From: Roland Schulz <roland@utk.edu>
Date: Tue, 20 Dec 2011 12:28:48 +0000 (-0500)
Subject: Merge release-4-5-patches into release-4-6
X-Git-Url: http://biod.pnpi.spb.ru/gitweb/?a=commitdiff_plain;h=30e460710761d7a0bb8446b19ebb1a17e0ff198e;p=alexxy%2Fgromacs.git

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
---

30e460710761d7a0bb8446b19ebb1a17e0ff198e
diff --cc admin/GerritBuild.bat
index f603724726,a373642e89..a343203117
--- a/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 719fe62512,147e2ae9ec..7eb47ecfd4
--- a/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 c3c32dbaff,59a6e8dd0d..0a9f5a652e
--- a/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 94db178b6b,06ccfed618..60ebc29013
--- a/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,