a lock */
};
-/** Names for different items that can be read/written with gmx_fio_do_*() */
-extern const char *eioNames[eioNR];
-
-/** check the number of items against the allowed number of items */
-void gmx_fio_check_nitem(int eio, int nitem, const char *file,
- int line);
-/** check the output type against allowed values */
-void gmx_fio_fe(t_fileio *fio, int eio, const char *desc, const char *srcfile,
- int line);
-
/** lock the mutex associated with a fio */
void gmx_fio_lock(t_fileio *fio);
/** unlock the mutex associated with a fio */
void gmx_fio_unlock(t_fileio *fio);
-/** xdr read/write routine */
-gmx_bool do_xdr(t_fileio *fio, void *item, int nitem, int eio,
- const char *desc, const char *srcfile, int line);
-
#endif
*/
#include "gmxpre.h"
+#include <stdio.h>
+#include <string.h>
+
#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/xdrf.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
#include "gmxfio-impl.h"
+static const char *eioNames[eioNR] =
+{
+ "REAL", "INT", "GMX_STE_T", "UCHAR", "NUCHAR", "USHORT", "RVEC", "NRVEC",
+ "IVEC", "STRING"
+};
+
+/* check the number of items given against the type */
+static void gmx_fio_check_nitem(int eio, int nitem, const char *file, int line)
+{
+ if ((nitem != 1) && !((eio == eioNRVEC) || (eio == eioNUCHAR)))
+ {
+ gmx_fatal(FARGS,
+ "nitem (%d) may differ from 1 only for %s or %s, not for %s"
+ "(%s, %d)", nitem, eioNames[eioNUCHAR], eioNames[eioNRVEC],
+ eioNames[eio], file, line);
+ }
+}
+
+
+/* output a data type error. */
+static void gmx_fio_fe(t_fileio *fio, int eio, const char *desc,
+ const char *srcfile, int line)
+{
+
+ gmx_fatal(FARGS, "Trying to %s %s type %d (%s), src %s, line %d",
+ fio->bRead ? "read" : "write", desc, eio,
+ ((eio >= 0) && (eio < eioNR)) ? eioNames[eio] : "unknown",
+ srcfile, line);
+}
+
+/* This is the part that reads xdr files. */
+
+static gmx_bool do_xdr(t_fileio *fio, void *item, int nitem, int eio,
+ const char *desc, const char *srcfile, int line)
+{
+ unsigned char ucdum, *ucptr;
+ bool_t res = 0;
+ float fvec[DIM];
+ double dvec[DIM];
+ int j, m, *iptr, idum;
+ gmx_int64_t sdum;
+ real *ptr;
+ unsigned short us;
+ double d = 0;
+ float f = 0;
+
+ gmx_fio_check_nitem(eio, nitem, srcfile, line);
+ switch (eio)
+ {
+ case eioREAL:
+ if (fio->bDouble)
+ {
+ if (item && !fio->bRead)
+ {
+ d = *((real *) item);
+ }
+ res = xdr_double(fio->xdr, &d);
+ if (item)
+ {
+ *((real *) item) = d;
+ }
+ }
+ else
+ {
+ if (item && !fio->bRead)
+ {
+ f = *((real *) item);
+ }
+ res = xdr_float(fio->xdr, &f);
+ if (item)
+ {
+ *((real *) item) = f;
+ }
+ }
+ break;
+ case eioFLOAT:
+ if (item && !fio->bRead)
+ {
+ f = *((float *) item);
+ }
+ res = xdr_float(fio->xdr, &f);
+ if (item)
+ {
+ *((float *) item) = f;
+ }
+ break;
+ case eioDOUBLE:
+ if (item && !fio->bRead)
+ {
+ d = *((double *) item);
+ }
+ res = xdr_double(fio->xdr, &d);
+ if (item)
+ {
+ *((double *) item) = d;
+ }
+ break;
+ case eioINT:
+ if (item && !fio->bRead)
+ {
+ idum = *(int *) item;
+ }
+ res = xdr_int(fio->xdr, &idum);
+ if (item)
+ {
+ *(int *) item = idum;
+ }
+ break;
+ case eioINT64:
+ if (item && !fio->bRead)
+ {
+ sdum = *(gmx_int64_t *) item;
+ }
+ res = xdr_int64(fio->xdr, &sdum);
+ if (item)
+ {
+ *(gmx_int64_t *) item = sdum;
+ }
+ break;
+ case eioUCHAR:
+ if (item && !fio->bRead)
+ {
+ ucdum = *(unsigned char *) item;
+ }
+ res = xdr_u_char(fio->xdr, &ucdum);
+ if (item)
+ {
+ *(unsigned char *) item = ucdum;
+ }
+ break;
+ case eioNUCHAR:
+ ucptr = (unsigned char *) item;
+ res = 1;
+ for (j = 0; (j < nitem) && res; j++)
+ {
+ res = xdr_u_char(fio->xdr, &(ucptr[j]));
+ }
+ break;
+ case eioUSHORT:
+ if (item && !fio->bRead)
+ {
+ us = *(unsigned short *) item;
+ }
+ res = xdr_u_short(fio->xdr, (unsigned short *) &us);
+ if (item)
+ {
+ *(unsigned short *) item = us;
+ }
+ break;
+ case eioRVEC:
+ if (fio->bDouble)
+ {
+ if (item && !fio->bRead)
+ {
+ for (m = 0; (m < DIM); m++)
+ {
+ dvec[m] = ((real *) item)[m];
+ }
+ }
+ res = xdr_vector(fio->xdr, (char *) dvec, DIM,
+ (unsigned int) sizeof(double),
+ (xdrproc_t) xdr_double);
+ if (item)
+ {
+ for (m = 0; (m < DIM); m++)
+ {
+ ((real *) item)[m] = dvec[m];
+ }
+ }
+ }
+ else
+ {
+ if (item && !fio->bRead)
+ {
+ for (m = 0; (m < DIM); m++)
+ {
+ fvec[m] = ((real *) item)[m];
+ }
+ }
+ res = xdr_vector(fio->xdr, (char *) fvec, DIM,
+ (unsigned int) sizeof(float),
+ (xdrproc_t) xdr_float);
+ if (item)
+ {
+ for (m = 0; (m < DIM); m++)
+ {
+ ((real *) item)[m] = fvec[m];
+ }
+ }
+ }
+ break;
+ case eioNRVEC:
+ ptr = NULL;
+ res = 1;
+ for (j = 0; (j < nitem) && res; j++)
+ {
+ if (item)
+ {
+ ptr = ((rvec *) item)[j];
+ }
+ res = do_xdr(fio, ptr, 1, eioRVEC, desc, srcfile, line);
+ }
+ break;
+ case eioIVEC:
+ iptr = (int *) item;
+ res = 1;
+ for (m = 0; (m < DIM) && res; m++)
+ {
+ if (item && !fio->bRead)
+ {
+ idum = iptr[m];
+ }
+ res = xdr_int(fio->xdr, &idum);
+ if (item)
+ {
+ iptr[m] = idum;
+ }
+ }
+ break;
+ case eioSTRING:
+ {
+ char *cptr;
+ int slen;
+
+ if (item)
+ {
+ if (!fio->bRead)
+ {
+ slen = strlen((char *) item) + 1;
+ }
+ else
+ {
+ slen = 0;
+ }
+ }
+ else
+ {
+ slen = 0;
+ }
+
+ if (xdr_int(fio->xdr, &slen) <= 0)
+ {
+ gmx_fatal(FARGS, "wrong string length %d for string %s"
+ " (source %s, line %d)", slen, desc, srcfile, line);
+ }
+ if (!item && fio->bRead)
+ {
+ snew(cptr, slen);
+ }
+ else
+ {
+ cptr = (char *)item;
+ }
+ if (cptr)
+ {
+ res = xdr_string(fio->xdr, &cptr, slen);
+ }
+ else
+ {
+ res = 1;
+ }
+ if (!item && fio->bRead)
+ {
+ sfree(cptr);
+ }
+ break;
+ }
+ default:
+ gmx_fio_fe(fio, eio, desc, srcfile, line);
+ }
+ if ((res == 0) && (fio->bDebug))
+ {
+ fprintf(stderr, "Error in xdr I/O %s %s to file %s (source %s, line %d)\n",
+ eioNames[eio], desc, fio->fn, srcfile, line);
+ }
+
+ return (res != 0);
+}
+
/*******************************************************************
*
* READ/WRITE FUNCTIONS
const char *desc, const char *srcfile, int line)
{
gmx_bool ret;
- int itmp;
gmx_fio_lock(fio);
if (fio->bRead)
{
- ret = do_xdr(fio, &itmp, 1, eioINT, desc, srcfile, line);
- *item = itmp;
+ int itmp = 0;
+ ret = do_xdr(fio, &itmp, 1, eioINT, desc, srcfile, line);
+ *item = itmp;
}
else
{
- itmp = *item;
- ret = do_xdr(fio, &itmp, 1, eioINT, desc, srcfile, line);
+ int itmp = *item;
+ ret = do_xdr(fio, &itmp, 1, eioINT, desc, srcfile, line);
}
gmx_fio_unlock(fio);
return ret;
const char *desc, const char *srcfile, int line)
{
gmx_bool ret = TRUE;
- int i, itmp;
+ int i;
gmx_fio_lock(fio);
for (i = 0; i < n; i++)
{
if (fio->bRead)
{
- ret = ret && do_xdr(fio, &itmp, 1, eioINT, desc,
- srcfile, line);
- item[i] = itmp;
+ int itmp = 0;
+ ret = ret && do_xdr(fio, &itmp, 1, eioINT, desc, srcfile, line);
+ item[i] = itmp;
}
else
{
- itmp = item[i];
- ret = ret && do_xdr(fio, &itmp, 1, eioINT, desc,
- srcfile, line);
+ int itmp = item[i];
+ ret = ret && do_xdr(fio, &itmp, 1, eioINT, desc, srcfile, line);
}
}
gmx_fio_unlock(fio);
during the simulation. */
static tMPI_Thread_mutex_t open_file_mutex = TMPI_THREAD_MUTEX_INITIALIZER;
-const char *eioNames[eioNR] =
-{
- "REAL", "INT", "GMX_STE_T", "UCHAR", "NUCHAR", "USHORT", "RVEC", "NRVEC",
- "IVEC", "STRING"
-};
-
/******************************************************************
*
* Internal functions:
return rc;
}
-
-/* check the number of items given against the type */
-void gmx_fio_check_nitem(int eio, int nitem, const char *file, int line)
-{
- if ((nitem != 1) && !((eio == eioNRVEC) || (eio == eioNUCHAR)))
- {
- gmx_fatal(FARGS,
- "nitem (%d) may differ from 1 only for %s or %s, not for %s"
- "(%s, %d)", nitem, eioNames[eioNUCHAR], eioNames[eioNRVEC],
- eioNames[eio], file, line);
- }
-}
-
-
-/* output a data type error. */
-void gmx_fio_fe(t_fileio *fio, int eio, const char *desc,
- const char *srcfile, int line)
-{
-
- gmx_fatal(FARGS, "Trying to %s %s type %d (%s), src %s, line %d",
- fio->bRead ? "read" : "write", desc, eio,
- ((eio >= 0) && (eio < eioNR)) ? eioNames[eio] : "unknown",
- srcfile, line);
-}
-
/* lock the mutex associated with this fio. This needs to be done for every
type of access to the fio's elements. */
void gmx_fio_lock(t_fileio *fio)
+++ /dev/null
-/*
- * 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) 2013,2014,2015, 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.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version 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 "gmxpre.h"
-
-#include <stdio.h>
-#include <string.h>
-
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/xdrf.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/utility/smalloc.h"
-
-#include "gmxfio-impl.h"
-
-/* This is the part that reads xdr files. */
-
-gmx_bool do_xdr(t_fileio *fio, void *item, int nitem, int eio,
- const char *desc, const char *srcfile, int line)
-{
- unsigned char ucdum, *ucptr;
- bool_t res = 0;
- float fvec[DIM];
- double dvec[DIM];
- int j, m, *iptr, idum;
- gmx_int64_t sdum;
- real *ptr;
- unsigned short us;
- double d = 0;
- float f = 0;
-
- gmx_fio_check_nitem(eio, nitem, srcfile, line);
- switch (eio)
- {
- case eioREAL:
- if (fio->bDouble)
- {
- if (item && !fio->bRead)
- {
- d = *((real *) item);
- }
- res = xdr_double(fio->xdr, &d);
- if (item)
- {
- *((real *) item) = d;
- }
- }
- else
- {
- if (item && !fio->bRead)
- {
- f = *((real *) item);
- }
- res = xdr_float(fio->xdr, &f);
- if (item)
- {
- *((real *) item) = f;
- }
- }
- break;
- case eioFLOAT:
- if (item && !fio->bRead)
- {
- f = *((float *) item);
- }
- res = xdr_float(fio->xdr, &f);
- if (item)
- {
- *((float *) item) = f;
- }
- break;
- case eioDOUBLE:
- if (item && !fio->bRead)
- {
- d = *((double *) item);
- }
- res = xdr_double(fio->xdr, &d);
- if (item)
- {
- *((double *) item) = d;
- }
- break;
- case eioINT:
- if (item && !fio->bRead)
- {
- idum = *(int *) item;
- }
- res = xdr_int(fio->xdr, &idum);
- if (item)
- {
- *(int *) item = idum;
- }
- break;
- case eioINT64:
- if (item && !fio->bRead)
- {
- sdum = *(gmx_int64_t *) item;
- }
- res = xdr_int64(fio->xdr, &sdum);
- if (item)
- {
- *(gmx_int64_t *) item = sdum;
- }
- break;
- case eioUCHAR:
- if (item && !fio->bRead)
- {
- ucdum = *(unsigned char *) item;
- }
- res = xdr_u_char(fio->xdr, &ucdum);
- if (item)
- {
- *(unsigned char *) item = ucdum;
- }
- break;
- case eioNUCHAR:
- ucptr = (unsigned char *) item;
- res = 1;
- for (j = 0; (j < nitem) && res; j++)
- {
- res = xdr_u_char(fio->xdr, &(ucptr[j]));
- }
- break;
- case eioUSHORT:
- if (item && !fio->bRead)
- {
- us = *(unsigned short *) item;
- }
- res = xdr_u_short(fio->xdr, (unsigned short *) &us);
- if (item)
- {
- *(unsigned short *) item = us;
- }
- break;
- case eioRVEC:
- if (fio->bDouble)
- {
- if (item && !fio->bRead)
- {
- for (m = 0; (m < DIM); m++)
- {
- dvec[m] = ((real *) item)[m];
- }
- }
- res = xdr_vector(fio->xdr, (char *) dvec, DIM,
- (unsigned int) sizeof(double),
- (xdrproc_t) xdr_double);
- if (item)
- {
- for (m = 0; (m < DIM); m++)
- {
- ((real *) item)[m] = dvec[m];
- }
- }
- }
- else
- {
- if (item && !fio->bRead)
- {
- for (m = 0; (m < DIM); m++)
- {
- fvec[m] = ((real *) item)[m];
- }
- }
- res = xdr_vector(fio->xdr, (char *) fvec, DIM,
- (unsigned int) sizeof(float),
- (xdrproc_t) xdr_float);
- if (item)
- {
- for (m = 0; (m < DIM); m++)
- {
- ((real *) item)[m] = fvec[m];
- }
- }
- }
- break;
- case eioNRVEC:
- ptr = NULL;
- res = 1;
- for (j = 0; (j < nitem) && res; j++)
- {
- if (item)
- {
- ptr = ((rvec *) item)[j];
- }
- res = do_xdr(fio, ptr, 1, eioRVEC, desc, srcfile, line);
- }
- break;
- case eioIVEC:
- iptr = (int *) item;
- res = 1;
- for (m = 0; (m < DIM) && res; m++)
- {
- if (item && !fio->bRead)
- {
- idum = iptr[m];
- }
- res = xdr_int(fio->xdr, &idum);
- if (item)
- {
- iptr[m] = idum;
- }
- }
- break;
- case eioSTRING:
- {
- char *cptr;
- int slen;
-
- if (item)
- {
- if (!fio->bRead)
- {
- slen = strlen((char *) item) + 1;
- }
- else
- {
- slen = 0;
- }
- }
- else
- {
- slen = 0;
- }
-
- if (xdr_int(fio->xdr, &slen) <= 0)
- {
- gmx_fatal(FARGS, "wrong string length %d for string %s"
- " (source %s, line %d)", slen, desc, srcfile, line);
- }
- if (!item && fio->bRead)
- {
- snew(cptr, slen);
- }
- else
- {
- cptr = (char *)item;
- }
- if (cptr)
- {
- res = xdr_string(fio->xdr, &cptr, slen);
- }
- else
- {
- res = 1;
- }
- if (!item && fio->bRead)
- {
- sfree(cptr);
- }
- break;
- }
- default:
- gmx_fio_fe(fio, eio, desc, srcfile, line);
- }
- if ((res == 0) && (fio->bDebug))
- {
- fprintf(stderr, "Error in xdr I/O %s %s to file %s (source %s, line %d)\n",
- eioNames[eio], desc, fio->fn, srcfile, line);
- }
-
- return (res != 0);
-}
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff