-/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
- * $Id: densorder.c,v 0.9
- *
- * This source code is part of
- *
- * G R O M A C S
- *
- * GROningen MAchine for Chemical Simulations
- *
- * VERSION 3.0
+/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 1991-2001
- * BIOSON Research Institute, Dept. of Biophysical Chemistry
- * University of Groningen, The Netherlands
+ * 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.
*
- * 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
* of the License, or (at your option) any later version.
*
- * If you want to redistribute modifications, please consider that
- * scientific software is very special. Version control is crucial -
- * bugs must be traceable. We will be happy to consider code for
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- * the papers on the package - you can find them in the top README file.
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*
- * Do check out http://www.gromacs.org , or mail us at gromacs@gromacs.org .
+ * 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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- * Gyas ROwers Mature At Cryogenic Speed
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*/
+#include "gmxpre.h"
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include <ctype.h>
#include <math.h>
-#include "sysstuff.h"
#include <string.h>
-#include "string2.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "macros.h"
+
+#include "gromacs/utility/cstringutil.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 "physics.h"
-#include "matio.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 "gromacs/math/units.h"
#include "dens_filter.h"
#include "binsearch.h"
#include "powerspect.h"
#include "gmx_ana.h"
-#include "copyrite.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/rmpbc.h"
#include "gromacs/utility/exceptions.h"
-#include "gromacs/utility/programinfo.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/smalloc.h"
#ifdef GMX_DOUBLE
#define FLOOR(x) ((int) floor(x))
dim[2] = yslices;
dim[3] = zslices;
- fldH = ffopen(fldfn, "w");
+ fldH = gmx_ffopen(fldfn, "w");
fwrite(dim, sizeof(int), 4, fldH);
for (n = 0; n < tdim; n++)
{
}
totdens /= (xslices*yslices*zslices*tdim);
fprintf(stderr, "Total density [kg/m^3] %8f", totdens);
- ffclose(fldH);
+ gmx_ffclose(fldH);
}
static void filterdensmap(real ****Densmap, int xslices, int yslices, int zslices, int tblocks, int ftsize)
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 = zbins*bwz;
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);
sfree(profile1);
sfree(yticks);
}
-static void writeraw(t_interf ***int1, t_interf ***int2, int tblocks, int xbins, int ybins, char **fnms)
+static void writeraw(t_interf ***int1, t_interf ***int2, int tblocks,
+ int xbins, int ybins, char **fnms,
+ const output_env_t oenv)
{
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");
try
{
gmx::BinaryInformationSettings settings;
settings.generatedByHeader(true);
settings.linePrefix("# ");
- gmx::printBinaryInformation(raw1, gmx::ProgramInfo::getInstance(),
+ gmx::printBinaryInformation(raw1, output_env_get_program_context(oenv),
settings);
- gmx::printBinaryInformation(raw2, gmx::ProgramInfo::getInstance(),
+ gmx::printBinaryInformation(raw2, output_env_get_program_context(oenv),
settings);
}
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
}
}
- ffclose(raw1);
- ffclose(raw2);
+ gmx_ffclose(raw1);
+ gmx_ffclose(raw2);
}
int gmx_densorder(int argc, char *argv[])
{
static const char *desc[] = {
- "A small program to reduce a two-phase density distribution",
- "along an axis, computed over a MD trajectory",
+ "[THISMODULE] reduces a two-phase density distribution",
+ "along an axis, computed over a MD trajectory,",
"to 2D surfaces fluctuating in time, by a fit to",
- "a functional profile for interfacial densities",
+ "a functional profile for interfacial densities.",
"A time-averaged spatial representation of the",
- "interfaces can be output with the option -tavg"
+ "interfaces can be output with the option [TT]-tavg[tt]."
};
/* Extra arguments - but note how you always get the begin/end
t_filenm fnm[] = {
- { efTPX, "-s", NULL, ffREAD }, /* this is for the topology */
+ { efTPR, "-s", NULL, ffREAD }, /* this is for the topology */
{ efTRX, "-f", NULL, ffREAD }, /* and this for the trajectory */
{ efNDX, "-n", NULL, ffREAD}, /* this is to select groups */
{ efDAT, "-o", "Density4D", ffOPTWR}, /* This is for outputting the entire 4D densityfield in binary format */
bRawOut = opt2bSet("-or", NFILE, fnm);
bGraph = opt2bSet("-og", NFILE, fnm);
bOut = opt2bSet("-o", NFILE, fnm);
- top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC);
+ top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC);
snew(grpname, 1);
snew(index, 1);
snew(ngx, 1);
{
gmx_fatal(FARGS, "No or not correct number (2) of output-files: %d", nfxpm);
}
- writeraw(surf1, surf2, tblock, xslices, yslices, rawfiles);
+ writeraw(surf1, surf2, tblock, xslices, yslices, rawfiles, oenv);
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff