/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.2.0
- * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
- * Copyright (c) 2001-2004, The GROMACS development team,
- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
+ * 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.
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+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
+#include <stdlib.h>
#include <string.h>
-#include "statutil.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "pbc.h"
-#include "copyrite.h"
-#include "futil.h"
-#include "statutil.h"
-#include "index.h"
-#include "mshift.h"
-#include "xvgr.h"
-#include "princ.h"
-#include "rmpbc.h"
-#include "txtdump.h"
-#include "tpxio.h"
+
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/fileio/xvgr.h"
+
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
#include "gmx_ana.h"
+#include "gromacs/utility/fatalerror.h"
+
typedef struct {
atom_id i;
real d2;
int gmx_trjorder(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]trjorder[tt] orders molecules according to the smallest distance",
+ "[THISMODULE] orders molecules according to the smallest distance",
"to atoms in a reference group",
"or on z-coordinate (with option [TT]-z[tt]).",
"With distance ordering, it will ask for a group of reference",
"be used instead of a reference atom by setting [TT]-da[tt] to 0.",
"All atoms in the trajectory are written",
"to the output trajectory.[PAR]",
- "[TT]trjorder[tt] can be useful for e.g. analyzing the n waters closest to a",
+ "[THISMODULE] can be useful for e.g. analyzing the n waters closest to a",
"protein.",
"In that case the reference group would be the protein and the group",
"of molecules would consist of all the water atoms. When an index group",
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &x, NULL, box, TRUE);
sfree(x);
}
out = open_trx(opt2fn("-o", NFILE, fnm), "w");
}
- gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms, box);
+ gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
do
{
gmx_rmpbc(gpbc, natoms, box, x);
write_trx(out, natoms, swi, &top.atoms, 0, t, box, x, NULL, NULL);
}
}
- while (read_next_x(oenv, status, &t, natoms, x, box));
+ while (read_next_x(oenv, status, &t, x, box));
close_trj(status);
if (out)
{
}
if (fp)
{
- ffclose(fp);
+ gmx_ffclose(fp);
}
gmx_rmpbc_done(gpbc);
- thanx(stderr);
-
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff