*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 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.
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
#include <ctype.h>
#include <math.h>
#include <stdlib.h>
#include <string.h>
-#include "gromacs/utility/cstringutil.h"
-#include "typedefs.h"
-#include "macros.h"
-#include "gstat.h"
-#include "viewit.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
-#include "gromacs/math/units.h"
-#include "gmx_ana.h"
-#include "macros.h"
-
#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/trxio.h"
#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
+#include "gromacs/math/units.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/fatalerror.h"
#include "gromacs/utility/futil.h"
#include "gromacs/utility/smalloc.h"
gmx_fatal(FARGS, "Invalid line in datafile at line %d\n", i+1);
}
(*eltab)[i].nr_el = tempnr;
- (*eltab)[i].atomname = strdup(tempname);
+ (*eltab)[i].atomname = gmx_strdup(tempname);
}
gmx_ffclose(in);
com[m] /= tmass;
}
calc_box_center(ecenterDEF, box, box_center);
- rvec_sub(box_center, com, shift);
+ rvec_sub(com, box_center, shift);
/* Important - while the center was calculated based on a group, we should move all atoms */
for (i = 0; (i < atoms->nr); i++)
slice = (z / (*slWidth));
}
sought.nr_el = 0;
- sought.atomname = strdup(*(top->atoms.atomname[index[n][i]]));
+ sought.atomname = gmx_strdup(*(top->atoms.atomname[index[n][i]]));
/* now find the number of electrons. This is not efficient. */
found = (t_electron *)
fprintf(den, "\n");
}
- gmx_ffclose(den);
+ xvgrclose(den);
}
int gmx_density(int argc, char *argv[])
"of an arbitrary group, in absolute box coordinates. If you are calculating",
"profiles along the Z axis box dimension bZ, output would be from -bZ/2 to",
"bZ/2 if you center based on the entire system.",
- "Note that this behaviour has changed in Gromacs 5.0; earlier versions",
+ "Note that this behaviour has changed in GROMACS 5.0; earlier versions",
"merely performed a static binning in (0,bZ) and shifted the output. Now",
"we compute the center for each frame and bin in (-bZ/2,bZ/2).[PAR]",
"Densities are in kg/m^3, and number densities or electron densities can also be",
"calculated. For electron densities, a file describing the number of",
"electrons for each type of atom should be provided using [TT]-ei[tt].",
- "It should look like:[BR]",
- " [TT]2[tt][BR]",
- " [TT]atomname = nrelectrons[tt][BR]",
- " [TT]atomname = nrelectrons[tt][BR]",
+ "It should look like::",
+ "",
+ " 2",
+ " atomname = nrelectrons",
+ " atomname = nrelectrons",
+ "",
"The first line contains the number of lines to read from the file.",
"There should be one line for each unique atom name in your system.",
"The number of electrons for each atom is modified by its atomic",
"The first problem that while both proteins and lipids have low volume",
"compressibility, lipids have quite high area compressiblity. This means the",
"shape of the box (thickness and area/lipid) will fluctuate substantially even",
- "for a fully relaxed system. Since Gromacs places the box between the origin",
+ "for a fully relaxed system. Since GROMACS places the box between the origin",
"and positive coordinates, this in turn means that a bilayer centered in the",
"box will move a bit up/down due to these fluctuations, and smear out your",
"profile. The easiest way to fix this (if you want pressure coupling) is",
t_filenm fnm[] = { /* files for g_density */
{ efTRX, "-f", NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
- { efTPX, NULL, NULL, ffREAD },
+ { efTPR, NULL, NULL, ffREAD },
{ efDAT, "-ei", "electrons", ffOPTRD }, /* file with nr. of electrons */
{ efXVG, "-o", "density", ffWRITE },
};
#define NFILE asize(fnm)
- 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, asize(bugs), bugs,
&oenv))
{
/* Calculate axis */
axis = toupper(axtitle[0]) - 'X';
- top = read_top(ftp2fn(efTPX, NFILE, fnm), &ePBC); /* read topology file */
+ top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC); /* read topology file */
if (dens_opt[0][0] == 'n')
{
for (i = 0; (i < top->atoms.nr); i++)
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff