Merge branch 'master' into pygromacs

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

diff --git a/src/gromacs/gmxana/gmx_saltbr.c b/src/gromacs/gmxana/gmx_saltbr.cpp
similarity index 96%
rename from src/gromacs/gmxana/gmx_saltbr.c
rename to src/gromacs/gmxana/gmx_saltbr.cpp
index cc4417213daa0cc39ce816d0227a35ca93273b60..85e05de0e8ada5a44a612635ea529a5155b1d401 100644 (file)
--- a/src/gromacs/gmxana/gmx_saltbr.c
+++ b/src/gromacs/gmxana/gmx_saltbr.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/filenm.h"
@@ -75,7 +75,7 @@ static t_charge *mk_charge(t_atoms *atoms, t_block *cgs, int *nncg)
         {
             qq += atoms->atom[j].q;
         }
-        if (fabs(qq) > 1.0e-5)
+        if (std::abs(qq) > 1.0e-5)
         {
             srenew(cg, ncg+1);
             cg[ncg].q  = qq;
@@ -124,7 +124,7 @@ static real calc_dist(t_pbc *pbc, rvec x[], t_block *cgs, int icg, int jcg)
             }
         }
     }
-    return sqrt(mindist2);
+    return std::sqrt(mindist2);
 }
 
 int gmx_saltbr(int argc, char *argv[])
@@ -170,14 +170,12 @@ int gmx_saltbr(int argc, char *argv[])
     int                ePBC;
     char              *buf;
     t_trxstatus       *status;
-    int                i, j, k, m, nnn, teller, ncg, n1, n2, n3, natoms;
+    int                i, j, k, m, nnn, teller, ncg;
     real               t, *time, qi, qj;
     t_charge          *cg;
     real            ***cgdist;
     int              **nWithin;
 
-    double             t0, dt;
-    char               label[234];
     t_pbc              pbc;
     rvec              *x;
     matrix             box;
@@ -199,7 +197,7 @@ int gmx_saltbr(int argc, char *argv[])
         snew(nWithin[i], ncg);
     }
 
-    natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
+    read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
 
     teller = 0;
     time   = NULL;