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Merge branch 'master' into pygromacs
[alexxy/gromacs.git]
/
src
/
gromacs
/
gmxana
/
gmx_vanhove.cpp
diff --git
a/src/gromacs/gmxana/gmx_vanhove.c
b/src/gromacs/gmxana/gmx_vanhove.cpp
similarity index 93%
rename from
src/gromacs/gmxana/gmx_vanhove.c
rename to
src/gromacs/gmxana/gmx_vanhove.cpp
index 8d046f4b6afa12190776315795c3abc443b5018a..340491acaeda9ae17f2d40c8593be426f3370010 100644
(file)
--- a/
src/gromacs/gmxana/gmx_vanhove.c
+++ b/
src/gromacs/gmxana/gmx_vanhove.cpp
@@
-36,10
+36,9
@@
*/
#include "gmxpre.h"
*/
#include "gmxpre.h"
-#include <assert.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
@@
-56,6
+55,7
@@
#include "gromacs/topology/index.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/futil.h"
#include "gromacs/topology/index.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/futil.h"
+#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/smalloc.h"
@@
-135,7
+135,7
@@
int gmx_vanhove(int argc, char *argv[])
int ePBC;
matrix boxtop, box, *sbox, avbox, corr;
rvec *xtop, *x, **sx;
int ePBC;
matrix boxtop, box, *sbox, avbox, corr;
rvec *xtop, *x, **sx;
- int isize, nalloc, nallocn
, natom
;
+ int isize, nalloc, nallocn;
t_trxstatus *status;
atom_id *index;
char *grpname;
t_trxstatus *status;
atom_id *index;
char *grpname;
@@
-189,7
+189,7
@@
int gmx_vanhove(int argc, char *argv[])
sx = NULL;
clear_mat(avbox);
sx = NULL;
clear_mat(avbox);
-
natom =
read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
+ read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
nfr = 0;
do
{
nfr = 0;
do
{
@@
-200,7
+200,8
@@
int gmx_vanhove(int argc, char *argv[])
srenew(sbox, nalloc);
srenew(sx, nalloc);
}
srenew(sbox, nalloc);
srenew(sx, nalloc);
}
- assert(time != NULL); assert(sbox != NULL);
+ GMX_RELEASE_ASSERT(time != NULL, "Memory allocation failure; time array is NULL");
+ GMX_RELEASE_ASSERT(sbox != NULL, "Memory allocation failure; sbox array is NULL");
time[nfr] = t;
copy_mat(box, sbox[nfr]);
time[nfr] = t;
copy_mat(box, sbox[nfr]);
@@
-226,7
+227,7
@@
int gmx_vanhove(int argc, char *argv[])
dt = (time[nfr-1] - time[0])/(nfr - 1);
/* Some ugly rounding to get nice nice times in the output */
dt = (time[nfr-1] - time[0])/(nfr - 1);
/* Some ugly rounding to get nice nice times in the output */
- dt =
(int)(10000.0*dt + 0.5)/10000.0
;
+ dt =
static_cast<int>((10000.0*dt + 0.5)/10000.0)
;
invbin = 1.0/rbin;
invbin = 1.0/rbin;
@@
-237,7
+238,7
@@
int gmx_vanhove(int argc, char *argv[])
fmmax = nfr - 1;
}
snew(mcount, fmmax);
fmmax = nfr - 1;
}
snew(mcount, fmmax);
- nbin =
(int)
(rmax*invbin + 0.5);
+ nbin =
static_cast<int>
(rmax*invbin + 0.5);
if (sbin == 0)
{
mat_nx = fmmax + 1;
if (sbin == 0)
{
mat_nx = fmmax + 1;
@@
-245,7
+246,7
@@
int gmx_vanhove(int argc, char *argv[])
else
{
invsbin = 1.0/sbin;
else
{
invsbin = 1.0/sbin;
- mat_nx = s
qrt(fmmax*dt)*invsbin + 1
;
+ mat_nx = s
tatic_cast<int>(std::sqrt(fmmax*dt)*invsbin + 1)
;
}
snew(mat, mat_nx);
for (f = 0; f < mat_nx; f++)
}
snew(mat, mat_nx);
for (f = 0; f < mat_nx; f++)
@@
-327,14
+328,14
@@
int gmx_vanhove(int argc, char *argv[])
}
else
{
}
else
{
- mbin =
(int)(
sqrt(fbin*dt)*invsbin + 0.5);
+ mbin =
static_cast<int>(std::
sqrt(fbin*dt)*invsbin + 0.5);
}
for (i = 0; i < isize; i++)
{
d2 = distance2(sx[f][i], sx[ff][i]);
if (mbin < mat_nx && d2 < rmax2)
{
}
for (i = 0; i < isize; i++)
{
d2 = distance2(sx[f][i], sx[ff][i]);
if (mbin < mat_nx && d2 < rmax2)
{
- bin =
(int)(
sqrt(d2)*invbin + 0.5);
+ bin =
static_cast<int>(std::
sqrt(d2)*invbin + 0.5);
if (bin < nbin)
{
mat[mbin][bin] += 1;
if (bin < nbin)
{
mat[mbin][bin] += 1;
@@
-365,7
+366,7
@@
int gmx_vanhove(int argc, char *argv[])
for (i = 0; i < isize; i++)
{
d2 = distance2(sx[f][i], sx[ff][i]);
for (i = 0; i < isize; i++)
{
d2 = distance2(sx[f][i], sx[ff][i]);
- bin =
(int)(
sqrt(d2)*invbin + 0.5);
+ bin =
static_cast<int>(std::
sqrt(d2)*invbin + 0.5);
if (bin >= nalloc)
{
nallocn = 10*(bin/10) + 11;
if (bin >= nalloc)
{
nallocn = 10*(bin/10) + 11;
@@
-452,8
+453,7
@@
int gmx_vanhove(int argc, char *argv[])
fprintf(fp, "%g", i*rbin);
for (fbin = 0; fbin < nr; fbin++)
{
fprintf(fp, "%g", i*rbin);
for (fbin = 0; fbin < nr; fbin++)
{
- fprintf(fp, " %g",
- (real)pr[fbin][i]/(rcount[fbin]*isize*rbin*(i == 0 ? 0.5 : 1)));
+ fprintf(fp, " %g", static_cast<real>(pr[fbin][i])/(rcount[fbin]*isize*rbin*(i == 0 ? 0.5 : 1.0)));
}
fprintf(fp, "\n");
}
}
fprintf(fp, "\n");
}
@@
-470,7
+470,7
@@
int gmx_vanhove(int argc, char *argv[])
}
for (f = 0; f <= ftmax; f++)
{
}
for (f = 0; f <= ftmax; f++)
{
- fprintf(fp, "%g %g\n", f*dt,
(real)pt[f]
/(tcount[f]*isize));
+ fprintf(fp, "%g %g\n", f*dt,
static_cast<real>(pt[f])
/(tcount[f]*isize));
}
xvgrclose(fp);
}
}
xvgrclose(fp);
}