-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
- * $Id: densorder.c,v 0.9
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
+ * Copyright (c) 2010,2011,2012,2013,2014, 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.
*
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.0
- *
- * Copyright (c) 1991-2001
- * BIOSON Research Institute, Dept. of Biophysical Chemistry
- * University of Groningen, The Netherlands
- *
- * 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
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
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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
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <math.h>
-#include <ctype.h>
-
-#include "sysstuff.h"
#include <string.h>
-#include "typedefs.h"
-#include "statutil.h"
-#include "smalloc.h"
-#include "macros.h"
+
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/macros.h"
#include "gstat.h"
-#include "vec.h"
-#include "xvgr.h"
-#include "pbc.h"
-#include "futil.h"
-#include "statutil.h"
-#include "index.h"
-#include "tpxio.h"
-#include "matio.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
#include "binsearch.h"
#include "powerspect.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
+
/* Print name of first atom in all groups in index file */
static void print_types(atom_id index[], atom_id a[], int ngrps,
char *groups[], t_topology *top)
fprintf(stderr, "Using following groups: \n");
for (i = 0; i < ngrps; i++)
{
- fprintf(stderr, "Groupname: %s First atomname: %s First atomnr %u\n",
+ fprintf(stderr, "Groupname: %s First atomname: %s First atomnr %d\n",
groups[i], *(top->atoms.atomname[a[index[i]]]), a[index[i]]);
}
fprintf(stderr, "\n");
yticks[j] += bw;
}
- xpmfile1 = ffopen(outfiles[0], "w");
- xpmfile2 = ffopen(outfiles[1], "w");
+ xpmfile1 = gmx_ffopen(outfiles[0], "w");
+ xpmfile2 = gmx_ffopen(outfiles[1], "w");
max1 = max2 = 0.0;
min1 = min2 = 1000.00;
write_xpm(xpmfile2, 3, numbuf, "Height", "x[nm]", "y[nm]", xbins, ybins, xticks, yticks, profile2, min2, max2, lo, hi, &maplevels);
}
- ffclose(xpmfile1);
- ffclose(xpmfile2);
+ gmx_ffclose(xpmfile1);
+ gmx_ffclose(xpmfile2);
FILE *raw1, *raw2;
int i, j, n;
- raw1 = ffopen(fnms[0], "w");
- raw2 = ffopen(fnms[1], "w");
+ raw1 = gmx_ffopen(fnms[0], "w");
+ raw2 = gmx_ffopen(fnms[1], "w");
fprintf(raw1, "#Legend\n#TBlock\n#Xbin Ybin Z t\n");
fprintf(raw2, "#Legend\n#TBlock\n#Xbin Ybin Z t\n");
for (n = 0; n < tblocks; n++)
}
}
- ffclose(raw1);
- ffclose(raw2);
+ gmx_ffclose(raw1);
+ gmx_ffclose(raw2);
}
int gmx_hydorder(int argc, char *argv[])
{
static const char *desc[] = {
- "g_hydorder computes the tetrahedrality order parameters around a ",
+ "[THISMODULE] computes the tetrahedrality order parameters around a ",
"given atom. Both angle an distance order parameters are calculated. See",
"P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518.",
- "for more details.[BR]"
- "This application calculates the orderparameter in a 3d-mesh in the box, and",
+ "for more details.[PAR]"
+ "[THISMODULE] calculates the order parameter in a 3d-mesh in the box, and",
"with 2 phases in the box gives the user the option to define a 2D interface in time",
- "separating the faces by specifying parameters -sgang1 and -sgang2 (It is important",
- "to select these judiciously)"
+ "separating the faces by specifying parameters [TT]-sgang1[tt] and",
+ "[TT]-sgang2[tt] (it is important to select these judiciously)."
};
int axis = 0;
t_filenm fnm[] = { /* files for g_order */
{ efTRX, "-f", NULL, ffREAD }, /* trajectory file */
{ efNDX, "-n", NULL, ffREAD }, /* index file */
- { efTPX, "-s", NULL, ffREAD }, /* topology file */
+ { efTPR, "-s", NULL, ffREAD }, /* topology file */
{ efXPM, "-o", "intf", ffWRMULT}, /* XPM- surface maps */
{ efOUT, "-or", "raw", ffOPTWRMULT }, /* xvgr output file */
{ efOUT, "-Spect", "intfspect", ffOPTWRMULT}, /* Fourier spectrum interfaces */
int nfspect, nfxpm, nfraw;
output_env_t oenv;
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
+ if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
ndxfnm = ftp2fn(efNDX, NFILE, fnm);
- tpsfnm = ftp2fn(efTPX, NFILE, fnm);
+ tpsfnm = ftp2fn(efTPR, NFILE, fnm);
trxfnm = ftp2fn(efTRX, NFILE, fnm);
/* Calculate axis */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff