/*
+ * 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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*
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+ * 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 <string.h>
-#include "sysstuff.h"
-#include "physics.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "futil.h"
-#include "statutil.h"
-#include "index.h"
-#include "macros.h"
-#include "gmx_fatal.h"
-#include "xvgr.h"
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/legacyheaders/macros.h"
#include "gstat.h"
-#include "vec.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gmx_ana.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
int gmx_rotacf(int argc, char *argv[])
{
const char *desc[] = {
- "[TT]g_rotacf[tt] calculates the rotational correlation function",
+ "[THISMODULE] calculates the rotational correlation function",
"for molecules. Atom triplets (i,j,k) must be given in the index",
"file, defining two vectors ij and jk. The rotational ACF",
"is calculated as the autocorrelation function of the vector",
"by specifying atom pairs (i,j) in the index file.",
"[PAR]",
"EXAMPLES[PAR]",
- "[TT]g_rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1",
+ "[TT]gmx rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1",
"-fa expfit-x-P1 -beginfit 2.5 -endfit 20.0[tt][PAR]",
"This will calculate the rotational correlation function using a first",
"order Legendre polynomial of the angle of a vector defined by the index",
int ePBC;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffREAD },
{ efXVG, "-o", "rotacf", ffWRITE }
};
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
- NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv);
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
+ NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
+ {
+ return 0;
+ }
rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
"these can not be atom doublets\n");
}
- top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
+ top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC);
snew(c1, nvec);
for (i = 0; (i < nvec); i++)
natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
snew(x_s, natoms);
- gpbc = gmx_rmpbc_init(&(top->idef), ePBC, natoms, box);
+ gpbc = gmx_rmpbc_init(&(top->idef), ePBC, natoms);
/* Start the loop over frames */
t1 = t0 = t;
/* Increment loop counter */
teller++;
}
- while (read_next_x(oenv, status, &t, natoms, x, box));
+ while (read_next_x(oenv, status, &t, x, box));
close_trj(status);
fprintf(stderr, "\nDone with trajectory\n");
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff