Merge branch 'master' of git@git.gromacs.org:gromacs

diff --combined CMakeLists.txt
index e73260d731dc85ff3a587c19ee0117a31af68e1e,9cf4e788f334212876f44fdc66c06598720d23b2..7238ed45c929fd06cd1a99d8db181f0a84aeb7eb
--- 1/CMakeLists.txt
--- 2/CMakeLists.txt
+++ b/CMakeLists.txt
@@@ -32,7 -32,7 +32,7 @@@ set(GMX_FFT_LIBRARY "fftw3
  option(GMX_DISABLE_FFTW_MEASURE 
         "Do not optimize FFTW setups (not needed with SSE)" OFF)
  set(GMX_QMMM_PROGRAM "none" 
-     CACHE STRING "QM package choices: none,gaussian,mopac,gamess")
+     CACHE STRING "QM package choices: none,gaussian,mopac,gamess,orca")
  option(GMX_BROKEN_CALLOC "Work around broken calloc()" OFF)
  option(BUILD_SHARED_LIBS "Enable shared libraries (can be problematic with MPI)" OFF)
  option(GMX_MPI_IN_PLACE "Enable MPI_IN_PLACE for MPIs that have it defined" ON)
@@@ -46,9 -46,6 +46,9 @@@ option(GMX_X86_64_ASM "Add SSE assembl
  option(USE_VERSION_H "Generate development version string/information" ON)
  option(GMX_DISABLE_GCC41_CHECK "Disable check for (buggy) gcc 4.1.x" OFF)
  
 +set(GMX_BINARY_SUFFIX "" CACHE STRING "Suffix for GROMACS binaries.")
 +
 +
  #######################################################################
  # Check for options incompatible with OpenMM build                    #
  #######################################################################
@@@ -66,7 -63,7 +66,7 @@@ if(GMX_OPENMM
      if(GMX_SOFTWARE_INVSQRT)
          set(GMX_SOFTWARE_INVSQRT OFF)
      endif(GMX_SOFTWARE_INVSQRT)
 -    if(NOT GMX_ACCELERATION MATCHES "none")    
 +    if(NOT GMX_ACCELERATION MATCHES "none|None|NONE" OR NOT ${GMX_ACCELERATION} STREQUAL "")
          message(WARNING "The OpenMM build does not support other acceleration modes!")
          set(GMX_ACCELERATION "none")
      endif()
@@@ -156,6 -153,8 +156,8 @@@ check_function_exists(strcasecm
  check_function_exists(strdup            HAVE_STRDUP)
  check_function_exists(vprintf           HAVE_VPRINTF)
  check_function_exists(memcmp            HAVE_MEMCMP)
+ check_function_exists(posix_memalign    HAVE_POSIX_MEMALIGN)
+ check_function_exists(memalign          HAVE_MEMALIGN)
  check_function_exists(gettimeofday      HAVE_GETTIMEOFDAY)
  check_function_exists(isnan             HAVE_ISNAN)
  check_function_exists(_isnan            HAVE__ISNAN)
@@@ -450,10 -449,12 +452,12 @@@ elseif(${GMX_QMMM_PROGRAM} STREQUAL "MO
      set(GMX_QMMM_MOPAC 1)
  elseif(${GMX_QMMM_PROGRAM} STREQUAL "GAMESS")
      set(GMX_QMMM_GAMESS 1)
+ elseif(${GMX_QMMM_PROGRAM} STREQUAL "ORCA")
+     set(GMX_QMMM_ORCA 1)
  elseif(${GMX_QMMM_PROGRAM} STREQUAL "NONE")
      # nothing to do
  else(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
-     MESSAGE(FATAL_ERROR "Invalid QM/MM program option: ${GMX_QMMM_PROGRAM}. Choose one of: Gaussian, Mopac, Gamess, None")
+     MESSAGE(FATAL_ERROR "Invalid QM/MM program option: ${GMX_QMMM_PROGRAM}. Choose one of: Gaussian, Mopac, Gamess, Orca, None")
  endif(${GMX_QMMM_PROGRAM} STREQUAL "GAUSSIAN")
  
  # Process FFT library settings - if not OpenMM build 
@@@ -569,4 -570,11 +573,11 @@@ add_subdirectory(man
  
  add_subdirectory(src)
  
+ ########################################################################
+ # Tests                                                                #
+ ########################################################################
+ 
+ enable_testing()
+ add_test(TestBuildAll make)
  
+ add_subdirectory(tests)

diff --combined src/tools/CMakeLists.txt
index fbe24534bad5f64054da4d8be66ac19544e3f0e4,45edce51f5b43523cb0806b9a64016d88519ac19..998997b8d0b08eba2f65ead924f0c81265c2727f
--- 1/src/tools/CMakeLists.txt
--- 2/src/tools/CMakeLists.txt
+++ b/src/tools/CMakeLists.txt
@@@ -28,10 -28,11 +28,11 @@@ add_library(gmxan
              gmx_trjconv.c   gmx_trjcat.c    gmx_trjorder.c  gmx_xpm2ps.c    
              gmx_editconf.c  gmx_genbox.c    gmx_genion.c    gmx_genconf.c   
              gmx_genpr.c     gmx_eneconv.c   gmx_vanhove.c   gmx_wheel.c     
-             addconf.c       calcpot.c       edittop.c       gmx_bar.c)
+             addconf.c       calcpot.c       edittop.c       gmx_bar.c
+             gmx_membed.c    )
  
  target_link_libraries(gmxana md ${GMX_EXTRA_LIBRARIES})
 -
 +set_target_properties(gmxana PROPERTIES OUTPUT_NAME "gmxana${GMX_BINARY_SUFFIX}")
  
  # List of programs with single corresponding .c source file,
  # used to create build rules automatically.
@@@ -49,6 -50,7 +50,7 @@@ set(GMX_TOOLS_PROGRAM
      g_rmsf g_rotacf g_saltbr g_sas g_select g_sgangle g_sham g_sorient
      g_spol g_sdf g_spatial g_tcaf g_traj g_tune_pme g_vanhove
      g_velacc g_clustsize g_mdmat g_wham g_kinetics g_sigeps g_bar
+     g_membed
      )
  
  
@@@ -56,7 -58,6 +58,7 @@@
  foreach(TOOL ${GMX_TOOLS_PROGRAMS})
      add_executable(${TOOL} ${TOOL}.c)
      target_link_libraries(${TOOL} gmxana)
 +    set_target_properties(${TOOL} PROPERTIES OUTPUT_NAME "${TOOL}${GMX_BINARY_SUFFIX}")
  endforeach(TOOL ${GMX_TOOLS_PROGRAMS})