Added some template CMake files and cleaned up the ignore files a bit

.gitignore

@@ -1,10 +1,14 @@
 # Whitelist ignore file: Ignore everything that isn't explicitly included
 *
+!*/
 !ctem/**
 !examples/**
-!/src/**
+!src/**
+!cmake/**
+!**/.gitignore
 !*.f90
 !*.py
+!*.cmake
 !README.md
 !ctem.in
 !craterlist.in
@@ -13,5 +17,9 @@
 !NPFextrap.dat
 !FassettCounts.txt
 !NonMareNonSpa-Highlands.csv
-
+!CMakeLists.txt
+!version.txt
+*.mod
+**/.idea
+**/__pycache__
 

CMakeLists.txt

@@ -0,0 +1,78 @@
+# Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+# This file is part of Swiftest.
+# Swiftest is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License 
+# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+# Swiftest is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty 
+# of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+# You should have received a copy of the GNU General Public License along with Swiftest. 
+# If not, see: https://www.gnu.org/licenses. 
+
+# CMake project file for Swiftest
+##################################################
+# Define the project and the depencies that it has
+##################################################
+CMAKE_MINIMUM_REQUIRED(VERSION 3.6.0...3.27.1)
+
+# Get version stored in text file
+FILE(READ "version.txt" VERSION)
+PROJECT(${SKBUILD_PROJECT_NAME} LANGUAGES C Fortran VERSION ${VERSION})
+
+IF (CMAKE_Fortran_COMPILER_ID MATCHES "^Intel")
+    SET(COMPILER_OPTIONS "Intel" CACHE STRING "Compiler identified as Intel")
+ELSEIF (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
+    SET(COMPILER_OPTIONS "GNU" CACHE STRING "Compiler identified as gfortran")
+ELSE ()
+    MESSAGE(FATAL_ERROR "Compiler ${CMAKE_Fortran_COMPILER_ID} not recognized!") 
+ENDIF ()
+
+# Set some options the user may choose
+OPTION(USE_COARRAY "Use Coarray Fortran for parallelization of test particles" OFF)
+OPTION(USE_OPENMP "Use OpenMP for parallelization" ON)
+OPTION(USE_SIMD "Use SIMD vectorization" ON)
+OPTION(BUILD_SHARED_LIBS "Build using shared libraries" OFF)
+
+# The following section is modified from Numpy f2py documentation
+IF(PROJECT_SOURCE_DIR STREQUAL PROJECT_BINARY_DIR)
+  MESSAGE(FATAL_ERROR "In-source builds not allowed. Please make a new directory (called a build directory) and run CMake from there.\n")
+ENDIF()
+
+# Ensure scikit-build modules
+FIND_PACKAGE(Python COMPONENTS Interpreter Development.Module REQUIRED)
+
+# Add our local modules to the module path
+FILE(TO_CMAKE_PATH "${CMAKE_SOURCE_DIR}/cmake/Modules" LOCAL_MODULE_PATH)
+LIST(APPEND CMAKE_MODULE_PATH ${LOCAL_MODULE_PATH})
+
+# Define some directories that are important to the build
+SET(SRC "${CMAKE_SOURCE_DIR}/src")
+SET(LIB "${CMAKE_SOURCE_DIR}/lib")
+SET(BIN "${CMAKE_SOURCE_DIR}/bin")
+SET(MOD "${CMAKE_SOURCE_DIR}/include")
+SET(PY "${CMAKE_SOURCE_DIR}/ctem")
+
+# Make sure paths are correct for Unix or Windows style
+FILE(TO_CMAKE_PATH ${SRC} SRC)
+FILE(TO_CMAKE_PATH ${LIB} LIB)
+FILE(TO_CMAKE_PATH ${BIN} BIN)
+FILE(TO_CMAKE_PATH ${MOD} MOD)
+FILE(TO_CMAKE_PATH ${PY} PY)
+
+set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${LIB})
+set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${LIB})
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${BIN})
+
+# Have the .mod files placed in the lib folder
+SET(CMAKE_Fortran_MODULE_DIRECTORY ${MOD})
+
+# Set the name of the ctem library
+SET(CTEM_LIBRARY ctem)
+
+# The source for the CTEM binary and have it placed in the bin folder
+ADD_SUBDIRECTORY(${SRC} ${BIN})
+
+ADD_SUBDIRECTORY(${PY})
+
+# Add a distclean target to the Makefile
+ADD_CUSTOM_TARGET(distclean 
+    COMMAND ${CMAKE_COMMAND} -P "${CMAKE_SOURCE_DIR}/distclean.cmake"
+)

cmake/Modules/FindCoarray_Fortran.cmake

@@ -0,0 +1,117 @@
+# Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+# This file is part of Swiftest.
+# Swiftest is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License 
+# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+# Swiftest is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty 
+# of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+# You should have received a copy of the GNU General Public License along with Swiftest. 
+# If not, see: https://www.gnu.org/licenses. 
+
+# - Finds Coarray support
+# This module can be used to detect Coarray support in a compiler.
+# If the compiler supports Coarray, the flags required to compile with
+# coarray support are set.  
+#
+# This module was modified from the standard FindOpenMP module to find Fortran
+# flags.
+#
+# The following variables are set:
+#   Coarray_Fortran_FLAGS - flags to add to the Fortran compiler for Coarray
+#                          support.  In general, you must use these at both
+#                          compile- and link-time.
+#   OMP_NUM_PROCS - the max number of processors available to Coarray
+
+#=============================================================================
+
+INCLUDE (FindPackageHandleStandardArgs)
+
+STRING(TOUPPER "${CMAKE_BUILD_TYPE}" BT)
+IF(BT STREQUAL "DEBUG")
+    IF (COMPILER_OPTIONS STREQUAL "Intel")
+        SET (Coarray_Fortran_FLAG_CANDIDATES
+            #Intel
+            "-coarray=single"
+            #Intel windows
+            "/Qcoarray:single" 
+            #Empty, if compiler automatically accepts coarray
+            " "
+        )
+    ELSEIF (COMPILER_OPTIONS STREQUAL "GNU")
+        SET (Coarray_Fortran_FLAG_CANDIDATES
+            #Gnu
+            "-fcoarray=single"
+            #Empty, if compiler automatically accepts coarray
+            " "
+    )
+    ENDIF()
+ELSE()
+    IF (COMPILER_OPTIONS STREQUAL "Intel")
+        SET (Coarray_Fortran_FLAG_CANDIDATES
+            #Intel
+            "-coarray=distributed"
+            #Intel windows
+            "/Qcoarray:distributed" 
+            #Empty, if compiler automatically accepts coarray
+            " "
+        )
+    ELSEIF (COMPILER_OPTIONS STREQUAL "GNU") 
+        SET (Coarray_Fortran_FLAG_CANDIDATES
+            #Gnu
+            "-fcoarray=lib -lcaf_mpi"
+            #Empty, if compiler automatically accepts coarray
+            " "
+        )
+ENDIF()
+
+
+IF (DEFINED Coarray_Fortran_FLAGS)
+    SET (Coarray_Fortran_FLAG_CANDIDATES)
+ENDIF (DEFINED Coarray_Fortran_FLAGS)
+
+# check fortran compiler. also determine number of processors
+FOREACH (FLAG ${Coarray_Fortran_FLAG_CANDIDATES})
+    SET (SAFE_CMAKE_REQUIRED_FLAGS "${CMAKE_REQUIRED_FLAGS}")
+    SET (CMAKE_REQUIRED_FLAGS "${FLAG}")
+    UNSET (Coarray_FLAG_DETECTED CACHE)
+    MESSAGE (STATUS "Try Coarray Fortran flag = [${FLAG}]")
+    FILE (WRITE "${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeTmp/testFortranCoarray.f90" 
+"
+program TestCoarray
+ integer, codimension[*] :: i
+ write(*,'(I2)',ADVANCE='NO') num_images()
+end program TestCoarray
+")
+    SET (MACRO_CHECK_FUNCTION_DEFINITIONS
+         "-DCoarray_FLAG_DETECTED ${CMAKE_REQUIRED_FLAGS}")
+    TRY_RUN (Coarray_RUN_FAILED Coarray_FLAG_DETECTED ${CMAKE_BINARY_DIR}
+        ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeTmp/testFortranCoarray.f90
+        COMPILE_DEFINITIONS ${CMAKE_REQUIRED_DEFINITIONS}
+        CMAKE_FLAGS -DCOMPILE_DEFINITIONS:STRING=${MACRO_CHECK_FUNCTION_DEFINITIONS}
+        COMPILE_OUTPUT_VARIABLE OUTPUT
+        RUN_OUTPUT_VARIABLE OMP_NUM_PROCS_INTERNAL)
+    IF (Coarray_FLAG_DETECTED)
+        FILE (APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeOutput.log
+             "Determining if the Fortran compiler supports Coarray passed with "
+             "the following output:\n${OUTPUT}\n\n")
+        SET (Coarray_FLAG_DETECTED 1)
+        IF (Coarray_RUN_FAILED)
+            MESSAGE (FATAL_ERROR "Coarray found, but test code did not run")
+        ENDIF (Coarray_RUN_FAILED)
+        SET (Coarray_Fortran_FLAGS_INTERNAL "${FLAG}")
+        BREAK ()
+    ELSE ()
+        FILE (APPEND ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeError.log
+             "Determining if the Fortran compiler supports Coarray failed with "
+             "the following output:\n${OUTPUT}\n\n")
+        SET (Coarray_FLAG_DETECTED 0)
+    ENDIF (Coarray_FLAG_DETECTED)
+ENDFOREACH (FLAG ${Coarray_Fortran_FLAG_CANDIDATES})
+
+SET (Coarray_Fortran_FLAGS "${Coarray_Fortran_FLAGS_INTERNAL}"
+     CACHE STRING "Fortran compiler flags for Coarray parallization")
+
+# handle the standard arguments for FIND_PACKAGE
+FIND_PACKAGE_HANDLE_STANDARD_ARGS (Coarray_Fortran DEFAULT_MSG 
+    Coarray_Fortran_FLAGS)
+
+MARK_AS_ADVANCED(Coarray_Fortran_FLAGS)

cmake/Modules/FindCython.cmake

@@ -0,0 +1,88 @@
+#.rst:
+#
+# Find ``cython`` executable.
+#
+# This module will set the following variables in your project:
+#
+#  ``CYTHON_EXECUTABLE``
+#    path to the ``cython`` program
+#
+#  ``CYTHON_VERSION``
+#    version of ``cython``
+#
+#  ``CYTHON_FOUND``
+#    true if the program was found
+#
+# For more information on the Cython project, see https://cython.org/.
+#
+# *Cython is a language that makes writing C extensions for the Python language
+# as easy as Python itself.*
+#
+#=============================================================================
+# Copyright 2011 Kitware, Inc.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#=============================================================================
+
+# Use the Cython executable that lives next to the Python executable
+# if it is a local installation.
+if(Python_EXECUTABLE)
+  get_filename_component(_python_path ${Python_EXECUTABLE} PATH)
+elseif(Python3_EXECUTABLE)
+  get_filename_component(_python_path ${Python3_EXECUTABLE} PATH)
+elseif(DEFINED PYTHON_EXECUTABLE)
+  get_filename_component(_python_path ${PYTHON_EXECUTABLE} PATH)
+endif()
+
+if(DEFINED _python_path)
+  find_program(CYTHON_EXECUTABLE
+               NAMES cython cython.bat cython3
+               HINTS ${_python_path}
+               DOC "path to the cython executable")
+else()
+  find_program(CYTHON_EXECUTABLE
+               NAMES cython cython.bat cython3
+               DOC "path to the cython executable")
+endif()
+
+if(CYTHON_EXECUTABLE)
+  set(CYTHON_version_command ${CYTHON_EXECUTABLE} --version)
+
+  execute_process(COMMAND ${CYTHON_version_command}
+                  OUTPUT_VARIABLE CYTHON_version_output
+                  ERROR_VARIABLE CYTHON_version_error
+                  RESULT_VARIABLE CYTHON_version_result
+                  OUTPUT_STRIP_TRAILING_WHITESPACE
+                  ERROR_STRIP_TRAILING_WHITESPACE)
+
+  if(NOT ${CYTHON_version_result} EQUAL 0)
+    set(_error_msg "Command \"${CYTHON_version_command}\" failed with")
+    set(_error_msg "${_error_msg} output:\n${CYTHON_version_error}")
+    message(SEND_ERROR "${_error_msg}")
+  else()
+    if("${CYTHON_version_output}" MATCHES "^[Cc]ython version ([^,]+)")
+      set(CYTHON_VERSION "${CMAKE_MATCH_1}")
+    else()
+      if("${CYTHON_version_error}" MATCHES "^[Cc]ython version ([^,]+)")
+        set(CYTHON_VERSION "${CMAKE_MATCH_1}")
+      endif()
+    endif()
+  endif()
+endif()
+
+include(FindPackageHandleStandardArgs)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(Cython REQUIRED_VARS CYTHON_EXECUTABLE)
+
+mark_as_advanced(CYTHON_EXECUTABLE)
+
+include(UseCython)

cmake/Modules/FindMKL.cmake

@@ -0,0 +1,17 @@
+# Copyright 2022 - David Minton, Carlisle Wishard, Jennifer Pouplin, Jake Elliott, & Dana Singh
+# This file is part of Swiftest.
+# Swiftest is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License 
+# as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+# Swiftest is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty 
+# of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+# You should have received a copy of the GNU General Public License along with Swiftest. 
+# If not, see: https://www.gnu.org/licenses. 
+
+# - Finds the Intel MKL libraries 
+find_path(MKL_INCLUDE_DIR NAMES mkl.h HINTS ENV MKLROOT PATH_SUFFIXES include)
+find_library(MKL_LIBRARY NAMES libmkl_core.a  HINTS ENV MKLROOT PATH_SUFFIXES lib lib/intel64 )
+
+set(MKL_FOUND TRUE)
+set(MKL_INCLUDE_DIRS ${MKL_INCLUDE_DIR})
+set(MKL_LIBRARIES ${MKL_LIBRARY})
+mark_as_advanced(MKL_LIBRARY MKL_INCLUDE_DIR)