01.cmake.patch

diff --git a/.gitignore b/.gitignore
index 4d26a143..db7c1603 100644
--- a/.gitignore
+++ b/.gitignore
@@ -62,3 +62,6 @@ meshtest.dat
 
 # compiled doxygen file
 doc/doxy*
+
+# build
+build/
diff --git a/CMakeLists.txt b/CMakeLists.txt
new file mode 100644
index 00000000..091514f9
--- /dev/null
+++ b/CMakeLists.txt
@@ -0,0 +1,60 @@
+# Installs athenapp library
+#
+#   library: libathenapp_debug.a
+#   library: libathenapp_release.a
+#
+# Define the following variables
+#
+#   ATHENAPP_INCLUDE_DIR
+#   ATHENAPP_LIBRARY_DEBUG
+#   ATHENAPP_LIBRARY_RELEASE
+#
+# Normal usage would be
+#
+#   include_directories( ${ATHENAPP_INCLUDE_DIR})
+#   target_link_libraries( ${ATHENAPP_LIBRARY_DEBUG})
+#
+cmake_minimum_required(VERSION 3.10)
+
+project(
+  ATHENAPP
+  LANGUAGES CXX
+  )
+set(CMAKE_CXX_STANDARD 14)
+message(STATUS "")
+message(STATUS "== Setting up athenapp library ==")
+
+if (NOT CMAKE_BUILD_TYPE)
+  set(CMAKE_BUILD_TYPE Release)
+  message(STATUS "Default Build Type = Release")
+  message(STATUS "")
+else()
+  message(STATUS "Build Type = ${CMAKE_BUILD_TYPE}")
+  message(STATUS "")
+endif()
+
+## 1. set up compiler flags ##
+message(STATUS "1. Set up project compiler flags ...")
+message(STATUS "Include ${CMAKE_SOURCE_DIR}/cmake/setup_compiler_flags.cmake")
+include(${CMAKE_SOURCE_DIR}/cmake/setup_compiler_flags.cmake)
+
+## 2. set up project specific configuration ##
+message(STATUS "2. Set up project specific configuration ...")
+message(STATUS "Include ${CMAKE_CURRENT_SOURCE_DIR}/cmake/setup_parameters.cmake")
+include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/setup_parameters.cmake)
+
+## 3. set up project system libraries ##
+message(STATUS "3. Set up project system libraries ...")
+if (${MPI_OPTION} STREQUAL "MPI_PARALLEL")
+    find_package(MPI REQUIRED)
+endif()
+
+## 4. set up project configure file and library ##
+message(STATUS "4. Set up project libraries ...")
+message(STATUS "Find project definitions in src/defs.hpp")
+configure_file(src/defs.hpp.in ${CMAKE_CURRENT_SOURCE_DIR}/src/defs.hpp @ONLY)
+add_subdirectory(src)
+
+#include_directories(
+#  ${CMAKE_CURRENT_BINARY_DIR}
+#  )
diff --git a/cmake/setup_compiler_flags.cmake b/cmake/setup_compiler_flags.cmake
new file mode 100644
index 00000000..9313021b
--- /dev/null
+++ b/cmake/setup_compiler_flags.cmake
@@ -0,0 +1,86 @@
+# Checks for compiler features (such as C++14 support) and compiler
+# specific bugs that
+#   - usually set up further configuration (such as preprocessor
+#     definitions)
+#   - disable a specific flag for a specific compiler version.
+#
+
+# General setup for GCC and compilers sufficiently close to GCC:
+#
+if (CMAKE_CXX_COMPILER_ID MATCHES "GNU")
+  set(CMAKE_CXX_FLAGS_RELEASE 
+    "-O2 -funroll-loops -funroll-all-loops -fstrict-aliasing"
+    )
+
+  set(CMAKE_CXX_FLAGS_DEBUG
+    "-g3"
+    )
+  set(CMAKE_C_FLAGS_RELEASE 
+    "-O2 -funroll-loops -funroll-all-loops -fstrict-aliasing"
+    )
+
+  set(CMAKE_C_FLAGS_DEBUG
+    "-g3"
+    )
+
+  #set(CMAKE_Fortran_FLAGS_RELEASE
+  #  "-O3"
+  #  )
+  set(KNOWN_COMPILER TRUE)
+endif()
+
+if (CMAKE_CXX_COMPILER_ID MATCHES "Clang" )
+  set(CMAKE_CXX_FLAGS_RELEASE 
+    "-O2 -funroll-loops -fstrict-aliasing"
+    )
+
+  set(CMAKE_CXX_FLAGS_DEBUG
+    "-g3"
+    )
+  set(CMAKE_C_FLAGS_RELEASE 
+    "-O2 -funroll-loops -fstrict-aliasing"
+    )
+
+  set(CMAKE_C_FLAGS_DEBUG
+    "-g3"
+    )
+
+  #set(CMAKE_Fortran_FLAGS_RELEASE
+  #  "-O3"
+  #  )
+  set(KNOWN_COMPILER TRUE)
+endif()
+
+#
+# Setup for ICC compiler (version >= 10):
+#
+if (CMAKE_CXX_COMPILER_ID MATCHES "Intel")
+	message(FATAL_ERROR "\n"
+		"Intel complier not implemented.\n\n"
+		)
+	#  set(_flags ${CMAKE_SOURCE_DIR}/cmake/compiler_flags_intel.cmake)
+	# message(STATUS "Include ${_flags}")
+	#  include(${_flags})
+	#  set(KNOWN_COMPILER TRUE)
+endif()
+
+#
+# Setup for MSVC compiler (version >= 2012):
+#
+if (CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
+	message(FATAL_ERROR "\n"
+		"MSVC compiler not implemented.\n\n"
+        )
+	#set(_flags ${CMAKE_SOURCE_DIR}/cmake/compiler_flags_msvc.cmake)
+	#message(STATUS "Include ${_flags}")
+	#include(${_flags})
+	#set(KNOWN_COMPILER TRUE)
+endif()
+
+if (NOT KNOWN_COMPILER)
+  message(FATAL_ERROR "\n"
+    "Unknown compiler!\n"
+    "If you're serious about it, set SETUP_DEFAULT_COMPILER_FLAGS=OFF "
+    "and set the relevant compiler options by hand.\n\n"
+    )
+endif()
diff --git a/cmake/setup_parameters.cmake b/cmake/setup_parameters.cmake
new file mode 100644
index 00000000..6aa8429d
--- /dev/null
+++ b/cmake/setup_parameters.cmake
@@ -0,0 +1,93 @@
+## defines default parameters
+
+## define a macro to set a variable if it is empty
+macro(SET_IF_EMPTY _variable)
+    if("${${_variable}}" STREQUAL "")
+        set(${_variable} ${ARGN})
+    endiF()
+endmacro()
+
+## populate the default values
+
+## configure.py dict(definitions) string values:
+# problem generator
+SET_IF_EMPTY(PROBLEM "shock_tube")
+
+# coordinate system
+SET_IF_EMPTY(COORDINATE_SYSTEM "cartesian")
+
+# Riemann solver
+SET_IF_EMPTY(RSOLVER "hllc")
+
+# Equation of state
+SET_IF_EMPTY(EQUATION_OF_STATE "adiabatic")
+
+## configure.py dict(definitions) Boolean values:
+# use general EOS framework default=0 (false).
+SET_IF_EMPTY(GENERAL_EOS 0)
+
+# use EOS table default=0 (false).
+SET_IF_EMPTY(EOS_TABLE_ENABLED 0)
+
+# non-barotropic equation of state (i.e. P not simply a func of rho)? default=1 (true)
+SET_IF_EMPTY(NON_BAROTROPIC_EOS 1)
+
+# include magnetic fields? default=0 (false)
+SET_IF_EMPTY(MAGNETIC_FIELDS_ENABLED 0)
+
+# include super-time-stepping? default=0 (false)
+SET_IF_EMPTY(STS_ENABLED 0)
+
+# include self gravity? default=0 (false)
+SET_IF_EMPTY(SELF_GRAVITY_ENABLED 0)
+
+# include radiative transfer? default=0 (false)
+SET_IF_EMPTY(RADIATION_ENABLED 0)
+
+# enable special or general relativity? default=0 (false)
+SET_IF_EMPTY(RELATIVISTIC_DYNAMICS 0)
+
+# enable general relativity? default=0 (false)
+SET_IF_EMPTY(GENERAL_RELATIVITY 0)
+
+# enable GR frame transformations? default=0 (false)
+SET_IF_EMPTY(FRAME_TRANSFORMATIONS 0)
+
+# use single precision floating-point values (binary32)? default=0 (false; use binary64)
+SET_IF_EMPTY(SINGLE_PRECISION_ENABLED 0)
+
+# use double precision for HDF5 output? default=0 (false; write out binary32)
+SET_IF_EMPTY(H5_DOUBLE_PRECISION_ENABLED 0)
+
+## configure.py dict(definitions) Boolean string macros:
+## (these options have the latter (false) option as defaults, unless noted otherwise)
+# make use of FFT? (FFT or NO_FFT)
+SET_IF_EMPTY(FFT_OPTION "NO_FFT")
+
+# MPI parallelization (MPI_PARALLEL or NOT_MPI_PARALLEL)
+SET_IF_EMPTY(MPI_OPTION "NOT_MPI_PARALLEL")
+
+# OpenMP parallelization (OPENMP_PARALLEL or NOT_OPENMP_PARALLEL)
+SET_IF_EMPTY(OPENMP_OPTION "NOT_OPENMP_PARALLEL")
+
+# HDF5 output (HDF5OUTPUT or NO_HDF5OUTPUT)
+SET_IF_EMPTY(HDF5_OPTION "NO_HDF5OUTPUT")
+
+# debug build macros (DEBUG or NOT_DEBUG)
+SET_IF_EMPTY(DEBUG_OPTION "NOT_DEBUG")
+
+# try/throw/catch C++ exception handling (ENABLE_EXCEPTIONS or DISABLE_EXCEPTIONS)
+SET_IF_EMPTY(EXCEPTION_HANDLING_OPTION "ENABLE_EXCEPTIONS")
+
+# compiler options
+SET_IF_EMPTY(COMPILER_CHOICE ${CMAKE_CXX_COMPILER_ID})
+SET_IF_EMPTY(COMPILER_COMMAND ${CMAKE_CXX_COMPILER})
+string(TOUPPER ${CMAKE_BUILD_TYPE} BUILD_TYPE)
+SET_IF_EMPTY(COMPILER_FLAGS ${CMAKE_CXX_FLAGS_${BUILD_TYPE}})
+
+# macros associated with numerical algorithm (rarely modified)
+SET_IF_EMPTY(NHYDRO_VARIABLES 5)
+SET_IF_EMPTY(NFIELD_VARIABLES 0)
+SET_IF_EMPTY(NWAVE_VALUE 5)
+SET_IF_EMPTY(NUMBER_PASSIVE_SCALARS 0)
+SET_IF_EMPTY(NUMBER_GHOST_CELLS 2)
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
new file mode 100644
index 00000000..9a026dd5
--- /dev/null
+++ b/src/CMakeLists.txt
@@ -0,0 +1,119 @@
+# Creates athenapp library
+
+set(namel athenapp)
+string(TOUPPER ${namel} nameu)
+
+# set GENERAL_EOS_FILE, EOS_FILE, RSOLVER_DIR, RSOLVER_FILE, PROBLEM_FILE
+set(GENERAL_EOS_FILE noop.cpp)
+set(EOS_FILE ${EQUATION_OF_STATE})
+set(RSOLVER_FILE ${RSOLVER})
+set(PROBLEM_FILE ${PROBLEM})
+
+if (MAGNETIC_FILEDS_ENABLED EQUAL 1)
+    set(EOS_FILE ${EOS_FILE}_mhd)
+    set(RSOLVER_DIR mhd/)
+    set(RSOLVER_FILE ${RSOLVER_FILE}_mhd)
+else()
+    set(EOS_FILE ${EOS_FILE}_hydro)
+    set(RSOLVER_DIR hydro/)
+endif()
+
+set(EOS_FILE ${EOS_FILE}.cpp)
+set(RSOLVER_FILE ${RSOLVER_FILE}.cpp)
+set(PROBLEM_FILE ${PROBLEM_FILE}.cpp)
+
+message(STATUS ${RSOLVER_DIR}${RSOLVER_FILE})
+
+# source files are defined in Makefile.in
+file(GLOB src_files
+    *.cpp
+    bvals/*.cpp
+    bvals/cc/*.cpp
+    bvals/cc/fft_grav/*.cpp
+    bvals/cc/hydro/*.cpp
+    bvals/cc/mg/*.cpp
+    bvals/fc/*.cpp
+    bvals/orbital/*.cpp
+    bvals/utils/*.cpp
+    coordinates/*.cpp
+    eos/general/${GENERAL_EOS_FILE}
+    eos/${EOS_FILE}
+    eos/eos_high_order.cpp
+    eos/eos_scalars.cpp
+    fft/*.cpp
+    field/*.cpp
+    field/field_diffusion/*.cpp
+    gravity/*.cpp
+    hydro/*.cpp
+    hydro/srcterms/*.cpp
+    hydro/hydro_diffusion/*.cpp
+    hydro/rsolvers/${RSOLVER_DIR}${RSOLVER_FILE}
+    inputs/*.cpp
+    mesh/*.cpp
+    multigrid/*.cpp
+    orbital_advection/*.cpp
+    outputs/*.cpp
+    pgen/default_pgen.cpp
+    pgen/${PROBLEM_FILE}
+    reconstruct/*.cpp
+    scalars/*.cpp
+    task_list/*.cpp
+    utils/*.cpp
+    ${MPIFFT_FILE}
+  )
+
+# remove main file
+if (EXISTS "${CMAKE_SOURCE_DIR}/src/main.cpp")
+    list(FILTER src_files EXCLUDE REGEX ".*/src/main\\.cpp$")
+endif()
+
+# user mod calcualte_fluxes
+if (EXISTS "${CMAKE_SOURCE_DIR}/mod/hydro/calculate_fluxes.cpp")
+    message(STATUS "Found calculate_fluxes.cpp in ${CMAKE_SOURCE_DIR}/mod/hydro/calculate_fluxes.cpp")
+    list(FILTER src_files EXCLUDE REGEX ".*/mod/hydro/calculate_fluxes\\.cpp$")
+endif()
+
+# user mod new_blockdt
+if (EXISTS "${CMAKE_SOURCE_DIR}/mod/hydro/new_blockdt.cpp")
+    message(STATUS "Found new_blockdt.cpp in ${CMAKE_SOURCE_DIR}/mod/hydro/new_blockdt.cpp")
+    list(FILTER src_files EXCLUDE REGEX ".*/mod/hydro/new_blockdt\\.cpp$")
+endif()
+
+# user mod outputs delegates
+if (EXISTS "${CMAKE_SOURCE_DIR}/mod/outputs/outputs.cpp")
+    message(STATUS "Found outputs.cpp in ${CMAKE_SOURCE_DIR}/mod/outputs/outputs.cpp")
+    list(FILTER src_files EXCLUDE REGEX ".*/mod/outputs/outputs\\.cpp$")
+endif()
+
+string(TOLOWER ${CMAKE_BUILD_TYPE} buildl)
+string(TOUPPER ${CMAKE_BUILD_TYPE} buildu)
+
+add_library(${namel}_${buildl} 
+    OBJECT 
+    ${src_files}
+    )
+
+set_target_properties(${namel}_${buildl}
+    PROPERTIES
+    COMPILE_FLAGS ${CMAKE_CXX_FLAGS_${buildu}}
+    )
+
+target_include_directories(${namel}_${buildl}
+    SYSTEM PRIVATE
+    ${MPI_CXX_INCLUDE_PATH}
+    )
+
+target_link_libraries(${namel}_${buildl}
+    ${MPI_CXX_LIBRARIES}
+    )
+
+set(${nameu}_LIBRARY_${buildu} ${namel}_${buildl}
+    CACHE STRING
+    "{namel} library ${buildu}"
+    )
+mark_as_advanced(${nameu}_LIBRARY_${buildu})
+
+set(ATHENAPP_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/src
+  CACHE PATH 
+  "${namel} include directory")
+mark_as_advanced(ATHENAPP_INCLUDE_DIR)