biod.pnpi.spb.ru
/
alexxy
/
gromacs.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge branch 'master' into pygromacs
[alexxy/gromacs.git]
/
src
/
gromacs
/
gmxana
/
gmx_potential.cpp
diff --git
a/src/gromacs/gmxana/gmx_potential.c
b/src/gromacs/gmxana/gmx_potential.cpp
similarity index 95%
rename from
src/gromacs/gmxana/gmx_potential.c
rename to
src/gromacs/gmxana/gmx_potential.cpp
index fb56240c3adee3119754814f5d9d2da34f635758..e07a38eda3cd999e68a7b9ad64272e6f6146a765 100644
(file)
--- a/
src/gromacs/gmxana/gmx_potential.c
+++ b/
src/gromacs/gmxana/gmx_potential.cpp
@@
-36,9
+36,9
@@
*/
#include "gmxpre.h"
*/
#include "gmxpre.h"
-#include <c
type.h
>
-#include <
math.
h>
-#include <
string.h
>
+#include <c
ctype
>
+#include <
cmat
h>
+#include <
cstring
>
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/trxio.h"
@@
-106,12
+106,11
@@
void calc_potential(const char *fn, atom_id **index, int gnx[],
double fudge_z, gmx_bool bSpherical, gmx_bool bCorrect,
const output_env_t oenv)
{
double fudge_z, gmx_bool bSpherical, gmx_bool bCorrect,
const output_env_t oenv)
{
- rvec *x0;
/* coordinates without pbc */
- matrix box;
/* box (3x3) */
- int natoms;
/* nr. atoms in trj */
+ rvec *x0; /* coordinates without pbc */
+ matrix box; /* box (3x3) */
+ int natoms; /* nr. atoms in trj */
t_trxstatus *status;
t_trxstatus *status;
- int **slCount, /* nr. of atoms in one slice for a group */
- i, j, n, /* loop indices */
+ int i, n, /* loop indices */
teller = 0,
ax1 = 0, ax2 = 0,
nr_frames = 0, /* number of frames */
teller = 0,
ax1 = 0, ax2 = 0,
nr_frames = 0, /* number of frames */
@@
-145,7
+144,7
@@
void calc_potential(const char *fn, atom_id **index, int gnx[],
if (!*nslices)
{
if (!*nslices)
{
- *nslices =
(int)(box[axis][axis] * 1
0); /* default value */
+ *nslices =
static_cast<int>(box[axis][axis] * 10.
0); /* default value */
}
fprintf(stderr, "\nDividing the box in %d slices\n", *nslices);
}
fprintf(stderr, "\nDividing the box in %d slices\n", *nslices);
@@
-190,7
+189,7
@@
void calc_potential(const char *fn, atom_id **index, int gnx[],
{
rvec_add(x0[index[n][i]], xcm, x0[index[n][i]]);
/* only distance from origin counts, not sign */
{
rvec_add(x0[index[n][i]], xcm, x0[index[n][i]]);
/* only distance from origin counts, not sign */
- slice =
norm(x0[index[n][i]])/(*slWidth
);
+ slice =
static_cast<int>(norm(x0[index[n][i]])/(*slWidth)
);
/* this is a nice check for spherical groups but not for
all water in a cubic box since a lot will fall outside
/* this is a nice check for spherical groups but not for
all water in a cubic box since a lot will fall outside
@@
-215,7
+214,7
@@
void calc_potential(const char *fn, atom_id **index, int gnx[],
z -= box[axis][axis];
}
/* determine which slice atom is in */
z -= box[axis][axis];
}
/* determine which slice atom is in */
- slice =
(z / (*slWidth
));
+ slice =
static_cast<int>((z / (*slWidth)
));
(*slCharge)[n][slice] += top->atoms.atom[index[n][i]].q;
}
}
(*slCharge)[n][slice] += top->atoms.atom[index[n][i]].q;
}
}
@@
-282,7
+281,7
@@
void calc_potential(const char *fn, atom_id **index, int gnx[],
qsum = 0;
for (i = 0; i < *nslices; i++)
{
qsum = 0;
for (i = 0; i < *nslices; i++)
{
- if (
f
abs((*slCharge)[n][i]) >= GMX_DOUBLE_MIN)
+ if (
std::
abs((*slCharge)[n][i]) >= GMX_DOUBLE_MIN)
{
nn++;
qsum += (*slCharge)[n][i];
{
nn++;
qsum += (*slCharge)[n][i];
@@
-291,7
+290,7
@@
void calc_potential(const char *fn, atom_id **index, int gnx[],
qsum /= nn;
for (i = 0; i < *nslices; i++)
{
qsum /= nn;
for (i = 0; i < *nslices; i++)
{
- if (
f
abs((*slCharge)[n][i]) >= GMX_DOUBLE_MIN)
+ if (
std::
abs((*slCharge)[n][i]) >= GMX_DOUBLE_MIN)
{
(*slCharge)[n][i] -= qsum;
}
{
(*slCharge)[n][i] -= qsum;
}
@@
-314,7
+313,7
@@
void calc_potential(const char *fn, atom_id **index, int gnx[],
qsum = 0;
for (i = 0; i < *nslices; i++)
{
qsum = 0;
for (i = 0; i < *nslices; i++)
{
- if (
f
abs((*slCharge)[n][i]) >= GMX_DOUBLE_MIN)
+ if (
std::
abs((*slCharge)[n][i]) >= GMX_DOUBLE_MIN)
{
nn++;
qsum += (*slField)[n][i];
{
nn++;
qsum += (*slField)[n][i];
@@
-323,7
+322,7
@@
void calc_potential(const char *fn, atom_id **index, int gnx[],
qsum /= nn;
for (i = 0; i < *nslices; i++)
{
qsum /= nn;
for (i = 0; i < *nslices; i++)
{
- if (
f
abs((*slCharge)[n][i]) >= GMX_DOUBLE_MIN)
+ if (
std::
abs((*slCharge)[n][i]) >= GMX_DOUBLE_MIN)
{
(*slField)[n][i] -= qsum;
}
{
(*slField)[n][i] -= qsum;
}