Merge branch 'master' into pygromacs

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

diff --git a/src/gromacs/gmxana/gmx_polystat.c b/src/gromacs/gmxana/gmx_polystat.cpp
similarity index 95%
rename from src/gromacs/gmxana/gmx_polystat.c
rename to src/gromacs/gmxana/gmx_polystat.cpp
index d174119ac54301394b32234d7852457921f6a5ad..48f8092ecabdd533101f6214399453a198684e45 100644 (file)
--- a/src/gromacs/gmxana/gmx_polystat.c
+++ b/src/gromacs/gmxana/gmx_polystat.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/tpxio.h"
@@ -86,7 +88,7 @@ static void gyro_eigen(double **gyr, double *eig, double **eigv, int *ord)
 /* Calculate mean square internal distances (Auhl et al., JCP 119, 12718) */
 static void calc_int_dist(double *intd, rvec *x, int i0, int i1)
 {
-    int       ii, jj;
+    int       ii;
     const int ml = i1 - i0 + 1; /* Number of beads in molecule. */
     int       bd;               /* Distance between beads */
     double    d;
@@ -211,8 +213,8 @@ int gmx_polystat(int argc, char *argv[])
     nat_max      = 0;
     for (mol = 0; mol < nmol; mol++)
     {
-        nat_min = min(nat_min, molind[mol+1]-molind[mol]);
-        nat_max = max(nat_max, molind[mol+1]-molind[mol]);
+        nat_min = std::min(nat_min, molind[mol+1]-molind[mol]);
+        nat_max = std::max(nat_max, molind[mol+1]-molind[mol]);
     }
     fprintf(stderr, "Group %s consists of %d molecules\n", grpname, nmol);
     fprintf(stderr, "Group size per molecule, min: %d atoms, max %d atoms\n",
@@ -405,13 +407,13 @@ int gmx_polystat(int argc, char *argv[])
 
         fprintf(out, "%10.3f %8.4f %8.4f %8.4f %8.4f %8.4f",
                 t*output_env_get_time_factor(oenv),
-                sqrt(sum_eed2), sqrt(sum_gyro),
-                sqrt(eig[ord[0]]), sqrt(eig[ord[1]]), sqrt(eig[ord[2]]));
+                std::sqrt(sum_eed2), sqrt(sum_gyro),
+                std::sqrt(eig[ord[0]]), std::sqrt(eig[ord[1]]), std::sqrt(eig[ord[2]]));
         if (bPC)
         {
             for (d = 0; d < DIM; d++)
             {
-                fprintf(out, " %8.4f", sqrt(sum_eig[d]/nmol));
+                fprintf(out, " %8.4f", std::sqrt(sum_eig[d]/nmol));
             }
         }
         fprintf(out, "\n");
@@ -438,7 +440,7 @@ int gmx_polystat(int argc, char *argv[])
             for (j = 0; j < nat_min/2; j += 2)
             {
                 sum_inp[j] /= ninp[j];
-                if (i == -1 && sum_inp[j] <= exp(-1.0))
+                if (i == -1 && sum_inp[j] <= std::exp(-1.0))
                 {
                     i = j;
                 }
@@ -450,8 +452,8 @@ int gmx_polystat(int argc, char *argv[])
             else
             {
                 /* Do linear interpolation on a log scale */
-                pers = i - 2
-                    + 2*(log(sum_inp[i-2]) + 1)/(log(sum_inp[i-2]) - log(sum_inp[i]));
+                pers = i - 2.0
+                    + 2.0*(std::log(sum_inp[i-2]) + 1.0)/(std::log(sum_inp[i-2]) - std::log(sum_inp[i]));
             }
             fprintf(outp, "%10.3f %8.4f\n", t*output_env_get_time_factor(oenv), pers);
             sum_pers_tot += pers;
@@ -479,9 +481,9 @@ int gmx_polystat(int argc, char *argv[])
     sum_gyro_tot /= frame;
     sum_pers_tot /= frame;
     fprintf(stdout, "\nAverage end to end distance: %.3f (nm)\n",
-            sqrt(sum_eed2_tot));
+            std::sqrt(sum_eed2_tot));
     fprintf(stdout, "\nAverage radius of gyration:  %.3f (nm)\n",
-            sqrt(sum_gyro_tot));
+            std::sqrt(sum_gyro_tot));
     if (opt2bSet("-p", NFILE, fnm))
     {
         fprintf(stdout, "\nAverage persistence length:  %.2f bonds\n",