*
* 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) 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.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-#include <string.h>
#include <math.h>
-#include "macros.h"
-#include "sysstuff.h"
-#include "smalloc.h"
-#include "typedefs.h"
+#include <stdlib.h>
+#include <string.h>
+
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/pdbio.h"
#include "gromacs/fileio/tngio.h"
#include "gromacs/fileio/tngio_for_tools.h"
-#include "gromacs/commandline/pargs.h"
-#include "gromacs/fileio/futil.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/confio.h"
-#include "names.h"
-#include "index.h"
-#include "vec.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xtcio.h"
-#include "do_fit.h"
-#include "rmpbc.h"
-#include "gromacs/fileio/g87io.h"
-#include "pbc.h"
-#include "xvgr.h"
-#include "gromacs/fileio/xdrf.h"
-#include "gmx_ana.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
#define TIME_EXPLICIT 0
#define TIME_CONTINUE 1
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_BE_NICE | PCA_TIME_UNIT, NFILE, fnm,
+ if (!parse_common_args(&argc, argv, PCA_TIME_UNIT, NFILE, fnm,
asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
{
if (nfile_out != nset)
{
- char *buf = strdup(fnms_out[0]);
+ char *buf = gmx_strdup(fnms_out[0]);
snew(fnms_out, nset);
for (i = 0; (i < nset); i++)
{
/* Fails if last frame is incomplete
* We can't do anything about it without overwriting
* */
- if (filetype == efXTC)
- {
- lasttime =
- xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio),
- gmx_fio_getxdr(stfio),
- fr.natoms, &bOK);
- fr.time = lasttime;
- if (!bOK)
- {
- gmx_fatal(FARGS, "Error reading last frame. Maybe seek not supported." );
- }
- }
- else if (filetype == efTNG)
+ if (filetype == efXTC || filetype == efTNG)
{
- tng_trajectory_t tng = trx_get_tng(status);
- if (!tng)
- {
- gmx_fatal(FARGS, "Error opening TNG file.");
- }
- lasttime = gmx_tng_get_time_of_final_frame(tng);
+ lasttime = trx_get_time_of_final_frame(status);
fr.time = lasttime;
}
else
{
gmx_fatal(FARGS, "Overwrite only supported for XTC." );
}
- last_frame_time =
- xdr_xtc_get_last_frame_time(gmx_fio_getfp(stfio),
- gmx_fio_getxdr(stfio),
- fr.natoms, &bOK);
- if (!bOK)
- {
- gmx_fatal(FARGS, "Error reading last frame. Maybe seek not supported." );
- }
+ last_frame_time = trx_get_time_of_final_frame(status);
+
/* xtc_seek_time broken for trajectories containing only 1 or 2 frames
* or when seek time = 0 */
if (nfile_in > 1 && settime[1] < last_frame_time+timest[0]*0.5)