/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
+ * Copyright (c) 2007,2008,2009,2010,2011,2012,2013,2014, 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
* of the License, or (at your option) any later version.
*
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+ * GROMACS is distributed in the hope that it will be useful,
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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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- * Gyas ROwers Mature At Cryogenic Speed
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
-
+#include "gmxpre.h"
+#include <math.h>
+#include <stdlib.h>
#include "gromacs/commandline/pargs.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "vec.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/math/vec.h"
#include "gromacs/fileio/tpxio.h"
#include "gromacs/fileio/trxio.h"
-#include <math.h>
-#include "index.h"
-#include "pbc.h"
-#include "rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
#include "gmx_ana.h"
-#include "macros.h"
-
+#include "gromacs/legacyheaders/macros.h"
static const double bohr = 0.529177249; /* conversion factor to compensate for VMD plugin conversion... */
-static void mequit(void)
-{
- printf("Memory allocation error\n");
- exit(1);
-}
-
int gmx_spatial(int argc, char *argv[])
{
const char *desc[] = {
"For a system of 32,000 atoms and a 50 ns trajectory, the SDF can be generated ",
"in about 30 minutes, with most of the time dedicated to the two runs through ",
"[TT]trjconv[tt] that are required to center everything properly. ",
- "This also takes a whole bunch of space (3 copies of the [TT].xtc[tt] file). ",
+ "This also takes a whole bunch of space (3 copies of the trajectory file). ",
"Still, the pictures are pretty and very informative when the fitted selection is properly made. ",
"3-4 atoms in a widely mobile group (like a free amino acid in solution) works ",
"well, or select the protein backbone in a stable folded structure to get the SDF ",
"Cartesian coordinate. To do that, simply omit the preliminary [gmx-trjconv] steps. \n",
"USAGE: \n",
"1. Use [gmx-make_ndx] to create a group containing the atoms around which you want the SDF \n",
- "2. [TT]gmx trjconv -s a.tpr -f a.xtc -o b.xtc -boxcenter tric -ur compact -pbc none[tt] \n",
- "3. [TT]gmx trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans[tt] \n",
- "4. run [THISMODULE] on the [TT].xtc[tt] output of step #3. \n",
+ "2. [TT]gmx trjconv -s a.tpr -f a.tng -o b.tng -boxcenter tric -ur compact -pbc none[tt] \n",
+ "3. [TT]gmx trjconv -s a.tpr -f b.tng -o c.tng -fit rot+trans[tt] \n",
+ "4. run [THISMODULE] on the [TT]c.tng[tt] output of step #3. \n",
"5. Load [TT]grid.cube[tt] into VMD and view as an isosurface. \n",
"[BB]Note[bb] that systems such as micelles will require [TT]gmx trjconv -pbc cluster[tt] between steps 1 and 2\n",
"WARNINGS:[BR]",
MINBIN[i] -= (double)iNAB*rBINWIDTH;
nbin[i] = (long)ceil((MAXBIN[i]-MINBIN[i])/rBINWIDTH);
}
- bin = (long ***)malloc(nbin[XX]*sizeof(long **));
- if (!bin)
- {
- mequit();
- }
+ snew(bin, nbin[XX]);
for (i = 0; i < nbin[XX]; ++i)
{
- bin[i] = (long **)malloc(nbin[YY]*sizeof(long *));
- if (!bin[i])
- {
- mequit();
- }
+ snew(bin[i], nbin[YY]);
for (j = 0; j < nbin[YY]; ++j)
{
- bin[i][j] = (long *)calloc(nbin[ZZ], sizeof(long));
- if (!bin[i][j])
- {
- mequit();
- }
+ snew(bin[i][j], nbin[ZZ]);
}
}
copy_mat(box, box_pbc);
}
/* OUTPUT */
- flp = ffopen("grid.cube", "w");
+ flp = gmx_ffopen("grid.cube", "w");
fprintf(flp, "Spatial Distribution Function\n");
fprintf(flp, "test\n");
fprintf(flp, "%5d%12.6f%12.6f%12.6f\n", nidxp, (MINBIN[XX]+(minx+iIGNOREOUTER)*rBINWIDTH)*10./bohr, (MINBIN[YY]+(miny+iIGNOREOUTER)*rBINWIDTH)*10./bohr, (MINBIN[ZZ]+(minz+iIGNOREOUTER)*rBINWIDTH)*10./bohr);
}
fprintf(flp, "\n");
}
- ffclose(flp);
+ gmx_ffclose(flp);
/* printf("x=%d to %d\n",minx,maxx); */
/* printf("y=%d to %d\n",miny,maxy); */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff