Merge branch 'master' into pygromacs

[alexxy/gromacs.git] / src / gromacs / gmxana / gmx_enemat.cpp

diff --git a/src/gromacs/gmxana/gmx_enemat.c b/src/gromacs/gmxana/gmx_enemat.cpp
similarity index 98%
rename from src/gromacs/gmxana/gmx_enemat.c
rename to src/gromacs/gmxana/gmx_enemat.cpp
index 69da88fb2986491aa76f1bb8f5b3694dcc406997..448eaa4d7c1dc175d1de415e1d9fd7bdb0fad0d8 100644 (file)
--- a/src/gromacs/gmxana/gmx_enemat.c
+++ b/src/gromacs/gmxana/gmx_enemat.cpp
@@ -36,8 +36,8 @@
  */
 #include "gmxpre.h"
 
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/enxio.h"
@@ -61,7 +61,7 @@
 static int search_str2(int nstr, char **str, char *key)
 {
     int  i, n;
-    int  keylen = strlen(key);
+    int  keylen = std::strlen(key);
     /* Linear search */
     n = 0;
     while ( (n < keylen) && ((key[n] < '0') || (key[n] > '9')) )
@@ -222,7 +222,7 @@ int gmx_enemat(int argc, char *argv[])
     fprintf(stderr, "Will read groupnames from inputfile\n");
     ngroups = get_lines(opt2fn("-groups", NFILE, fnm), &groups);
     fprintf(stderr, "Read %d groups\n", ngroups);
-    snew(set, sqr(ngroups)*egNR/2);
+    snew(set, static_cast<size_t>(sqr(ngroups)*egNR/2));
     n     = 0;
     prevk = 0;
     for (i = 0; (i < ngroups); i++)
@@ -240,7 +240,7 @@ int gmx_enemat(int argc, char *argv[])
 #endif
                     for (k = prevk; (k < prevk+nre); k++)
                     {
-                        if (strcmp(enm[k%nre].name, groupname) == 0)
+                        if (std::strcmp(enm[k%nre].name, groupname) == 0)
                         {
                             set[n++] = k;
                             break;
@@ -402,9 +402,9 @@ int gmx_enemat(int argc, char *argv[])
                 expE = 0;
                 for (k = 0; (k < nenergy); k++)
                 {
-                    expE += exp(beta*(e[i][k]-eaver[i]));
+                    expE += std::exp(beta*(e[i][k]-eaver[i]));
                 }
-                efree[i] = log(expE/nenergy)/beta + eaver[i];
+                efree[i] = std::log(expE/nenergy)/beta + eaver[i];
                 if (bRef)
                 {
                     n = search_str2(neref, erefres, groups[i]);