/*
+ * 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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+ * 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.
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-
-#include "sysstuff.h"
#include <string.h>
-#include "typedefs.h"
-#include "smalloc.h"
-#include "macros.h"
-#include "princ.h"
-#include "rmpbc.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "pbc.h"
-#include "gromacs/fileio/futil.h"
-#include "statutil.h"
-#include "index.h"
-#include "gmx_ana.h"
-#include "gromacs/fileio/trxio.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/princ.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
/****************************************************************************/
/* This program calculates the ordering of water molecules across a box, as */
factor*dipole[slice][ZZ], order[slice]);
}
- ffclose(ord);
+ gmx_ffclose(ord);
}
int gmx_h2order(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]g_h2order[tt] computes the orientation of water molecules with respect to the normal",
+ "[THISMODULE] computes the orientation of water molecules with respect to the normal",
"of the box. The program determines the average cosine of the angle",
"between the dipole moment of water and an axis of the box. The box is",
"divided in slices and the average orientation per slice is printed.",
{ efTRX, "-f", NULL, ffREAD }, /* trajectory file */
{ efNDX, NULL, NULL, ffREAD }, /* index file */
{ efNDX, "-nm", NULL, ffOPTRD }, /* index with micelle atoms */
- { efTPX, NULL, NULL, ffREAD }, /* topology file */
+ { efTPR, NULL, NULL, ffREAD }, /* topology file */
{ efXVG, "-o", "order", ffWRITE }, /* xvgr output file */
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv,
- PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE, NFILE,
+ PCA_CAN_VIEW | PCA_CAN_TIME, NFILE,
fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
bMicel = opt2bSet("-nm", NFILE, fnm);
- top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC); /* read topology file */
+ top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC); /* read topology file */
rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &ngx, &index, &grpname);
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff