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Merge branch 'master' into pygromacs
[alexxy/gromacs.git]
/
src
/
gromacs
/
gmxlib
/
checkpoint.cpp
diff --git
a/src/gromacs/gmxlib/checkpoint.cpp
b/src/gromacs/gmxlib/checkpoint.cpp
index e38563f9c95446411ec6ea473492da16111252ca..4f3634d5f7f4771116c818bec7e8e3c50b19f4bd 100644
(file)
--- a/
src/gromacs/gmxlib/checkpoint.cpp
+++ b/
src/gromacs/gmxlib/checkpoint.cpp
@@
-41,9
+41,9
@@
#include "config.h"
#include "config.h"
-#include <
errno.h
>
-#include <
stdlib.h
>
-#include <
string.h
>
+#include <
cerrno
>
+#include <
cstdlib
>
+#include <
cstring
>
#include <fcntl.h>
#ifdef GMX_NATIVE_WINDOWS
#include <fcntl.h>
#ifdef GMX_NATIVE_WINDOWS
@@
-189,14
+189,11
@@
static void cp_error()
static void do_cpt_string_err(XDR *xd, gmx_bool bRead, const char *desc, char **s, FILE *list)
{
static void do_cpt_string_err(XDR *xd, gmx_bool bRead, const char *desc, char **s, FILE *list)
{
- bool_t res = 0;
-
if (bRead)
{
snew(*s, CPTSTRLEN);
}
if (bRead)
{
snew(*s, CPTSTRLEN);
}
- res = xdr_string(xd, s, CPTSTRLEN);
- if (res == 0)
+ if (xdr_string(xd, s, CPTSTRLEN) == 0)
{
cp_error();
}
{
cp_error();
}
@@
-209,10
+206,7
@@
static void do_cpt_string_err(XDR *xd, gmx_bool bRead, const char *desc, char **
static int do_cpt_int(XDR *xd, const char *desc, int *i, FILE *list)
{
static int do_cpt_int(XDR *xd, const char *desc, int *i, FILE *list)
{
- bool_t res = 0;
-
- res = xdr_int(xd, i);
- if (res == 0)
+ if (xdr_int(xd, i) == 0)
{
return -1;
}
{
return -1;
}
@@
-225,13
+219,12
@@
static int do_cpt_int(XDR *xd, const char *desc, int *i, FILE *list)
static int do_cpt_u_chars(XDR *xd, const char *desc, int n, unsigned char *i, FILE *list)
{
static int do_cpt_u_chars(XDR *xd, const char *desc, int n, unsigned char *i, FILE *list)
{
- bool_t res = 1;
- int j;
if (list)
{
fprintf(list, "%s = ", desc);
}
if (list)
{
fprintf(list, "%s = ", desc);
}
- for (j = 0; j < n && res; j++)
+ bool_t res = 1;
+ for (int j = 0; j < n && res; j++)
{
res &= xdr_u_char(xd, &i[j]);
if (list)
{
res &= xdr_u_char(xd, &i[j]);
if (list)
@@
-261,11
+254,9
@@
static void do_cpt_int_err(XDR *xd, const char *desc, int *i, FILE *list)
static void do_cpt_step_err(XDR *xd, const char *desc, gmx_int64_t *i, FILE *list)
{
static void do_cpt_step_err(XDR *xd, const char *desc, gmx_int64_t *i, FILE *list)
{
- bool_t res = 0;
char buf[STEPSTRSIZE];
char buf[STEPSTRSIZE];
- res = xdr_int64(xd, i);
- if (res == 0)
+ if (xdr_int64(xd, i) == 0)
{
cp_error();
}
{
cp_error();
}
@@
-277,10
+268,7
@@
static void do_cpt_step_err(XDR *xd, const char *desc, gmx_int64_t *i, FILE *lis
static void do_cpt_double_err(XDR *xd, const char *desc, double *f, FILE *list)
{
static void do_cpt_double_err(XDR *xd, const char *desc, double *f, FILE *list)
{
- bool_t res = 0;
-
- res = xdr_double(xd, f);
- if (res == 0)
+ if (xdr_double(xd, f) == 0)
{
cp_error();
}
{
cp_error();
}
@@
-292,12
+280,10
@@
static void do_cpt_double_err(XDR *xd, const char *desc, double *f, FILE *list)
static void do_cpt_real_err(XDR *xd, real *f)
{
static void do_cpt_real_err(XDR *xd, real *f)
{
- bool_t res = 0;
-
#ifdef GMX_DOUBLE
#ifdef GMX_DOUBLE
- res = xdr_double(xd, f);
+
bool_t
res = xdr_double(xd, f);
#else
#else
- res = xdr_float(xd, f);
+
bool_t
res = xdr_float(xd, f);
#endif
if (res == 0)
{
#endif
if (res == 0)
{
@@
-307,11
+293,9
@@
static void do_cpt_real_err(XDR *xd, real *f)
static void do_cpt_n_rvecs_err(XDR *xd, const char *desc, int n, rvec f[], FILE *list)
{
static void do_cpt_n_rvecs_err(XDR *xd, const char *desc, int n, rvec f[], FILE *list)
{
- int i, j;
-
- for (i = 0; i < n; i++)
+ for (int i = 0; i < n; i++)
{
{
- for (j = 0; j < DIM; j++)
+ for (
int
j = 0; j < DIM; j++)
{
do_cpt_real_err(xd, &f[i][j]);
}
{
do_cpt_real_err(xd, &f[i][j]);
}
@@
-404,14
+388,14
@@
static int do_cpte_reals_low(XDR *xd, int cptp, int ecpt, int sflags,
{
if (dtc == xdr_datatype_float)
{
{
if (dtc == xdr_datatype_float)
{
- vf =
(float *)vp
;
+ vf =
reinterpret_cast<float *>(vp)
;
}
else
{
snew(vf, nf);
}
}
else
{
snew(vf, nf);
}
- res = xdr_vector(xd,
(char *)vf
, nf,
-
(unsigned int)sizeof(float
), (xdrproc_t)xdr_float);
+ res = xdr_vector(xd,
reinterpret_cast<char *>(vf)
, nf,
+
static_cast<unsigned int>(sizeof(float)
), (xdrproc_t)xdr_float);
if (res == 0)
{
return -1;
if (res == 0)
{
return -1;
@@
-437,8
+421,8
@@
static int do_cpte_reals_low(XDR *xd, int cptp, int ecpt, int sflags,
{
snew(vd, nf);
}
{
snew(vd, nf);
}
- res = xdr_vector(xd,
(char *)vd
, nf,
-
(unsigned int)sizeof(double
), (xdrproc_t)xdr_double);
+ res = xdr_vector(xd,
reinterpret_cast<char *>(vd)
, nf,
+
static_cast<unsigned int>(sizeof(double)
), (xdrproc_t)xdr_double);
if (res == 0)
{
return -1;
if (res == 0)
{
return -1;
@@
-545,8
+529,8
@@
static int do_cpte_ints(XDR *xd, int cptp, int ecpt, int sflags,
}
vp = *v;
}
}
vp = *v;
}
- res = xdr_vector(xd,
(char *)vp
, nf,
-
(unsigned int)sizeof(int
), (xdrproc_t)xdr_int);
+ res = xdr_vector(xd,
reinterpret_cast<char *>(vp)
, nf,
+
static_cast<unsigned int>(sizeof(int)
), (xdrproc_t)xdr_int);
if (res == 0)
{
return -1;
if (res == 0)
{
return -1;
@@
-612,8
+596,8
@@
static int do_cpte_doubles(XDR *xd, int cptp, int ecpt, int sflags,
}
vp = *v;
}
}
vp = *v;
}
- res = xdr_vector(xd,
(char *)vp
, nf,
-
(unsigned int)sizeof(double
), (xdrproc_t)xdr_double);
+ res = xdr_vector(xd,
reinterpret_cast<char *>(vp)
, nf,
+
static_cast<unsigned int>(sizeof(double)
), (xdrproc_t)xdr_double);
if (res == 0)
{
return -1;
if (res == 0)
{
return -1;
@@
-650,7
+634,7
@@
static int do_cpte_matrix(XDR *xd, int cptp, int ecpt, int sflags,
real *vr;
int ret;
real *vr;
int ret;
- vr =
(real *)
&(v[0][0]);
+ vr = &(v[0][0]);
ret = do_cpte_reals_low(xd, cptp, ecpt, sflags,
DIM*DIM, NULL, &vr, NULL, ecprMATRIX);
ret = do_cpte_reals_low(xd, cptp, ecpt, sflags,
DIM*DIM, NULL, &vr, NULL, ecprMATRIX);
@@
-1390,7
+1374,7
@@
static int do_cpt_files(XDR *xd, gmx_bool bRead,
if (bRead)
{
do_cpt_string_err(xd, bRead, "output filename", &buf, list);
if (bRead)
{
do_cpt_string_err(xd, bRead, "output filename", &buf, list);
- strncpy(outputfiles[i].filename, buf, CPTSTRLEN-1);
+ st
d::st
rncpy(outputfiles[i].filename, buf, CPTSTRLEN-1);
if (list == NULL)
{
sfree(buf);
if (list == NULL)
{
sfree(buf);
@@
-1404,7
+1388,7
@@
static int do_cpt_files(XDR *xd, gmx_bool bRead,
{
return -1;
}
{
return -1;
}
- outputfiles[i].offset = (
((gmx_off_t) offset_high) << 32 ) | ( (gmx_off_t) offset_low
& mask );
+ outputfiles[i].offset = (
static_cast<gmx_off_t>(offset_high) << 32 ) | ( static_cast<gmx_off_t>(offset_low)
& mask );
}
else
{
}
else
{
@@
-1419,8
+1403,8
@@
static int do_cpt_files(XDR *xd, gmx_bool bRead,
}
else
{
}
else
{
- offset_low =
(int)
(offset & mask);
- offset_high =
(int)
((offset >> 32) & mask);
+ offset_low =
static_cast<int>
(offset & mask);
+ offset_high =
static_cast<int>
((offset >> 32) & mask);
}
if (do_cpt_int(xd, "file_offset_high", &offset_high, list) != 0)
{
}
if (do_cpt_int(xd, "file_offset_high", &offset_high, list) != 0)
{
@@
-1489,18
+1473,18
@@
void write_checkpoint(const char *fn, gmx_bool bNumberAndKeep,
#if !GMX_NO_RENAME
/* make the new temporary filename */
#if !GMX_NO_RENAME
/* make the new temporary filename */
- snew(fntemp, strlen(fn)+5+STEPSTRSIZE);
- strcpy(fntemp, fn);
- fntemp[st
rlen(fn) -
strlen(ftp2ext(fn2ftp(fn))) - 1] = '\0';
+ snew(fntemp, st
d::st
rlen(fn)+5+STEPSTRSIZE);
+ st
d::st
rcpy(fntemp, fn);
+ fntemp[st
d::strlen(fn) - std::
strlen(ftp2ext(fn2ftp(fn))) - 1] = '\0';
sprintf(suffix, "_%s%s", "step", gmx_step_str(step, sbuf));
sprintf(suffix, "_%s%s", "step", gmx_step_str(step, sbuf));
- strcat(fntemp, suffix);
- st
rcat(fntemp, fn+strlen(fn) -
strlen(ftp2ext(fn2ftp(fn))) - 1);
+ st
d::st
rcat(fntemp, suffix);
+ st
d::strcat(fntemp, fn+std::strlen(fn) - std::
strlen(ftp2ext(fn2ftp(fn))) - 1);
#else
/* if we can't rename, we just overwrite the cpt file.
* dangerous if interrupted.
*/
#else
/* if we can't rename, we just overwrite the cpt file.
* dangerous if interrupted.
*/
- snew(fntemp, strlen(fn));
- strcpy(fntemp, fn);
+ snew(fntemp, st
d::st
rlen(fn));
+ st
d::st
rcpy(fntemp, fn);
#endif
gmx_format_current_time(timebuf, STRLEN);
#endif
gmx_format_current_time(timebuf, STRLEN);
@@
-1648,10
+1632,10
@@
void write_checkpoint(const char *fn, gmx_bool bNumberAndKeep,
if (gmx_fexist(fn))
{
/* Rename the previous checkpoint file */
if (gmx_fexist(fn))
{
/* Rename the previous checkpoint file */
- strcpy(buf, fn);
- buf[st
rlen(fn) -
strlen(ftp2ext(fn2ftp(fn))) - 1] = '\0';
- strcat(buf, "_prev");
- st
rcat(buf, fn+strlen(fn) -
strlen(ftp2ext(fn2ftp(fn))) - 1);
+ st
d::st
rcpy(buf, fn);
+ buf[st
d::strlen(fn) - std::
strlen(ftp2ext(fn2ftp(fn))) - 1] = '\0';
+ st
d::st
rcat(buf, "_prev");
+ st
d::strcat(buf, fn+std::strlen(fn) - std::
strlen(ftp2ext(fn2ftp(fn))) - 1);
#ifndef GMX_FAHCORE
/* we copy here so that if something goes wrong between now and
* the rename below, there's always a state.cpt.
#ifndef GMX_FAHCORE
/* we copy here so that if something goes wrong between now and
* the rename below, there's always a state.cpt.
@@
-1725,7
+1709,7
@@
static void check_string(FILE *fplog, const char *type, const char *p,
{
FILE *fp = fplog ? fplog : stderr;
{
FILE *fp = fplog ? fplog : stderr;
- if (strcmp(p, f) != 0)
+ if (st
d::st
rcmp(p, f) != 0)
{
fprintf(fp, " %s mismatch,\n", type);
fprintf(fp, " current program: %s\n", p);
{
fprintf(fp, " %s mismatch,\n", type);
fprintf(fp, " current program: %s\n", p);
@@
-2153,7
+2137,7
@@
static void read_checkpoint(const char *fn, FILE **pfplog,
else
{
gmx_fatal(FARGS, "Failed to lock: %s. %s.",
else
{
gmx_fatal(FARGS, "Failed to lock: %s. %s.",
- outputfiles[i].filename, strerror(errno));
+ outputfiles[i].filename, st
d::st
rerror(errno));
}
}
}
}
}
}
@@
-2173,7
+2157,7
@@
static void read_checkpoint(const char *fn, FILE **pfplog,
{
if (gmx_fio_seek(chksum_file, outputfiles[i].offset))
{
{
if (gmx_fio_seek(chksum_file, outputfiles[i].offset))
{
- gmx_fatal(FARGS, "Seek error! Failed to truncate log-file: %s.", strerror(errno));
+ gmx_fatal(FARGS, "Seek error! Failed to truncate log-file: %s.", st
d::st
rerror(errno));
}
}
#endif
}
}
#endif