Merge branch 'master' into pygromacs

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

diff --git a/src/gromacs/gmxana/gmx_density.c b/src/gromacs/gmxana/gmx_density.cpp
similarity index 96%
rename from src/gromacs/gmxana/gmx_density.c
rename to src/gromacs/gmxana/gmx_density.cpp
index 29bd719c4380249654e5134386405de7e8543bce..f63db4e7f836c5f58fdfea6c380c8477c0137331 100644 (file)
--- a/src/gromacs/gmxana/gmx_density.c
+++ b/src/gromacs/gmxana/gmx_density.cpp
@@ -36,10 +36,10 @@
  */
 #include "gmxpre.h"
 
-#include <ctype.h>
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cctype>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/trxio.h"
@@ -57,6 +57,7 @@
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
+#include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
 
 typedef struct {
@@ -75,7 +76,7 @@ int compare(void *a, void *b)
     t_electron *tmp1, *tmp2;
     tmp1 = (t_electron *)a; tmp2 = (t_electron *)b;
 
-    return strcmp(tmp1->atomname, tmp2->atomname);
+    return std::strcmp(tmp1->atomname, tmp2->atomname);
 }
 
 int get_electrons(t_electron **eltab, const char *fn)
@@ -204,7 +205,7 @@ void calc_electron_density(const char *fn, atom_id **index, int gnx[],
 
     if (!*nslices)
     {
-        *nslices = (int)(box[axis][axis] * 10); /* default value */
+        *nslices = static_cast<int>(box[axis][axis] * 10); /* default value */
         fprintf(stderr, "\nDividing the box in %d slices\n", *nslices);
     }
 
@@ -265,11 +266,11 @@ void calc_electron_density(const char *fn, atom_id **index, int gnx[],
                 /* determine which slice atom is in */
                 if (bCenter)
                 {
-                    slice = floor( (z-(boxSz/2.0)) / (*slWidth) ) + *nslices/2;
+                    slice = static_cast<int>(std::floor( (z-(boxSz/2.0)) / (*slWidth) ) + *nslices/2);
                 }
                 else
                 {
-                    slice = (z / (*slWidth));
+                    slice = static_cast<int>(z / (*slWidth));
                 }
                 sought.nr_el    = 0;
                 sought.atomname = gmx_strdup(*(top->atoms.atomname[index[n][i]]));
@@ -336,15 +337,12 @@ void calc_density(const char *fn, atom_id **index, int gnx[],
     double       invvol;
     int          natoms;        /* nr. atoms in trj */
     t_trxstatus *status;
-    int        **slCount,       /* nr. of atoms in one slice for a group */
-                 i, j, n,       /* loop indices */
-                 ax1       = 0, ax2 = 0,
+    int          i, n,          /* loop indices */
                  nr_frames = 0, /* number of frames */
                  slice;         /* current slice */
     real         t,
                  z;
     real         boxSz, aveBox;
-    char        *buf;    /* for tmp. keeping atomname */
     gmx_rmpbc_t  gpbc = NULL;
 
     if (axis < 0 || axis >= DIM)
@@ -361,7 +359,7 @@ void calc_density(const char *fn, atom_id **index, int gnx[],
 
     if (!*nslices)
     {
-        *nslices = (int)(box[axis][axis] * 10); /* default value */
+        *nslices = static_cast<int>(box[axis][axis] * 10); /* default value */
         fprintf(stderr, "\nDividing the box in %d slices\n", *nslices);
     }
 
@@ -422,11 +420,11 @@ void calc_density(const char *fn, atom_id **index, int gnx[],
                 /* determine which slice atom is in */
                 if (bCenter)
                 {
-                    slice = floor( (z-(boxSz/2.0)) / (*slWidth) ) + *nslices/2;
+                    slice = static_cast<int>(std::floor( (z-(boxSz/2.0)) / (*slWidth) ) + *nslices/2);
                 }
                 else
                 {
-                    slice = floor(z / (*slWidth));
+                    slice = static_cast<int>(std::floor(z / (*slWidth)));
                 }
 
                 /* Slice should already be 0<=slice<nslices, but we just make
@@ -504,6 +502,8 @@ void plot_density(double *slDensity[], const char *afile, int nslices,
         xlabel = bRelative ? "Average coordinate (nm)" : "Coordinate (nm)";
     }
 
+    GMX_RELEASE_ASSERT(dens_opt[0] != NULL, "Option setting inconsistency; dens_opt[0] is NULL");
+
     switch (dens_opt[0][0])
     {
         case 'm': ylabel = "Density (kg m\\S-3\\N)"; break;
@@ -724,7 +724,8 @@ int gmx_density(int argc, char *argv[])
     }
     else
     {
-        ncenter = 0;
+        ncenter      = 0;
+        index_center = NULL;
     }
 
     fprintf(stderr, "\nSelect %d group%s to calculate density for:\n", ngrps, (ngrps > 1) ? "s" : "");