/*
+ * 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.
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- * check out http://www.gromacs.org for more information.
-
- * This program is free software; you can redistribute it and/or
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- * 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
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
#include <math.h>
#include <string.h>
-#include "statutil.h"
-#include "sysstuff.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "vec.h"
-#include "statutil.h"
-#include "index.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/topology/index.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
#include "princ.h"
-#include "do_fit.h"
-#include "copyrite.h"
-#include "rmpbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
#include "gmx_ana.h"
+#include "gromacs/math/do_fit.h"
int gmx_filter(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]g_filter[tt] performs frequency filtering on a trajectory.",
+ "[THISMODULE] performs frequency filtering on a trajectory.",
"The filter shape is cos([GRK]pi[grk] t/A) + 1 from -A to +A, where A is given",
"by the option [TT]-nf[tt] times the time step in the input trajectory.",
"This filter reduces fluctuations with period A by 85%, with period",
};
#define NFILE asize(fnm)
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
highfile = opt2fn_null("-oh", NFILE, fnm);
if (highfile)
&xtop, NULL, topbox, TRUE);
if (bTop)
{
- gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr, topbox);
+ gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr);
gmx_rmpbc(gpbc, top.atoms.nr, topbox, xtop);
}
}
x[nffr - 1] = ptr;
fr++;
}
- while (read_next_x(oenv, in, &(t[nffr - 1]), nat, x[nffr - 1], box[nffr - 1]));
+ while (read_next_x(oenv, in, &(t[nffr - 1]), x[nffr - 1], box[nffr - 1]));
if (bTop)
{