 862                 return fnm[i].fns[0];
 863         }
 864     fprintf(stderr, "No option %s\n", opt);
 865     return NULL;
 866 }
 867
 868 const char *ftp2fn_null(int ftp, int nfile, const t_filenm fnm[])
 869 {
 870     int i;
 871
 872     for (i = 0; (i < nfile); i++)
 873         if (ftp == fnm[i].ftp)
 874         {
 875             if (IS_OPT(fnm[i]) && !IS_SET(fnm[i]))
 876                 return NULL;
 877             else
 878                 return fnm[i].fns[0];
 879         }
 880     fprintf(stderr, "ftp2fn: No filetype %s\n", deffile[ftp].ext);
 881     return NULL;
 882 }
 883
 884 #if 0
 885 static void add_filters(char *filter,int *n,int nf,const int ftp[])
 886 {
 887     char buf[8];
 888     int i;
 889
 890     sprintf(filter,"*.{");
 891     for(i=0; (i<nf); i++)
 892     {
 893         sprintf(buf,"%s",ftp2ext(ftp[i]));
 894         if (*n > 0)
 895             strcat(filter,",");
 896         strcat(filter,buf);
 897         (*n) ++;
 898     }
 899     strcat(filter,"}");
 900 }
 901
 902 char *ftp2filter(int ftp)
 903 {
 904     int n;
 905     static char filter[128];
 906
 907     filter[0] = '\0';
 908     n = 0;
 909     switch (ftp)
 910     {
 911     case efTRX:
 912         add_filters(filter,&n,NTRXS,trxs);
 913         break;
 914     case efTRN:
 915         add_filters(filter,&n,NTRNS,trns);
 916         break;
 917     case efSTO:
 918         add_filters(filter,&n,NSTOS,stos);
 919         break;
 920     case efSTX:
 921         add_filters(filter,&n,NSTXS,stxs);
 922         break;
 923     case efTPX:
 924         add_filters(filter,&n,NTPXS,tpxs);
 925         break;
 926     default:
 927         sprintf(filter,"*%s",ftp2ext(ftp));
 928         break;
 929     }
 930     return filter;
 931 }
 932 #endif
 933
 934 gmx_bool is_optional(const t_filenm *fnm)
 935 {
 936     return ((fnm->flag & ffOPT) == ffOPT);
 937 }
 938
 939 gmx_bool is_output(const t_filenm *fnm)
 940 {
 941     return ((fnm->flag & ffWRITE) == ffWRITE);
 942 }
 943
 944 gmx_bool is_set(const t_filenm *fnm)
 945 {
 946     return ((fnm->flag & ffSET) == ffSET);
 947 }
 948
 949 int add_suffix_to_output_names(t_filenm *fnm, int nfile, const char *suffix)
 950 {
 951     int i, j, pos;
 952     char buf[STRLEN], newname[STRLEN];
 953     char *extpos;
 954
 955     for (i = 0; i < nfile; i++)
 956     {
 957         if (is_output(&fnm[i]) && fnm[i].ftp != efCPT)
 958         {
 959             /* We never use multiple _outputs_, but we might as well check
 960              for it, just in case... */
 961             for (j = 0; j < fnm[i].nfiles; j++)
 962             {
 963                 strncpy(buf, fnm[i].fns[j], STRLEN - 1);
 964                 extpos = strrchr(buf, '.');
 965                 *extpos = '\0';
 966                 sprintf(newname, "%s%s.%s", buf, suffix, extpos + 1);
 967                 free(fnm[i].fns[j]);
 968                 fnm[i].fns[j] = strdup(newname);
 969             }
 970         }
 971     }
 972     return 0;
 973 }
 974
 975 t_filenm *dup_tfn(int nf, const t_filenm tfn[])
 976 {
 977     int i, j;
 978     t_filenm *ret;
 979
 980     snew(ret, nf);
 981     for (i = 0; i < nf; i++)
 982     {
 983         ret[i] = tfn[i]; /* just directly copy all non-string fields */
 984         if (tfn[i].opt)
 985             ret[i].opt = strdup(tfn[i].opt);
 986         else
 987             ret[i].opt = NULL;
 988
 989         if (tfn[i].fn)
 990             ret[i].fn = strdup(tfn[i].fn);
 991         else
 992             ret[i].fn = NULL;
 993
 994         if (tfn[i].nfiles > 0)
 995         {
 996             snew(ret[i].fns,tfn[i].nfiles);
 997             for (j = 0; j < tfn[i].nfiles; j++)
 998             {
 999                 ret[i].fns[j] = strdup(tfn[i].fns[j]);
1000             }
1001         }
1002     }
1003     return ret;
1004 }
1005
1006 void done_filenms(int nf, t_filenm fnm[])
1007 {
1008     int i, j;
1009
1010     for (i = 0; i < nf; ++i)
1011     {
1012         for (j = 0; j < fnm[i].nfiles; ++j)
1013         {
1014             sfree(fnm[i].fns[j]);
1015         }
1016         sfree(fnm[i].fns);
1017         fnm[i].fns = NULL;
1018     }
1019 }