Merge branch 'master' into pygromacs

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

diff --git a/src/gromacs/gmxana/gmx_mdmat.c b/src/gromacs/gmxana/gmx_mdmat.cpp
similarity index 97%
rename from src/gromacs/gmxana/gmx_mdmat.c
rename to src/gromacs/gmxana/gmx_mdmat.cpp
index 8d2ac08527ab1a3d5367d54d667db66d3cfcfd83..d832088c9051cdf4e91e6190ef092b8eaf112958 100644 (file)
--- a/src/gromacs/gmxana/gmx_mdmat.c
+++ b/src/gromacs/gmxana/gmx_mdmat.cpp
@@ -36,8 +36,10 @@
  */
 #include "gmxpre.h"
 
-#include <math.h>
-#include <string.h>
+#include <cmath>
+#include <cstring>
+
+#include <algorithm>
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
@@ -134,7 +136,7 @@ static void calc_mat(int nres, int natoms, int rndx[],
                 nmat[resi][j]++;
                 nmat[resj][i]++;
             }
-            mdmat[resi][resj] = min(r2, mdmat[resi][resj]);
+            mdmat[resi][resj] = std::min(r2, mdmat[resi][resj]);
         }
     }
 
@@ -143,7 +145,7 @@ static void calc_mat(int nres, int natoms, int rndx[],
         mdmat[resi][resi] = 0;
         for (resj = resi+1; (resj < nres); resj++)
         {
-            r                 = sqrt(mdmat[resi][resj]);
+            r                 = std::sqrt(mdmat[resi][resj]);
             mdmat[resi][resj] = r;
             mdmat[resj][resi] = r;
         }
@@ -183,7 +185,6 @@ int gmx_mdmat(int argc, char *argv[])
         "The output can be processed with [gmx-xpm2ps] to make a PostScript (tm) plot."
     };
     static real     truncate = 1.5;
-    static gmx_bool bAtom    = FALSE;
     static int      nlevels  = 40;
     t_pargs         pa[]     = {
         { "-t",   FALSE, etREAL, {&truncate},
@@ -210,9 +211,8 @@ int gmx_mdmat(int argc, char *argv[])
     char          *grpname;
     int           *rndx, *natm, prevres, newres;
 
-    int            i, j, nres, natoms, nframes, it, trxnat;
+    int            i, j, nres, natoms, nframes, trxnat;
     t_trxstatus   *status;
-    int            nr0;
     gmx_bool       bCalcN, bFrames;
     real           t, ratio;
     char           title[256], label[234];