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_nmens.cpp
diff --git
a/src/gromacs/gmxana/gmx_nmens.c
b/src/gromacs/gmxana/gmx_nmens.cpp
similarity index 93%
rename from
src/gromacs/gmxana/gmx_nmens.c
rename to
src/gromacs/gmxana/gmx_nmens.cpp
index 4028f46b455d8e4995fb8c9a56c3cca099d8eeb3..b53f3b0d602d44ecfdc9765187efc2a90f563465 100644
(file)
--- a/
src/gromacs/gmxana/gmx_nmens.c
+++ b/
src/gromacs/gmxana/gmx_nmens.cpp
@@
-36,8
+36,8
@@
*/
#include "gmxpre.h"
*/
#include "gmxpre.h"
-#include <
math.
h>
-#include <
string.h
>
+#include <
cmat
h>
+#include <
cstring
>
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
@@
-86,7
+86,6
@@
int gmx_nmens(int argc, char *argv[])
#define NPA asize(pa)
t_trxstatus *out;
#define NPA asize(pa)
t_trxstatus *out;
- int status, trjout;
t_topology top;
int ePBC;
t_atoms *atoms;
t_topology top;
int ePBC;
t_atoms *atoms;
@@
-95,18
+94,17
@@
int gmx_nmens(int argc, char *argv[])
int nvec, *eignr = NULL;
rvec **eigvec = NULL;
matrix box;
int nvec, *eignr = NULL;
rvec **eigvec = NULL;
matrix box;
- real *eigval,
totmass,
*invsqrtm, t, disp;
- int natoms
, neigval
;
+ real *eigval, *invsqrtm, t, disp;
+ int natoms;
char *grpname, title[STRLEN];
const char *indexfile;
int i, j, d, s, v;
int nout, *iout, noutvec, *outvec;
atom_id *index;
char *grpname, title[STRLEN];
const char *indexfile;
int i, j, d, s, v;
int nout, *iout, noutvec, *outvec;
atom_id *index;
- real rfac, invfr, rhalf, jr;
- int * eigvalnr;
+ real rfac, rhalf, jr;
output_env_t oenv;
gmx_rng_t rng;
output_env_t oenv;
gmx_rng_t rng;
-
unsigned long
jran;
+
int
jran;
const unsigned long im = 0xffff;
const unsigned long ia = 1093;
const unsigned long ic = 18257;
const unsigned long im = 0xffff;
const unsigned long ia = 1093;
const unsigned long ic = 18257;
@@
-215,7
+213,7
@@
int gmx_nmens(int argc, char *argv[])
if (seed == -1)
{
if (seed == -1)
{
- seed =
(int)gmx_rng_make_seed(
);
+ seed =
static_cast<int>(gmx_rng_make_seed()
);
rng = gmx_rng_init(seed);
}
else
rng = gmx_rng_init(seed);
}
else
@@
-227,7
+225,7
@@
int gmx_nmens(int argc, char *argv[])
snew(xout1, natoms);
snew(xout2, atoms->nr);
out = open_trx(ftp2fn(efTRO, NFILE, fnm), "w");
snew(xout1, natoms);
snew(xout2, atoms->nr);
out = open_trx(ftp2fn(efTRO, NFILE, fnm), "w");
- jran =
(unsigned long)((real)
im*gmx_rng_uniform_real(rng));
+ jran =
static_cast<int>(
im*gmx_rng_uniform_real(rng));
gmx_rng_destroy(rng);
for (s = 0; s < nstruct; s++)
{
gmx_rng_destroy(rng);
for (s = 0; s < nstruct; s++)
{
@@
-241,18
+239,18
@@
int gmx_nmens(int argc, char *argv[])
/* (r-0.5) n times: var_n = n * var_1 = n/12
n=4: var_n = 1/3, so multiply with 3 */
/* (r-0.5) n times: var_n = n * var_1 = n/12
n=4: var_n = 1/3, so multiply with 3 */
- rfac = sqrt(3.0 * BOLTZ*temp/eigval[iout[j]]);
+ rfac = s
td::s
qrt(3.0 * BOLTZ*temp/eigval[iout[j]]);
rhalf = 2.0*rfac;
rhalf = 2.0*rfac;
- rfac = rfac/
(real)
im;
+ rfac = rfac/im;
jran = (jran*ia+ic) & im;
jran = (jran*ia+ic) & im;
- jr =
(real)
jran;
+ jr = jran;
jran = (jran*ia+ic) & im;
jran = (jran*ia+ic) & im;
- jr +=
(real)
jran;
+ jr += jran;
jran = (jran*ia+ic) & im;
jran = (jran*ia+ic) & im;
- jr +=
(real)
jran;
+ jr += jran;
jran = (jran*ia+ic) & im;
jran = (jran*ia+ic) & im;
- jr +=
(real)
jran;
+ jr += jran;
disp = rfac * jr - rhalf;
for (i = 0; i < natoms; i++)
disp = rfac * jr - rhalf;
for (i = 0; i < natoms; i++)