/*
+ * This file is part of the GROMACS molecular simulation package.
*
- * This source code is part of
+ * Copyright (c) 2007,2008,2009,2010,2011,2012,2013,2014,2015, 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
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+ * as published by the Free Software Foundation; either version 2.1
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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 "statutil.h"
-#include "typedefs.h"
-#include "smalloc.h"
-#include "vec.h"
-#include "statutil.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.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/confio.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/cstringutil.h"
+#include "gromacs/utility/futil.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 ",
- "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). ",
- "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",
- "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 -boxcenter 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",
- "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",
- "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 ",
- "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. ",
- "It is up to the user to ensure that this is the case. \n",
- "BUGS:[BR]",
- "When the allocated memory is not large enough, a segmentation fault may occur. This is usually detected ",
- "and the program is halted prior to the fault while displaying a warning message suggesting the use of the [TT]-nab[tt] (Number of Additional Bins)",
- "option. However, the program does not detect all such events. If you encounter a segmentation fault, run it again ",
- "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]. ",
- "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"
+ "[THISMODULE] calculates the spatial distribution function and",
+ "outputs it in a form that can be read by VMD as Gaussian98 cube format.",
+ "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 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 [gmx-trjconv] steps.",
+ "",
+ "Usage:",
+ "",
+ "1. Use [gmx-make_ndx] to create a group containing the atoms around which you want the SDF",
+ "2. [TT]gmx trjconv -s a.tpr -f a.tng -o b.tng -boxcenter tric -ur compact -pbc none[tt]",
+ "3. [TT]gmx trjconv -s a.tpr -f b.tng -o c.tng -fit rot+trans[tt]",
+ "4. run [THISMODULE] on the [TT]c.tng[tt] output of step #3.",
+ "5. Load [TT]grid.cube[tt] into VMD and view as an isosurface.",
+ "",
+ "[BB]Note[bb] that systems such as micelles will require [TT]gmx trjconv -pbc cluster[tt] between steps 1 and 2.",
+ "",
+ "Warnings",
+ "^^^^^^^^",
+ "",
+ "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 [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.",
+ "It is up to the user to ensure that this is the case.",
+ "",
+ "Risky options",
+ "^^^^^^^^^^^^^",
+ "",
+ "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 [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."
+ };
+ const char *bugs[] = {
+ "When the allocated memory is not large enough, a segmentation fault may occur. This is usually detected "
+ "and the program is halted prior to the fault while displaying a warning message suggesting the use of the [TT]-nab[tt] (Number of Additional Bins) "
+ "option. However, the program does not detect all such events. If you encounter a segmentation fault, run it again "
+ "with an increased [TT]-nab[tt] value."
};
static gmx_bool bPBC = FALSE;
/* This is the routine responsible for adding default options,
* calling the X/motif interface, etc. */
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
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