Merge branch '4-write-a-basic-test-simulation-and-user-guide-for-sphe…

…rical-harmonics-use' into 3-convert-the-basic-installation-instructions-from-the-readmemd-file-to-the-first-section-of-the-getting-started-section-of-the-documentation
MintonGroup · Feb 29, 2024 · 259314b · 259314b
2 parents a56dd5d + 4b3f764
commit 259314b
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diff --git a/.gitignore b/.gitignore
@@ -37,13 +37,15 @@ swiftest-*
 __pycache__*
 _cmake*
 _dependencies
+!SHTOOLS
+!SHTOOLS/**
 
 
 #Documentation
 !.readthedocs.yaml
 !docs/
 !docs/**/*
-docs/_build/
+!docs/_build/
 docs/_build/**/*
 docs/generated/
 docs/generated/**/*
@@ -64,14 +66,14 @@ docs/_static/fortran_docs/*/**
 !environment.yml
 !.dockerignore
 
+swiftest/_bindings.cpython*
 bin/
 build/*
-hdf5-*
-netcdf-c-*
-netcdf-fortran-*
-zlib-*
+lib*
 
 actions-runner*
 
 env/**
 venv/**
+
+sandbox/**
diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "SHTOOLS"]
+	path = SHTOOLS
+	url = https://github.com/profminton/SHTOOLS
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -11,7 +11,7 @@
 ##################################################
 # Define the project and the depencies that it has
 ##################################################
-CMAKE_MINIMUM_REQUIRED(VERSION 3.6.0...3.27.1)
+CMAKE_MINIMUM_REQUIRED(VERSION 3.23.1...3.28.3)
 SET(SKBUILD_PROJECT_NAME "swiftest" CACHE STRING "Name of project set by scikit-build")
 
 # Get version stored in text file
@@ -28,27 +28,44 @@ ELSE()
         CMAKE_POLICY(SET CMP0148 OLD)
     ENDIF ()
 
+    # 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()
+
     # 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" ON)
 
+    # Define the paths to the source code and python files
+    SET(SRC "${CMAKE_SOURCE_DIR}/src")
+    SET(PY "${CMAKE_SOURCE_DIR}/swiftest")
+
+    # Make sure paths are correct for Unix or Windows style
+    FILE(TO_CMAKE_PATH ${SRC} SRC)
+    FILE(TO_CMAKE_PATH ${PY} PY)
+
     INCLUDE(GNUInstallDirs)
     IF (SKBUILD)
-        SET(INSTALL_BINDIR ${SKBUILD_PLATLIB_DIR}/${SKBUILD_PROJECT_NAME}) 
-        SET(INSTALL_LIBDIR ${SKBUILD_PLATLIB_DIR}/${SKBUILD_PROJECT_NAME}) 
-        SET(INSTALL_INCLUDEDIR ${INSTALL_LIBDIR}) 
+        SET(INSTALL_BINDIR ${SKBUILD_SCRIPTS_DIR})
+        SET(INSTALL_LIBDIR ${SKBUILD_DATA_DIR}/lib) 
+        SET(INSTALL_INCLUDEDIR ${SKBUILD_HEADERS_DIR}) 
+        SET(INSTALL_PYPROJ ${SKBUILD_PLATLIB_DIR}/${SKBUILD_PROJECT_NAME}) 
         IF (APPLE)
-            SET(CMAKE_INSTALL_RPATH "@loader_path")
+            SET(CMAKE_INSTALL_RPATH "@loader_path;${CMAKE_BINARY_DIR}/bin")
         ELSEIF (LINUX)
-            SET(CMAKE_INSTALL_RPATH $ORIGIN)
+            SET(CMAKE_INSTALL_RPATH "@ORIGIN;${CMAKE_BINARY_DIR}/bin")
         ENDIF ()
     ELSE ()
+        SET(INSTALL_PYPROJ ${PY})
         SET(INSTALL_BINDIR ${CMAKE_INSTALL_BINDIR})
         SET(INSTALL_LIBDIR ${CMAKE_INSTALL_LIBDIR})
         SET(INSTALL_INCLUDEDIR ${CMAKE_INSTALL_INCLUDEDIR})
     ENDIF ()
+
+    SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
 
     # Have the .mod files placed in the include folder
     SET(CMAKE_Fortran_MODULE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/mod)
@@ -57,6 +74,7 @@ ELSE()
     FILE(TO_CMAKE_PATH "${CMAKE_SOURCE_DIR}/cmake/Modules" LOCAL_MODULE_PATH)
     LIST(APPEND CMAKE_MODULE_PATH ${LOCAL_MODULE_PATH})
 
+    # Add in the external dependency libraries 
     IF (CMAKE_Fortran_COMPILER_ID MATCHES "^Intel")
         SET(COMPILER_OPTIONS "Intel" CACHE STRING "Compiler identified as Intel")
     ELSEIF (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU")
@@ -65,10 +83,22 @@ ELSE()
         MESSAGE(FATAL_ERROR "Compiler ${CMAKE_Fortran_COMPILER_ID} not recognized!") 
     ENDIF ()
 
-    # 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")
+    IF (COMPILER_OPTIONS STREQUAL "GNU")
+        IF (APPLE)
+            SET(BLA_VENDOR "Apple" CACHE STRING "BLAS vendor")
+        ELSE ()
+            SET(BLA_VENDOR "OpenBLAS" CACHE STRING "BLAS vendor")
+        ENDIF ()
+    ELSEIF (COMPILER_OPTIONS STREQUAL "INTEL")
+        SET(BLA_VENDOR "Intel10_64lp" CACHE STRING "BLAS vendor")
     ENDIF()
+    SET(BLA_STATIC ON)
+    FIND_PACKAGE(BLAS REQUIRED)
+    FIND_PACKAGE(LAPACK REQUIRED)
+    FIND_PACKAGE(FFTW3 REQUIRED)
+    FIND_PACKAGE(SHTOOLS REQUIRED)
+
+
 
     FIND_PACKAGE(NETCDF_Fortran REQUIRED)
     IF (MSVC)
@@ -85,9 +115,6 @@ ELSE()
     FIND_PACKAGE(Python COMPONENTS Interpreter Development.Module REQUIRED)
 
 
-    SET(SRC "${CMAKE_SOURCE_DIR}/src")
-    SET(PY "${CMAKE_SOURCE_DIR}/swiftest")
-
     #####################################
     # Tell how to install this executable
     #####################################
@@ -99,11 +126,6 @@ ELSE()
         SET(CMAKE_INSTALL_PREFIX /usr/local CACHE PATH "Path for install")
     ENDIF()
 
-
-    # Make sure paths are correct for Unix or Windows style
-    FILE(TO_CMAKE_PATH ${SRC} SRC)
-    FILE(TO_CMAKE_PATH ${PY} PY)
-
     # Set the name of the swiftest library
     SET(SWIFTEST_LIBRARY ${SKBUILD_PROJECT_NAME})
 
@@ -113,13 +135,11 @@ ELSE()
     ENDIF(NOT CMAKE_Fortran_COMPILER_SUPPORTS_F90)
     INCLUDE(SetParallelizationLibrary)
 
-    IF (COMPILER_OPTIONS STREQUAL "Intel" AND NOT CMAKE_SYSTEM_NAME STREQUAL "Windows")
-        INCLUDE(SetMKL)
-    ENDIF ()
     INCLUDE(SetSwiftestFlags) 
 
-
-
+    IF (NOT BUILD_SHARED_LIBS)
+        SET(CMAKE_POSITION_INDEPENDENT_CODE ON)
+    ENDIF()
     # The source for the SWIFTEST binary and have it placed in the bin folder
     ADD_SUBDIRECTORY(${SRC} ${CMAKE_INSTALL_BINDIR})
     ADD_SUBDIRECTORY(${PY})

diff --git a/README_tables/add_body_kwargs.md b/README_tables/add_body_kwargs.md
@@ -15,7 +15,7 @@
 | ```Gmass```     | Gravitational mass value(s) of bodies. Only for massive bodies. Only  ```mass``` **OR** ```Gmass``` may be set.                         | float or array-like of floats
 | ```radius```    | Radius value(s) of bodies. Only for massive bodies.                                                                                     | float or array-like of floats
 | ```rhill```     | Hill Radius value(s) of bodies. Only for massive bodies.                                                                                | float or array-like of floats
-| ```rot```       | Rotation rate vector(s) of bodies in degrees/sec. Only for massive bodies. Only used if ```rotation``` is set to ```True```.                           | (n,3) array-like of floats
+| ```rot```       | Rotation rate vector(s) of bodies in degrees/TU. Only for massive bodies. Only used if ```rotation``` is set to ```True```.                           | (n,3) array-like of floats
 | ```Ip```        | Principal axes moments of inertia vector(s) of bodies. Only for massive bodies. Only used if ```rotation``` is set to ```True```.       | (n,3) array-like of floats
 | ```J2```        | The unitless value of the spherical harmonic term equal to J2*R^2 where R is the radius of the central body.                                                                                                     | float or array-like of floats
 | ```J4```        | The unitless value of the spherical harmonic term equal to J4*R^4 where R is the radius of the central body.                                                                                                     | float or array-like of floats
diff --git a/SHTOOLS b/SHTOOLS
diff --git a/buildscripts/_build_getopts.sh b/buildscripts/_build_getopts.sh
@@ -14,7 +14,8 @@ SCRIPT_DIR=$(realpath $(dirname $0))
 ROOT_DIR=$(realpath ${SCRIPT_DIR}/..)
 
 # Get platform and architecture
-read -r OS ARCH < <($SCRIPT_DIR/get_platform.sh)
+OS=$(uname -s)
+ARCH=$(uname -m)
 
 # Parse arguments
 USTMT="Usage: ${0} [-d /path/to/dependency/source] [-p /prefix/path] [-m MACOSX_DEPLOYMENT_TARGET]"
@@ -53,8 +54,22 @@ BUILD_DIR=${BUILD_DIR:-"${HOME}/Downloads"}
 PREFIX=${PREFIX:-"/usr/local"}
 DEPENDENCY_DIR=${DEPENDENCY_DIR:-${BUILD_DIR}}
 
-mkdir -p ${DEPENDENCY_DIR}
-mkdir -p ${PREFIX}/lib
-mkdir -p ${PREFIX}/include
-mkdir -p ${PREFIX}/share
-mkdir -p ${PREFIX}/bin
+
+case $OS in
+    Linux*)
+        . ${SCRIPT_DIR}/set_environment_linux.sh
+        ;;
+    MacOSX|Darwin)
+        . ${SCRIPT_DIR}/set_environment_macos.sh
+        ;;
+
+    *)
+        printf "Unknown compiler type: ${OS}\n"
+        echo "Valid options are Linux, MacOSX, or Darwin"
+        printf $USTMT
+        exit 1
+        ;;
+esac
+
+
+mkdir -p ${DEPENDENCY_DIR}
diff --git a/buildscripts/build_dependencies.sh b/buildscripts/build_dependencies.sh
@@ -50,6 +50,7 @@ ${SCRIPT_DIR}/build_zlib.sh ${ARGS}
 ${SCRIPT_DIR}/build_hdf5.sh ${ARGS}
 ${SCRIPT_DIR}/build_netcdf-c.sh ${ARGS}
 ${SCRIPT_DIR}/build_netcdf-fortran.sh ${ARGS}
+${SCRIPT_DIR}/build_shtools.sh ${ARGS}
 
 printf "\n"
 printf "*********************************************************\n"

diff --git a/buildscripts/build_hdf5.sh b/buildscripts/build_hdf5.sh
@@ -11,8 +11,8 @@
 # You should have received a copy of the GNU General Public License along with Swiftest. 
 # If not, see: https://www.gnu.org/licenses. 
 
-HDF5_VER="1_14_2"
-ZLIB_VER="1.3"
+HDF5_VER="1_14_3"
+ZLIB_VER="1.3.1"
 
 SCRIPT_DIR=$(realpath $(dirname $0))
 set -a
@@ -27,7 +27,7 @@ printf "*********************************************************\n"
 printf "*          STARTING DEPENDENCY BUILD                    *\n"
 printf "*********************************************************\n"
 printf "Using ${OS} compilers:\nFC: ${FC}\nCC: ${CC}\nCXX: ${CXX}\n"
-printf "Installing to ${PREFIX}\n"
+printf "Installing to ${HDF5_ROOT}\n"
 printf "\n"
 
 printf "*********************************************************\n"
@@ -60,13 +60,11 @@ printf "CPPFLAGS: ${CPPFLAGS}\n"
 printf "CPATH: ${CPATH}\n"
 printf "LD_LIBRARY_PATH: ${LD_LIBRARY_PATH}\n"
 printf "LDFLAGS: ${LDFLAGS}\n"
+printf "INSTALL_PREFIX: ${HDF5_ROOT}\n"
 printf "*********************************************************\n"
 
 cd ${DEPENDENCY_DIR}/hdfsrc
 
-HDF5_ROOT=${PREFIX}
-ZLIB_ROOT=${PREFIX}
-SZIP_ROOT=${PREFIX}
 if [ $OS = "MacOSX" ]; then
     ZLIB_LIBRARY="${ZLIB_ROOT}/lib/libz.dylib"
 else
@@ -85,6 +83,7 @@ ARGLIST="-DCMAKE_INSTALL_PREFIX:PATH=${HDF5_ROOT} \
     -DHDF5_BUILD_FORTRAN:BOOL=OFF \
     -DHDF5_BUILD_EXAMPLES:BOOL=ON \
     -DBUILD_TESTING:BOOL=ON \
+    -DBUILD_STATIC_LIBS:BOOL=OFF \
     -DHDF5_BUILD_JAVA:BOOL=OFF"
 
 if [ $OS = "MacOSX" ]; then
@@ -94,7 +93,7 @@ fi
 cmake -B build -C ./config/cmake/cacheinit.cmake -G Ninja ${ARGLIST} .
 
 cmake --build build -j${NPROC} --config Release
-if [ -w ${PREFIX} ]; then
+if [ -w ${HDF5_ROOT} ]; then
     cmake --install build 
 else
     sudo cmake --install build 

diff --git a/buildscripts/build_netcdf-c.sh b/buildscripts/build_netcdf-c.sh
@@ -22,7 +22,7 @@ printf "*********************************************************\n"
 printf "*          STARTING DEPENDENCY BUILD                    *\n"
 printf "*********************************************************\n"
 printf "Using ${OS} compilers:\nFC: ${FC}\nCC: ${CC}\nCXX: ${CXX}\n"
-printf "Installing to ${PREFIX}\n"
+printf "Installing to ${NCDIR}\n"
 printf "\n"
 
 NC_VER="4.9.2"
@@ -48,16 +48,15 @@ printf "CPATH: ${CPATH}\n"
 printf "LD_LIBRARY_PATH: ${LD_LIBRARY_PATH}\n"
 printf "LDFLAGS: ${LDFLAGS}\n"
 printf "HDF5_ROOT: ${HDF5_ROOT}\n"
+printf "INSTALL_PREFIX: ${NCDIR}\n"
 printf "*********************************************************\n"
 
 cd ${DEPENDENCY_DIR}/netcdf-c-*
-NCDIR="${PREFIX}"
-ZLIB_ROOT=${PREFIX}
 cmake -B build -S . -G Ninja  \
     -DCMAKE_BUILD_TYPE:STRING="Release" \
     -DHDF5_DIR:PATH=${HDF5_ROOT}/cmake \
     -DHDF5_ROOT:PATH=${HDF5_ROOT} \
-    -DCMAKE_FIND_ROOT_PATH:PATH="${PREFIX}" \
+    -DCMAKE_FIND_ROOT_PATH:PATH="${NCDIR}" \
     -DCMAKE_INSTALL_PREFIX:STRING="${NCDIR}" \
     -DENABLE_DAP:BOOL=OFF \
     -DENABLE_BYTERANGE:BOOL=OFF \
@@ -68,7 +67,7 @@ cmake -B build -S . -G Ninja  \
     -DENABLE_REMOTE_FORTRAN_BOOTSTRAP:BOOL=ON
 
 cmake --build build -j${NPROC} 
-if [ -w ${PREFIX} ]; then
+if [ -w ${NCDIR} ]; then
     cmake --install build 
 else
     sudo cmake --install build 

diff --git a/buildscripts/build_netcdf-fortran.sh b/buildscripts/build_netcdf-fortran.sh
@@ -22,7 +22,7 @@ printf "*********************************************************\n"
 printf "*          STARTING DEPENDENCY BUILD                    *\n"
 printf "*********************************************************\n"
 printf "Using ${OS} compilers:\nFC: ${FC}\nCC: ${CC}\nCXX: ${CXX}\n"
-printf "Installing to ${PREFIX}\n"
+printf "Installing to ${NFDIR}\n"
 printf "\n"
 
 NF_VER="4.6.1"
@@ -49,7 +49,6 @@ printf "LDFLAGS: ${LDFLAGS}\n"
 printf "*********************************************************\n"
 
 cd ${DEPENDENCY_DIR}/netcdf-fortran-*
-NFDIR="${PREFIX}"
 NCLIBDIR=$(${NCDIR}/bin/nc-config --libdir)
 if [ $OS = "MacOSX" ]; then
     netCDF_LIBRARIES="${NCLIBDIR}/libnetcdf.dylib"
@@ -62,7 +61,7 @@ cmake -B build -S . -G Ninja \
     -DCMAKE_INSTALL_PREFIX:PATH=${NFDIR} \
     -DCMAKE_INSTALL_LIBDIR="lib"
 cmake --build build -j${NPROC} 
-if [ -w ${PREFIX} ]; then
+if [ -w ${NFDIR} ]; then
     cmake --install build 
 else
     sudo cmake --install build