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Merge branch 'master' into pygromacs
[alexxy/gromacs.git]
/
src
/
gromacs
/
gmxana
/
gmx_traj.cpp
diff --git
a/src/gromacs/gmxana/gmx_traj.c
b/src/gromacs/gmxana/gmx_traj.cpp
similarity index 98%
rename from
src/gromacs/gmxana/gmx_traj.c
rename to
src/gromacs/gmxana/gmx_traj.cpp
index 7560cec153d82974784b366b5e4c442401493380..3cb4ead8184e090cf246189271f36e5a62ad9e57 100644
(file)
--- a/
src/gromacs/gmxana/gmx_traj.c
+++ b/
src/gromacs/gmxana/gmx_traj.cpp
@@
-36,9
+36,11
@@
*/
#include "gmxpre.h"
*/
#include "gmxpre.h"
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
+
+#include <algorithm>
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
#include "gromacs/commandline/pargs.h"
#include "gromacs/fileio/confio.h"
@@
-424,7
+426,6
@@
static void write_pdb_bfac(const char *fname, const char *xname,
real max, len2, scale;
atom_id maxi;
int i, m, onedim;
real max, len2, scale;
atom_id maxi;
int i, m, onedim;
- gmx_bool bOne;
if ((nfr_x == 0) || (nfr_v == 0))
{
if ((nfr_x == 0) || (nfr_v == 0))
{
@@
-495,12
+496,12
@@
static void write_pdb_bfac(const char *fname, const char *xname,
}
else
{
}
else
{
- scale = 10.0/sqrt(max);
+ scale = 10.0/s
td::s
qrt(max);
}
}
printf("Maximum %s is %g on atom %d %s, res. %s %d\n",
}
}
printf("Maximum %s is %g on atom %d %s, res. %s %d\n",
- title, sqrt(max), maxi+1, *(atoms->atomname[maxi]),
+ title, s
td::s
qrt(max), maxi+1, *(atoms->atomname[maxi]),
*(atoms->resinfo[atoms->atom[maxi].resind].name),
atoms->resinfo[atoms->atom[maxi].resind].nr);
*(atoms->resinfo[atoms->atom[maxi].resind].name),
atoms->resinfo[atoms->atom[maxi].resind].nr);
@@
-520,7
+521,7
@@
static void write_pdb_bfac(const char *fname, const char *xname,
len2 += sqr(sum[index[i]][m]);
}
}
len2 += sqr(sum[index[i]][m]);
}
}
- atoms->pdbinfo[index[i]].bfac = sqrt(len2)*scale;
+ atoms->pdbinfo[index[i]].bfac = s
td::s
qrt(len2)*scale;
}
}
else
}
}
else
@@
-546,16
+547,16
@@
static void update_histo(int gnx, atom_id index[], rvec v[],
for (i = 0; (i < gnx); i++)
{
vn = norm(v[index[i]]);
for (i = 0; (i < gnx); i++)
{
vn = norm(v[index[i]]);
- vnmax = max(vn, vnmax);
+ vnmax =
std::
max(vn, vnmax);
}
vnmax *= 2;
}
vnmax *= 2;
- *nhisto =
1+(vnmax/binwidth
);
+ *nhisto =
static_cast<int>(1+(vnmax/binwidth)
);
snew(*histo, *nhisto);
}
for (i = 0; (i < gnx); i++)
{
vn = norm(v[index[i]]);
snew(*histo, *nhisto);
}
for (i = 0; (i < gnx); i++)
{
vn = norm(v[index[i]]);
- in =
vn/binwidth
;
+ in =
static_cast<int>(vn/binwidth)
;
if (in >= *nhisto)
{
nnn = in+100;
if (in >= *nhisto)
{
nnn = in+100;
@@
-667,7
+668,7
@@
int gmx_traj(int argc, char *argv[])
t_trxstatus *status;
t_trxstatus *status_out = NULL;
gmx_rmpbc_t gpbc = NULL;
t_trxstatus *status;
t_trxstatus *status_out = NULL;
gmx_rmpbc_t gpbc = NULL;
- int i, j
, n
;
+ int i, j;
int nr_xfr, nr_vfr, nr_ffr;
char **grpname;
int *isize0, *isize;
int nr_xfr, nr_vfr, nr_ffr;
char **grpname;
int *isize0, *isize;
@@
-676,7
+677,7
@@
int gmx_traj(int argc, char *argv[])
t_block *mols;
gmx_bool bTop, bOX, bOXT, bOV, bOF, bOB, bOT, bEKT, bEKR, bCV, bCF;
gmx_bool bDim[4], bDum[4], bVD;
t_block *mols;
gmx_bool bTop, bOX, bOXT, bOV, bOF, bOB, bOT, bEKT, bEKR, bCV, bCF;
gmx_bool bDim[4], bDum[4], bVD;
- char
*sffmt, sffmt6[1024
];
+ char
sffmt[STRLEN], sffmt6[STRLEN
];
const char *box_leg[6] = { "XX", "YY", "ZZ", "YX", "ZX", "ZY" };
output_env_t oenv;
const char *box_leg[6] = { "XX", "YY", "ZZ", "YX", "ZX", "ZY" };
output_env_t oenv;
@@
-736,11
+737,11
@@
int gmx_traj(int argc, char *argv[])
if (bFP)
{
if (bFP)
{
- s
ffmt = "\t" gmx_real_fullprecision_pfmt
;
+ s
printf(sffmt, "\t%s", gmx_real_fullprecision_pfmt)
;
}
else
{
}
else
{
- s
ffmt = "\t%g"
;
+ s
printf(sffmt, "\t%%g")
;
}
sprintf(sffmt6, "%s%s%s%s%s%s", sffmt, sffmt, sffmt, sffmt, sffmt, sffmt);
}
sprintf(sffmt6, "%s%s%s%s%s%s", sffmt, sffmt, sffmt, sffmt, sffmt, sffmt);