/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
- *
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- * 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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-
- * This program is free software; you can redistribute it and/or
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+ * 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 "gromacs/fileio/filenm.h"
-#include "smalloc.h"
-#include "macros.h"
#include <math.h>
-#include "typedefs.h"
-#include "xvgr.h"
-#include "statutil.h"
+#include <string.h>
+
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/tpxio.h"
-#include "string2.h"
-#include "vec.h"
-#include "index.h"
-#include "pbc.h"
-#include "gmx_fatal.h"
-#include "gromacs/fileio/futil.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/fileio/pdbio.h"
-#include "txtdump.h"
-#include "do_fit.h"
-#include "viewit.h"
-#include "rmpbc.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/pbcutil/rmpbc.h"
#include "gmx_ana.h"
+#include "gromacs/math/do_fit.h"
void calc_rm_cm(int isize, atom_id index[], t_atoms *atoms, rvec x[], rvec xcm)
{
{
if (debug)
{
- fprintf(debug, "{%d %d}", *i1+bFW ? dx : dy, *i2+bFW ? dy : dx );
+ fprintf(debug, "{%d %d}", *i1 + (bFW ? dx : dy), *i2 + (bFW ? dy : dx) );
}
if (bFW)
{
real *msds;
- if (!parse_common_args(&argc, argv, PCA_BE_NICE | PCA_CAN_VIEW,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
find_matching_names(&isize1, index1, atoms1, &isize2, index2, atoms2);
if (matchndxfile)
{
- fp = ffopen(matchndxfile, "w");
+ fp = gmx_ffopen(matchndxfile, "w");
fprintf(fp, "; Matching atoms between %s from %s and %s from %s\n",
groupnames1, conf1file, groupnames2, conf2file);
fprintf(fp, "[ Match_%s_%s ]\n", conf1file, groupnames1);
/* atoms2->resinfo[atoms2->atom[index2[i]].resind].chain = 'B'; */
}
}
- fp = ffopen(outfile, "w");
+ fp = gmx_ffopen(outfile, "w");
if (!bOne)
{
write_pdbfile(fp, title1, atoms1, x1, ePBC1, box1, ' ', 1, NULL, TRUE);
}
write_pdbfile(fp, title2, atoms2, x2, ePBC2, box2, ' ', bOne ? -1 : 2, NULL, TRUE);
- ffclose(fp);
+ gmx_ffclose(fp);
break;
case efGRO:
if (bBfac)
{
fprintf(stderr, "WARNING: cannot write B-factor values to gro file\n");
}
- fp = ffopen(outfile, "w");
+ fp = gmx_ffopen(outfile, "w");
if (!bOne)
{
write_hconf_p(fp, title1, atoms1, 3, x1, v1, box1);
}
write_hconf_p(fp, title2, atoms2, 3, x2, v2, box2);
- ffclose(fp);
+ gmx_ffclose(fp);
break;
default:
if (bBfac)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff