Merge release-4-5-patches into release-4-6

Conflicts:
	admin/GerritBuild.bat
	include/gstat.h
	src/tools/anadih.c
	src/tools/gmx_chi.c

Change-Id: If70475e8f38978aeb52652afce2ca2a62d355987

diff --cc CMakeLists.txt
Simple merge

diff --cc admin/GerritBuild.bat
index f603724726900c7a756afc12a570bec5c1791ded,a373642e8912ce77069d468a197f88f6fb4f9c43..a3432031173ebd10377c37afd871db628a786c5d
--- 1/admin/GerritBuild.bat
--- 2/admin/GerritBuild.bat
+++ b/admin/GerritBuild.bat
@@@ -1,6 -1,7 +1,6 @@@
  REM Requires Windows SDK and CMake to be in the path
  REM Run Windows SDK SetEnv script
- SetEnv && ^
- cmake -G "Visual Studio 10 Win64" -D GMX_DOUBLE=%GMX_DOUBLE% -D GMX_MPI=%GMX_MPI% -D GMX_OPENMP=%GMX_OPENMP% -DGMX_DEFAULT_SUFFIX=off -DCMAKE_BUILD_TYPE=Debug . && ^
- msbuild All_Build.vcxproj && ^
- ctest -D ExperimentalTest -C Debug -V
+ SetEnv /Release && ^
+ cmake -G "Visual Studio 10 Win64" -D GMX_DOUBLE=%GMX_DOUBLE% -D GMX_MPI=%GMX_MPI% -D GMX_OPENMP=%GMX_OPENMP% -DGMX_DEFAULT_SUFFIX=off . && ^
+ msbuild /m:2 /p:Configuration=MinSizeRel All_Build.vcxproj && ^
+ ctest -D ExperimentalTest -C MinSizeRel -V
 -

diff --cc include/gstat.h
index 719fe625125e43794b70da7347e3013086b7c9f0,147e2ae9ecb609d05c0eaff9366495a99d52b80b..7eb47ecfd45f1cf3ffd9dbb4f721eebb4b06ba9a
--- 1/include/gstat.h
--- 2/include/gstat.h
+++ b/include/gstat.h
@@@ -269,9 -269,9 +269,9 @@@ void low_ana_dih_trans(gmx_bool bTrans
                              gmx_bool bHisto, const char *fn_histo, int maxchi, 
                              real **dih, int nlist, t_dlist dlist[], 
                                int nframes, int nangles, const char *grpname, 
-                              int multiplicity[], real t0, real dt, gmx_bool bRb, 
 -                              int xity[], real *time, gmx_bool bRb,
++                              int multiplicity[], real *time, gmx_bool bRb,
                                real core_frac, const output_env_t oenv); 
 -  /* as above but passes dlist so can copy occupancies into it, and xity[] 
 +  /* as above but passes dlist so can copy occupancies into it, and multiplicity[] 
     *  (1..nangles, corresp to dih[this][], so can have non-3 multiplicity of
     * rotamers. Also production of xvg output files is conditional 
     * and the fractional width of each rotamer can be set ie for a 3 fold 

diff --cc src/tools/anadih.c
index c3c32dbaff19ae14d63ec0afab02f1a0563e1cdd,59a6e8dd0d7a11ea4ef7cddc54a1f443842d15a5..0a9f5a652e1f2bef311e21ec3d3292c2ce1f4dfc
--- 1/src/tools/anadih.c
--- 2/src/tools/anadih.c
+++ b/src/tools/anadih.c
@@@ -131,17 -131,17 +131,17 @@@ void ana_dih_trans(const char *fn_trans
  
    low_ana_dih_trans(TRUE, fn_trans,TRUE, fn_histo, maxchi, 
                      dih, nlist, dlist, nframes,
-                   nangles, grpname, multiplicity, t0, dt, bRb, 0.5,oenv); 
 -                  nangles, grpname, xity, time, bRb, 0.5,oenv);
++                  nangles, grpname, multiplicity, time, bRb, 0.5,oenv);
    sfree(dlist); 
 -  sfree(xity); 
 +  sfree(multiplicity); 
    
  }
  
  void low_ana_dih_trans(gmx_bool bTrans, const char *fn_trans,
                       gmx_bool bHisto, const char *fn_histo, int maxchi, 
                       real **dih, int nlist, t_dlist dlist[], int nframes,
-                      int nangles, const char *grpname, int multiplicity[], 
-                      real t0, real dt, gmx_bool bRb, real core_frac,
 -                     int nangles, const char *grpname, int xity[],
++                     int nangles, const char *grpname, int multiplicity[],
+                      real *time, gmx_bool bRb, real core_frac,
                         const output_env_t oenv)
  {
    FILE *fp;

diff --cc src/tools/gmx_chi.c
index 94db178b6b71ba096df2def57e8b4baedccd8b13,06ccfed618f37b554d52486a63747ca4aa4dd3f7..60ebc2901306767e5796a384bb400adc9ea791a2
--- 1/src/tools/gmx_chi.c
--- 2/src/tools/gmx_chi.c
+++ b/src/tools/gmx_chi.c
@@@ -1270,8 -1272,8 +1272,8 @@@ int gmx_chi(int argc,char *argv[]
  
    low_ana_dih_trans(bDo_ot, opt2fn("-ot",NFILE,fnm),
                    bDo_oh, opt2fn("-oh",NFILE,fnm),maxchi, 
 -                  dih, nlist, dlist, nf, nactdih, grpname, xity, 
 +                  dih, nlist, dlist, nf, nactdih, grpname, multiplicity, 
-                   *time,  dt, FALSE, core_frac,oenv) ; 
+                   time, FALSE, core_frac,oenv);
  
    /* Order parameters */  
    order_params(log,opt2fn("-o",NFILE,fnm),maxchi,nlist,dlist,