Update waves

Created by: acrovato

Context

This pull request brings the last developments from the flow module as well as some upgrade to waves.

Major changes in flow

• flow is now able to compute 3D flows
• The Jacobian (tangent) matrix for the Netwton method is now fully analytical
• The adjacent elements identification is now based on ```std::unordered_set````

Major changes in waves

• tbox and fwk are now included in a namespace
• waves is now fully included in a namespace
• All elements now have a private memory (Mem) which can be publicly accessed
• All elements now have a cache including Gauss points (Gauss) which can be publicly accessed
• MshDeformation now uses a linear elasticity solver
• MshCrack class implemented (creates duplicate internal boundaries in meshes)

Test

The ctest battery has been run on gaston, 100% tests passed under 110s.

Future work

• Use automated indentation rules for the whole code
• Move methods using VTK outside of MshData
• Clean tbox (mainly MshData, Tri3, Tera4 and Hex8)

CMakeLists.txt

@@ -37,6 +37,9 @@ OPTION(WAVES_USE_SPH         "Compile sph module"              ON)
 OPTION(WAVES_USE_TLNOS       "Compile tlnos module"            OFF)
 OPTION(WAVES_USE_WAVES       "Compile waves module"            ON)
 
+# build the doxygen documentation
+option(BUILD_DOC             "Build documentation"             OFF)
+
 # macros/fcts
 INCLUDE(fwkMacros)
 
@@ -89,6 +92,29 @@ ELSE()
     SET(CMAKE_SWIG_OUTDIR "${EXECUTABLE_OUTPUT_PATH}")
 ENDIF()
 
+# -- Doxygen (https://vicrucann.github.io/tutorials/quick-cmake-doxygen/)
+# check if Doxygen is installed
+find_package(Doxygen)
+IF(DOXYGEN_FOUND)
+    # set input and output files
+    set(DOXYGEN_IN ${PROJECT_SOURCE_DIR}/Doxyfile.in)
+    set(DOXYGEN_OUT ${PROJECT_BINARY_DIR}/Doxyfile)
+
+    # request to configure the file
+    configure_file(${DOXYGEN_IN} ${DOXYGEN_OUT} @ONLY)
+    #message("Doxygen build started")
+
+    # note the option ALL which allows to build the docs together with the application
+    # "make dox" rebuilds the doc
+    add_custom_target( dox #ALL
+        COMMAND ${DOXYGEN_EXECUTABLE} ${DOXYGEN_OUT}
+        WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+        COMMENT "Generating API documentation with Doxygen"
+        VERBATIM )
+ELSE(DOXYGEN_FOUND)
+    message("Doxygen need to be installed to generate the doxygen documentation")
+ENDIF(DOXYGEN_FOUND)
+
 # -- CTest
 enable_testing()