Merge branch 'master' into pygromacs

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

diff --git a/src/gromacs/gmxana/gmx_nmens.c b/src/gromacs/gmxana/gmx_nmens.cpp
similarity index 93%
rename from src/gromacs/gmxana/gmx_nmens.c
rename to src/gromacs/gmxana/gmx_nmens.cpp
index 4028f46b455d8e4995fb8c9a56c3cca099d8eeb3..b53f3b0d602d44ecfdc9765187efc2a90f563465 100644 (file)
--- a/src/gromacs/gmxana/gmx_nmens.c
+++ b/src/gromacs/gmxana/gmx_nmens.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/confio.h"
@@ -86,7 +86,6 @@ int gmx_nmens(int argc, char *argv[])
 #define NPA asize(pa)
 
     t_trxstatus        *out;
-    int                 status, trjout;
     t_topology          top;
     int                 ePBC;
     t_atoms            *atoms;
@@ -95,18 +94,17 @@ int gmx_nmens(int argc, char *argv[])
     int                 nvec, *eignr = NULL;
     rvec              **eigvec = NULL;
     matrix              box;
-    real               *eigval, totmass, *invsqrtm, t, disp;
-    int                 natoms, neigval;
+    real               *eigval, *invsqrtm, t, disp;
+    int                 natoms;
     char               *grpname, title[STRLEN];
     const char         *indexfile;
     int                 i, j, d, s, v;
     int                 nout, *iout, noutvec, *outvec;
     atom_id            *index;
-    real                rfac, invfr, rhalf, jr;
-    int          *      eigvalnr;
+    real                rfac, rhalf, jr;
     output_env_t        oenv;
     gmx_rng_t           rng;
-    unsigned long       jran;
+    int                 jran;
     const unsigned long im = 0xffff;
     const unsigned long ia = 1093;
     const unsigned long ic = 18257;
@@ -215,7 +213,7 @@ int gmx_nmens(int argc, char *argv[])
 
     if (seed == -1)
     {
-        seed = (int)gmx_rng_make_seed();
+        seed = static_cast<int>(gmx_rng_make_seed());
         rng  = gmx_rng_init(seed);
     }
     else
@@ -227,7 +225,7 @@ int gmx_nmens(int argc, char *argv[])
     snew(xout1, natoms);
     snew(xout2, atoms->nr);
     out  = open_trx(ftp2fn(efTRO, NFILE, fnm), "w");
-    jran = (unsigned long)((real)im*gmx_rng_uniform_real(rng));
+    jran = static_cast<int>(im*gmx_rng_uniform_real(rng));
     gmx_rng_destroy(rng);
     for (s = 0; s < nstruct; s++)
     {
@@ -241,18 +239,18 @@ int gmx_nmens(int argc, char *argv[])
             /* (r-0.5) n times:  var_n = n * var_1 = n/12
                n=4:  var_n = 1/3, so multiply with 3 */
 
-            rfac  = sqrt(3.0 * BOLTZ*temp/eigval[iout[j]]);
+            rfac  = std::sqrt(3.0 * BOLTZ*temp/eigval[iout[j]]);
             rhalf = 2.0*rfac;
-            rfac  = rfac/(real)im;
+            rfac  = rfac/im;
 
             jran = (jran*ia+ic) & im;
-            jr   = (real)jran;
+            jr   = jran;
             jran = (jran*ia+ic) & im;
-            jr  += (real)jran;
+            jr  += jran;
             jran = (jran*ia+ic) & im;
-            jr  += (real)jran;
+            jr  += jran;
             jran = (jran*ia+ic) & im;
-            jr  += (real)jran;
+            jr  += jran;
             disp = rfac * jr - rhalf;
 
             for (i = 0; i < natoms; i++)