/*
+ * 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
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*
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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
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*
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- * Gyas ROwers Mature At Cryogenic Speed
+ * To help us fund GROMACS development, we humbly ask that you cite
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*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
-
-
-#include "statutil.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "vec.h"
-#include "copyrite.h"
-#include "statutil.h"
-#include "tpxio.h"
#include <math.h>
-#include "index.h"
-#include "pbc.h"
-#include "rmpbc.h"
-#include "gmx_ana.h"
-#include "macros.h"
-
+#include <stdlib.h>
+
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/smalloc.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[] = {
- "[TT]g_spatial[tt] calculates the spatial distribution function and ",
+ "[THISMODULE] calculates the spatial distribution function and ",
"outputs it in a form that can be read by VMD as Gaussian98 cube format. ",
- "This was developed from template.c (GROMACS-3.3). ",
"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 ",
"of solvent and look at the time-averaged solvation shell. ",
"It is also possible using this program to generate the SDF based on some arbitrary ",
- "Cartesian coordinate. To do that, simply omit the preliminary [TT]trjconv[tt] steps. \n",
+ "Cartesian coordinate. To do that, simply omit the preliminary [gmx-trjconv] steps. \n",
"USAGE: \n",
- "1. Use [TT]make_ndx[tt] to create a group containing the atoms around which you want the SDF \n",
- "2. [TT]trjconv -s a.tpr -f a.xtc -o b.xtc -center tric -ur compact -pbc none[tt] \n",
- "3. [TT]trjconv -s a.tpr -f b.xtc -o c.xtc -fit rot+trans[tt] \n",
- "4. run [TT]g_spatial[tt] on the [TT].xtc[tt] output of step #3. \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.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]trjconv -pbc cluster[tt] between steps 1 and 2\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]",
"The SDF will be generated for a cube that contains all bins that have some non-zero occupancy. ",
- "However, the preparatory [TT]-fit rot+trans[tt] option to [TT]trjconv[tt] implies that your system will be rotating ",
+ "However, the preparatory [TT]-fit rot+trans[tt] option to [gmx-trjconv] implies that your system will be rotating ",
"and translating in space (in order that the selected group does not). Therefore the values that are ",
"returned will only be valid for some region around your central group/coordinate that has full overlap ",
"with system volume throughout the entire translated/rotated system over the course of the trajectory. ",
"with an increased [TT]-nab[tt] value. \n",
"RISKY OPTIONS:[BR]",
"To reduce the amount of space and time required, you can output only the coords ",
- "that are going to be used in the first and subsequent run through [TT]trjconv[tt]. ",
+ "that are going to be used in the first and subsequent run through [gmx-trjconv]. ",
"However, be sure to set the [TT]-nab[tt] option to a sufficiently high value since ",
"memory is allocated for cube bins based on the initial coordinates and the [TT]-nab[tt] ",
"option value. \n"
/* This is the routine responsible for adding default options,
* calling the X/motif interface, etc. */
- parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
+ 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;
+ }
read_tps_conf(ftp2fn(efTPS, NFILE, fnm), title, &top, &ePBC, &xtop, NULL, box, TRUE);
sfree(xtop);
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);
if (bPBC)
{
- gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms, box);
+ gpbc = gmx_rmpbc_init(&top.idef, ePBC, natoms);
}
/* This is the main loop over frames */
do
}
/* 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); */
printf("Raw data: average %le, min %le, max %le\n", 1.0/norm, (double)min/(double)numfr, (double)max/(double)numfr);
}
- thanx(stderr);
-
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff