fix gitignore

.gitignore

@@ -3,6 +3,7 @@ build/*
 CMakeFiles/
 CMakeCache.txt
 *.cmake
+!cmake/*.cmake
 Makefile
 .ninja*
 build.ninja

cmake/setup_application.cmake

@@ -0,0 +1,138 @@
+# General setup for a PRISMS-PF application
+
+message(STATUS "")
+message(STATUS "=========================================================")
+message(STATUS "Configuring PRISMS-PF application")
+message(STATUS "=========================================================")
+message(STATUS "")
+
+# Setup the build type (debug, release, debugrelease)
+if("${CMAKE_BUILD_TYPE}" STREQUAL "")
+  set(CMAKE_BUILD_TYPE "DebugRelease" 
+      CACHE STRING
+      "Choose the type of build, options are: Debug, Release and DebugRelease."
+      FORCE)
+endif()
+
+# Convert build type into the debug and release builds, which may or may 
+# not be built.
+if("${CMAKE_BUILD_TYPE}" STREQUAL "Release" OR
+   "${CMAKE_BUILD_TYPE}" STREQUAL "Debug" OR
+   "${CMAKE_BUILD_TYPE}" STREQUAL "DebugRelease" )
+  message(STATUS "Setting up PRISMS-PF application for ${CMAKE_BUILD_TYPE} mode.")
+else()
+  message(FATAL_ERROR
+    "CMAKE_BUILD_TYPE must either be 'Release', 'Debug', or 'DebugRelease', but is set to '${CMAKE_BUILD_TYPE}'.")
+endif()
+
+if("${CMAKE_BUILD_TYPE}" STREQUAL "Debug" OR 
+   "${CMAKE_BUILD_TYPE}" STREQUAL "DebugRelease")
+  set(PRISMS_PF_BUILD_DEBUG "ON")
+else()
+  set(PRISMS_PF_BUILD_DEBUG "OFF")
+endif()
+
+if("${CMAKE_BUILD_TYPE}" STREQUAL "Release" OR 
+   "${CMAKE_BUILD_TYPE}" STREQUAL "DebugRelease")
+  set(PRISMS_PF_BUILD_RELEASE "ON")
+else()
+  set(PRISMS_PF_BUILD_RELEASE "OFF")
+endif()
+
+
+# Find deal.II installation
+find_package(deal.II 9.6.0 QUIET
+	HINTS ${DEAL_II_DIR} $ENV{DEAL_II_DIR}
+  )
+if(NOT ${deal.II_FOUND})
+  message(FATAL_ERROR "\n*** Could not find a recent version of deal.II. ***\n"
+  "You may want to either pass a flag -DDEAL_II_DIR=/path/to/deal.II to cmake "
+  "or set an environment variable \"DEAL_II_DIR\" that contains a path to a "
+  "recent version of deal.II."
+  )
+endif()
+
+message(STATUS "Found deal.II version ${DEAL_II_PACKAGE_VERSION} at '${deal.II_DIR}'\n")
+
+set(DEALII_INSTALL_VALID ON)
+
+if(NOT DEAL_II_WITH_P4EST)
+    message(SEND_ERROR
+      "\n**deal.II was built without support for p4est!\n"
+      )
+    set(DEALII_INSTALL_VALID OFF)
+endif()
+
+if(NOT DEAL_II_WITH_MPI)
+    message(SEND_ERROR
+      "\n**deal.II was built without support for MPI!\n"
+      )
+    set(DEALII_INSTALL_VALID OFF)
+endif()
+
+if(NOT DEALII_INSTALL_VALID)
+  message(FATAL_ERROR
+    "\nPRISMS-PF requires a deal.II installation with certain features enabled!\n"
+    )
+endif()
+
+# Load deal.II cached variables
+deal_ii_initialize_cached_variables()
+
+# Make and ninja build options
+if(CMAKE_GENERATOR MATCHES "Ninja")
+  set(_make_command "$ ninja")
+else()
+  set(_make_command " $ make")
+endif()
+
+# Debug and release targets
+if(${DEAL_II_BUILD_TYPE} MATCHES "DebugRelease")
+  add_custom_target(release
+    COMMAND ${CMAKE_COMMAND} -D CMAKE_BUILD_TYPE=Release .
+    COMMAND ${CMAKE_COMMAND} -E echo "***"
+    COMMAND ${CMAKE_COMMAND} -E echo "*** Switched to Release mode. Now recompile with: ${_make_command}"
+    COMMAND ${CMAKE_COMMAND} -E echo "***"
+    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    VERBATIM
+    COMMENT "switching to RELEASE mode..."
+  )
+
+  add_custom_target(debug
+    COMMAND ${CMAKE_COMMAND} -D CMAKE_BUILD_TYPE=Debug .
+    COMMAND ${CMAKE_COMMAND} -E echo "***"
+    COMMAND ${CMAKE_COMMAND} -E echo "*** Switched to Debug mode. Now recompile with: ${_make_command}"
+    COMMAND ${CMAKE_COMMAND} -E echo "***"
+    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    VERBATIM
+    COMMENT "switching to DEBUG mode..."
+  )
+
+  add_custom_target(debugrelease
+    COMMAND ${CMAKE_COMMAND} -D CMAKE_BUILD_TYPE=DebugRelease .
+    COMMAND ${CMAKE_COMMAND} -E echo "***"
+    COMMAND ${CMAKE_COMMAND} -E echo "*** Switched to Debug and Release mode. Now recompile with: ${_make_command}"
+    COMMAND ${CMAKE_COMMAND} -E echo "***"
+    WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
+    VERBATIM
+    COMMENT "switching to DEBUG/RELEASE mode..."
+  )
+endif()
+
+# Add distclean target to clean build
+add_custom_target(distclean
+  COMMAND ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target clean
+  COMMAND ${CMAKE_COMMAND} -E remove_directory CMakeFiles
+  COMMAND ${CMAKE_COMMAND} -E remove
+    CMakeCache.txt cmake_install.cmake Makefile
+    build.ninja rules.ninja .ninja_deps .ninja_log
+  COMMENT "distclean invoked"
+  )
+
+# Add postprocess.cc and nucleation.cc if they exist
+if(EXISTS "postprocess.cc")
+	add_definitions(-DPOSTPROCESS_FILE_EXISTS)
+endif()
+if(EXISTS "nucleation.cc")
+	add_definitions(-DNUCLEATION_FILE_EXISTS)
+endif()