* This file is part of the GROMACS molecular simulation package.
*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2001-2004, The GROMACS development team.
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#include "filenm.h"
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "filenm.h"
+#include <stdio.h>
#include <string.h>
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "string2.h"
-#include "gmx_fatal.h"
-#include "futil.h"
-#include "xdrf.h"
-#include "macros.h"
-
-#include "gromacs/onlinehelp/wman.h"
-
-#ifdef GMX_THREAD_MPI
-#include "thread_mpi.h"
-#endif
-/* NOTE: this was a cesspool of thread-unsafe code, has now been
- properly proteced by mutexes (hopefully). */
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+
+#include "gromacs/utility/basedefinitions.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
/* XDR should be available on all platforms now,
* but we keep the possibility of turning it off...
/* Use bitflag ... */
#define IS_SET(fn) ((fn.flag & ffSET) != 0)
#define IS_OPT(fn) ((fn.flag & ffOPT) != 0)
-#define IS_MULT(fn) ((fn.flag & ffMULT) != 0)
-#define UN_SET(fn) (fn.flag = (fn.flag & ~ffSET))
-#define DO_SET(fn) (fn.flag = (fn.flag | ffSET))
enum
{
- eftASC, eftBIN, eftXDR, eftGEN, eftNR
+ eftASC, eftBIN, eftXDR, eftTNG, eftGEN, eftNR
};
/* To support multiple file types with one general (eg TRX) we have
#ifdef USE_XDR
efXTC, efTRR, efCPT,
#endif
- efTRJ, efGRO, efG96, efPDB, efG87
+ efGRO, efG96, efPDB, efTNG
};
#define NTRXS asize(trxs)
+static const int trcompressed[] =
+{
+#ifdef USE_XDR
+ efXTC,
+#endif
+ efTNG
+};
+#define NTRCOMPRESSED asize(trcompressed)
+
static const int tros[] =
{
#ifdef USE_XDR
efXTC, efTRR,
#endif
- efTRJ, efGRO, efG96, efPDB, efG87
+ efGRO, efG96, efPDB, efTNG
};
#define NTROS asize(tros)
#ifdef USE_XDR
efTRR, efCPT,
#endif
- efTRJ
+ efTNG
};
#define NTRNS asize(trns)
static const int stos[] =
-{ efGRO, efG96, efPDB, efBRK, efENT, efESP, efXYZ };
+{ efGRO, efG96, efPDB, efBRK, efENT, efESP };
#define NSTOS asize(stos)
static const int stxs[] =
{
- efGRO, efG96, efPDB, efBRK, efENT, efESP, efXYZ,
+ efGRO, efG96, efPDB, efBRK, efENT, efESP
#ifdef USE_XDR
- efTPR,
+ , efTPR
#endif
- efTPB, efTPA
};
#define NSTXS asize(stxs)
-static const int tpxs[] =
-{
-#ifdef USE_XDR
- efTPR,
-#endif
- efTPB, efTPA
-};
-#define NTPXS asize(tpxs)
-
static const int tpss[] =
{
#ifdef USE_XDR
efTPR,
#endif
- efTPB, efTPA, efGRO, efG96, efPDB, efBRK, efENT
+ efGRO, efG96, efPDB, efBRK, efENT
};
#define NTPSS asize(tpss)
deffile[efNR] =
{
{ eftASC, ".mdp", "grompp", "-f", "grompp input file with MD parameters" },
- { eftGEN, ".???", "traj", "-f",
- "Trajectory: xtc trr trj gro g96 pdb cpt", NTRXS, trxs },
- { eftGEN, ".???", "trajout", "-f",
- "Trajectory: xtc trr trj gro g96 pdb", NTROS, tros },
+ { eftGEN, ".???", "traj", "-f", "Trajectory", NTRXS, trxs },
+ { eftGEN, ".???", "trajout", "-f", "Trajectory", NTROS, tros },
{ eftGEN, ".???", "traj", NULL,
- "Full precision trajectory: trr trj cpt", NTRNS, trns },
+ "Full precision trajectory", NTRNS, trns },
{ eftXDR, ".trr", "traj", NULL, "Trajectory in portable xdr format" },
- { eftBIN, ".trj", "traj", NULL, "Trajectory file (architecture specific)" },
+ { eftGEN, ".???", "traj_comp", NULL,
+ "Compressed trajectory (tng format or portable xdr format)", NTRCOMPRESSED, trcompressed},
{ eftXDR, ".xtc", "traj", NULL,
- "Compressed trajectory (portable xdr format)" },
- { eftASC, ".g87", "gtraj", NULL, "Gromos-87 ASCII trajectory format" },
+ "Compressed trajectory (portable xdr format): xtc" },
+ { eftTNG, ".tng", "traj", NULL,
+ "Trajectory file (tng format)" },
{ eftXDR, ".edr", "ener", NULL, "Energy file"},
- { eftGEN, ".???", "conf", "-c", "Structure file: gro g96 pdb tpr etc.",
- NSTXS, stxs },
- { eftGEN, ".???", "out", "-o", "Structure file: gro g96 pdb etc.",
- NSTOS, stos },
+ { eftGEN, ".???", "conf", "-c", "Structure file", NSTXS, stxs },
+ { eftGEN, ".???", "out", "-o", "Structure file", NSTOS, stos },
{ eftASC, ".gro", "conf", "-c", "Coordinate file in Gromos-87 format" },
{ eftASC, ".g96", "conf", "-c", "Coordinate file in Gromos-96 format" },
{ eftASC, ".pdb", "eiwit", "-f", "Protein data bank file"},
{ eftASC, ".ent", "eiwit", "-f", "Entry in the protein date bank" },
{ eftASC, ".esp", "conf", "-f", "Coordinate file in Espresso format" },
{ eftASC, ".pqr", "state", "-o", "Coordinate file for MEAD"},
- { eftASC, ".xyz", "conf", "-o", "Coordinate file for some other programs" },
{ eftXDR, ".cpt", "state", "-cp", "Checkpoint file"},
{ eftASC, ".log", "run", "-l", "Log file"},
{ eftASC, ".xvg", "graph", "-o", "xvgr/xmgr file"},
{ eftASC, ".ndx", "index", "-n", "Index file", },
{ eftASC, ".top", "topol", "-p", "Topology file"},
{ eftASC, ".itp", "topinc", NULL, "Include file for topology"},
- { eftGEN, ".???", "topol", "-s", "Run input file: tpr tpb tpa",
- NTPXS, tpxs },
- { eftGEN, ".???", "topol", "-s",
- "Structure+mass(db): tpr tpb tpa gro g96 pdb", NTPSS, tpss },
+ { eftGEN, ".???", "topol", "-s", "Structure+mass(db)", NTPSS, tpss },
{ eftXDR, ".tpr", "topol", "-s", "Portable xdr run input file"},
- { eftASC, ".tpa", "topol", "-s", "Ascii run input file"},
- { eftBIN, ".tpb", "topol", "-s", "Binary run input file"},
{ eftASC, ".tex", "doc", "-o", "LaTeX file"},
{ eftASC, ".rtp", "residue", NULL, "Residue Type file used by pdb2gmx" },
{ eftASC, ".atp", "atomtp", NULL, "Atomtype file used by pdb2gmx" },
{ eftASC, "", "rundir", NULL, "Run directory" }
};
-static char *default_file_name = NULL;
-
-#ifdef GMX_THREAD_MPI
-static tMPI_Thread_mutex_t filenm_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
-#endif
-
#define NZEXT 2
-const char *z_ext[NZEXT] =
+static const char *z_ext[NZEXT] =
{ ".gz", ".Z" };
-void set_default_file_name(const char *name)
-{
- int i;
-#ifdef GMX_THREAD_MPI
- tMPI_Thread_mutex_lock(&filenm_mutex);
-#endif
- default_file_name = strdup(name);
-#ifdef GMX_THREAD_MPI
- tMPI_Thread_mutex_unlock(&filenm_mutex);
-#endif
-
-}
-
const char *ftp2ext(int ftp)
{
if ((0 <= ftp) && (ftp < efNR))
return "sto";
case efSTX:
return "stx";
- case efTPX:
- return "tpx";
case efTPS:
return "tps";
default:
return "Binary";
case eftXDR:
return "XDR portable";
+ case eftTNG:
+ return "TNG";
case eftGEN:
return "";
default:
const char *ftp2defnm(int ftp)
{
- const char *buf = NULL;
-
-#ifdef GMX_THREAD_MPI
- tMPI_Thread_mutex_lock(&filenm_mutex);
-#endif
-
- if (default_file_name)
+ if ((0 <= ftp) && (ftp < efNR))
{
- buf = default_file_name;
+ return deffile[ftp].defnm;
}
else
{
- if ((0 <= ftp) && (ftp < efNR))
- {
- buf = deffile[ftp].defnm;
- }
+ return NULL;
}
-#ifdef GMX_THREAD_MPI
- tMPI_Thread_mutex_unlock(&filenm_mutex);
-#endif
-
- return buf;
}
-void pr_fns(FILE *fp, int nf, const t_filenm tfn[])
+const char *ftp2defopt(int ftp)
{
- int i, f;
- size_t j;
- char buf[256], *wbuf, opt_buf[32];
-#define OPTLEN 4
-#define NAMELEN 14
- fprintf(fp, "%6s %12s %-12s %s\n", "Option", "Filename", "Type",
- "Description");
- fprintf(fp,
- "------------------------------------------------------------\n");
- for (i = 0; (i < nf); i++)
- {
- for (f = 0; (f < tfn[i].nfiles); f++)
- {
- sprintf(buf, "%4s %14s %-12s ", (f == 0) ? tfn[i].opt : "",
- tfn[i].fns[f], (f == 0) ? fileopt(tfn[i].flag, opt_buf)
- : "");
- if (f < tfn[i].nfiles - 1)
- {
- fprintf(fp, "%s\n", buf);
- }
- }
- if (tfn[i].nfiles > 0)
- {
- strcat(buf, deffile[tfn[i].ftp].descr);
- if ((strlen(tfn[i].opt) > OPTLEN)
- && (strlen(tfn[i].opt) <= ((OPTLEN + NAMELEN)
- - strlen(tfn[i].fns[tfn[i].nfiles - 1]))))
- {
- for (j = strlen(tfn[i].opt); j < strlen(buf)
- - (strlen(tfn[i].opt) - OPTLEN) + 1; j++)
- {
- buf[j] = buf[j + strlen(tfn[i].opt) - OPTLEN];
- }
- }
- wbuf = wrap_lines(buf, 78, 35, FALSE);
- fprintf(fp, "%s\n", wbuf);
- sfree(wbuf);
- }
- }
- fprintf(fp, "\n");
- fflush(fp);
-}
-
-void pr_fopts(FILE *fp, int nf, const t_filenm tfn[], int shell)
-{
- int i, j;
-
- switch (shell)
+ if ((0 <= ftp) && (ftp < efNR))
{
- case eshellCSH:
- for (i = 0; (i < nf); i++)
- {
- fprintf(fp, " \"n/%s/f:*.", tfn[i].opt);
- if (deffile[tfn[i].ftp].ntps)
- {
- fprintf(fp, "{");
- for (j = 0; j < deffile[tfn[i].ftp].ntps; j++)
- {
- if (j > 0)
- {
- fprintf(fp, ",");
- }
- fprintf(fp, "%s", deffile[deffile[tfn[i].ftp].tps[j]].ext
- + 1);
- }
- fprintf(fp, "}");
- }
- else
- {
- fprintf(fp, "%s", deffile[tfn[i].ftp].ext + 1);
- }
- fprintf(fp, "{");
- for (j = 0; j < NZEXT; j++)
- {
- fprintf(fp, ",%s", z_ext[j]);
- }
- fprintf(fp, "}/\"");
- }
- break;
- case eshellBASH:
- for (i = 0; (i < nf); i++)
- {
- fprintf(fp, "%s) COMPREPLY=( $(compgen -X '!*.", tfn[i].opt);
- if (deffile[tfn[i].ftp].ntps)
- {
- fprintf(fp, "+(");
- for (j = 0; j < deffile[tfn[i].ftp].ntps; j++)
- {
- if (j > 0)
- {
- fprintf(fp, "|");
- }
- fprintf(fp, "%s", deffile[deffile[tfn[i].ftp].tps[j]].ext
- + 1);
- }
- fprintf(fp, ")");
- }
- else
- {
- fprintf(fp, "%s", deffile[tfn[i].ftp].ext + 1);
- }
- fprintf(fp, "*(");
- for (j = 0; j < NZEXT; j++)
- {
- if (j > 0)
- {
- fprintf(fp, "|");
- }
- fprintf(fp, "%s", z_ext[j]);
- }
- fprintf(fp, ")' -f $c ; compgen -S '/' -X '.*' -d $c ));;\n");
- }
- break;
- case eshellZSH:
- for (i = 0; (i < nf); i++)
- {
- fprintf(fp, "- 'c[-1,%s]' -g '*.", tfn[i].opt);
- if (deffile[tfn[i].ftp].ntps)
- {
- fprintf(fp, "(");
- for (j = 0; j < deffile[tfn[i].ftp].ntps; j++)
- {
- if (j > 0)
- {
- fprintf(fp, "|");
- }
- fprintf(fp, "%s", deffile[deffile[tfn[i].ftp].tps[j]].ext
- + 1);
- }
- fprintf(fp, ")");
- }
- else
- {
- fprintf(fp, "%s", deffile[tfn[i].ftp].ext + 1);
- }
- fprintf(fp, "(");
- for (j = 0; j < NZEXT; j++)
- {
- fprintf(fp, "|%s", z_ext[j]);
- }
- fprintf(fp, ") *(/)' ");
- }
- break;
+ return deffile[ftp].defopt;
}
-}
-
-static void check_opts(int nf, t_filenm fnm[])
-{
- int i;
- const t_deffile *df;
-
- for (i = 0; (i < nf); i++)
+ else
{
- df = &(deffile[fnm[i].ftp]);
- if (fnm[i].opt == NULL)
- {
- if (df->defopt == NULL)
- {
- gmx_fatal(FARGS, "No default cmd-line option for %s (type %d)\n",
- deffile[fnm[i].ftp].ext, fnm[i].ftp);
- }
- else
- {
- fnm[i].opt = df->defopt;
- }
- }
+ return NULL;
}
}
return i;
}
-static void set_extension(char *buf, int ftp)
-{
- int len, extlen;
- const t_deffile *df;
-
- /* check if extension is already at end of filename */
- df = &(deffile[ftp]);
- len = strlen(buf);
- extlen = strlen(df->ext);
- if ((len <= extlen) || (gmx_strcasecmp(&(buf[len - extlen]), df->ext) != 0))
- {
- strcat(buf, df->ext);
- }
-}
-
-static void add_filenm(t_filenm *fnm, const char *filenm)
-{
- srenew(fnm->fns, fnm->nfiles+1);
- fnm->fns[fnm->nfiles] = strdup(filenm);
- fnm->nfiles++;
-}
-
-static void set_grpfnm(t_filenm *fnm, const char *name, gmx_bool bCanNotOverride)
-{
- char buf[256], buf2[256];
- int i, type;
- gmx_bool bValidExt;
- int nopts;
- const int *ftps;
-
- nopts = deffile[fnm->ftp].ntps;
- ftps = deffile[fnm->ftp].tps;
- if ((nopts == 0) || (ftps == NULL))
- {
- gmx_fatal(FARGS, "nopts == 0 || ftps == NULL");
- }
-
- bValidExt = FALSE;
- if (name && (bCanNotOverride || (default_file_name == NULL)))
- {
- strcpy(buf, name);
- /* First check whether we have a valid filename already */
- type = fn2ftp(name);
- if ((fnm->flag & ffREAD) && (fnm->ftp == efTRX))
- {
- /*if file exist don't add an extension for trajectory reading*/
- bValidExt = gmx_fexist(name);
- }
- for (i = 0; (i < nopts) && !bValidExt; i++)
- {
- if (type == ftps[i])
- {
- bValidExt = TRUE;
- }
- }
- }
- else
- {
- /* No name given, set the default name */
- strcpy(buf, ftp2defnm(fnm->ftp));
- }
-
- if (!bValidExt && (fnm->flag & ffREAD))
- {
- /* for input-files only: search for filenames in the directory */
- for (i = 0; (i < nopts) && !bValidExt; i++)
- {
- type = ftps[i];
- strcpy(buf2, buf);
- set_extension(buf2, type);
- if (gmx_fexist(buf2))
- {
- bValidExt = TRUE;
- strcpy(buf, buf2);
- }
- }
- }
-
- if (!bValidExt)
- {
- /* Use the first extension type */
- set_extension(buf, ftps[0]);
- }
-
- add_filenm(fnm, buf);
-}
-
-static void set_filenm(t_filenm *fnm, const char *name, gmx_bool bCanNotOverride,
- gmx_bool bReadNode)
-{
- /* Set the default filename, extension and option for those fields that
- * are not already set. An extension is added if not present, if fn = NULL
- * or empty, the default filename is given.
- */
- char buf[256];
- int i, len, extlen;
-
- if ((fnm->flag & ffREAD) && !bReadNode)
- {
- return;
- }
-
- if ((fnm->ftp < 0) || (fnm->ftp >= efNR))
- {
- gmx_fatal(FARGS, "file type out of range (%d)", fnm->ftp);
- }
-
- if (name)
- {
- strcpy(buf, name);
- }
- if ((fnm->flag & ffREAD) && name && gmx_fexist(name))
- {
- /* check if filename ends in .gz or .Z, if so remove that: */
- len = strlen(name);
- for (i = 0; i < NZEXT; i++)
- {
- extlen = strlen(z_ext[i]);
- if (len > extlen)
- {
- if (gmx_strcasecmp(name+len-extlen, z_ext[i]) == 0)
- {
- buf[len-extlen] = '\0';
- break;
- }
- }
- }
- }
-
- if (deffile[fnm->ftp].ntps)
- {
- set_grpfnm(fnm, name ? buf : NULL, bCanNotOverride);
- }
- else
- {
- if ((name == NULL) || !(bCanNotOverride || (default_file_name == NULL)))
- {
- const char *defnm = ftp2defnm(fnm->ftp);
- strcpy(buf, defnm);
- }
- set_extension(buf, fnm->ftp);
-
- add_filenm(fnm, buf);
- }
-}
-
-static void set_filenms(int nf, t_filenm fnm[], gmx_bool bReadNode)
-{
- int i;
-
- for (i = 0; (i < nf); i++)
- {
- if (!IS_SET(fnm[i]))
- {
- set_filenm(&(fnm[i]), fnm[i].fn, FALSE, bReadNode);
- }
- }
-}
-
-void parse_file_args(int *argc, char *argv[], int nf, t_filenm fnm[],
- gmx_bool bKeep, gmx_bool bReadNode)
-{
- int i, j;
- gmx_bool *bRemove;
-
- check_opts(nf, fnm);
-
- for (i = 0; (i < nf); i++)
- {
- UN_SET(fnm[i]);
- }
-
- if (*argc > 1)
- {
- snew(bRemove, (*argc)+1);
- i = 1;
- do
- {
- for (j = 0; (j < nf); j++)
- {
- if (strcmp(argv[i], fnm[j].opt) == 0)
- {
- DO_SET(fnm[j]);
- bRemove[i] = TRUE;
- i++;
- /* check if we are out of arguments for this option */
- if ((i >= *argc) || (argv[i][0] == '-'))
- {
- set_filenm(&fnm[j], fnm[j].fn, FALSE, bReadNode);
- }
- /* sweep up all file arguments for this option */
- while ((i < *argc) && (argv[i][0] != '-'))
- {
- set_filenm(&fnm[j], argv[i], TRUE, bReadNode);
- bRemove[i] = TRUE;
- i++;
- /* only repeat for 'multiple' file options: */
- if (!IS_MULT(fnm[j]))
- {
- break;
- }
- }
-
- break; /* jump out of 'j' loop */
- }
- }
- /* No file found corresponding to option argv[i] */
- if (j == nf)
- {
- i++;
- }
- }
- while (i < *argc);
-
- if (!bKeep)
- {
- /* Remove used entries */
- for (i = j = 0; (i <= *argc); i++)
- {
- if (!bRemove[i])
- {
- argv[j++] = argv[i];
- }
- }
- (*argc) = j - 1;
- }
- sfree(bRemove);
- }
-
- set_filenms(nf, fnm, bReadNode);
-
-}
-
const char *opt2fn(const char *opt, int nfile, const t_filenm fnm[])
{
int i;
extpos = strrchr(buf, '.');
*extpos = '\0';
sprintf(newname, "%s%s.%s", buf, suffix, extpos + 1);
- free(fnm[i].fns[j]);
- fnm[i].fns[j] = strdup(newname);
+ sfree(fnm[i].fns[j]);
+ fnm[i].fns[j] = gmx_strdup(newname);
}
}
}
ret[i] = tfn[i]; /* just directly copy all non-string fields */
if (tfn[i].opt)
{
- ret[i].opt = strdup(tfn[i].opt);
+ ret[i].opt = gmx_strdup(tfn[i].opt);
}
else
{
if (tfn[i].fn)
{
- ret[i].fn = strdup(tfn[i].fn);
+ ret[i].fn = gmx_strdup(tfn[i].fn);
}
else
{
snew(ret[i].fns, tfn[i].nfiles);
for (j = 0; j < tfn[i].nfiles; j++)
{
- ret[i].fns[j] = strdup(tfn[i].fns[j]);
+ ret[i].fns[j] = gmx_strdup(tfn[i].fns[j]);
}
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff