Merge branch 'master' into pygromacs

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

diff --git a/src/gromacs/gmxana/gmx_traj.c b/src/gromacs/gmxana/gmx_traj.cpp
similarity index 98%
rename from src/gromacs/gmxana/gmx_traj.c
rename to src/gromacs/gmxana/gmx_traj.cpp
index 7560cec153d82974784b366b5e4c442401493380..3cb4ead8184e090cf246189271f36e5a62ad9e57 100644 (file)
--- a/src/gromacs/gmxana/gmx_traj.c
+++ b/src/gromacs/gmxana/gmx_traj.cpp
@@ -36,9 +36,11 @@
  */
 #include "gmxpre.h"
 
-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
+
+#include <algorithm>
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
@@ -424,7 +426,6 @@ static void write_pdb_bfac(const char *fname, const char *xname,
     real        max, len2, scale;
     atom_id     maxi;
     int         i, m, onedim;
-    gmx_bool    bOne;
 
     if ((nfr_x == 0) || (nfr_v == 0))
     {
@@ -495,12 +496,12 @@ static void write_pdb_bfac(const char *fname, const char *xname,
             }
             else
             {
-                scale = 10.0/sqrt(max);
+                scale = 10.0/std::sqrt(max);
             }
         }
 
         printf("Maximum %s is %g on atom %d %s, res. %s %d\n",
-               title, sqrt(max), maxi+1, *(atoms->atomname[maxi]),
+               title, std::sqrt(max), maxi+1, *(atoms->atomname[maxi]),
                *(atoms->resinfo[atoms->atom[maxi].resind].name),
                atoms->resinfo[atoms->atom[maxi].resind].nr);
 
@@ -520,7 +521,7 @@ static void write_pdb_bfac(const char *fname, const char *xname,
                         len2 += sqr(sum[index[i]][m]);
                     }
                 }
-                atoms->pdbinfo[index[i]].bfac = sqrt(len2)*scale;
+                atoms->pdbinfo[index[i]].bfac = std::sqrt(len2)*scale;
             }
         }
         else
@@ -546,16 +547,16 @@ static void update_histo(int gnx, atom_id index[], rvec v[],
         for (i = 0; (i < gnx); i++)
         {
             vn    = norm(v[index[i]]);
-            vnmax = max(vn, vnmax);
+            vnmax = std::max(vn, vnmax);
         }
         vnmax  *= 2;
-        *nhisto = 1+(vnmax/binwidth);
+        *nhisto = static_cast<int>(1+(vnmax/binwidth));
         snew(*histo, *nhisto);
     }
     for (i = 0; (i < gnx); i++)
     {
         vn = norm(v[index[i]]);
-        in = vn/binwidth;
+        in = static_cast<int>(vn/binwidth);
         if (in >= *nhisto)
         {
             nnn = in+100;
@@ -667,7 +668,7 @@ int gmx_traj(int argc, char *argv[])
     t_trxstatus    *status;
     t_trxstatus    *status_out = NULL;
     gmx_rmpbc_t     gpbc       = NULL;
-    int             i, j, n;
+    int             i, j;
     int             nr_xfr, nr_vfr, nr_ffr;
     char          **grpname;
     int            *isize0, *isize;
@@ -676,7 +677,7 @@ int gmx_traj(int argc, char *argv[])
     t_block        *mols;
     gmx_bool        bTop, bOX, bOXT, bOV, bOF, bOB, bOT, bEKT, bEKR, bCV, bCF;
     gmx_bool        bDim[4], bDum[4], bVD;
-    char           *sffmt, sffmt6[1024];
+    char            sffmt[STRLEN], sffmt6[STRLEN];
     const char     *box_leg[6] = { "XX", "YY", "ZZ", "YX", "ZX", "ZY" };
     output_env_t    oenv;
 
@@ -736,11 +737,11 @@ int gmx_traj(int argc, char *argv[])
 
     if (bFP)
     {
-        sffmt = "\t" gmx_real_fullprecision_pfmt;
+        sprintf(sffmt, "\t%s", gmx_real_fullprecision_pfmt);
     }
     else
     {
-        sffmt = "\t%g";
+        sprintf(sffmt, "\t%%g");
     }
     sprintf(sffmt6, "%s%s%s%s%s%s", sffmt, sffmt, sffmt, sffmt, sffmt, sffmt);