Merge branch 'master' into pygromacs

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

diff --git a/src/gromacs/gmxana/gmx_trjorder.c b/src/gromacs/gmxana/gmx_trjorder.cpp
similarity index 98%
rename from src/gromacs/gmxana/gmx_trjorder.c
rename to src/gromacs/gmxana/gmx_trjorder.cpp
index 8b9e56ad9a7c0cf6721738911ed8338576216f13..70c8d7f4b644a0c3067775a3873dcd877e96a84a 100644 (file)
--- a/src/gromacs/gmxana/gmx_trjorder.c
+++ b/src/gromacs/gmxana/gmx_trjorder.cpp
@@ -36,9 +36,9 @@
  */
 #include "gmxpre.h"
 
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
@@ -260,7 +260,7 @@ int gmx_trjorder(int argc, char *argv[])
                         xsol[i][d] += mass*x[sa][d];
                     }
                 }
-                svmul(1/totmass, xsol[i], xsol[i]);
+                svmul(1.0/totmass, xsol[i], xsol[i]);
             }
         }
         else
@@ -318,7 +318,6 @@ int gmx_trjorder(int argc, char *argv[])
                 sr = ind_ref[j];
                 for (i = 0; (i < nwat); i++)
                 {
-                    sa = ind_sol[na*i];
                     pbc_dx(&pbc, x[sr], xsol[i], dx);
                     n2 = norm2(dx);
                     if (n2 < order[i].d2)
@@ -359,7 +358,7 @@ int gmx_trjorder(int argc, char *argv[])
                 {
                     for (j = 0; (j < na); j++)
                     {
-                        top.atoms.pdbinfo[order[i].i+j].bfac = sqrt(order[i].d2);
+                        top.atoms.pdbinfo[order[i].i+j].bfac = std::sqrt(order[i].d2);
                     }
                 }
             }