Merge branch 'master' into pygromacs

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

diff --git a/src/gromacs/gmxana/gmx_tcaf.c b/src/gromacs/gmxana/gmx_tcaf.cpp
similarity index 96%
rename from src/gromacs/gmxana/gmx_tcaf.c
rename to src/gromacs/gmxana/gmx_tcaf.cpp
index eef238878a838552fa2f93d21d61225212536ad0..c139df52ed8f72004f8d0ed337995a33d6847b8f 100644 (file)
--- a/src/gromacs/gmxana/gmx_tcaf.c
+++ b/src/gromacs/gmxana/gmx_tcaf.cpp
@@ -36,9 +36,9 @@
  */
 #include "gmxpre.h"
 
-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/correlationfunctions/autocorr.h"
@@ -59,6 +59,7 @@
 #include "gromacs/topology/index.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
+#include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
 
 #define NK  24
@@ -106,9 +107,9 @@ static void process_tcaf(int nframes, real dt, int nkc, real **tc, rvec *kfac,
     }
 
     ncorr = (nframes+1)/2;
-    if (ncorr > (int)(5*wt/dt+0.5))
+    if (ncorr > static_cast<int>(5*wt/dt+0.5))
     {
-        ncorr = (int)(5*wt/dt+0.5)+1;
+        ncorr = static_cast<int>(5*wt/dt+0.5)+1;
     }
     snew(tcaf, nk);
     for (k = 0; k < nk; k++)
@@ -126,7 +127,7 @@ static void process_tcaf(int nframes, real dt, int nkc, real **tc, rvec *kfac,
     snew(sig, ncorr);
     for (i = 0; i < ncorr; i++)
     {
-        sig[i] = exp(0.5*i*dt/wt);
+        sig[i] = std::exp(0.5*i*dt/wt);
     }
 
     low_do_autocorr(fn_tca, oenv, "Transverse Current Autocorrelation Functions",
@@ -306,7 +307,7 @@ int gmx_tcaf(int argc, char *argv[])
     int             ePBC;
     t_trxframe      fr;
     matrix          box;
-    gmx_bool        bTPS, bTop; /* ,bCubic; */
+    gmx_bool        bTop;
     int             gnx;
     atom_id        *index, *atndx = NULL, at;
     char           *grpname;
@@ -316,7 +317,7 @@ int gmx_tcaf(int argc, char *argv[])
     int             nframes, n_alloc, i, j, k, d;
     rvec            mv_mol, cm_mol, kfac[NK];
     int             nkc, nk, ntc;
-    real          **c1, **tc;
+    real          **tc;
     output_env_t    oenv;
 
 #define NHISTO 360
@@ -402,14 +403,9 @@ int gmx_tcaf(int argc, char *argv[])
     n_alloc = 0;
     nframes = 0;
     rho     = 0;
-    /* bCubic = TRUE; */
+
     do
     {
-        /*
-           bCubic = bCubic && !TRICLINIC(fr.box) &&
-           fabs(fr.box[XX][XX]-fr.box[YY][YY]) < 0.001*fr.box[XX][XX] &&
-           fabs(fr.box[XX][XX]-fr.box[ZZ][ZZ]) < 0.001*fr.box[XX][XX];
-         */
 
         if (nframes >= n_alloc)
         {
@@ -466,8 +462,8 @@ int gmx_tcaf(int argc, char *argv[])
             j = 0;
             for (k = 0; k < nk; k++)
             {
-                sx              = sin(iprod(kfac[k], cm_mol));
-                cx              = cos(iprod(kfac[k], cm_mol));
+                sx              = std::sin(iprod(kfac[k], cm_mol));
+                cx              = std::cos(iprod(kfac[k], cm_mol));
                 tc[j][nframes] += sx*iprod(v1[k], mv_mol);
                 j++;
                 tc[j][nframes] += cx*iprod(v1[k], mv_mol);