modularity

CMakeLists.txt

@@ -9,7 +9,6 @@ endif()
 enable_language(C)
 enable_language(CXX)
 enable_testing()
-option(ENABLE_PROJ "Enable PROJ" ON)
 option(ENABLE_PETSC "Enable PETSc" ON)
 option(ENABLE_PETSC4PY "Enable PETSc4Py" ON)
 
@@ -82,63 +81,12 @@ if(ENABLE_PETSC)
   endif(PETSC_FOUND)
 endif(ENABLE_PETSC)
 
-macro(dg_set_module_option VARNAME STRING)
-  set(${VARNAME} TRUE PARENT_SCOPE)
-  list(APPEND DG_CONFIG_OPTIONS " ${STRING}")
-  set(DG_CONFIG_OPTIONS "${DG_CONFIG_OPTIONS}" PARENT_SCOPE)
-  message(STATUS "Found " ${STRING})
-endmacro(dg_set_module_option)
-
-macro(dg_add_library LIBNAME)
-  list(APPEND EXTERNAL_LIBRARIES ${LIBNAME})
-  set(EXTERNAL_LIBRARIES ${EXTERNAL_LIBRARIES} PARENT_SCOPE)
-endmacro(dg_add_library)
-
-if(ENABLE_PROJ)
-  find_library (PROJ_LIB proj)
-  if (PROJ_LIB)
-    find_path (PROJ_INC "proj_api.h" PATH_SUFFIXES include)
-    if (PROJ_INC)
-      set(HAVE_PROJ TRUE)
-      set_dg_config_option(HAVE_PROJ "Proj")
-      list(APPEND EXTERNAL_LIBRARIES ${PROJ_LIB})
-      list(APPEND EXTERNAL_INCLUDES ${PROJ_INC})
-    endif(PROJ_INC)
-  endif(PROJ_LIB)
-endif(ENABLE_PROJ)
-
 find_library(REALTIME_LIB rt)
 if (REALTIME_LIB)
   list(APPEND EXTERNAL_LIBRARIES ${REALTIME_LIB})
   set_dg_config_option(HAVE_REALTIME "RealTime")
 endif (REALTIME_LIB)
 
-find_package(SWIG REQUIRED)
-find_package(PythonLibs REQUIRED)
-if(SWIG_FOUND AND PYTHONLIBS_FOUND)
-  message(STATUS "Found SWIG version " ${SWIG_VERSION})
-  set_dg_config_option(HAVE_SWIG "Swig")
-endif(SWIG_FOUND AND PYTHONLIBS_FOUND)
-
-if(SWIG_FOUND AND PYTHONLIBS_FOUND)
-  find_package(SWIG)
-  find_package(PythonLibs)
-  find_package(PythonInterp)
-  include(${SWIG_USE_FILE})
-  include_directories(${PYTHON_INCLUDE_PATH})
-  include_directories(${CMAKE_CURRENT_BINARY_DIR}/..)
-  if (NOT NUMPY_INC)
-    EXEC_PROGRAM (${PYTHON_EXECUTABLE}
-      ARGS "-c \"import numpy; print(numpy.get_include())\""
-      OUTPUT_VARIABLE NUMPY_INC
-      RETURN_VALUE NUMPY_NOT_FOUND)
-  endif(NOT NUMPY_INC)
-  if(NUMPY_INC)
-    list(APPEND EXTERNAL_INCLUDES ${NUMPY_INC})
-    set_dg_config_option(HAVE_NUMPY "Numpy")
-  endif(NUMPY_INC)
-endif(SWIG_FOUND AND PYTHONLIBS_FOUND)
-
 macro(dg_add_source FILES)
   foreach(FILE ${FILES})
     list(APPEND LIST ${CMAKE_CURRENT_SOURCE_DIR}/${FILE})
@@ -146,14 +94,7 @@ macro(dg_add_source FILES)
   set(DG_SRC ${DG_SRC};${LIST} PARENT_SCOPE)
 endmacro(dg_add_source)
 
-macro(dg_add_swig_module module filename libname)
-  list(APPEND DG_SWIG_MODULES ${module})
-  string(REPLACE "${CMAKE_SOURCE_DIR}/" "" RELATIVE_SOURCE "${CMAKE_CURRENT_SOURCE_DIR}")
-  list(APPEND DG_SWIG_MODULES ${RELATIVE_SOURCE})
-  list(APPEND DG_SWIG_MODULES ${filename})
-  list(APPEND DG_SWIG_MODULES ${libname})
-  set(DG_SWIG_MODULES ${DG_SWIG_MODULES} PARENT_SCOPE)
-endmacro(dg_add_swig_module)
+include(dgpy/dgpy.cmake)
 
 macro(dg_add_test_directory directory email)
   get_filename_component(ABSPATH ${directory} ABSOLUTE)
@@ -197,13 +138,12 @@ macro(dg_add_module_ module FILES)
   endif(BLAS_LINKER_FLAGS)
 endmacro(dg_add_module_)
 
-
 dg_add_module_(dg "${DG_SRC}")
 target_link_libraries(dg ${EXTERNAL_LIBRARIES})
 
-macro(dg_add_module module FILES)
+macro(dg_add_module module FILES LIBS)
   dg_add_module_(${module} "${FILES}")
-  target_link_libraries(${module} dg ${EXTERNAL_LIBRARIES})
+  target_link_libraries(${module} dg ${EXTERNAL_LIBRARIES} ${LIBS})
 endmacro(dg_add_module)
 
 add_subdirectory(modules/atmosphere)
@@ -229,5 +169,16 @@ configure_file(dgftpupload ${CMAKE_CURRENT_BINARY_DIR}/dgftpupload @ONLY)
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/dgConfig.h.in
                ${CMAKE_CURRENT_BINARY_DIR}/dgConfig.h)
 
+set (EXTERNAL_LIBRARIES_COMMAND_LINE "")
+FOREACH(lib ${EXTERNAL_LIBRARIES})
+  IF ("${lib}" MATCHES "^[-/].*")
+    set (EXTERNAL_LIBRARIES_COMMAND_LINE "${EXTERNAL_LIBRARIES_COMMAND_LINE} ${lib}")
+  ELSE()
+    set (EXTERNAL_LIBRARIES_COMMAND_LINE "${EXTERNAL_LIBRARIES_COMMAND_LINE} -l${lib}")
+  ENDIF()
+ENDFOREACH(lib)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/external_libraries.make.in 
+               ${CMAKE_CURRENT_BINARY_DIR}/external_libraries.make)
+
 
-message("Dg has been configured for ${GMSH_OS} with the following options: " ${DG_CONFIG_OPTIONS})
+message("Dg has been configured with the following options: " ${DG_CONFIG_OPTIONS})

conservationLaw/dgConservationLawFunction.cpp

@@ -918,7 +918,7 @@ class dgIPTerm : public functor {
         }
         else
           Msg::Fatal("The setup with anisotropic and different diffusivities for different fields is not implemented");
-        val(iPt, k)             = - (meanNormalFlux + solutionJumpPenalty);
+        val(iPt, k)            = - (meanNormalFlux + solutionJumpPenalty);
         val(iPt, k + nbFields) =   (meanNormalFlux + solutionJumpPenalty);
       }
     }

dgConfig.h.in

 #ifndef _DG_CONFIG_H_
 #define _DG_CONFIG_H_
 
-#cmakedefine HAVE_FES
-#cmakedefine HAVE_GOTM
 #cmakedefine HAVE_GPERFTOOLSPROFILER
 #cmakedefine HAVE_METIS
 #cmakedefine HAVE_MPI
-#cmakedefine HAVE_NETCDF
-#cmakedefine HAVE_NETCDFCPP
-#cmakedefine HAVE_PNETCDF
 #cmakedefine HAVE_NUMPY
 #cmakedefine HAVE_PETSC
 #cmakedefine HAVE_PETSC4PY
-#cmakedefine HAVE_PROJ
 #cmakedefine HAVE_REALTIME
 
-#ifdef HAVE_FES
-#define FES_DATA "${FES_DATA}"
-#endif
-
 #endif

dgpy/CMakeLists.txt

-
-#see CMake bug 4147 (modified to remove dgConfig.h)
-MACRO(SWIG_GET_WRAPPER_DEPENDENCIES swigFile genWrapper language DEST_VARIABLE)
-  GET_FILENAME_COMPONENT(swig_getdeps_basename ${swigFile} NAME_WE)
-  GET_FILENAME_COMPONENT(swig_getdeps_outdir ${genWrapper} PATH)
-  GET_SOURCE_FILE_PROPERTY(swig_getdeps_extra_flags "${swigFile}" SWIG_FLAGS)
-  IF("${swig_getdeps_extra_flags}" STREQUAL "NOTFOUND")
-    SET(swig_getdeps_extra_flags "")
-  ENDIF("${swig_getdeps_extra_flags}" STREQUAL "NOTFOUND")
-
-  IF(NOT swig_getdeps_outdir)
-    SET(swig_getdeps_outdir ${CMAKE_CURRENT_BINARY_DIR})
-  ENDIF(NOT swig_getdeps_outdir)
-  SET(swig_getdeps_depsfile
-    ${swig_getdeps_outdir}/swig_${swig_getdeps_basename}_deps.txt)
-  GET_DIRECTORY_PROPERTY(swig_getdeps_include_directories INCLUDE_DIRECTORIES)
-  SET(swig_getdeps_include_dirs)
-  FOREACH(it ${swig_getdeps_include_directories})
-    SET(swig_getdeps_include_dirs ${swig_getdeps_include_dirs} "-I${it}")
-  ENDFOREACH(it)
-  EXECUTE_PROCESS(
-    COMMAND ${SWIG_EXECUTABLE}
-    -MM -MF ${swig_getdeps_depsfile} ${swig_getdeps_extra_flags}
-    ${CMAKE_SWIG_FLAGS} -${language}
-    -o ${genWrapper} ${swig_getdeps_include_dirs} ${swigFile}
-    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-    RESULT_VARIABLE swig_getdeps_result
-    ERROR_VARIABLE swig_getdeps_error
-    OUTPUT_STRIP_TRAILING_WHITESPACE)
-  IF(NOT EXISTS ${swig_getdeps_depsfile})
-    SET(swig_getdeps_dependencies "")
-  ELSE(NOT EXISTS ${swig_getdeps_depsfile})
-    FILE(READ ${swig_getdeps_depsfile} ${DEST_VARIABLE})
-    # Remove the first line
-    STRING(REGEX REPLACE "^.+: +\\\\\n +" ""
-      ${DEST_VARIABLE} "${${DEST_VARIABLE}}")
-    # Clean the end of each line
-    STRING(REGEX REPLACE " +(\\\\)?\n" "\n" ${DEST_VARIABLE}
-      "${${DEST_VARIABLE}}")
-    # Clean beginning of each line
-    STRING(REGEX REPLACE "\n +" "\n"
-      ${DEST_VARIABLE} "${${DEST_VARIABLE}}")
-    # clean paths
-    STRING(REGEX REPLACE "\\\\\\\\" "/" ${DEST_VARIABLE}
-      "${${DEST_VARIABLE}}")
-    STRING(REGEX REPLACE "\n" ";"
-      ${DEST_VARIABLE} "${${DEST_VARIABLE}}")
-  ENDIF(NOT EXISTS ${swig_getdeps_depsfile})
-ENDMACRO(SWIG_GET_WRAPPER_DEPENDENCIES)
-
-
-set (EXTERNAL_LIBRARIES_COMMAND_LINE "")
-FOREACH(lib ${EXTERNAL_LIBRARIES})
-  IF ("${lib}" MATCHES "^[-/].*")
-    set (EXTERNAL_LIBRARIES_COMMAND_LINE "${EXTERNAL_LIBRARIES_COMMAND_LINE} ${lib}")
-  ELSE()
-    set (EXTERNAL_LIBRARIES_COMMAND_LINE "${EXTERNAL_LIBRARIES_COMMAND_LINE} -l${lib}")
-  ENDIF()
-ENDFOREACH(lib)
-
-configure_file(${CMAKE_CURRENT_SOURCE_DIR}/external_libraries.make.in 
-               ${CMAKE_CURRENT_BINARY_DIR}/external_libraries.make)
-
-find_package(SWIG)
-find_package(PythonLibs)
-find_package(PythonInterp)
-include(${SWIG_USE_FILE})
-include_directories(${PYTHON_INCLUDE_PATH})
-include_directories(${CMAKE_CURRENT_BINARY_DIR}/..)
-
-list(LENGTH DG_SWIG_MODULES N)
-set(CMAKE_SWIG_FLAGS -features autodoc=1)
-include_directories(${CMAKE_BINARY_DIR})
-include_directories(${CMAKE_SOURCE_DIR}/../../wrappers/gmshpy/)
-while (${N} GREATER 0)
-  list(GET DG_SWIG_MODULES 0 module)
-  list(GET DG_SWIG_MODULES 1 directory)
-  list(GET DG_SWIG_MODULES 2 filename)
-  list(GET DG_SWIG_MODULES 3 libname)
-  list(REMOVE_AT DG_SWIG_MODULES 0)
-  list(REMOVE_AT DG_SWIG_MODULES 0)
-  list(REMOVE_AT DG_SWIG_MODULES 0)
-  list(REMOVE_AT DG_SWIG_MODULES 0)
-  list(LENGTH DG_SWIG_MODULES N)
-  set (filename  "../${directory}/${filename}")
-  set_source_files_properties(${filename} PROPERTIES CPLUSPLUS ON)
-  # see CMake bug 4147
-  SWIG_GET_WRAPPER_DEPENDENCIES(${filename} ${CMAKE_CURRENT_BINARY_DIR}/${module}PYTHON_wrap.cxx python swig_extra_dependencies)
-  LIST(APPEND SWIG_MODULE_${module}_EXTRA_DEPS ${swig_extra_dependencies})
-  swig_add_module(${module} python ${filename})
-  swig_link_libraries(${module} ${PYTHON_LIBRARIES} ${libname})
-  #target_include_directories not present in cmake < 2.8.11
-  #target_include_directories(_${module} PRIVATE ../${directory})
-  #INCLUDE_DIRECTORIES is read only on cmake < 2.8.9
-  #get_property(IDIR TARGET _${module} PROPERTY INCLUDE_DIRECTORIES)    
-  #set_property(TARGET _${module} PROPERTY INCLUDE_DIRECTORIES ${IDIR};${CMAKE_SOURCE_DIR}/${directory})
-
-  set_target_properties("_${module}" PROPERTIES COMPILE_FLAGS "-Wno-literal-suffix")
-  include_directories(${CMAKE_SOURCE_DIR}/${directory})
-  if(APPLE)
-    set_target_properties("_${module}" PROPERTIES LINK_FLAGS "-undefined suppress -flat_namespace")
-  endif(APPLE)
-  SET(DG_PYTHON_MODULES_INCLUDE_CODE "${DG_PYTHON_MODULES_INCLUDE_CODE}from dgpy.${module} import *\n")
-  list(APPEND DGPY_DEPENDS "_${module}")
-endwhile (${N} GREATER 0)
-
-add_custom_target("_dgpy" DEPENDS ${DGPY_DEPENDS})
-
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/__init__.py.in 
                ${CMAKE_CURRENT_BINARY_DIR}/__init__.py)
 

dgpy/dgpy.cmake

+find_package(SWIG REQUIRED)
+find_package(PythonLibs REQUIRED)
+find_package(PythonInterp REQUIRED)
+if(SWIG_FOUND AND PYTHONLIBS_FOUND)
+  message(STATUS "Found SWIG version " ${SWIG_VERSION})
+  set_dg_config_option(HAVE_SWIG "Swig")
+  include(${SWIG_USE_FILE})
+  include_directories(${PYTHON_INCLUDE_PATH})
+  include_directories(${CMAKE_CURRENT_BINARY_DIR}/..)
+  if (NOT NUMPY_INC)
+    EXEC_PROGRAM (${PYTHON_EXECUTABLE}
+      ARGS "-c \"import numpy; print(numpy.get_include())\""
+      OUTPUT_VARIABLE NUMPY_INC
+      RETURN_VALUE NUMPY_NOT_FOUND)
+  endif(NOT NUMPY_INC)
+  if(NUMPY_INC)
+    list(APPEND EXTERNAL_INCLUDES ${NUMPY_INC})
+    set_dg_config_option(HAVE_NUMPY "Numpy")
+  endif(NUMPY_INC)
+endif(SWIG_FOUND AND PYTHONLIBS_FOUND)
+
+#include_directories(${PYTHON_INCLUDE_PATH})
+#include_directories(${CMAKE_CURRENT_BINARY_DIR}/..)
+#
+#include_directories(${CMAKE_BINARY_DIR})
+
+#see CMake bug 4147 (modified to remove dgConfig.h)
+MACRO(SWIG_GET_WRAPPER_DEPENDENCIES swigFile genWrapper language DEST_VARIABLE)
+  GET_FILENAME_COMPONENT(swig_getdeps_basename ${swigFile} NAME_WE)
+  GET_FILENAME_COMPONENT(swig_getdeps_outdir ${genWrapper} PATH)
+  GET_SOURCE_FILE_PROPERTY(swig_getdeps_extra_flags "${swigFile}" SWIG_FLAGS)
+  IF("${swig_getdeps_extra_flags}" STREQUAL "NOTFOUND")
+    SET(swig_getdeps_extra_flags "")
+  ENDIF("${swig_getdeps_extra_flags}" STREQUAL "NOTFOUND")
+
+  IF(NOT swig_getdeps_outdir)
+    SET(swig_getdeps_outdir ${CMAKE_CURRENT_BINARY_DIR})
+  ENDIF(NOT swig_getdeps_outdir)
+  SET(swig_getdeps_depsfile
+    ${swig_getdeps_outdir}/swig_${swig_getdeps_basename}_deps.txt)
+  GET_DIRECTORY_PROPERTY(swig_getdeps_include_directories INCLUDE_DIRECTORIES)
+  SET(swig_getdeps_include_dirs)
+  FOREACH(it ${swig_getdeps_include_directories})
+    SET(swig_getdeps_include_dirs ${swig_getdeps_include_dirs} "-I${it}")
+  ENDFOREACH(it)
+  EXECUTE_PROCESS(
+    COMMAND ${SWIG_EXECUTABLE}
+    -MM -MF ${swig_getdeps_depsfile} ${swig_getdeps_extra_flags}
+    ${CMAKE_SWIG_FLAGS} -${language}
+    -o ${genWrapper} ${swig_getdeps_include_dirs} ${swigFile}
+    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    RESULT_VARIABLE swig_getdeps_result
+    ERROR_VARIABLE swig_getdeps_error
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+  IF(NOT EXISTS ${swig_getdeps_depsfile})
+    SET(swig_getdeps_dependencies "")
+  ELSE(NOT EXISTS ${swig_getdeps_depsfile})
+    FILE(READ ${swig_getdeps_depsfile} ${DEST_VARIABLE})
+    # Remove the first line
+    STRING(REGEX REPLACE "^.+: +\\\\\n +" ""
+      ${DEST_VARIABLE} "${${DEST_VARIABLE}}")
+    # Clean the end of each line
+    STRING(REGEX REPLACE " +(\\\\)?\n" "\n" ${DEST_VARIABLE}
+      "${${DEST_VARIABLE}}")
+    # Clean beginning of each line
+    STRING(REGEX REPLACE "\n +" "\n"
+      ${DEST_VARIABLE} "${${DEST_VARIABLE}}")
+    # clean paths
+    STRING(REGEX REPLACE "\\\\\\\\" "/" ${DEST_VARIABLE}
+      "${${DEST_VARIABLE}}")
+    STRING(REGEX REPLACE "\n" ";"
+      ${DEST_VARIABLE} "${${DEST_VARIABLE}}")
+  ENDIF(NOT EXISTS ${swig_getdeps_depsfile})
+ENDMACRO(SWIG_GET_WRAPPER_DEPENDENCIES)
+
+macro(dg_add_swig_module module filename libname)
+  if(SWIG_FOUND AND PYTHONLIBS_FOUND)
+    set(CMAKE_SWIG_OUTDIR ${CMAKE_BINARY_DIR}/dgpy)
+    set(CMAKE_SWIG_FLAGS -features autodoc=1)
+    get_directory_property(defs COMPILE_DEFINITIONS)
+    set(ddefs "")
+    foreach(d ${defs})
+      list(APPEND ddefs "-D${d}")
+    endforeach()
+    set_property(SOURCE ${filename} PROPERTY CPLUSPLUS ON)
+    set_property(SOURCE ${filename} PROPERTY SWIG_FLAGS "${ddefs}")
+    # see CMake bug 4147
+    SWIG_GET_WRAPPER_DEPENDENCIES(${filename} ${CMAKE_CURRENT_BINARY_DIR}/${module}PYTHON_wrap.cxx python swig_extra_dependencies)
+    LIST(APPEND SWIG_MODULE_${module}_EXTRA_DEPS ${swig_extra_dependencies})
+    swig_add_module(${module} python ${filename})
+    swig_link_libraries(${module} ${PYTHON_LIBRARIES} ${libname})
+    set_target_properties(${SWIG_MODULE_${module}_REAL_NAME} PROPERTIES COMPILE_FLAGS "-Wno-literal-suffix")
+    include_directories(${CMAKE_CURRENT_SOURCE_DIR})
+    if(APPLE)
+      set_target_properties(${SWIG_MODULE_${module}_REAL_NAME} PROPERTIES LINK_FLAGS "-undefined suppress -flat_namespace")
+    endif(APPLE)
+
+    set_target_properties(${SWIG_MODULE_${module}_REAL_NAME}
+      PROPERTIES
+      LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/dgpy
+      RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/dgpy
+    )
+    SET(DG_PYTHON_MODULES_INCLUDE_CODE "${DG_PYTHON_MODULES_INCLUDE_CODE}from dgpy.${module} import *\n")
+    SET(DG_PYTHON_MODULES_INCLUDE_CODE "${DG_PYTHON_MODULES_INCLUDE_CODE}" PARENT_SCOPE)
+    list(APPEND DGPY_DEPENDS "_${module}")
+  endif()
+endmacro(dg_add_swig_module)

function/functionGeneric.cpp

@@ -565,7 +565,7 @@ void functionC::buildLibraryFromFile(const std::string &cfilename, const std::st
   /* Compiling string. */
   const std::string compilingString =
     std::string ("include $(DG_BUILD_DIR)/CMakeFiles/dg.dir/flags.make\n")
-    + "include $(DG_BUILD_DIR)/dgpy/external_libraries.make\n"
+    + "include $(DG_BUILD_DIR)/external_libraries.make\n"
     + "%s : %s\n"
     + "\tg++ $< -fPIC -shared -o $@ $(CXX_FLAGS) $(CXX_INCLUDES) -L$(DG_BUILD_DIR) -ldg $(CXX_DEFINES) ${EXTERNAL_LIBRARIES} "
     + optionalFlags + '\n';
@@ -845,8 +845,8 @@ const fullMatrix<double> &functionPrecomputed::faceData(functorCache::Mode m, in
   }
   if (m != functorCache::INTEGRATION_GROUP_MODE)
     Msg::Fatal("only NODE_GROUP_MODE and INTEGRATION_GROUP_MODE are valid argument for functionPrecomputed");
-    if ((size_t)iGroup >= _faceData.size() || (size_t)iConn >= _faceData[iGroup].size() || _faceData[iGroup][iConn].size1() == 0)
-      Msg::Fatal("functionPrecomputed not pre computed for face group %i %i in INTEGRATION_GROUP_MODE", iGroup, iConn);
+  if ((size_t)iGroup >= _faceData.size() || (size_t)iConn >= _faceData[iGroup].size() || _faceData[iGroup][iConn].size1() == 0)
+    Msg::Fatal("functionPrecomputed not pre computed for face group %i %i in INTEGRATION_GROUP_MODE", iGroup, iConn);
   return _faceData[iGroup][iConn];
 }
 

mesh/dgGroupOfElements.cpp

@@ -538,9 +538,9 @@ void dgGroupCollection::setCoordinates(dgDofContainer* xyzCoordDof)
   fullMatrix<double> coord, mod;
   for (int i = 0; i < getNbElementGroups() + getNbGhostGroups(); i++) {
     dgGroupOfElements *group = getElementGroup(i);
-  if(xyzCoordDof->nField(*group) != 6)
-    Msg::Error("dgGroupCollection::setCoordinates require a dof of 6 fields. The original mesh nodes "
-               "are modified as f0 * x + f1, f2 * y + f3, f4 * z + f5.");
+    if(xyzCoordDof->nField(*group) != 6)
+      Msg::Error("dgGroupCollection::setCoordinates require a dof of 6 fields. The original mesh nodes "
+          "are modified as f0 * x + f1, f2 * y + f3, f4 * z + f5.");
     const nodalBasis &fsGeo = _mesh->elementVector(group->elementVectorId()).functionSpace();
     const nodalBasis &fs = group->getFunctionSpace();
     fullMatrix<double> phiGeo(fsGeo.points.size1(), fs.points.size1());
@@ -558,10 +558,10 @@ void dgGroupCollection::setCoordinates(dgDofContainer* xyzCoordDof)
       coord.setAll(0.);
       for (int l = 0; l < fs.points.size1(); ++l) {
         /*        for (int k = 0; k < coordEVp.size1(); ++ k) {
-         coord(l,0) += coord(k, 0) * phiGeo(k, l);
-         coord(l,1) += coord(k, 1) * phiGeo(k, l);
-         coord(l,2) += coord(k, 2) * phiGeo(k, l);
-         }*/
+                  coord(l,0) += coord(k, 0) * phiGeo(k, l);
+                  coord(l,1) += coord(k, 1) * phiGeo(k, l);
+                  coord(l,2) += coord(k, 2) * phiGeo(k, l);
+                  }*/
         coord(l,0) = coordEVp(l,0) * mod(l,0) + mod(l,1);
         coordEVp(l,0) = coord(l,0);
         coord(l,1) = coordEVp(l,1) * mod(l,2) + mod(l,3);

modules/atmosphere/CMakeLists.txt

@@ -7,6 +7,6 @@ set(SRC
   simplePhysics/atmBoundaryLayer.cpp
 )
 
-dg_add_module(dgAtmosphere "${SRC}")
+dg_add_module(dgAtmosphere "${SRC}" "")
 dg_add_swig_module(atmosphere atmosphere.i dgAtmosphere)
 dg_add_test_directory(tests sebastien.blaise@uclouvain.be)

modules/elastodynamics/CMakeLists.txt

@@ -2,6 +2,6 @@ set(SRC
   dgConservationLawElastodynamics.cpp
 )
 
-dg_add_module(dgElastodynamics "${SRC}")
+dg_add_module(dgElastodynamics "${SRC}" "")
 dg_add_swig_module(elastodynamics elastodynamics.i dgElastodynamics)
 #dg_add_test_directory(tests axel.modave@uclouvain.be)

modules/generic/CMakeLists.txt

@@ -5,6 +5,6 @@ set(SRC
   dgConservationLawODE.cpp
 )
 
-dg_add_module(dgGeneric "${SRC}")
+dg_add_module(dgGeneric "${SRC}" "")
 dg_add_swig_module(generic generic.i dgGeneric)
 dg_add_test_directory(tests sebastien.blaise@uclouvain.be)

modules/lee/CMakeLists.txt

@@ -2,6 +2,6 @@ set(SRC
   dgConservationLawLEE.cpp
 )
 
-dg_add_module(dgLee "${SRC}")
+dg_add_module(dgLee "${SRC}" "")
 dg_add_swig_module(lee lee.i dgLee)
 #dg_add_test_directory(tests thomas.toulorge@uclouvain.be)

modules/maxwell/CMakeLists.txt

@@ -4,6 +4,6 @@ set(SRC
   dgConservationLawMaxwellPml.cpp
 )
 
-dg_add_module(dgMaxwell "${SRC}")
+dg_add_module(dgMaxwell "${SRC}" "")
 dg_add_swig_module(maxwell maxwell.i dgMaxwell)
 #dg_add_test_directory(tests axel.modave@uclouvain.be)

modules/navierStokesIncomp/CMakeLists.txt

@@ -5,6 +5,6 @@ set(SRC
   dgConservationLawStokes3d.cpp
 )
 
-dg_add_module(dgNavierStokesIncomp "${SRC}")
+dg_add_module(dgNavierStokesIncomp "${SRC}" "")
 dg_add_swig_module(navierStokesIncomp navierStokesIncomp.i dgNavierStokesIncomp)
 #dg_add_test_directory(tests emilie.marchandise@uclouvain.be)

modules/perfectGas/CMakeLists.txt

@@ -3,6 +3,6 @@ set(SRC
   dgConservationLawPerfectGasALE.cpp
 )
 
-dg_add_module(dgPerfectGas "${SRC}")
+dg_add_module(dgPerfectGas "${SRC}" "")
 dg_add_swig_module(perfectGas perfectGas.i dgPerfectGas)
 #dg_add_test_directory(tests jean-francois.remacle@uclouvain.be)

modules/shallowWater/CMakeLists.txt

@@ -8,6 +8,6 @@ set(SRC
   slimMovingBathWettingDrying.cpp
 )
 
-dg_add_module(dgShallowWater "${SRC}")
+dg_add_module(dgShallowWater "${SRC}" "")
 dg_add_swig_module(shallowWater shallowWater.i dgShallowWater)
 dg_add_test_directory(tests karim.slaoui@uclouvain.be)

modules/slim3d/CMakeLists.txt

-option(ENABLE_PNETCDF "Enable PNETCDF" OFF)
-if(ENABLE_PNETCDF)
-  find_library (PNETCDF_LIB pnetcdf)
-  if (PNETCDF_LIB)
-    find_path (PNETCDF_INC "pnetcdf.h" PATH_SUFFIXES include)
-    if (PNETCDF_INC)
-      dg_set_module_option(HAVE_PNETCDF "PNetcdf")
-      dg_add_library(${PNETCDF_LIB})
-      include_directories(${PNETCDF_INC})
-    endif(PNETCDF_INC)
-  endif(PNETCDF_LIB)
-endif(ENABLE_PNETCDF)
 
 set(SRC
   dgConservationLawSW3dContinuity.cpp
@@ -28,6 +16,22 @@ set(SRC
   slim3dNetCDFIO.cpp
 )
 
+set (LIBS "")
+
+option(ENABLE_PNETCDF "Enable PNETCDF" OFF)
+if(ENABLE_PNETCDF)
+  find_library (PNETCDF_LIB pnetcdf)
+  if (PNETCDF_LIB)
+    find_path (PNETCDF_INC "pnetcdf.h" PATH_SUFFIXES include)
+    if (PNETCDF_INC)
+      add_definitions("-DHAVE_PNETCDF")
+      list(APPEND LIBS "${PNETCDF_LIB}")
+      include_directories(${PNETCDF_INC})
+      message("slim3d configured with PNETCDF")
+    endif(PNETCDF_INC)
+  endif(PNETCDF_LIB)
+endif(ENABLE_PNETCDF)
+
 option(ENABLE_GOTM "Enable GOTM" OFF)
 if(ENABLE_GOTM)
   include(ExternalProject)
@@ -57,13 +61,13 @@ if(ENABLE_GOTM)
   # if(NOT ${FortranCInterface_GLOBAL_FOUND})
   #  configure_file(${CMAKE_CURRENT_SOURCE_DIR}/gotm.h.fallback ${CMAKE_CURRENT_BINARY_DIR}/gotm.h COPYONLY)
   #endif(NOT ${FortranCInterface_GLOBAL_FOUND})
-  dg_set_module_option(HAVE_GOTM "Gotm")
-  dg_add_library("${CMAKE_CURRENT_BINARY_DIR}/gotm/build/libgotm.a")
-  dg_add_library("${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES}")
+  add_definitions("-DHAVE_GOTM")
+  message("slim3d configured with Gotm")
+  list(APPEND LIBS "${CMAKE_CURRENT_BINARY_DIR}/gotm/build/libgotm.a")
+  list(APPEND LIBS "${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES}")
   include_directories("${CMAKE_CURRENT_BINARY_DIR}")
 endif(ENABLE_GOTM)
 
-dg_add_module(dgSlim3D "${SRC}")
+dg_add_module(dgSlim3D "${SRC}" "${LIBS}")
 dg_add_swig_module(slim3d slim3d.i dgSlim3D)
 dg_add_test_directory(tests philippe.delandmeter@uclouvain.be)
-

modules/slim3d/dgGOTMWrapper.h

 #ifndef _DG_GOTM_WRAPPER__H_
 #define _DG_GOTM_WRAPPER__H_
-#include "dgConfig.h"
 #ifdef HAVE_GOTM
 #include <string>
 class dgGOTMinterface {

modules/slim3d/dgSW3dTurbulenceGOTM.h

 #ifndef DG_SW3D_TURBULENCE_GOTM_H_
 #define DG_SW3D_TURBULENCE_GOTM_H_
-#include "dgConfig.h"
 #include "dgSW3dVerticalModel.h"
 #include "dgGOTMWrapper.h"
 #ifdef HAVE_GOTM

modules/slim3d/slim3dEquations.cpp

@@ -4,7 +4,6 @@
 #include "dgSW3dVerticalModel.h"
 #include "dgSW3dTurbulenceGOTM.h"
 #include "dgExtrusion.h"
-#include "dgConfig.h"
 
 slim3dSolverDofs::slim3dSolverDofs(slim3dSolver *solver): _solver(solver) {
   // init all dofs to NULL