/*
+ * 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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+ * 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 "statutil.h"
#include <string.h>
-#include "smalloc.h"
-#include "typedefs.h"
+
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/legacyheaders/typedefs.h"
#include "gromacs/fileio/confio.h"
-#include "gromacs/fileio/futil.h"
-#include "macros.h"
-#include "vec.h"
-#include "index.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
#include "gmx_ana.h"
int gmx_genpr(int argc, char *argv[])
{
const char *desc[] = {
- "[THISMODULE] produces an include file for a topology containing",
+ "[THISMODULE] produces an #include file for a topology containing",
"a list of atom numbers and three force constants for the",
- "[IT]x[it]-, [IT]y[it]-, and [IT]z[it]-direction. A single isotropic force constant may",
+ "[IT]x[it]-, [IT]y[it]-, and [IT]z[it]-direction based on",
+ "the contents of the [TT]-f[tt] file. A single isotropic force constant may",
"be given on the command line instead of three components.[PAR]",
- "WARNING: position restraints only work for the one molecule at a time.",
- "Position restraints are interactions within molecules, therefore",
- "they should be included within the correct [TT][ moleculetype ][tt]",
- "block in the topology. Since the atom numbers in every moleculetype",
- "in the topology start at 1 and the numbers in the input file for",
- "[THISMODULE] number consecutively from 1, [THISMODULE] will only",
- "produce a useful file for the first molecule.[PAR]",
+ "WARNING: Position restraints are interactions within molecules, therefore",
+ "they must be included within the correct [TT][ moleculetype ][tt]",
+ "block in the topology. The atom indices within the",
+ "[TT][ position_restraints ][tt] block must be within the range of the",
+ "atom indices for that molecule type. Since the atom numbers in every",
+ "moleculetype in the topology start at 1 and the numbers in the input file",
+ "for [THISMODULE] number consecutively from 1, [THISMODULE] will only",
+ "produce a useful file for the first molecule. You may wish to",
+ "edit the resulting index file to remove the lines for later atoms,",
+ "or construct a suitable index group to provide",
+ "as input to [THISMODULE].[PAR]",
"The [TT]-of[tt] option produces an index file that can be used for",
"freezing atoms. In this case, the input file must be a [TT].pdb[tt] file.[PAR]",
"With the [TT]-disre[tt] option, half a matrix of distance restraints",
fprintf(out, "%d\n", i+1);
}
}
- ffclose(out);
+ gmx_ffclose(out);
}
else if ((bDisre || bConstr) && x)
{
hi = d+dd;
fprintf(out, "%5d %5d %1d %5d %10d %10g %10g %10g %10g\n",
ind_grp[i]+1, ind_grp[j]+1, 1, k, 1,
- lo, hi, hi+1, 1.0);
+ lo, hi, hi+disre_up2, 1.0);
}
}
}
}
- ffclose(out);
+ gmx_ffclose(out);
}
else
{
fprintf(out, "%4d %4d %10g %10g %10g\n",
ind_grp[i]+1, 1, fc[XX], fc[YY], fc[ZZ]);
}
- ffclose(out);
+ gmx_ffclose(out);
}
if (xfn)
{
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff