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_THREADS
  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 };
 202
 203 static char *default_file_name = NULL;
 204
 205 #ifdef GMX_THREADS
 206 static tMPI_Thread_mutex_t filenm_mutex=TMPI_THREAD_MUTEX_INITIALIZER;
 207 #endif
 208
 209 #define NZEXT 2
 210 const char *z_ext[NZEXT] =
 211     { ".gz", ".Z" };
 212
 213 void set_default_file_name(const char *name)
 214 {
 215     int i;
 216 #ifdef GMX_THREADS
 217     tMPI_Thread_mutex_lock(&filenm_mutex);
 218 #endif
 219     default_file_name = strdup(name);
 220 #ifdef GMX_THREADS
 221     tMPI_Thread_mutex_unlock(&filenm_mutex);
 222 #endif
 223
 224 #if 0
 225     for(i=0; i<efNR; i++)
 226     deffile[i].defnm = default_file_name;
 227 #endif
 228 }
 229
 230 const char *ftp2ext(int ftp)
 231 {
 232     if ((0 <= ftp) && (ftp < efNR))
 233         return deffile[ftp].ext + 1;
 234     else
 235         return "unknown";
 236 }
 237
 238 const char *ftp2ext_generic(int ftp)
 239 {
 240     if ((0 <= ftp) && (ftp < efNR))
 241     {
 242         switch (ftp)
 243         {
 244         case efTRX:
 245             return "trx";
 246         case efTRN:
 247             return "trn";
 248         case efSTO:
 249             return "sto";
 250         case efSTX:
 251             return "stx";
 252         case efTPX:
 253             return "tpx";
 254         case efTPS:
 255             return "tps";
 256         default:
 257             return ftp2ext(ftp);
 258         }
 259     }
 260     else
 261         return "unknown";
 262 }
 263
 264 const char *ftp2desc(int ftp)
 265 {
 266     if ((0 <= ftp) && (ftp < efNR))
 267         return deffile[ftp].descr;
 268     else
 269         return "unknown filetype";
 270 }
 271
 272 const char *ftp2ftype(int ftp)
 273 {
 274     if ((ftp >= 0) && (ftp < efNR))
 275     {
 276         switch (deffile[ftp].ftype)
 277         {
 278         case eftASC:
 279             return "ASCII";
 280         case eftBIN:
 281             return "Binary";
 282         case eftXDR:
 283             return "XDR portable";
 284         case eftGEN:
 285             return "";
 286         default:
 287             gmx_fatal(FARGS, "Unknown filetype %d in ftp2ftype",deffile[ftp].ftype);
 288             break;
 289         }
 290     }
 291     return "unknown";
 292 }
 293
 294 const char *ftp2defnm(int ftp)
 295 {
 296     const char *buf = NULL;
 297
 298 #ifdef GMX_THREADS
 299     tMPI_Thread_mutex_lock(&filenm_mutex);
 300 #endif
 301
 302     if (default_file_name)
 303     {
 304         buf = default_file_name;
 305     }
 306     else
 307     {
 308         if ((0 <= ftp) && (ftp < efNR))
 309         {
 310             buf = deffile[ftp].defnm;
 311         }
 312     }
 313 #ifdef GMX_THREADS
 314     tMPI_Thread_mutex_unlock(&filenm_mutex);
 315 #endif
 316
 317     return buf;
 318 }
 319
 320 void pr_def(FILE *fp, int ftp)
 321 {
 322     const t_deffile *df;
 323     const char *s = NULL;
 324     char *flst, *tmp, *desc;
 325     const char *ext;
 326     const char *defnm;
 327
 328     df = &(deffile[ftp]);
 329     defnm = ftp2defnm(ftp);
 330     /* find default file extension and \tt-ify description */
 331     /* FIXME: The constness should not be cast away */
 332     flst = (char *) "";
 333     desc = strdup(df->descr);
 334
 335     if (df->ntps)
 336     {
 337         ext = deffile[df->tps[0]].ext;
 338         tmp = strstr(desc, ": ") + 1;
 339         if (tmp)
 340         {
 341             tmp[0] = '\0';
 342             tmp++;
 343             snew(flst,strlen(tmp)+6);
 344             strcpy(flst, " \\tt ");
 345             strcat(flst, tmp);
 346         }
 347     }
 348     else
 349     {
 350         ext = df->ext;
 351     }
 352     /* now skip dot */
 353     if (ext[0])
 354         ext++;
 355     else
 356         ext = "";
 357     /* set file contents type */
 358     switch (df->ftype)
 359     {
 360     case eftASC:
 361         s = "Asc";
 362         break;
 363     case eftBIN:
 364         s = "Bin";
 365         break;
 366     case eftXDR:
 367         s = "xdr";
 368         break;
 369     case eftGEN:
 370         s = "";
 371         break;
 372     default:
 373         gmx_fatal(FARGS, "Unimplemented filetype %d %d",ftp,
 374         df->ftype);
 375     }
 376     fprintf(fp,"\\tt %8s & \\tt %3s & %3s & \\tt %2s & %s%s \\\\[-0.1ex]\n",
 377         defnm, ext, s, df->defopt ? df->defopt : "",
 378         check_tex(desc),check_tex(flst));
 379     free(desc);
 380 }
 381
 382 void pr_fns(FILE *fp, int nf, const t_filenm tfn[])
 383 {
 384     int i, f;
 385     size_t j;
 386     char buf[256], *wbuf, opt_buf[32];
 387 #define OPTLEN 4
 388 #define NAMELEN 14
 389     fprintf(fp, "%6s %12s  %-12s %s\n", "Option", "Filename", "Type",
 390             "Description");
 391     fprintf(fp,
 392             "------------------------------------------------------------\n");
 393     for (i = 0; (i < nf); i++)
 394     {
 395         for (f = 0; (f < tfn[i].nfiles); f++)
 396         {
 397             sprintf(buf, "%4s %14s  %-12s ", (f == 0) ? tfn[i].opt : "",
 398                     tfn[i].fns[f], (f == 0) ? fileopt(tfn[i].flag, opt_buf, 32)
 399                         : "");
 400             if (f < tfn[i].nfiles - 1)
 401                 fprintf(fp, "%s\n", buf);
 402         }
 403         if (tfn[i].nfiles > 0)
 404         {
 405             strcat(buf, deffile[tfn[i].ftp].descr);
 406             if ((strlen(tfn[i].opt) > OPTLEN)
 407                 && (strlen(tfn[i].opt) <= ((OPTLEN + NAMELEN)
 408                     - strlen(tfn[i].fns[tfn[i].nfiles - 1]))))
 409             {
 410                 for (j = strlen(tfn[i].opt); j < strlen(buf)
 411                     - (strlen(tfn[i].opt) - OPTLEN) + 1; j++)
 412                     buf[j] = buf[j + strlen(tfn[i].opt) - OPTLEN];
 413             }
 414             wbuf = wrap_lines(buf, 78, 35, FALSE);
 415             fprintf(fp, "%s\n", wbuf);
 416             sfree(wbuf);
 417         }
 418     }
 419     fprintf(fp, "\n");
 420     fflush(fp);
 421 }
 422
 423 void pr_fopts(FILE *fp, int nf, const t_filenm tfn[], int shell)
 424 {
 425     int i, j;
 426
 427     switch (shell)
 428     {
 429     case eshellCSH:
 430         for (i = 0; (i < nf); i++)
 431         {
 432             fprintf(fp, " \"n/%s/f:*.", tfn[i].opt);
 433             if (deffile[tfn[i].ftp].ntps)
 434             {
 435                 fprintf(fp, "{");
 436                 for (j = 0; j < deffile[tfn[i].ftp].ntps; j++)
 437                 {
 438                     if (j > 0)
 439                         fprintf(fp, ",");
 440                     fprintf(fp, "%s", deffile[deffile[tfn[i].ftp].tps[j]].ext
 441                             + 1);
 442                 }
 443                 fprintf(fp, "}");
 444             }
 445             else
 446                 fprintf(fp, "%s", deffile[tfn[i].ftp].ext + 1);
 447             fprintf(fp, "{");
 448             for (j = 0; j < NZEXT; j++)
 449                 fprintf(fp, ",%s", z_ext[j]);
 450             fprintf(fp, "}/\"");
 451         }
 452         break;
 453     case eshellBASH:
 454         for (i = 0; (i < nf); i++)
 455         {
 456             fprintf(fp, "%s) COMPREPLY=( $(compgen -X '!*.", tfn[i].opt);
 457             if (deffile[tfn[i].ftp].ntps)
 458             {
 459                 fprintf(fp, "+(");
 460                 for (j = 0; j < deffile[tfn[i].ftp].ntps; j++)
 461                 {
 462                     if (j > 0)
 463                         fprintf(fp, "|");
 464                     fprintf(fp, "%s", deffile[deffile[tfn[i].ftp].tps[j]].ext
 465                             + 1);
 466                 }
 467                 fprintf(fp, ")");
 468             }
 469             else
 470                 fprintf(fp, "%s", deffile[tfn[i].ftp].ext + 1);
 471             fprintf(fp, "*(");
 472             for (j = 0; j < NZEXT; j++)
 473             {
 474                 if (j > 0)
 475                     fprintf(fp, "|");
 476                 fprintf(fp, "%s", z_ext[j]);
 477             }
 478             fprintf(fp, ")' -f $c ; compgen -S '/' -X '.*' -d $c ));;\n");
 479         }
 480         break;
 481     case eshellZSH:
 482         for (i = 0; (i < nf); i++)
 483         {
 484             fprintf(fp, "- 'c[-1,%s]' -g '*.", tfn[i].opt);
 485             if (deffile[tfn[i].ftp].ntps)
 486             {
 487                 fprintf(fp, "(");
 488                 for (j = 0; j < deffile[tfn[i].ftp].ntps; j++)
 489                 {
 490                     if (j > 0)
 491                         fprintf(fp, "|");
 492                     fprintf(fp, "%s", deffile[deffile[tfn[i].ftp].tps[j]].ext
 493                             + 1);
 494                 }
 495                 fprintf(fp, ")");
 496             }
 497             else
 498                 fprintf(fp, "%s", deffile[tfn[i].ftp].ext + 1);
 499             fprintf(fp, "(");
 500             for (j = 0; j < NZEXT; j++)
 501                 fprintf(fp, "|%s", z_ext[j]);
 502             fprintf(fp, ") *(/)' ");
 503         }
 504         break;
 505     }
 506 }
 507
 508 static void check_opts(int nf, t_filenm fnm[])
 509 {
 510     int i;
 511     const t_deffile *df;
 512
 513     for (i = 0; (i < nf); i++)
 514     {
 515         df = &(deffile[fnm[i].ftp]);
 516         if (fnm[i].opt == NULL)
 517         {
 518             if (df->defopt == NULL)
 519             {
 520                 gmx_fatal(FARGS, "No default cmd-line option for %s (type %d)\n",
 521                           deffile[fnm[i].ftp].ext,fnm[i].ftp);
 522             }
 523             else
 524             {
 525                 fnm[i].opt=df->defopt;
 526             }
 527         }
 528     }
 529 }
 530
 531 int fn2ftp(const char *fn)
 532 {
 533     int i, len;
 534     const char *feptr;
 535     const char *eptr;
 536
 537     if (!fn)
 538         return efNR;
 539
 540     len = strlen(fn);
 541     if ((len >= 4) && (fn[len - 4] == '.'))
 542         feptr = &(fn[len - 4]);
 543     else
 544         return efNR;
 545
 546     for (i = 0; (i < efNR); i++)
 547         if ((eptr = deffile[i].ext) != NULL)
 548             if (gmx_strcasecmp(feptr, eptr) == 0)
 549                 break;
 550
 551     return i;
 552 }
 553
 554 static void set_extension(char *buf, int ftp)
 555 {
 556     int len, extlen;
 557     const t_deffile *df;
 558
 559     /* check if extension is already at end of filename */
 560     df = &(deffile[ftp]);
 561     len = strlen(buf);
 562     extlen = strlen(df->ext);
 563     if ((len <= extlen) || (gmx_strcasecmp(&(buf[len - extlen]), df->ext) != 0))
 564         strcat(buf, df->ext);
 565 }
 566
 567 static void add_filenm(t_filenm *fnm, const char *filenm)
 568 {
 569     srenew(fnm->fns, fnm->nfiles+1);
 570     fnm->fns[fnm->nfiles] = strdup(filenm);
 571     fnm->nfiles++;
 572 }
 573
 574 static void set_grpfnm(t_filenm *fnm, const char *name, gmx_bool bCanNotOverride)
 575 {
 576     char buf[256], buf2[256];
 577     int i, type;
 578     gmx_bool bValidExt;
 579     int nopts;
 580     const int *ftps;
 581
 582     nopts = deffile[fnm->ftp].ntps;
 583     ftps = deffile[fnm->ftp].tps;
 584     if ((nopts == 0) || (ftps == NULL))
 585         gmx_fatal(FARGS, "nopts == 0 || ftps == NULL");
 586
 587     bValidExt = FALSE;
 588     if (name && (bCanNotOverride || (default_file_name == NULL)))
 589     {
 590         strcpy(buf,name);
 591         /* First check whether we have a valid filename already */
 592         type = fn2ftp(name);
 593         if ((fnm->flag & ffREAD) && (fnm->ftp == efTRX))
 594         {
 595             /*if file exist don't add an extension for trajectory reading*/
 596             bValidExt = gmx_fexist(name);
 597         }
 598         for(i=0; (i<nopts) && !bValidExt; i++)
 599         {
 600             if (type == ftps[i])
 601             {
 602                 bValidExt = TRUE;
 603             }
 604         }
 605     }
 606     else
 607         /* No name given, set the default name */
 608         strcpy(buf,ftp2defnm(fnm->ftp));
 609
 610     if (!bValidExt && (fnm->flag & ffREAD))
 611     {
 612         /* for input-files only: search for filenames in the directory */
 613         for(i=0; (i<nopts) && !bValidExt; i++)
 614         {
 615             type = ftps[i];
 616             strcpy(buf2,buf);
 617             set_extension(buf2,type);
 618             if (gmx_fexist(buf2))
 619             {
 620                 bValidExt = TRUE;
 621                 strcpy(buf,buf2);
 622             }
 623         }
 624     }
 625
 626     if (!bValidExt)
 627     {
 628         /* Use the first extension type */
 629         set_extension(buf,ftps[0]);
 630     }
 631
 632     add_filenm(fnm, buf);
 633 }
 634
 635 static void set_filenm(t_filenm *fnm, const char *name, gmx_bool bCanNotOverride,
 636                        gmx_bool bReadNode)
 637 {
 638     /* Set the default filename, extension and option for those fields that
 639      * are not already set. An extension is added if not present, if fn = NULL
 640      * or empty, the default filename is given.
 641      */
 642     char buf[256];
 643     int i, len, extlen;
 644
 645     if ((fnm->flag & ffREAD) && !bReadNode)
 646     {
 647         return;
 648     }
 649
 650     if ((fnm->ftp < 0) || (fnm->ftp >= efNR))
 651         gmx_fatal(FARGS, "file type out of range (%d)",fnm->ftp);
 652
 653     if (name)
 654         strcpy(buf, name);
 655     if ((fnm->flag & ffREAD) && name && gmx_fexist(name))
 656     {
 657         /* check if filename ends in .gz or .Z, if so remove that: */
 658         len = strlen(name);
 659         for (i=0; i<NZEXT; i++)
 660         {
 661             extlen = strlen(z_ext[i]);
 662             if (len > extlen)
 663             {
 664                 if (gmx_strcasecmp(name+len-extlen,z_ext[i]) == 0)
 665                 {
 666                     buf[len-extlen]='\0';
 667                     break;
 668                 }
 669             }
 670         }
 671     }
 672
 673     if (deffile[fnm->ftp].ntps)
 674     {
 675         set_grpfnm(fnm,name ? buf : NULL,bCanNotOverride);
 676     }
 677     else
 678     {
 679         if ((name == NULL) || !(bCanNotOverride || (default_file_name ==NULL)))
 680         {
 681             const char *defnm=ftp2defnm(fnm->ftp);
 682             strcpy(buf,defnm);
 683         }
 684         set_extension(buf,fnm->ftp);
 685
 686         add_filenm(fnm, buf);
 687     }
 688 }
 689
 690 static void set_filenms(int nf, t_filenm fnm[], gmx_bool bReadNode)
 691 {
 692     int i;
 693
 694     for (i = 0; (i < nf); i++)
 695         if (!IS_SET(fnm[i]))
 696             set_filenm(&(fnm[i]), fnm[i].fn, FALSE, bReadNode);
 697 }
 698
 699 void parse_file_args(int *argc, char *argv[], int nf, t_filenm fnm[],
 700                      gmx_bool bKeep, gmx_bool bReadNode)
 701 {
 702     int i, j;
 703     gmx_bool *bRemove;
 704
 705     check_opts(nf, fnm);
 706
 707     for (i = 0; (i < nf); i++)
 708         UN_SET(fnm[i]);
 709
 710     if (*argc > 1)
 711     {
 712         snew(bRemove,(*argc)+1);
 713         i = 1;
 714         do
 715         {
 716             for (j = 0; (j < nf); j++)
 717             {
 718                 if (strcmp(argv[i], fnm[j].opt) == 0)
 719                 {
 720                     DO_SET(fnm[j]);
 721                     bRemove[i] = TRUE;
 722                     i++;
 723                     /* check if we are out of arguments for this option */
 724                     if ((i >= *argc) || (argv[i][0] == '-'))
 725                         set_filenm(&fnm[j], fnm[j].fn, FALSE, bReadNode);
 726                     /* sweep up all file arguments for this option */
 727                     while ((i < *argc) && (argv[i][0] != '-'))
 728                     {
 729                         set_filenm(&fnm[j], argv[i], TRUE, bReadNode);
 730                         bRemove[i] = TRUE;
 731                         i++;
 732                         /* only repeat for 'multiple' file options: */
 733                         if (!IS_MULT(fnm[j]))
 734                             break;
 735                     }
 736
 737                     break; /* jump out of 'j' loop */
 738                 }
 739             }
 740             /* No file found corresponding to option argv[i] */
 741             if (j == nf)
 742                 i++;
 743         } while (i < *argc);
 744
 745         if (!bKeep)
 746         {
 747             /* Remove used entries */
 748             for (i = j = 0; (i <= *argc); i++)
 749             {
 750                 if (!bRemove[i])
 751                     argv[j++] = argv[i];
 752             }
 753             (*argc) = j - 1;
 754         }
 755         sfree(bRemove);
 756     }
 757
 758     set_filenms(nf, fnm, bReadNode);
 759
 760 }
 761
 762 const char *opt2fn(const char *opt, int nfile, const t_filenm fnm[])
 763 {
 764     int i;
 765
 766     for (i = 0; (i < nfile); i++)
 767         if (strcmp(opt, fnm[i].opt) == 0)
 768         {
 769             return fnm[i].fns[0];
 770         }
 771
 772     fprintf(stderr, "No option %s\n", opt);
 773
 774     return NULL;
 775 }
 776
 777 const char *opt2fn_master(const char *opt, int nfile, const t_filenm fnm[],
 778                           t_commrec *cr)
 779 {
 780     return SIMMASTER(cr) ? opt2fn(opt, nfile, fnm) : NULL;
 781 }
 782
 783 int opt2fns(char **fns[], const char *opt, int nfile, const t_filenm fnm[])
 784 {
 785     int i;
 786
 787     for (i = 0; (i < nfile); i++)
 788         if (strcmp(opt, fnm[i].opt) == 0)
 789         {
 790             *fns = fnm[i].fns;
 791             return fnm[i].nfiles;
 792         }
 793
 794     fprintf(stderr, "No option %s\n", opt);
 795     return 0;
 796 }
 797
 798 const char *ftp2fn(int ftp, int nfile, const t_filenm fnm[])
 799 {
 800     int i;
 801
 802     for (i = 0; (i < nfile); i++)
 803         if (ftp == fnm[i].ftp)
 804             return fnm[i].fns[0];
 805
 806     fprintf(stderr, "ftp2fn: No filetype %s\n", deffile[ftp].ext);
 807     return NULL;
 808 }
 809
 810 int ftp2fns(char **fns[], int ftp, int nfile, const t_filenm fnm[])
 811 {
 812     int i;
 813
 814     for (i = 0; (i < nfile); i++)
 815         if (ftp == fnm[i].ftp)
 816         {
 817             *fns = fnm[i].fns;
 818             return fnm[i].nfiles;
 819         }
 820
 821     fprintf(stderr, "ftp2fn: No filetype %s\n", deffile[ftp].ext);
 822     return 0;
 823 }
 824
 825 gmx_bool ftp2bSet(int ftp, int nfile, const t_filenm fnm[])
 826 {
 827     int i;
 828
 829     for (i = 0; (i < nfile); i++)
 830         if (ftp == fnm[i].ftp)
 831             return (gmx_bool) IS_SET(fnm[i]);
 832
 833     fprintf(stderr, "ftp2bSet: No filetype %s\n", deffile[ftp].ext);
 834
 835     return FALSE;
 836 }
 837
 838 gmx_bool opt2bSet(const char *opt, int nfile, const t_filenm fnm[])
 839 {
 840     int i;
 841
 842     for (i = 0; (i < nfile); i++)
 843         if (strcmp(opt, fnm[i].opt) == 0)
 844             return (gmx_bool) IS_SET(fnm[i]);
 845
 846     fprintf(stderr, "No option %s\n", opt);
 847
 848     return FALSE;
 849 }
 850
 851 const char *opt2fn_null(const char *opt, int nfile, const t_filenm fnm[])
 852 {
 853     int i;
 854
 855     for (i = 0; (i < nfile); i++)
 856         if (strcmp(opt, fnm[i].opt) == 0)
 857         {
 858             if (IS_OPT(fnm[i]) && !IS_SET(fnm[i]))
 859                 return NULL;
 860             else
 861                 return fnm[i].fns[0];
 862         }
 863     fprintf(stderr, "No option %s\n", opt);
 864     return NULL;
 865 }
 866
 867 const char *ftp2fn_null(int ftp, int nfile, const t_filenm fnm[])
 868 {
 869     int i;
 870
 871     for (i = 0; (i < nfile); i++)
 872         if (ftp == fnm[i].ftp)
 873         {
 874             if (IS_OPT(fnm[i]) && !IS_SET(fnm[i]))
 875                 return NULL;
 876             else
 877                 return fnm[i].fns[0];
 878         }
 879     fprintf(stderr, "ftp2fn: No filetype %s\n", deffile[ftp].ext);
 880     return NULL;
 881 }
 882
 883 #if 0
 884 static void add_filters(char *filter,int *n,int nf,const int ftp[])
 885 {
 886     char buf[8];
 887     int i;
 888
 889     sprintf(filter,"*.{");
 890     for(i=0; (i<nf); i++)
 891     {
 892         sprintf(buf,"%s",ftp2ext(ftp[i]));
 893         if (*n > 0)
 894             strcat(filter,",");
 895         strcat(filter,buf);
 896         (*n) ++;
 897     }
 898     strcat(filter,"}");
 899 }
 900
 901 char *ftp2filter(int ftp)
 902 {
 903     int n;
 904     static char filter[128];
 905
 906     filter[0] = '\0';
 907     n = 0;
 908     switch (ftp)
 909     {
 910     case efTRX:
 911         add_filters(filter,&n,NTRXS,trxs);
 912         break;
 913     case efTRN:
 914         add_filters(filter,&n,NTRNS,trns);
 915         break;
 916     case efSTO:
 917         add_filters(filter,&n,NSTOS,stos);
 918         break;
 919     case efSTX:
 920         add_filters(filter,&n,NSTXS,stxs);
 921         break;
 922     case efTPX:
 923         add_filters(filter,&n,NTPXS,tpxs);
 924         break;
 925     default:
 926         sprintf(filter,"*%s",ftp2ext(ftp));
 927         break;
 928     }
 929     return filter;
 930 }
 931 #endif
 932
 933 gmx_bool is_optional(const t_filenm *fnm)
 934 {
 935     return ((fnm->flag & ffOPT) == ffOPT);
 936 }
 937
 938 gmx_bool is_output(const t_filenm *fnm)
 939 {
 940     return ((fnm->flag & ffWRITE) == ffWRITE);
 941 }
 942
 943 gmx_bool is_set(const t_filenm *fnm)
 944 {
 945     return ((fnm->flag & ffSET) == ffSET);
 946 }
 947
 948 int add_suffix_to_output_names(t_filenm *fnm, int nfile, const char *suffix)
 949 {
 950     int i, j, pos;
 951     char buf[STRLEN], newname[STRLEN];
 952     char *extpos;
 953
 954     for (i = 0; i < nfile; i++)
 955     {
 956         if (is_output(&fnm[i]) && fnm[i].ftp != efCPT)
 957         {
 958             /* We never use multiple _outputs_, but we might as well check
 959              for it, just in case... */
 960             for (j = 0; j < fnm[i].nfiles; j++)
 961             {
 962                 strncpy(buf, fnm[i].fns[j], STRLEN - 1);
 963                 extpos = strrchr(buf, '.');
 964                 *extpos = '\0';
 965                 sprintf(newname, "%s%s.%s", buf, suffix, extpos + 1);
 966                 free(fnm[i].fns[j]);
 967                 fnm[i].fns[j] = strdup(newname);
 968             }
 969         }
 970     }
 971     return 0;
 972 }
 973
 974 t_filenm *dup_tfn(int nf, const t_filenm tfn[])
 975 {
 976     int i, j;
 977     t_filenm *ret;
 978
 979     snew(ret, nf);
 980     for (i = 0; i < nf; i++)
 981     {
 982         ret[i] = tfn[i]; /* just directly copy all non-string fields */
 983         if (tfn[i].opt)
 984             ret[i].opt = strdup(tfn[i].opt);
 985         else
 986             ret[i].opt = NULL;
 987
 988         if (tfn[i].fn)
 989             ret[i].fn = strdup(tfn[i].fn);
 990         else
 991             ret[i].fn = NULL;
 992
 993         if (tfn[i].nfiles > 0)
 994         {
 995             snew(ret[i].fns,tfn[i].nfiles);
 996             for (j = 0; j < tfn[i].nfiles; j++)
 997             {
 998                 ret[i].fns[j] = strdup(tfn[i].fns[j]);
 999             }
1000         }
1001     }
1002     return ret;
1003 }
1004
1005 void done_filenms(int nf, t_filenm fnm[])
1006 {
1007     int i, j;
1008
1009     for (i = 0; i < nf; ++i)
1010     {
1011         for (j = 0; j < fnm[i].nfiles; ++j)
1012         {
1013             sfree(fnm[i].fns[j]);
1014         }
1015         sfree(fnm[i].fns);
1016         fnm[i].fns = NULL;
1017     }
1018 }