/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
- *
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- *
- * 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 <math.h>
+#include <stdlib.h>
#include <string.h>
-#include "typedefs.h"
-#include "macros.h"
-#include "mshift.h"
-#include "xvgr.h"
-#include "vec.h"
-#include "do_fit.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/pbcutil/mshift.h"
+#include "gromacs/legacyheaders/viewit.h"
#include "gromacs/fileio/confio.h"
-#include "smalloc.h"
-#include "nrnb.h"
-#include "disre.h"
-#include "gromacs/commandline/pargs.h"
-#include "force.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/legacyheaders/force.h"
#include "gstat.h"
-#include "main.h"
+#include "gromacs/legacyheaders/main.h"
#include "gromacs/fileio/pdbio.h"
-#include "index.h"
-#include "mdatoms.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/legacyheaders/mdatoms.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include "mdrun.h"
-#include "names.h"
-#include "gromacs/fileio/matio.h"
-#include "mtop_util.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/topology/mtop_util.h"
#include "gmx_ana.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
typedef struct {
int n;
hi = max_dr;
}
printf("Highest level in the matrix will be %g\n", hi);
- fp = ffopen(fn, "w");
+ fp = gmx_ffopen(fn, "w");
write_xpm(fp, 0, "Distance Violations", "<V> (nm)", "Residue", "Residue",
n_res, n_res, t_res, t_res, matrix, 0, hi, rlo, rhi, &nlevels);
- ffclose(fp);
+ gmx_ffclose(fp);
}
int gmx_disre(int argc, char *argv[])
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
+ 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;
}
ir.dr_tau = 0.0;
- init_disres(fplog, &mtop, &ir, NULL, FALSE, &fcd, NULL, FALSE);
+ init_disres(fplog, &mtop, &ir, NULL, &fcd, NULL, FALSE);
natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
snew(f, 5*natoms);
}
mdatoms = init_mdatoms(fplog, &mtop, ir.efep != efepNO);
- atoms2md(&mtop, &ir, 0, NULL, 0, mtop.natoms, mdatoms);
+ atoms2md(&mtop, &ir, 0, NULL, mtop.natoms, mdatoms);
update_mdatoms(mdatoms, ir.fepvals->init_lambda);
init_nrnb(&nrnb);
if (ir.ePBC != epbcNONE)
}
dump_disre_matrix(opt2fn_null("-x", NFILE, fnm), &dr, fcd.disres.nres,
j, &top->idef, &mtop, max_dr, nlevels, bThird);
- ffclose(out);
- ffclose(aver);
- ffclose(numv);
- ffclose(maxxv);
+ gmx_ffclose(out);
+ gmx_ffclose(aver);
+ gmx_ffclose(numv);
+ gmx_ffclose(maxxv);
if (isize > 0)
{
- ffclose(xvg);
+ gmx_ffclose(xvg);
do_view(oenv, opt2fn("-dr", NFILE, fnm), "-nxy");
}
do_view(oenv, opt2fn("-dn", NFILE, fnm), "-nxy");
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff