diff --git a/.github/workflows/esmf-8.0.1_jasper-2.0.22_nceplibs-1.3.0.yml b/.github/workflows/esmf-8.0.1_jasper-2.0.22_nceplibs-1.3.0.yml new file mode 100644 index 000000000..48fe75cef --- /dev/null +++ b/.github/workflows/esmf-8.0.1_jasper-2.0.22_nceplibs-1.3.0.yml @@ -0,0 +1,155 @@ +name: esmf-8.0.1_jasper-2.0.22_nceplibs-1.3.0 +on: [push, pull_request] + +jobs: + build: + runs-on: ${{ matrix.os }} + env: + CC: gcc-9 + FC: gfortran-9 + CXX: g++-9 + strategy: + matrix: + os: [macos-10.15, ubuntu-20.04] + compiler: [gcc-9] + + steps: + + - name: cache-mpich + id: cache-mpich + uses: actions/cache@v2 + with: + path: ~/mpich + key: mpich-${{ runner.os }}-3.3.2-1 + + - name: build-mpich + if: steps.cache-mpich.outputs.cache-hit != 'true' + run: | + if [[ ${{ matrix.os }} == "macos-10.15" ]]; then + wget http://www.mpich.org/static/downloads/3.3.2/mpich-3.3.2.tar.gz &> /dev/null + tar -xzf mpich-3.3.2.tar.gz + pushd mpich-3.3.2 + ./configure --prefix=$HOME/mpich + make + sudo make install + popd + fi + + - name: install-dependencies + run: | + echo "$HOME/mpich/bin" >> $GITHUB_PATH + if [[ ${{ matrix.os }} == "ubuntu-20.04" ]]; then + sudo apt-get update + sudo apt-get install libmpich-dev + sudo apt-get install doxygen + sudo apt-get install libnetcdf-dev libnetcdff-dev netcdf-bin pkg-config + sudo apt-get install libpng-dev + sudo apt-get install libjpeg-dev + elif [[ ${{ matrix.os }} == "macos-10.15" ]]; then + brew update + brew install doxygen + brew install mpich + brew install netcdf + brew install wget + if [[ ${{ matrix.compiler }} == "gcc-9" ]]; then + sudo ln -sf /usr/local/bin/gfortran-9 /usr/local/bin/gfortran + elif [[ ${{ matrix.compiler }} == "gcc-10" ]]; then + sudo ln -sf /usr/local/bin/gfortran-10 /usr/local/bin/gfortran + fi + fi + + - name: cache-esmf + id: cache-esmf + uses: actions/cache@v2 + with: + path: ~/esmf + key: esmf-${{ runner.os }}-8.0.1-2 + + - name: build-esmf + if: steps.cache-esmf.outputs.cache-hit != 'true' + run: | + set -x + pushd ~ + export ESMF_DIR=~/esmf-ESMF_8_0_1 + wget https://github.com/esmf-org/esmf/archive/ESMF_8_0_1.tar.gz &> /dev/null && ls -l + tar zxf ESMF_8_0_1.tar.gz && ls -l + cd esmf-ESMF_8_0_1 + export ESMF_COMM=mpich3 + export ESMF_INSTALL_BINDIR=bin + export ESMF_INSTALL_LIBDIR=lib + export ESMF_INSTALL_MODDIR=mod + export ESMF_COMPILER=gfortran + export ESMF_INSTALL_PREFIX=~/esmf + export ESMF_NETCDF=split + if [[ ${{ matrix.os }} == "ubuntu-20.04" ]]; then + export ESMF_NETCDF_INCLUDE=/usr/include + export ESMF_NETCDF_LIBPATH=/usr/x86_64-linux-gnu + elif [[ ${{ matrix.os }} == "macos-10.15" ]]; then + export ESMF_NETCDF_INCLUDE=/usr/local/include + export ESMF_NETCDF_LIBPATH=/usr/local/lib + fi + make -j2 + make install + + - name: cache-jasper + id: cache-jasper + uses: actions/cache@v2 + with: + path: ~/jasper + key: jasper-${{ runner.os }}-2.0.22 + + - name: build-jasper + if: steps.cache-jasper.outputs.cache-hit != 'true' + run: | + set -x + pwd + wget https://github.com/jasper-software/jasper/archive/version-2.0.22.tar.gz &> /dev/null && ls -l + tar zxf version-2.0.22.tar.gz && ls -l + cd jasper-version-2.0.22 + mkdir build-jasper && cd build-jasper + cmake .. -DCMAKE_INSTALL_PREFIX=~/jasper + make -j2 + make install + + - name: checkout-nceplibs + uses: actions/checkout@v2 + with: + repository: NOAA-EMC/NCEPLIBS + path: nceplibs + + - name: cache-nceplibs + id: cache-nceplibs + uses: actions/cache@v2 + with: + path: ~/nceplibs + key: nceplibs-${{ runner.os }}-1.3.0 + + - name: build-nceplibs + if: steps.cache-nceplibs.outputs.cache-hit != 'true' + run: | + set -x + export ESMFMKFILE=~/esmf/lib/esmf.mk + wget https://github.com/NOAA-EMC/NCEPLIBS/archive/v1.3.0.tar.gz &> /dev/null + tar zxf v1.3.0.tar.gz && ls -l + cd NCEPLIBS-1.3.0 + mkdir build && cd build + cmake .. -DCMAKE_PREFIX_PATH='~;~/jasper' -DCMAKE_INSTALL_PREFIX='~/nceplibs' -DFLAT=ON + make -j2 + + - name: checkout-ufs-utils + uses: actions/checkout@v2 + with: + path: ufs_utils + + - name: build-ufs-utils + run: | + set -x + mpicc --version + mpifort --version + pwd + export ESMFMKFILE=~/esmf/lib/esmf.mk + cd ufs_utils + mkdir build && cd build + cmake .. -DCMAKE_PREFIX_PATH='~;~/jasper;~/nceplibs' -DENABLE_DOCS=On + make -j2 + make test diff --git a/.github/workflows/esmf-8.0.1_jasper-2.0.22_nceplibs-develop.yml b/.github/workflows/esmf-8.0.1_jasper-2.0.22_nceplibs-develop.yml new file mode 100644 index 000000000..618f0e4e9 --- /dev/null +++ b/.github/workflows/esmf-8.0.1_jasper-2.0.22_nceplibs-develop.yml @@ -0,0 +1,163 @@ +name: esmf-8.0.1_jasper-2.0.22_nceplibs-develop +on: [push, pull_request] + +jobs: + build: + runs-on: ${{ matrix.os }} + env: + CC: gcc-9 + FC: gfortran-9 + CXX: g++-9 + strategy: + matrix: + os: [macos-10.15, ubuntu-20.04] + compiler: [gcc-9] + + steps: + - name: cache-mpich + id: cache-mpich + uses: actions/cache@v2 + with: + path: ~/mpich + key: mpich-${{ runner.os }}-3.3.2-1 + + - name: build-mpich + if: steps.cache-mpich.outputs.cache-hit != 'true' + run: | + if [[ ${{ matrix.os }} == "macos-10.15" ]]; then + wget http://www.mpich.org/static/downloads/3.3.2/mpich-3.3.2.tar.gz &> /dev/null + tar -xzf mpich-3.3.2.tar.gz + pushd mpich-3.3.2 + ./configure --prefix=$HOME/mpich + make + sudo make install + popd + fi + + - name: install-dependencies + run: | + echo "/home/runner/mpich/bin" >> $GITHUB_PATH + if [[ ${{ matrix.os }} == "ubuntu-20.04" ]]; then + sudo apt-get update + sudo apt-get install libmpich-dev + sudo apt-get install doxygen + sudo apt-get install libnetcdf-dev libnetcdff-dev netcdf-bin pkg-config + sudo apt-get install libpng-dev + sudo apt-get install libjpeg-dev + elif [[ ${{ matrix.os }} == "macos-10.15" ]]; then + echo "$HOME/mpich/bin" >> $GITHUB_PATH + brew update + brew install doxygen + brew install mpich + brew install netcdf + brew install wget + if [[ ${{ matrix.compiler }} == "gcc-9" ]]; then + sudo ln -sf /usr/local/bin/gfortran-9 /usr/local/bin/gfortran + elif [[ ${{ matrix.compiler }} == "gcc-10" ]]; then + sudo ln -sf /usr/local/bin/gfortran-10 /usr/local/bin/gfortran + fi + fi + python3 -m pip install gcovr + + - name: cache-esmf + id: cache-esmf + uses: actions/cache@v2 + with: + path: ~/esmf + key: esmf-${{ runner.os }}-8.0.1-2 + + - name: build-esmf + if: steps.cache-esmf.outputs.cache-hit != 'true' + run: | + set -x + pushd ~ + export ESMF_DIR=~/esmf-ESMF_8_0_1 + wget https://github.com/esmf-org/esmf/archive/ESMF_8_0_1.tar.gz &> /dev/null && ls -l + tar zxf ESMF_8_0_1.tar.gz && ls -l + cd esmf-ESMF_8_0_1 + export ESMF_COMM=mpich3 + export ESMF_INSTALL_BINDIR=bin + export ESMF_INSTALL_LIBDIR=lib + export ESMF_INSTALL_MODDIR=mod + export ESMF_COMPILER=gfortran + export ESMF_INSTALL_PREFIX=~/esmf + export ESMF_NETCDF=split + if [[ ${{ matrix.os }} == "ubuntu-20.04" ]]; then + export ESMF_NETCDF_INCLUDE=/usr/include + export ESMF_NETCDF_LIBPATH=/usr/x86_64-linux-gnu + elif [[ ${{ matrix.os }} == "macos-10.15" ]]; then + export ESMF_NETCDF_INCLUDE=/usr/local/include + export ESMF_NETCDF_LIBPATH=/usr/local/lib + fi + make -j2 + make install + + - name: cache-jasper + id: cache-jasper + uses: actions/cache@v2 + with: + path: ~/jasper + key: jasper-${{ runner.os }}-2.0.22 + + - name: build-jasper + if: steps.cache-jasper.outputs.cache-hit != 'true' + run: | + set -x + pwd + wget https://github.com/jasper-software/jasper/archive/version-2.0.22.tar.gz &> /dev/null && ls -l + tar zxf version-2.0.22.tar.gz && ls -l + cd jasper-version-2.0.22 + mkdir build-jasper && cd build-jasper + cmake .. -DCMAKE_INSTALL_PREFIX=~/jasper + make -j2 + make install + + - name: checkout-nceplibs + uses: actions/checkout@v2 + with: + repository: NOAA-EMC/NCEPLIBS + path: nceplibs + + - name: get-git-hash + run: | + cd nceplibs + git rev-parse HEAD > hash.txt + + - name: cache-nceplibs-develop + id: cache-nceplibs-develop + uses: actions/cache@v2 + with: + path: ~/nceplibs + key: nceplibs-develop-${{ runner.os }}-${{ hashFiles('nceplibs/hash.txt') }} + + - name: build-nceplibs + if: steps.cache-nceplibs-develop.outputs.cache-hit != 'true' + run: | + set -x + export ESMFMKFILE=~/esmf/lib/esmf.mk + cd nceplibs + mkdir build && cd build + cmake .. -DCMAKE_PREFIX_PATH='~;~/jasper' -DCMAKE_INSTALL_PREFIX='~/nceplibs' -DFLAT=ON + make -j2 + + - name: checkout-ufs-utils + uses: actions/checkout@v2 + with: + path: ufs_utils + + - name: build-ufs-utils + run: | + export ESMFMKFILE=~/esmf/lib/esmf.mk + cd ufs_utils + mkdir build && cd build + cmake .. -DCMAKE_PREFIX_PATH='~/jasper;~/nceplibs' -DENABLE_DOCS=On -DCMAKE_Fortran_FLAGS="-g -fprofile-arcs -ftest-coverage -O0" + make -j2 + make test + export PATH="/home/runner/.local/bin:$PATH" + gcovr -r .. --html-details -o test-coverage.html + + - uses: actions/upload-artifact@v2 + if: ${{ matrix.os == 'ubuntu-20.04' }} + with: + name: test-coverage + path: ufs_utils/build/*.html diff --git a/.gitignore b/.gitignore new file mode 100644 index 000000000..22aa75a65 --- /dev/null +++ b/.gitignore @@ -0,0 +1,15 @@ +build/ +install/ +exec/ + +*.[ao] +*.mod +*.so +*.exe +*.x + +*.swp +*.o +emcsfc_ice_blend +ml01rg2.x + diff --git a/CMakeLists.txt b/CMakeLists.txt new file mode 100644 index 000000000..11b467cf5 --- /dev/null +++ b/CMakeLists.txt @@ -0,0 +1,88 @@ +# This is the main CMake file for NCEPLIBS-ip. +# +# George Gayno +cmake_minimum_required(VERSION 3.15) + +# Get the version from the VERSION file. +file(STRINGS "VERSION" pVersion) + +project( + ufs_util + VERSION ${pVersion} + LANGUAGES C Fortran) +list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake") + +# User options. +option(OPENMP "use OpenMP threading" ON) +option(ENABLE_DOCS "Enable generation of doxygen-based documentation." OFF) + +if(NOT CMAKE_BUILD_TYPE MATCHES "^(Debug|Release|RelWithDebInfo|MinSizeRel)$") + message(STATUS "Setting build type to 'Release' as none was specified.") + set(CMAKE_BUILD_TYPE + "Release" + CACHE STRING "Choose the type of build." FORCE) + set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" + "MinSizeRel" "RelWithDebInfo") + message(STATUS "Set BUILD_TESTING to YES and build unit testing package under tests") + set(BUILD_TESTING "YES") +endif() + +# Set compiler flags. +if(CMAKE_Fortran_COMPILER_ID MATCHES "^(Intel)$") + set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -traceback") + set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -fp-model precise") + set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -check -check noarg_temp_created -check nopointer -fp-stack-check -fstack-protector-all -fpe0 -debug -ftrapuv") +elseif(CMAKE_Fortran_COMPILER_ID MATCHES "^(GNU)$") + set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -fbacktrace") + set(CMAKE_Fortran_FLAGS_RELEASE "-O3") + set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -ggdb -fno-unsafe-math-optimizations -frounding-math -fsignaling-nans -ffpe-trap=invalid,zero,overflow -fbounds-check") +endif() + +if(CMAKE_C_COMPILER_ID MATCHES "^(Intel)$") + set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g -traceback") + set(CMAKE_C_FLAGS_RELEASE "-O2") + set(CMAKE_C_FLAGS_DEBUG "-O0") +endif() + +# Find packages. +find_package(NetCDF 4.3.3 REQUIRED C Fortran) +find_package(MPI REQUIRED C Fortran) +find_package(ESMF 8.0.0 REQUIRED) + +if(OPENMP) + find_package(OpenMP REQUIRED COMPONENTS Fortran) +endif() + +find_package(sfcio 1.4.0 REQUIRED) +find_package(w3nco 2.4.0 REQUIRED) +find_package(bacio 2.4.0 REQUIRED) +find_package(nemsio 2.5.0 REQUIRED) +find_package(sigio 2.3.0 REQUIRED) +find_package(sp 2.3.3 REQUIRED) +find_package(ip 3.3.3 REQUIRED) +find_package(g2 3.4.0 REQUIRED) +find_package(wgrib2 2.0.8 REQUIRED) + +# EMC requires executables in ./exec +set(exec_dir bin) +if(EMC_EXEC_DIR) + set(exec_dir exec) +endif() + +# If doxygen documentation we enabled, build it. This must come before +# adding the source code directories; the main documentation build +# must happen before any of the utility document builds. +if(ENABLE_DOCS) + find_package(Doxygen REQUIRED) + set(abs_top_srcdir "${CMAKE_SOURCE_DIR}") + add_subdirectory(docs) +endif() + +add_subdirectory(sorc) + +# Run unit tests. +include(CTest) +if(BUILD_TESTING) + add_subdirectory(tests) +endif() + diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 000000000..b7395d372 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,17 @@ +Copyright 2020 National Oceanic and Atmospheric Administration (by assignment from I. M. Systems Group) + +The ufs_utils code incorporated in the Unified Forecast System (UFS) was jointly developed by the +National Oceanic and Atmospheric Administration and the I. M. Systems Group. The gold standard copy +of the Code will be maintained by NOAA at https://github.com/NOAA-EMC/UFS_UTILS + +The National Oceanic and Atmospheric Administration is releasing this code under the GNU Lesser +General Public License v3.0 (the "License"); you may not use this code except in compliance +with the License. + +You may obtain a copy of the License at + https://www.gnu.org/licenses/lgpl-3.0.en.html + +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. diff --git a/README.md b/README.md new file mode 100644 index 000000000..47003be0d --- /dev/null +++ b/README.md @@ -0,0 +1,126 @@ + +# UFS_UTILS + +Utilities for the NCEP models. This is part of the +[NCEPLIBS](https://github.com/NOAA-EMC/NCEPLIBS) project. + +Documentation for the chgres_cube utility can be found at +https://noaa-emcufs-utils.readthedocs.io/en/latest/. + +Complete documentation can be found at +https://noaa-emc.github.io/UFS_UTILS/. + +## Authors + +Utility | Programmer(s) +--------|---------- +chgres_cube | George Gayno, Jeff Beck, Larissa Reames +emcsfc_ice_blend | George Gayno +emcsfc_snow2mdl | George Gayno +fvcom_tools | David Wright, University of Michigan, Ming Hu, GSD/AMB +global_cycle | George Gayno, Shrinivas Moorthi, Mark Iredell, Xu Li, Hang Lei +grid_tools | R. J. Purser (regional_esg_grid), Tom Black/Ben Blake (shave.fd), Gerard Ketefian (global_equiv_resol), Tsukasa Fujita, JMA (pmat2), GFDL programmer (topo filtering code). +orog_mask_tools | Ning Wang, Jordan Alpert, Shan Sun and Ning Wang +sfc_climo_gen | George Gayno +vcoord_gen | Fanglin Yang, Mark Iredell + +UFS_UTILS Code managers: George Gayno, Kyle Gerheiser + +## Prerequisites + +This package requires the following NCEPLIBS packages: + - [NCEPLIBS-sfcio](https://github.com/NOAA-EMC/NCEPLIBS-sfcio) + - [NCEPLIBS-w3nco](https://github.com/NOAA-EMC/NCEPLIBS-w3nco) + - [NCEPLIBS-bacio](https://github.com/NOAA-EMC/NCEPLIBS-bacio) + - [NCEPLIBS-nemsio](https://github.com/NOAA-EMC/NCEPLIBS-nemsio) + - [NCEPLIBS-sigio](https://github.com/NOAA-EMC/NCEPLIBS-sigio) + - [NCEPLIBS-sp](https://github.com/NOAA-EMC/NCEPLIBS-sp) + - [NCEPLIBS-ip](https://github.com/NOAA-EMC/NCEPLIBS-ip) + - [NCEPLIBS-g2](https://github.com/NOAA-EMC/NCEPLIBS-g2) + - [NCEPLIBS-wgrib2](https://github.com/NOAA-EMC/NCEPLIBS-wgrib2) + +This package also requires: + + - [netcdf-c Library](https://github.com/Unidata/netcdf-c) + - [netcdf-fortran Library](https://github.com/Unidata/netcdf-fortran) + - [ESMF](https://github.com/esmf-org/esmf) + - [Jasper](https://github.com/jasper-software/jasper) + + +## Installing + +``` +mkdir build +cd build +cmake -DCMAKE_INSTALL_PREFIX=/path/to/install .. +make -j2 +make install +``` + +## Contents + +The UFS_UTILS package contains the following utilities (under the sorc +directory): +- chgres_cube +- emcsfc_ice_blend +- emcsfc_snow2mdl +- fre-nctools +- fvcom_tools +- global_cycle +- grid_tools +- orog_mask_tools +- sfc_climo_gen +- vcoord_gen + +The reg_tests directory contains the consistency test code. + +The fix directory is where we set links to directories containing +large, static data files used by UFS_UTILS programs. + +The tests directory contains unit tests. + +The ush directory contains scripts to run UFS_UTILS programs. Most +are called from driver scripts. + +The util directory contains utility scripts to create coldstart +initial conditions for GFS parallels, and to run the vertical +coordinate generator. + +The parm directory contains variable mapping parameter tables used by +the chgres_cube program. + +The driver_scripts directory contains high-level driver scripts to +create a model grid on officially supported HPC platforms. + +The modulefiles directory contains modules loaded when building +UFS_UTILS on supported HPC platforms. They are also loaded at runtime +by utility and consistency test scripts. + +The docs directory contains the control file for the doxygen +documentation build, as well as some markdown files which are part of +the documentation. It also contains (in the source subdirectory) the +ReadTheDocs documentation files. + +## References + +Gayno G., Beck J., Carson L., [Pre-Processing: +chgres_cube](./docs/20201105-0945a-pre-processing-chgres-cube-gayno-final.pdf), +UFS MRW App Training, 5 November 2020. + +## Disclaimer + +The United States Department of Commerce (DOC) GitHub project code is +provided on an "as is" basis and the user assumes responsibility for +its use. DOC has relinquished control of the information and no longer +has responsibility to protect the integrity, confidentiality, or +availability of the information. Any claims against the Department of +Commerce stemming from the use of its GitHub project will be governed +by all applicable Federal law. Any reference to specific commercial +products, processes, or services by service mark, trademark, +manufacturer, or otherwise, does not constitute or imply their +endorsement, recommendation or favoring by the Department of +Commerce. The Department of Commerce seal and logo, or the seal and +logo of a DOC bureau, shall not be used in any manner to imply +endorsement of any commercial product or activity by DOC or the United +States Government. + diff --git a/VERSION b/VERSION new file mode 100644 index 000000000..f0bb29e76 --- /dev/null +++ b/VERSION @@ -0,0 +1 @@ +1.3.0 diff --git a/build_all.sh b/build_all.sh new file mode 100755 index 000000000..bc6a00c1c --- /dev/null +++ b/build_all.sh @@ -0,0 +1,40 @@ +#! /usr/bin/env bash +# +# This build script is only used on NOAA WCOSS systems. All other +# users should set module files as needed, and build directly with +# CMake. +# +# George Gayno + +set -eux + +target=${target:-"NULL"} +compiler=${compiler:-"intel"} + +export MOD_PATH + +if [[ "$target" == "linux.*" || "$target" == "macosx.*" ]]; then + unset -f module + set +x + source ./modulefiles/build.$target > /dev/null + set -x +else + set +x + source ./sorc/machine-setup.sh + module use ./modulefiles + module load build.$target.$compiler > /dev/null + module list + set -x +fi + +CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=../ -DEMC_EXEC_DIR=ON" + +rm -fr ./build +mkdir ./build && cd ./build + +cmake .. ${CMAKE_FLAGS} + +make -j 8 VERBOSE=1 +make install + +exit diff --git a/cmake/FindESMF.cmake b/cmake/FindESMF.cmake new file mode 100644 index 000000000..5d0790fa2 --- /dev/null +++ b/cmake/FindESMF.cmake @@ -0,0 +1,130 @@ +# - Try to find ESMF +# +# Requires setting ESMFMKFILE to the filepath of esmf.mk. If this is NOT set, +# then ESMF_FOUND will always be FALSE. If ESMFMKFILE exists, then ESMF_FOUND=TRUE +# and all ESMF makefile variables will be set in the global scope. Optionally, +# set ESMF_MKGLOBALS to a string list to filter makefile variables. For example, +# to globally scope only ESMF_LIBSDIR and ESMF_APPSDIR variables, use this CMake +# command in CMakeLists.txt: +# +# set(ESMF_MKGLOBALS "LIBSDIR" "APPSDIR") + + +# Add the ESMFMKFILE path to the cache if defined as system env variable +if (DEFINED ENV{ESMFMKFILE} AND NOT DEFINED ESMFMKFILE) + set(ESMFMKFILE $ENV{ESMFMKFILE} CACHE FILEPATH "Path to ESMF mk file") +endif () + +# Found the mk file and ESMF exists on the system +if (EXISTS ${ESMFMKFILE}) + set(ESMF_FOUND TRUE CACHE BOOL "ESMF mk file found" FORCE) + # Did not find the ESMF mk file +else() + set(ESMF_FOUND FALSE CACHE BOOL "ESMF mk file NOT found" FORCE) + # Best to warn users that without the mk file there is no way to find ESMF + if (NOT DEFINED ESMFMKFILE) + message(FATAL_ERROR "ESMFMKFILE not defined. This is the path to esmf.mk file. \ +Without this filepath, ESMF_FOUND will always be FALSE.") + endif () +endif() + +# Only parse the mk file if it is found +if (ESMF_FOUND) + # Read the mk file + file(STRINGS "${ESMFMKFILE}" esmfmkfile_contents) + # Parse each line in the mk file + foreach(str ${esmfmkfile_contents}) + # Only consider uncommented lines + string(REGEX MATCH "^[^#]" def ${str}) + # Line is not commented + if (def) + # Extract the variable name + string(REGEX MATCH "^[^=]+" esmf_varname ${str}) + # Extract the variable's value + string(REGEX MATCH "=.+$" esmf_vardef ${str}) + # Only for variables with a defined value + if (esmf_vardef) + # Get rid of the assignment string + string(SUBSTRING ${esmf_vardef} 1 -1 esmf_vardef) + # Remove whitespace + string(STRIP ${esmf_vardef} esmf_vardef) + # A string or single-valued list + if(NOT DEFINED ESMF_MKGLOBALS) + # Set in global scope + set(${esmf_varname} ${esmf_vardef}) + # Don't display by default in GUI + mark_as_advanced(esmf_varname) + else() # Need to filter global promotion + foreach(m ${ESMF_MKGLOBALS}) + string(FIND ${esmf_varname} ${m} match) + # Found the string + if(NOT ${match} EQUAL -1) + # Promote to global scope + set(${esmf_varname} ${esmf_vardef}) + # Don't display by default in the GUI + mark_as_advanced (esmf_varname) + # No need to search for the current string filter + break() + endif() + endforeach() + endif() + endif() + endif() + endforeach() + + # Construct ESMF_VERSION from ESMF_VERSION_STRING_GIT + if(ESMF_FOUND) + # ESMF_VERSION_MAJOR and ESMF_VERSION_MINOR are defined in ESMFMKFILE + set(ESMF_VERSION 0) + set(ESMF_VERSION_PATCH ${ESMF_VERSION_REVISION}) + set(ESMF_BETA_RELEASE FALSE) + if(ESMF_VERSION_BETASNAPSHOT MATCHES "^('T')$") + set(ESMF_BETA_RELEASE TRUE) + string(REGEX REPLACE ".*beta_snapshot_*\([0-9]*\).*" "\\1" ESMF_BETA_SNAPSHOT "${ESMF_VERSION_STRING_GIT}") + endif() + set(ESMF_VERSION "${ESMF_VERSION_MAJOR}.${ESMF_VERSION_MINOR}.${ESMF_VERSION_PATCH}") + endif() + + separate_arguments(ESMF_F90COMPILEPATHS NATIVE_COMMAND ${ESMF_F90COMPILEPATHS}) + foreach (ITEM ${ESMF_F90COMPILEPATHS}) + string(REGEX REPLACE "^-I" "" ITEM "${ITEM}") + list(APPEND tmp ${ITEM}) + endforeach() + set(ESMF_F90COMPILEPATHS ${tmp}) + + add_library(esmf UNKNOWN IMPORTED) + # Look for static library, if not found try dynamic library + find_library(esmf_lib NAMES libesmf.a PATHS ${ESMF_LIBSDIR}) + if(esmf_lib MATCHES "esmf_lib-NOTFOUND") + message(STATUS "Static ESMF library not found, searching for dynamic library instead") + find_library(esmf_lib NAMES esmf_fullylinked PATHS ${ESMF_LIBSDIR}) + if(esmf_lib MATCHES "esmf_lib-NOTFOUND") + message(FATAL_ERROR "Neither the dynamic nor the static ESMF library was found") + endif() + set(ESMF_INTERFACE_LINK_LIBRARIES "") + else() + # When linking the static library, also need the ESMF linker flags; strip any leading/trailing whitespaces + string(STRIP "${ESMF_F90ESMFLINKRPATHS} ${ESMF_F90ESMFLINKPATHS} ${ESMF_F90LINKPATHS} ${ESMF_F90LINKLIBS} ${ESMF_F90LINKOPTS}" ESMF_INTERFACE_LINK_LIBRARIES) + endif() + + message(STATUS "Found ESMF library: ${esmf_lib}") + if(ESMF_BETA_RELEASE) + message(STATUS "Detected ESMF Beta snapshot ${ESMF_BETA_SNAPSHOT}") + endif() + + set_target_properties(esmf PROPERTIES + IMPORTED_LOCATION ${esmf_lib} + INTERFACE_INCLUDE_DIRECTORIES "${ESMF_F90COMPILEPATHS}" + INTERFACE_LINK_LIBRARIES "${ESMF_INTERFACE_LINK_LIBRARIES}") + +endif() + +## Finalize find_package +include(FindPackageHandleStandardArgs) + +find_package_handle_standard_args( ${CMAKE_FIND_PACKAGE_NAME} + REQUIRED_VARS ESMF_LIBSDIR + ESMF_INTERFACE_LINK_LIBRARIES + ESMF_F90COMPILEPATHS + VERSION_VAR ESMF_VERSION + HANDLE_COMPONENTS ) diff --git a/cmake/FindNetCDF.cmake b/cmake/FindNetCDF.cmake new file mode 100644 index 000000000..9e32378ff --- /dev/null +++ b/cmake/FindNetCDF.cmake @@ -0,0 +1,347 @@ +# (C) Copyright 2011- ECMWF. +# +# This software is licensed under the terms of the Apache Licence Version 2.0 +# which can be obtained at http://www.apache.org/licenses/LICENSE-2.0. +# In applying this licence, ECMWF does not waive the privileges and immunities +# granted to it by virtue of its status as an intergovernmental organisation nor +# does it submit to any jurisdiction. + +# Try to find NetCDF includes and library. +# Supports static and shared libaries and allows each component to be found in sepearte prefixes. +# +# This module defines +# +# - NetCDF_FOUND - System has NetCDF +# - NetCDF_INCLUDE_DIRS - the NetCDF include directories +# - NetCDF_VERSION - the version of NetCDF +# - NetCDF_CONFIG_EXECUTABLE - the netcdf-config executable if found +# - NetCDF_PARALLEL - Boolean True if NetCDF4 has parallel IO support via hdf5 and/or pnetcdf +# - NetCDF_HAS_PNETCDF - Boolean True if NetCDF4 has pnetcdf support +# +# Deprecated Defines +# - NetCDF_LIBRARIES - [Deprecated] Use NetCDF::NetCDF_ targets instead. +# +# +# Following components are available: +# +# - C - C interface to NetCDF (netcdf) +# - CXX - CXX4 interface to NetCDF (netcdf_c++4) +# - Fortran - Fortran interface to NetCDF (netcdff) +# +# For each component the following are defined: +# +# - NetCDF__FOUND - whether the component is found +# - NetCDF__LIBRARIES - the libraries for the component +# - NetCDF__LIBRARY_SHARED - Boolean is true if libraries for component are shared +# - NetCDF__INCLUDE_DIRS - the include directories for specified component +# - NetCDF::NetCDF_ - target of component to be used with target_link_libraries() +# +# The following paths will be searched in order if set in CMake (first priority) or environment (second priority) +# +# - NetCDF_ROOT - root of NetCDF installation +# - NetCDF_PATH - root of NetCDF installation +# +# The search process begins with locating NetCDF Include headers. If these are in a non-standard location, +# set one of the following CMake or environment variables to point to the location: +# +# - NetCDF_INCLUDE_DIR or NetCDF_${comp}_INCLUDE_DIR +# - NetCDF_INCLUDE_DIRS or NetCDF_${comp}_INCLUDE_DIR +# +# Notes: +# +# - Use "NetCDF::NetCDF_" targets only. NetCDF_LIBRARIES exists for backwards compatibility and should not be used. +# - These targets have all the knowledge of include directories and library search directories, and a single +# call to target_link_libraries will provide all these transitive properties to your target. Normally all that is +# needed to build and link against NetCDF is, e.g.: +# target_link_libraries(my_c_tgt PUBLIC NetCDF::NetCDF_C) +# - "NetCDF" is always the preferred naming for this package, its targets, variables, and environment variables +# - For compatibility, some variables are also set/checked using alternate names NetCDF4, NETCDF, or NETCDF4 +# - Environments relying on these older environment variable names should move to using a "NetCDF_ROOT" environment variable +# - Preferred component capitalization follows the CMake LANGUAGES variables: i.e., C, Fortran, CXX +# - For compatibility, alternate capitalizations are supported but should not be used. +# - If no components are defined, all components will be searched +# + +list( APPEND _possible_components C CXX Fortran ) + +## Include names for each component +set( NetCDF_C_INCLUDE_NAME netcdf.h ) +set( NetCDF_CXX_INCLUDE_NAME netcdf ) +set( NetCDF_Fortran_INCLUDE_NAME netcdf.mod ) + +## Library names for each component +set( NetCDF_C_LIBRARY_NAME netcdf ) +set( NetCDF_CXX_LIBRARY_NAME netcdf_c++4 ) +set( NetCDF_Fortran_LIBRARY_NAME netcdff ) + +## Enumerate search components +foreach( _comp ${_possible_components} ) + string( TOUPPER "${_comp}" _COMP ) + set( _arg_${_COMP} ${_comp} ) + set( _name_${_COMP} ${_comp} ) +endforeach() + +set( _search_components C) +foreach( _comp ${${CMAKE_FIND_PACKAGE_NAME}_FIND_COMPONENTS} ) + string( TOUPPER "${_comp}" _COMP ) + set( _arg_${_COMP} ${_comp} ) + list( APPEND _search_components ${_name_${_COMP}} ) + if( NOT _name_${_COMP} ) + message(SEND_ERROR "Find${CMAKE_FIND_PACKAGE_NAME}: COMPONENT ${_comp} is not a valid component. Valid components: ${_possible_components}" ) + endif() +endforeach() +list( REMOVE_DUPLICATES _search_components ) + +## Search hints for finding include directories and libraries +foreach( _comp IN ITEMS "_" "_C_" "_Fortran_" "_CXX_" ) + foreach( _name IN ITEMS NetCDF4 NetCDF NETCDF4 NETCDF ) + foreach( _var IN ITEMS ROOT PATH ) + list(APPEND _search_hints ${${_name}${_comp}${_var}} $ENV{${_name}${_comp}${_var}} ) + list(APPEND _include_search_hints + ${${_name}${_comp}INCLUDE_DIR} $ENV{${_name}${_comp}INCLUDE_DIR} + ${${_name}${_comp}INCLUDE_DIRS} $ENV{${_name}${_comp}INCLUDE_DIRS} ) + endforeach() + endforeach() +endforeach() +#Old-school HPC module env variable names +foreach( _name IN ITEMS NetCDF4 NetCDF NETCDF4 NETCDF ) + foreach( _comp IN ITEMS "_C" "_Fortran" "_CXX" ) + list(APPEND _search_hints ${${_name}} $ENV{${_name}}) + list(APPEND _search_hints ${${_name}${_comp}} $ENV{${_name}${_comp}}) + endforeach() +endforeach() + +## Find headers for each component +set(NetCDF_INCLUDE_DIRS) +set(_new_search_components) +foreach( _comp IN LISTS _search_components ) + if(NOT ${PROJECT_NAME}_NetCDF_${_comp}_FOUND) + list(APPEND _new_search_components ${_comp}) + endif() + find_file(NetCDF_${_comp}_INCLUDE_FILE + NAMES ${NetCDF_${_comp}_INCLUDE_NAME} + DOC "NetCDF ${_comp} include directory" + HINTS ${_include_search_hints} ${_search_hints} + PATH_SUFFIXES include include/netcdf + ) + mark_as_advanced(NetCDF_${_comp}_INCLUDE_FILE) + message(DEBUG "NetCDF_${_comp}_INCLUDE_FILE: ${NetCDF_${_comp}_INCLUDE_FILE}") + if( NetCDF_${_comp}_INCLUDE_FILE ) + get_filename_component(NetCDF_${_comp}_INCLUDE_FILE ${NetCDF_${_comp}_INCLUDE_FILE} ABSOLUTE) + get_filename_component(NetCDF_${_comp}_INCLUDE_DIR ${NetCDF_${_comp}_INCLUDE_FILE} DIRECTORY) + list(APPEND NetCDF_INCLUDE_DIRS ${NetCDF_${_comp}_INCLUDE_DIR}) + endif() +endforeach() +if(NetCDF_INCLUDE_DIRS) + list(REMOVE_DUPLICATES NetCDF_INCLUDE_DIRS) +endif() +set(NetCDF_INCLUDE_DIRS "${NetCDF_INCLUDE_DIRS}" CACHE STRING "NetCDF Include directory paths" FORCE) + +## Find n*-config executables for search components +foreach( _comp IN LISTS _search_components ) + if( _comp MATCHES "^(C)$" ) + set(_conf "c") + elseif( _comp MATCHES "^(Fortran)$" ) + set(_conf "f") + elseif( _comp MATCHES "^(CXX)$" ) + set(_conf "cxx4") + endif() + find_program( NetCDF_${_comp}_CONFIG_EXECUTABLE + NAMES n${_conf}-config + HINTS ${NetCDF_INCLUDE_DIRS} ${_include_search_hints} ${_search_hints} + PATH_SUFFIXES bin Bin ../bin ../../bin + DOC "NetCDF n${_conf}-config helper" ) + message(DEBUG "NetCDF_${_comp}_CONFIG_EXECUTABLE: ${NetCDF_${_comp}_CONFIG_EXECUTABLE}") +endforeach() + +set(_C_libs_flag --libs) +set(_Fortran_libs_flag --flibs) +set(_CXX_libs_flag --libs) +set(_C_includes_flag --includedir) +set(_Fortran_includes_flag --includedir) +set(_CXX_includes_flag --includedir) +function(netcdf_config exec flag output_var) + set(${output_var} False PARENT_SCOPE) + if( exec ) + execute_process( COMMAND ${exec} ${flag} RESULT_VARIABLE _ret OUTPUT_VARIABLE _val) + if( _ret EQUAL 0 ) + string( STRIP ${_val} _val ) + set( ${output_var} ${_val} PARENT_SCOPE ) + endif() + endif() +endfunction() + +## Detect additional package properties +netcdf_config(${NetCDF_C_CONFIG_EXECUTABLE} --has-parallel4 _val) +if( NOT _val MATCHES "^(yes|no)$" ) + netcdf_config(${NetCDF_C_CONFIG_EXECUTABLE} --has-parallel _val) +endif() +if( _val MATCHES "^(yes)$" ) + set(NetCDF_PARALLEL TRUE CACHE STRING "NetCDF has parallel IO capability via pnetcdf or hdf5." FORCE) +else() + set(NetCDF_PARALLEL FALSE CACHE STRING "NetCDF has no parallel IO capability." FORCE) +endif() + +if(NetCDF_PARALLEL) + find_package(MPI REQUIRED) +endif() + +## Find libraries for each component +set( NetCDF_LIBRARIES ) +foreach( _comp IN LISTS _search_components ) + string( TOUPPER "${_comp}" _COMP ) + + find_library( NetCDF_${_comp}_LIBRARY + NAMES ${NetCDF_${_comp}_LIBRARY_NAME} + DOC "NetCDF ${_comp} library" + HINTS ${NetCDF_${_comp}_INCLUDE_DIRS} ${_search_hints} + PATH_SUFFIXES lib64 lib ../lib64 ../lib ../../lib64 ../../lib ) + mark_as_advanced( NetCDF_${_comp}_LIBRARY ) + get_filename_component(NetCDF_${_comp}_LIBRARY ${NetCDF_${_comp}_LIBRARY} ABSOLUTE) + set(NetCDF_${_comp}_LIBRARY ${NetCDF_${_comp}_LIBRARY} CACHE STRING "NetCDF ${_comp} library" FORCE) + message(DEBUG "NetCDF_${_comp}_LIBRARY: ${NetCDF_${_comp}_LIBRARY}") + + if( NetCDF_${_comp}_LIBRARY ) + if( NetCDF_${_comp}_LIBRARY MATCHES ".a$" ) + set( NetCDF_${_comp}_LIBRARY_SHARED FALSE ) + set( _library_type STATIC) + else() + list( APPEND NetCDF_LIBRARIES ${NetCDF_${_comp}_LIBRARY} ) + set( NetCDF_${_comp}_LIBRARY_SHARED TRUE ) + set( _library_type SHARED) + endif() + endif() + + #Use nc-config to set per-component LIBRARIES variable if possible + netcdf_config( ${NetCDF_${_comp}_CONFIG_EXECUTABLE} ${_${_comp}_libs_flag} _val ) + if( _val ) + set( NetCDF_${_comp}_LIBRARIES ${_val} ) + if(NOT NetCDF_${_comp}_LIBRARY_SHARED AND NOT NetCDF_${_comp}_FOUND) #Static targets should use nc_config to get a proper link line with all necessary static targets. + list( APPEND NetCDF_LIBRARIES ${NetCDF_${_comp}_LIBRARIES} ) + endif() + else() + set( NetCDF_${_comp}_LIBRARIES ${NetCDF_${_comp}_LIBRARY} ) + if(NOT NetCDF_${_comp}_LIBRARY_SHARED) + message(SEND_ERROR "Unable to properly find NetCDF. Found static libraries at: ${NetCDF_${_comp}_LIBRARY} but could not run nc-config: ${NetCDF_CONFIG_EXECUTABLE}") + endif() + endif() + + #Use nc-config to set per-component INCLUDE_DIRS variable if possible + netcdf_config( ${NetCDF_${_comp}_CONFIG_EXECUTABLE} ${_${_comp}_includes_flag} _val ) + if( _val ) + string( REPLACE " " ";" _val ${_val} ) + set( NetCDF_${_comp}_INCLUDE_DIRS ${_val} ) + else() + set( NetCDF_${_comp}_INCLUDE_DIRS ${NetCDF_${_comp}_INCLUDE_DIR} ) + endif() + + if( NetCDF_${_comp}_LIBRARIES AND NetCDF_${_comp}_INCLUDE_DIRS ) + set( ${CMAKE_FIND_PACKAGE_NAME}_${_arg_${_COMP}}_FOUND TRUE ) + if (NOT TARGET NetCDF::NetCDF_${_comp}) + add_library(NetCDF::NetCDF_${_comp} ${_library_type} IMPORTED) + set_target_properties(NetCDF::NetCDF_${_comp} PROPERTIES + IMPORTED_LOCATION ${NetCDF_${_comp}_LIBRARY} + INTERFACE_INCLUDE_DIRECTORIES "${NetCDF_${_comp}_INCLUDE_DIRS}" + INTERFACE_LINK_LIBRARIES ${NetCDF_${_comp}_LIBRARIES} ) + if( NOT _comp MATCHES "^(C)$" ) + target_link_libraries(NetCDF::NetCDF_${_comp} INTERFACE NetCDF::NetCDF_C) + endif() + if(MPI_${_comp}_FOUND) + target_link_libraries(NetCDF::NetCDF_${_comp} INTERFACE MPI::MPI_${_comp}) + endif() + endif() + endif() +endforeach() +if(NetCDF_LIBRARIES AND NetCDF_${_comp}_LIBRARY_SHARED) + list(REMOVE_DUPLICATES NetCDF_LIBRARIES) +endif() +set(NetCDF_LIBRARIES "${NetCDF_LIBRARIES}" CACHE STRING "NetCDF library targets" FORCE) + +## Find version via netcdf-config if possible +if (NetCDF_INCLUDE_DIRS) + if( NetCDF_C_CONFIG_EXECUTABLE ) + netcdf_config( ${NetCDF_C_CONFIG_EXECUTABLE} --version _vers ) + if( _vers ) + string(REGEX REPLACE ".* ((([0-9]+)\\.)+([0-9]+)).*" "\\1" NetCDF_VERSION "${_vers}" ) + endif() + else() + foreach( _dir IN LISTS NetCDF_INCLUDE_DIRS) + if( EXISTS "${_dir}/netcdf_meta.h" ) + file(STRINGS "${_dir}/netcdf_meta.h" _netcdf_version_lines + REGEX "#define[ \t]+NC_VERSION_(MAJOR|MINOR|PATCH|NOTE)") + string(REGEX REPLACE ".*NC_VERSION_MAJOR *\([0-9]*\).*" "\\1" _netcdf_version_major "${_netcdf_version_lines}") + string(REGEX REPLACE ".*NC_VERSION_MINOR *\([0-9]*\).*" "\\1" _netcdf_version_minor "${_netcdf_version_lines}") + string(REGEX REPLACE ".*NC_VERSION_PATCH *\([0-9]*\).*" "\\1" _netcdf_version_patch "${_netcdf_version_lines}") + string(REGEX REPLACE ".*NC_VERSION_NOTE *\"\([^\"]*\)\".*" "\\1" _netcdf_version_note "${_netcdf_version_lines}") + set(NetCDF_VERSION "${_netcdf_version_major}.${_netcdf_version_minor}.${_netcdf_version_patch}${_netcdf_version_note}") + unset(_netcdf_version_major) + unset(_netcdf_version_minor) + unset(_netcdf_version_patch) + unset(_netcdf_version_note) + unset(_netcdf_version_lines) + endif() + endforeach() + endif() +endif () + +## Finalize find_package +include(FindPackageHandleStandardArgs) + +if(NOT NetCDF_FOUND OR _new_search_components) + find_package_handle_standard_args( ${CMAKE_FIND_PACKAGE_NAME} + REQUIRED_VARS NetCDF_INCLUDE_DIRS NetCDF_LIBRARIES + VERSION_VAR NetCDF_VERSION + HANDLE_COMPONENTS ) +endif() + +foreach( _comp IN LISTS _search_components ) + if( NetCDF_${_comp}_FOUND ) + #Record found components to avoid duplication in NetCDF_LIBRARIES for static libraries + set(NetCDF_${_comp}_FOUND ${NetCDF_${_comp}_FOUND} CACHE BOOL "NetCDF ${_comp} Found" FORCE) + #Set a per-package, per-component found variable to communicate between multiple calls to find_package() + set(${PROJECT_NAME}_NetCDF_${_comp}_FOUND True) + endif() +endforeach() + +if( ${CMAKE_FIND_PACKAGE_NAME}_FOUND AND NOT ${CMAKE_FIND_PACKAGE_NAME}_FIND_QUIETLY AND _new_search_components) + message( STATUS "Find${CMAKE_FIND_PACKAGE_NAME} defines targets:" ) + message( STATUS " - NetCDF_VERSION [${NetCDF_VERSION}]") + message( STATUS " - NetCDF_PARALLEL [${NetCDF_PARALLEL}]") + foreach( _comp IN LISTS _new_search_components ) + string( TOUPPER "${_comp}" _COMP ) + message( STATUS " - NetCDF_${_comp}_CONFIG_EXECUTABLE [${NetCDF_${_comp}_CONFIG_EXECUTABLE}]") + if( ${CMAKE_FIND_PACKAGE_NAME}_${_arg_${_COMP}}_FOUND ) + get_filename_component(_root ${NetCDF_${_comp}_INCLUDE_DIR}/.. ABSOLUTE) + if( NetCDF_${_comp}_LIBRARY_SHARED ) + message( STATUS " - NetCDF::NetCDF_${_comp} [SHARED] [Root: ${_root}] Lib: ${NetCDF_${_comp}_LIBRARY} ") + else() + message( STATUS " - NetCDF::NetCDF_${_comp} [STATIC] [Root: ${_root}] Lib: ${NetCDF_${_comp}_LIBRARY} ") + endif() + endif() + endforeach() +endif() + +foreach( _prefix NetCDF NetCDF4 NETCDF NETCDF4 ${CMAKE_FIND_PACKAGE_NAME} ) + set( ${_prefix}_INCLUDE_DIRS ${NetCDF_INCLUDE_DIRS} ) + set( ${_prefix}_LIBRARIES ${NetCDF_LIBRARIES}) + set( ${_prefix}_VERSION ${NetCDF_VERSION} ) + set( ${_prefix}_FOUND ${${CMAKE_FIND_PACKAGE_NAME}_FOUND} ) + set( ${_prefix}_CONFIG_EXECUTABLE ${NetCDF_CONFIG_EXECUTABLE} ) + set( ${_prefix}_PARALLEL ${NetCDF_PARALLEL} ) + + foreach( _comp ${_search_components} ) + string( TOUPPER "${_comp}" _COMP ) + set( _arg_comp ${_arg_${_COMP}} ) + set( ${_prefix}_${_comp}_FOUND ${${CMAKE_FIND_PACKAGE_NAME}_${_arg_comp}_FOUND} ) + set( ${_prefix}_${_COMP}_FOUND ${${CMAKE_FIND_PACKAGE_NAME}_${_arg_comp}_FOUND} ) + set( ${_prefix}_${_arg_comp}_FOUND ${${CMAKE_FIND_PACKAGE_NAME}_${_arg_comp}_FOUND} ) + + set( ${_prefix}_${_comp}_LIBRARIES ${NetCDF_${_comp}_LIBRARIES} ) + set( ${_prefix}_${_COMP}_LIBRARIES ${NetCDF_${_comp}_LIBRARIES} ) + set( ${_prefix}_${_arg_comp}_LIBRARIES ${NetCDF_${_comp}_LIBRARIES} ) + + set( ${_prefix}_${_comp}_INCLUDE_DIRS ${NetCDF_${_comp}_INCLUDE_DIRS} ) + set( ${_prefix}_${_COMP}_INCLUDE_DIRS ${NetCDF_${_comp}_INCLUDE_DIRS} ) + set( ${_prefix}_${_arg_comp}_INCLUDE_DIRS ${NetCDF_${_comp}_INCLUDE_DIRS} ) + endforeach() +endforeach() diff --git a/cmake/LibMPI.cmake b/cmake/LibMPI.cmake new file mode 100644 index 000000000..bf43069c5 --- /dev/null +++ b/cmake/LibMPI.cmake @@ -0,0 +1,217 @@ +# This file contains CMake code related to MPI. (Taken from the +# ParallelIO project.) + +# Jim Edwards +include (CMakeParseArguments) + +# Find Valgrind to perform memory leak check +if (PIO_VALGRIND_CHECK) + find_program (VALGRIND_COMMAND NAMES valgrind) + if (VALGRIND_COMMAND) + set (VALGRIND_COMMAND_OPTIONS --leak-check=full --show-reachable=yes) + else () + message (WARNING "Valgrind not found: memory leak check could not be performed") + set (VALGRIND_COMMAND "") + endif () +endif () + +# +# - Functions for parallel testing with CTest +# + +#============================================================================== +# - Get the machine platform-specific +# +# Syntax: platform_name (RETURN_VARIABLE) +# +function (platform_name RETURN_VARIABLE) + + # Determine platform name from site name... + site_name (SITENAME) + + # hera + if (SITENAME MATCHES "^hfe01" OR + SITENAME MATCHES "^hfe02" OR + SITENAME MATCHES "^hfe03" OR + SITENAME MATCHES "^hfe04" OR + SITENAME MATCHES "^hfe05" OR + SITENAME MATCHES "^hfe06" OR + SITENAME MATCHES "^hfe07" OR + SITENAME MATCHES "^hfe08" OR + SITENAME MATCHES "^hfe09" OR + SITENAME MATCHES "^hfe10" OR + SITENAME MATCHES "^hfe11" OR + SITENAME MATCHES "^hfe12") + + set (${RETURN_VARIABLE} "hera" PARENT_SCOPE) + + # wcoss_cray (Luna) + elseif (SITENAME MATCHES "^llogin1" OR + SITENAME MATCHES "^llogin2" OR + SITENAME MATCHES "^llogin3") + + set (${RETURN_VARIABLE} "wcoss_cray" PARENT_SCOPE) + + # wcoss_cray (Surge) + elseif (SITENAME MATCHES "^slogin1" OR + SITENAME MATCHES "^slogin2" OR + SITENAME MATCHES "^slogin3") + + set (${RETURN_VARIABLE} "wcoss_cray" PARENT_SCOPE) + + # wcoss_dell_p3 (Venus) + elseif (SITENAME MATCHES "^v71a1.ncep.noaa.gov" OR + SITENAME MATCHES "^v71a2.ncep.noaa.gov" OR + SITENAME MATCHES "^v71a3.ncep.noaa.gov" OR + SITENAME MATCHES "^v72a1.ncep.noaa.gov" OR + SITENAME MATCHES "^v72a2.ncep.noaa.gov" OR + SITENAME MATCHES "^v72a3.ncep.noaa.gov") + + set (${RETURN_VARIABLE} "wcoss_dell_p3" PARENT_SCOPE) + + # wcoss_dell_p3 (Mars) + elseif (SITENAME MATCHES "^m71a1.ncep.noaa.gov" OR + SITENAME MATCHES "^m71a2.ncep.noaa.gov" OR + SITENAME MATCHES "^m71a3.ncep.noaa.gov" OR + SITENAME MATCHES "^m72a1.ncep.noaa.gov" OR + SITENAME MATCHES "^m72a2.ncep.noaa.gov" OR + SITENAME MATCHES "^m72a3.ncep.noaa.gov") + + set (${RETURN_VARIABLE} "wcoss_dell_p3" PARENT_SCOPE) + + # wcoss2 + elseif (SITENAME MATCHES "^along01" OR + SITENAME MATCHES "^alogin02") + + set (${RETURN_VARIABLE} "wcoss2" PARENT_SCOPE) + + # gaea + elseif (SITENAME MATCHES "^gaea9" OR + SITENAME MATCHES "^gaea10" OR + SITENAME MATCHES "^gaea11" OR + SITENAME MATCHES "^gaea12" OR + SITENAME MATCHES "^gaea13" OR + SITENAME MATCHES "^gaea14" OR + SITENAME MATCHES "^gaea15" OR + SITENAME MATCHES "^gaea16" OR + SITENAME MATCHES "^gaea9.ncrc.gov" OR + SITENAME MATCHES "^gaea10.ncrc.gov" OR + SITENAME MATCHES "^gaea11.ncrc.gov" OR + SITENAME MATCHES "^gaea12.ncrc.gov" OR + SITENAME MATCHES "^gaea13.ncrc.gov" OR + SITENAME MATCHES "^gaea14.ncrc.gov" OR + SITENAME MATCHES "^gaea15.ncrc.gov" OR + SITENAME MATCHES "^gaea16.ncrc.gov") + + set (${RETURN_VARIABLE} "gaea" PARENT_SCOPE) + + # jet + elseif (SITENAME MATCHES "^fe1" OR + SITENAME MATCHES "^fe2" OR + SITENAME MATCHES "^fe3" OR + SITENAME MATCHES "^fe4" OR + SITENAME MATCHES "^fe5" OR + SITENAME MATCHES "^fe6" OR + SITENAME MATCHES "^fe7" OR + SITENAME MATCHES "^fe8" OR + SITENAME MATCHES "^tfe1" OR + SITENAME MATCHES "^tfe2") + + set (${RETURN_VARIABLE} "jet" PARENT_SCOPE) + + elseif (SITENAME MATCHES "^Orion-login-1.HPC.MsState.Edu" OR + SITENAME MATCHES "^Orion-login-2.HPC.MsState.Edu" OR + SITENAME MATCHES "^Orion-login-3.HPC.MsState.Edu" OR + SITENAME MATCHES "^Orion-login-4.HPC.MsState.Edu") + + set (${RETURN_VARIABLE} "orion" PARENT_SCOPE) + + elseif (SITENAME MATCHES "^cheyenne1.cheyenne.ucar.edu" OR + SITENAME MATCHES "^cheyenne1.cheyenne.ucar.edu" OR + SITENAME MATCHES "^cheyenne2.cheyenne.ucar.edu" OR + SITENAME MATCHES "^cheyenne3.cheyenne.ucar.edu" OR + SITENAME MATCHES "^cheyenne4.cheyenne.ucar.edu" OR + SITENAME MATCHES "^cheyenne5.cheyenne.ucar.edu" OR + SITENAME MATCHES "^cheyenne6.cheyenne.ucar.edu" OR + SITENAME MATCHES "^cheyenne1.ib0.cheyenne.ucar.edu" OR + SITENAME MATCHES "^cheyenne2.ib0.cheyenne.ucar.edu" OR + SITENAME MATCHES "^cheyenne3.ib0.cheyenne.ucar.edu" OR + SITENAME MATCHES "^cheyenne4.ib0.cheyenne.ucar.edu" OR + SITENAME MATCHES "^cheyenne5.ib0.cheyenne.ucar.edu" OR + SITENAME MATCHES "^cheyenne6.ib0.cheyenne.ucar.edu" OR + SITENAME MATCHES "^chadmin1.ib0.cheyenne.ucar.edu" OR + SITENAME MATCHES "^chadmin2.ib0.cheyenne.ucar.edu" OR + SITENAME MATCHES "^chadmin3.ib0.cheyenne.ucar.edu" OR + SITENAME MATCHES "^chadmin4.ib0.cheyenne.ucar.edu" OR + SITENAME MATCHES "^chadmin5.ib0.cheyenne.ucar.edu" OR + SITENAME MATCHES "^chadmin6.ib0.cheyenne.ucar.edu") + + set (${RETURN_VARIABLE} "cheyenne" PARENT_SCOPE) + elseif (SITENAME MATCHES "^login1.stampede2.tacc.utexas.edu" OR + SITENAME MATCHES "^login2.stampede2.tacc.utexas.edu" OR + SITENAME MATCHES "^login3.stampede2.tacc.utexas.edu" OR + SITENAME MATCHES "^login4.stampede2.tacc.utexas.edu") + + + set (${RETURN_VARIABLE} "stampede" PARENT_SCOPE) + + else () + + set (${RETURN_VARIABLE} "unknown" PARENT_SCOPE) + + endif () +endfunction () + +#============================================================================== +# - Add a new parallel test +# +# Syntax: add_mpi_test ( +# EXECUTABLE +# ARGUMENTS ... +# NUMPROCS +# TIMEOUT ) +function (add_mpi_test TESTNAME) + + # Parse the input arguments + set (options) + set (oneValueArgs NUMPROCS TIMEOUT EXECUTABLE) + set (multiValueArgs ARGUMENTS) + cmake_parse_arguments (${TESTNAME} "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN}) + + # Store parsed arguments for convenience + set (exec_file ${${TESTNAME}_EXECUTABLE}) + set (exec_args ${${TESTNAME}_ARGUMENTS}) + set (num_procs ${${TESTNAME}_NUMPROCS}) + set (timeout ${${TESTNAME}_TIMEOUT}) + + # Get the platform name + platform_name (PLATFORM) + + get_property(WITH_MPIEXEC GLOBAL PROPERTY WITH_MPIEXEC) + if (WITH_MPIEXEC) + set(MPIEXEC "${WITH_MPIEXEC}") + endif () + + # Default ("unknown" platform) execution + if (PLATFORM STREQUAL "unknown") + + # Run tests directly from the command line + set(EXE_CMD ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${num_procs} + ${MPIEXEC_PREFLAGS} ${VALGRIND_COMMAND} ${VALGRIND_COMMAND_OPTIONS} ${exec_file} + ${MPIEXEC_POSTFLAGS} ${exec_args}) + + else () + + # Run tests from the platform-specific executable + set (EXE_CMD ${CMAKE_SOURCE_DIR}/cmake/mpiexec.${PLATFORM} + ${num_procs} ${VALGRIND_COMMAND} ${VALGRIND_COMMAND_OPTIONS} ${exec_file} ${exec_args}) + + endif () + + # Add the test to CTest + add_test(NAME ${TESTNAME} COMMAND ${EXE_CMD}) + + # Adjust the test timeout + set_tests_properties(${TESTNAME} PROPERTIES TIMEOUT ${timeout}) + +endfunction() diff --git a/cmake/mpiexec.hera b/cmake/mpiexec.hera new file mode 100755 index 000000000..332b33e29 --- /dev/null +++ b/cmake/mpiexec.hera @@ -0,0 +1,15 @@ +#!/bin/bash +# +# Arguments: +# +# $1 - Number of MPI Tasks +# $2+ - Executable and its arguments +# + +ACCOUNT= +QOS=debug + +NP=$1 +shift + +srun -A $ACCOUNT -q $QOS -n $NP $@ diff --git a/cmake/mpiexec.jet b/cmake/mpiexec.jet new file mode 100755 index 000000000..332b33e29 --- /dev/null +++ b/cmake/mpiexec.jet @@ -0,0 +1,15 @@ +#!/bin/bash +# +# Arguments: +# +# $1 - Number of MPI Tasks +# $2+ - Executable and its arguments +# + +ACCOUNT= +QOS=debug + +NP=$1 +shift + +srun -A $ACCOUNT -q $QOS -n $NP $@ diff --git a/cmake/mpiexec.orion b/cmake/mpiexec.orion new file mode 100755 index 000000000..332b33e29 --- /dev/null +++ b/cmake/mpiexec.orion @@ -0,0 +1,15 @@ +#!/bin/bash +# +# Arguments: +# +# $1 - Number of MPI Tasks +# $2+ - Executable and its arguments +# + +ACCOUNT= +QOS=debug + +NP=$1 +shift + +srun -A $ACCOUNT -q $QOS -n $NP $@ diff --git a/docs/20201105-0945a-pre-processing-chgres-cube-gayno-final.pdf b/docs/20201105-0945a-pre-processing-chgres-cube-gayno-final.pdf new file mode 100644 index 000000000..90011630f Binary files /dev/null and b/docs/20201105-0945a-pre-processing-chgres-cube-gayno-final.pdf differ diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt new file mode 100644 index 000000000..04e72c8fb --- /dev/null +++ b/docs/CMakeLists.txt @@ -0,0 +1,15 @@ +# This is the CMake file for building the docs directory of NCEPLIBS +# UFS_UTILS project. +# +# Ed Hartnett 10/5/20 + +# Create doxyfile. +configure_file(${CMAKE_CURRENT_SOURCE_DIR}/Doxyfile.in ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile @ONLY) + +# Build documentation with target all. +add_custom_target(doc ALL + ${DOXYGEN_EXECUTABLE} ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile + WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR} + COMMENT "Generating API Documentation with Doxygen" VERBATIM) + + diff --git a/docs/Doxyfile.in b/docs/Doxyfile.in new file mode 100644 index 000000000..c0874346c --- /dev/null +++ b/docs/Doxyfile.in @@ -0,0 +1,2571 @@ +# Doxyfile 1.9.1 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project. +# +# All text after a double hash (##) is considered a comment and is placed in +# front of the TAG it is preceding. +# +# All text after a single hash (#) is considered a comment and will be ignored. +# The format is: +# TAG = value [value, ...] +# For lists, items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (\" \"). + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the configuration +# file that follow. The default is UTF-8 which is also the encoding used for all +# text before the first occurrence of this tag. Doxygen uses libiconv (or the +# iconv built into libc) for the transcoding. See +# https://www.gnu.org/software/libiconv/ for the list of possible encodings. +# The default value is: UTF-8. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by +# double-quotes, unless you are using Doxywizard) that should identify the +# project for which the documentation is generated. This name is used in the +# title of most generated pages and in a few other places. +# The default value is: My Project. + +PROJECT_NAME = UFS_UTILS + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. This +# could be handy for archiving the generated documentation or if some version +# control system is used. + +PROJECT_NUMBER = @PROJECT_VERSION@ + +# Using the PROJECT_BRIEF tag one can provide an optional one line description +# for a project that appears at the top of each page and should give viewer a +# quick idea about the purpose of the project. Keep the description short. + +PROJECT_BRIEF = + +# With the PROJECT_LOGO tag one can specify a logo or an icon that is included +# in the documentation. The maximum height of the logo should not exceed 55 +# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy +# the logo to the output directory. + +PROJECT_LOGO = + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path +# into which the generated documentation will be written. If a relative path is +# entered, it will be relative to the location where doxygen was started. If +# left blank the current directory will be used. + +OUTPUT_DIRECTORY = + +# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub- +# directories (in 2 levels) under the output directory of each output format and +# will distribute the generated files over these directories. Enabling this +# option can be useful when feeding doxygen a huge amount of source files, where +# putting all generated files in the same directory would otherwise causes +# performance problems for the file system. +# The default value is: NO. + +CREATE_SUBDIRS = NO + +# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII +# characters to appear in the names of generated files. If set to NO, non-ASCII +# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode +# U+3044. +# The default value is: NO. + +ALLOW_UNICODE_NAMES = NO + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese, +# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States), +# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian, +# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages), +# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian, +# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian, +# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish, +# Ukrainian and Vietnamese. +# The default value is: English. + +OUTPUT_LANGUAGE = English + +# The OUTPUT_TEXT_DIRECTION tag is used to specify the direction in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all generated output in the proper direction. +# Possible values are: None, LTR, RTL and Context. +# The default value is: None. + +OUTPUT_TEXT_DIRECTION = None + +# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member +# descriptions after the members that are listed in the file and class +# documentation (similar to Javadoc). Set to NO to disable this. +# The default value is: YES. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief +# description of a member or function before the detailed description +# +# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. +# The default value is: YES. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator that is +# used to form the text in various listings. Each string in this list, if found +# as the leading text of the brief description, will be stripped from the text +# and the result, after processing the whole list, is used as the annotated +# text. Otherwise, the brief description is used as-is. If left blank, the +# following values are used ($name is automatically replaced with the name of +# the entity):The $name class, The $name widget, The $name file, is, provides, +# specifies, contains, represents, a, an and the. + +ABBREVIATE_BRIEF = + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# doxygen will generate a detailed section even if there is only a brief +# description. +# The default value is: NO. + +ALWAYS_DETAILED_SEC = YES + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. +# The default value is: NO. + +INLINE_INHERITED_MEMB = YES + +# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path +# before files name in the file list and in the header files. If set to NO the +# shortest path that makes the file name unique will be used +# The default value is: YES. + +FULL_PATH_NAMES = YES + +# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path. +# Stripping is only done if one of the specified strings matches the left-hand +# part of the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the path to +# strip. +# +# Note that you can specify absolute paths here, but also relative paths, which +# will be relative from the directory where doxygen is started. +# This tag requires that the tag FULL_PATH_NAMES is set to YES. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the +# path mentioned in the documentation of a class, which tells the reader which +# header file to include in order to use a class. If left blank only the name of +# the header file containing the class definition is used. Otherwise one should +# specify the list of include paths that are normally passed to the compiler +# using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but +# less readable) file names. This can be useful is your file systems doesn't +# support long names like on DOS, Mac, or CD-ROM. +# The default value is: NO. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the +# first line (until the first dot) of a Javadoc-style comment as the brief +# description. If set to NO, the Javadoc-style will behave just like regular Qt- +# style comments (thus requiring an explicit @brief command for a brief +# description.) +# The default value is: NO. + +JAVADOC_AUTOBRIEF = YES + +# If the JAVADOC_BANNER tag is set to YES then doxygen will interpret a line +# such as +# /*************** +# as being the beginning of a Javadoc-style comment "banner". If set to NO, the +# Javadoc-style will behave just like regular comments and it will not be +# interpreted by doxygen. +# The default value is: NO. + +JAVADOC_BANNER = NO + +# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first +# line (until the first dot) of a Qt-style comment as the brief description. If +# set to NO, the Qt-style will behave just like regular Qt-style comments (thus +# requiring an explicit \brief command for a brief description.) +# The default value is: NO. + +QT_AUTOBRIEF = YES + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a +# multi-line C++ special comment block (i.e. a block of //! or /// comments) as +# a brief description. This used to be the default behavior. The new default is +# to treat a multi-line C++ comment block as a detailed description. Set this +# tag to YES if you prefer the old behavior instead. +# +# Note that setting this tag to YES also means that rational rose comments are +# not recognized any more. +# The default value is: NO. + +MULTILINE_CPP_IS_BRIEF = YES + +# By default Python docstrings are displayed as preformatted text and doxygen's +# special commands cannot be used. By setting PYTHON_DOCSTRING to NO the +# doxygen's special commands can be used and the contents of the docstring +# documentation blocks is shown as doxygen documentation. +# The default value is: YES. + +PYTHON_DOCSTRING = YES + +# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the +# documentation from any documented member that it re-implements. +# The default value is: YES. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new +# page for each member. If set to NO, the documentation of a member will be part +# of the file/class/namespace that contains it. +# The default value is: NO. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen +# uses this value to replace tabs by spaces in code fragments. +# Minimum value: 1, maximum value: 16, default value: 4. + +TAB_SIZE = 4 + +# This tag can be used to specify a number of aliases that act as commands in +# the documentation. An alias has the form: +# name=value +# For example adding +# "sideeffect=@par Side Effects:\n" +# will allow you to put the command \sideeffect (or @sideeffect) in the +# documentation, which will result in a user-defined paragraph with heading +# "Side Effects:". You can put \n's in the value part of an alias to insert +# newlines (in the resulting output). You can put ^^ in the value part of an +# alias to insert a newline as if a physical newline was in the original file. +# When you need a literal { or } or , in the value part of an alias you have to +# escape them by means of a backslash (\), this can lead to conflicts with the +# commands \{ and \} for these it is advised to use the version @{ and @} or use +# a double escape (\\{ and \\}) + +ALIASES = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources +# only. Doxygen will then generate output that is more tailored for C. For +# instance, some of the names that are used will be different. The list of all +# members will be omitted, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_FOR_C = YES + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or +# Python sources only. Doxygen will then generate output that is more tailored +# for that language. For instance, namespaces will be presented as packages, +# qualified scopes will look different, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources. Doxygen will then generate output that is tailored for Fortran. +# The default value is: NO. + +OPTIMIZE_FOR_FORTRAN = YES + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for VHDL. +# The default value is: NO. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Set the OPTIMIZE_OUTPUT_SLICE tag to YES if your project consists of Slice +# sources only. Doxygen will then generate output that is more tailored for that +# language. For instance, namespaces will be presented as modules, types will be +# separated into more groups, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_SLICE = NO + +# Doxygen selects the parser to use depending on the extension of the files it +# parses. With this tag you can assign which parser to use for a given +# extension. Doxygen has a built-in mapping, but you can override or extend it +# using this tag. The format is ext=language, where ext is a file extension, and +# language is one of the parsers supported by doxygen: IDL, Java, JavaScript, +# Csharp (C#), C, C++, D, PHP, md (Markdown), Objective-C, Python, Slice, VHDL, +# Fortran (fixed format Fortran: FortranFixed, free formatted Fortran: +# FortranFree, unknown formatted Fortran: Fortran. In the later case the parser +# tries to guess whether the code is fixed or free formatted code, this is the +# default for Fortran type files). For instance to make doxygen treat .inc files +# as Fortran files (default is PHP), and .f files as C (default is Fortran), +# use: inc=Fortran f=C. +# +# Note: For files without extension you can use no_extension as a placeholder. +# +# Note that for custom extensions you also need to set FILE_PATTERNS otherwise +# the files are not read by doxygen. When specifying no_extension you should add +# * to the FILE_PATTERNS. +# +# Note see also the list of default file extension mappings. + +EXTENSION_MAPPING = + +# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments +# according to the Markdown format, which allows for more readable +# documentation. See https://daringfireball.net/projects/markdown/ for details. +# The output of markdown processing is further processed by doxygen, so you can +# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in +# case of backward compatibilities issues. +# The default value is: YES. + +MARKDOWN_SUPPORT = YES + +# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up +# to that level are automatically included in the table of contents, even if +# they do not have an id attribute. +# Note: This feature currently applies only to Markdown headings. +# Minimum value: 0, maximum value: 99, default value: 5. +# This tag requires that the tag MARKDOWN_SUPPORT is set to YES. + +TOC_INCLUDE_HEADINGS = 5 + +# When enabled doxygen tries to link words that correspond to documented +# classes, or namespaces to their corresponding documentation. Such a link can +# be prevented in individual cases by putting a % sign in front of the word or +# globally by setting AUTOLINK_SUPPORT to NO. +# The default value is: YES. + +AUTOLINK_SUPPORT = YES + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should set this +# tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); +# versus func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. +# The default value is: NO. + +BUILTIN_STL_SUPPORT = NO + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. +# The default value is: NO. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip (see: +# https://www.riverbankcomputing.com/software/sip/intro) sources only. Doxygen +# will parse them like normal C++ but will assume all classes use public instead +# of private inheritance when no explicit protection keyword is present. +# The default value is: NO. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate +# getter and setter methods for a property. Setting this option to YES will make +# doxygen to replace the get and set methods by a property in the documentation. +# This will only work if the methods are indeed getting or setting a simple +# type. If this is not the case, or you want to show the methods anyway, you +# should set this option to NO. +# The default value is: YES. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. +# The default value is: NO. + +DISTRIBUTE_GROUP_DOC = YES + +# If one adds a struct or class to a group and this option is enabled, then also +# any nested class or struct is added to the same group. By default this option +# is disabled and one has to add nested compounds explicitly via \ingroup. +# The default value is: NO. + +GROUP_NESTED_COMPOUNDS = NO + +# Set the SUBGROUPING tag to YES to allow class member groups of the same type +# (for instance a group of public functions) to be put as a subgroup of that +# type (e.g. under the Public Functions section). Set it to NO to prevent +# subgrouping. Alternatively, this can be done per class using the +# \nosubgrouping command. +# The default value is: YES. + +SUBGROUPING = YES + +# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions +# are shown inside the group in which they are included (e.g. using \ingroup) +# instead of on a separate page (for HTML and Man pages) or section (for LaTeX +# and RTF). +# +# Note that this feature does not work in combination with +# SEPARATE_MEMBER_PAGES. +# The default value is: NO. + +INLINE_GROUPED_CLASSES = YES + +# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions +# with only public data fields or simple typedef fields will be shown inline in +# the documentation of the scope in which they are defined (i.e. file, +# namespace, or group documentation), provided this scope is documented. If set +# to NO, structs, classes, and unions are shown on a separate page (for HTML and +# Man pages) or section (for LaTeX and RTF). +# The default value is: NO. + +INLINE_SIMPLE_STRUCTS = YES + +# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or +# enum is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically be +# useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. +# The default value is: NO. + +TYPEDEF_HIDES_STRUCT = NO + +# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This +# cache is used to resolve symbols given their name and scope. Since this can be +# an expensive process and often the same symbol appears multiple times in the +# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small +# doxygen will become slower. If the cache is too large, memory is wasted. The +# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range +# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536 +# symbols. At the end of a run doxygen will report the cache usage and suggest +# the optimal cache size from a speed point of view. +# Minimum value: 0, maximum value: 9, default value: 0. + +LOOKUP_CACHE_SIZE = 0 + +# The NUM_PROC_THREADS specifies the number threads doxygen is allowed to use +# during processing. When set to 0 doxygen will based this on the number of +# cores available in the system. You can set it explicitly to a value larger +# than 0 to get more control over the balance between CPU load and processing +# speed. At this moment only the input processing can be done using multiple +# threads. Since this is still an experimental feature the default is set to 1, +# which efficively disables parallel processing. Please report any issues you +# encounter. Generating dot graphs in parallel is controlled by the +# DOT_NUM_THREADS setting. +# Minimum value: 0, maximum value: 32, default value: 1. + +NUM_PROC_THREADS = 1 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in +# documentation are documented, even if no documentation was available. Private +# class members and static file members will be hidden unless the +# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES. +# Note: This will also disable the warnings about undocumented members that are +# normally produced when WARNINGS is set to YES. +# The default value is: NO. + +EXTRACT_ALL = NO + +# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will +# be included in the documentation. +# The default value is: NO. + +EXTRACT_PRIVATE = YES + +# If the EXTRACT_PRIV_VIRTUAL tag is set to YES, documented private virtual +# methods of a class will be included in the documentation. +# The default value is: NO. + +EXTRACT_PRIV_VIRTUAL = NO + +# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal +# scope will be included in the documentation. +# The default value is: NO. + +EXTRACT_PACKAGE = YES + +# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be +# included in the documentation. +# The default value is: NO. + +EXTRACT_STATIC = YES + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined +# locally in source files will be included in the documentation. If set to NO, +# only classes defined in header files are included. Does not have any effect +# for Java sources. +# The default value is: YES. + +EXTRACT_LOCAL_CLASSES = NO + +# This flag is only useful for Objective-C code. If set to YES, local methods, +# which are defined in the implementation section but not in the interface are +# included in the documentation. If set to NO, only methods in the interface are +# included. +# The default value is: NO. + +EXTRACT_LOCAL_METHODS = NO + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base name of +# the file that contains the anonymous namespace. By default anonymous namespace +# are hidden. +# The default value is: NO. + +EXTRACT_ANON_NSPACES = YES + +# If this flag is set to YES, the name of an unnamed parameter in a declaration +# will be determined by the corresponding definition. By default unnamed +# parameters remain unnamed in the output. +# The default value is: YES. + +RESOLVE_UNNAMED_PARAMS = YES + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all +# undocumented members inside documented classes or files. If set to NO these +# members will be included in the various overviews, but no documentation +# section is generated. This option has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. If set +# to NO, these classes will be included in the various overviews. This option +# has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend +# declarations. If set to NO, these declarations will be included in the +# documentation. +# The default value is: NO. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any +# documentation blocks found inside the body of a function. If set to NO, these +# blocks will be appended to the function's detailed documentation block. +# The default value is: NO. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation that is typed after a +# \internal command is included. If the tag is set to NO then the documentation +# will be excluded. Set it to YES to include the internal documentation. +# The default value is: NO. + +INTERNAL_DOCS = NO + +# With the correct setting of option CASE_SENSE_NAMES doxygen will better be +# able to match the capabilities of the underlying filesystem. In case the +# filesystem is case sensitive (i.e. it supports files in the same directory +# whose names only differ in casing), the option must be set to YES to properly +# deal with such files in case they appear in the input. For filesystems that +# are not case sensitive the option should be be set to NO to properly deal with +# output files written for symbols that only differ in casing, such as for two +# classes, one named CLASS and the other named Class, and to also support +# references to files without having to specify the exact matching casing. On +# Windows (including Cygwin) and MacOS, users should typically set this option +# to NO, whereas on Linux or other Unix flavors it should typically be set to +# YES. +# The default value is: system dependent. + +CASE_SENSE_NAMES = YES + +# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with +# their full class and namespace scopes in the documentation. If set to YES, the +# scope will be hidden. +# The default value is: NO. + +HIDE_SCOPE_NAMES = NO + +# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will +# append additional text to a page's title, such as Class Reference. If set to +# YES the compound reference will be hidden. +# The default value is: NO. + +HIDE_COMPOUND_REFERENCE= NO + +# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of +# the files that are included by a file in the documentation of that file. +# The default value is: YES. + +SHOW_INCLUDE_FILES = YES + +# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each +# grouped member an include statement to the documentation, telling the reader +# which file to include in order to use the member. +# The default value is: NO. + +SHOW_GROUPED_MEMB_INC = NO + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include +# files with double quotes in the documentation rather than with sharp brackets. +# The default value is: NO. + +FORCE_LOCAL_INCLUDES = YES + +# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the +# documentation for inline members. +# The default value is: YES. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the +# (detailed) documentation of file and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. +# The default value is: YES. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief +# descriptions of file, namespace and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. Note that +# this will also influence the order of the classes in the class list. +# The default value is: NO. + +SORT_BRIEF_DOCS = YES + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the +# (brief and detailed) documentation of class members so that constructors and +# destructors are listed first. If set to NO the constructors will appear in the +# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS. +# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief +# member documentation. +# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting +# detailed member documentation. +# The default value is: NO. + +SORT_MEMBERS_CTORS_1ST = YES + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy +# of group names into alphabetical order. If set to NO the group names will +# appear in their defined order. +# The default value is: NO. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by +# fully-qualified names, including namespaces. If set to NO, the class list will +# be sorted only by class name, not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the alphabetical +# list. +# The default value is: NO. + +SORT_BY_SCOPE_NAME = NO + +# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper +# type resolution of all parameters of a function it will reject a match between +# the prototype and the implementation of a member function even if there is +# only one candidate or it is obvious which candidate to choose by doing a +# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still +# accept a match between prototype and implementation in such cases. +# The default value is: NO. + +STRICT_PROTO_MATCHING = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo +# list. This list is created by putting \todo commands in the documentation. +# The default value is: YES. + +GENERATE_TODOLIST = NO + +# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test +# list. This list is created by putting \test commands in the documentation. +# The default value is: YES. + +GENERATE_TESTLIST = NO + +# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug +# list. This list is created by putting \bug commands in the documentation. +# The default value is: YES. + +GENERATE_BUGLIST = NO + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO) +# the deprecated list. This list is created by putting \deprecated commands in +# the documentation. +# The default value is: YES. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional documentation +# sections, marked by \if ... \endif and \cond +# ... \endcond blocks. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the +# initial value of a variable or macro / define can have for it to appear in the +# documentation. If the initializer consists of more lines than specified here +# it will be hidden. Use a value of 0 to hide initializers completely. The +# appearance of the value of individual variables and macros / defines can be +# controlled using \showinitializer or \hideinitializer command in the +# documentation regardless of this setting. +# Minimum value: 0, maximum value: 10000, default value: 30. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at +# the bottom of the documentation of classes and structs. If set to YES, the +# list will mention the files that were used to generate the documentation. +# The default value is: YES. + +SHOW_USED_FILES = YES + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This +# will remove the Files entry from the Quick Index and from the Folder Tree View +# (if specified). +# The default value is: YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces +# page. This will remove the Namespaces entry from the Quick Index and from the +# Folder Tree View (if specified). +# The default value is: YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command command input-file, where command is the value of the +# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided +# by doxygen. Whatever the program writes to standard output is used as the file +# version. For an example see the documentation. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed +# by doxygen. The layout file controls the global structure of the generated +# output files in an output format independent way. To create the layout file +# that represents doxygen's defaults, run doxygen with the -l option. You can +# optionally specify a file name after the option, if omitted DoxygenLayout.xml +# will be used as the name of the layout file. +# +# Note that if you run doxygen from a directory containing a file called +# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE +# tag is left empty. + +LAYOUT_FILE = + +# The CITE_BIB_FILES tag can be used to specify one or more bib files containing +# the reference definitions. This must be a list of .bib files. The .bib +# extension is automatically appended if omitted. This requires the bibtex tool +# to be installed. See also https://en.wikipedia.org/wiki/BibTeX for more info. +# For LaTeX the style of the bibliography can be controlled using +# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the +# search path. See also \cite for info how to create references. + +CITE_BIB_FILES = + +#--------------------------------------------------------------------------- +# Configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated to +# standard output by doxygen. If QUIET is set to YES this implies that the +# messages are off. +# The default value is: NO. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES +# this implies that the warnings are on. +# +# Tip: Turn warnings on while writing the documentation. +# The default value is: YES. + +WARNINGS = YES + +# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate +# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag +# will automatically be disabled. +# The default value is: YES. + +WARN_IF_UNDOCUMENTED = YES + +# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some parameters +# in a documented function, or documenting parameters that don't exist or using +# markup commands wrongly. +# The default value is: YES. + +WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that +# are documented, but have no documentation for their parameters or return +# value. If set to NO, doxygen will only warn about wrong or incomplete +# parameter documentation, but not about the absence of documentation. If +# EXTRACT_ALL is set to YES then this flag will automatically be disabled. +# The default value is: NO. + +WARN_NO_PARAMDOC = YES + +# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when +# a warning is encountered. If the WARN_AS_ERROR tag is set to FAIL_ON_WARNINGS +# then doxygen will continue running as if WARN_AS_ERROR tag is set to NO, but +# at the end of the doxygen process doxygen will return with a non-zero status. +# Possible values are: NO, YES and FAIL_ON_WARNINGS. +# The default value is: NO. + +WARN_AS_ERROR = YES + +# The WARN_FORMAT tag determines the format of the warning messages that doxygen +# can produce. The string should contain the $file, $line, and $text tags, which +# will be replaced by the file and line number from which the warning originated +# and the warning text. Optionally the format may contain $version, which will +# be replaced by the version of the file (if it could be obtained via +# FILE_VERSION_FILTER) +# The default value is: $file:$line: $text. + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning and error +# messages should be written. If left blank the output is written to standard +# error (stderr). + +WARN_LOGFILE = + +#--------------------------------------------------------------------------- +# Configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag is used to specify the files and/or directories that contain +# documented source files. You may enter file names like myfile.cpp or +# directories like /usr/src/myproject. Separate the files or directories with +# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING +# Note: If this tag is empty the current directory is searched. + +INPUT = @abs_top_srcdir@/docs/user_guide.md + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses +# libiconv (or the iconv built into libc) for the transcoding. See the libiconv +# documentation (see: +# https://www.gnu.org/software/libiconv/) for the list of possible encodings. +# The default value is: UTF-8. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and +# *.h) to filter out the source-files in the directories. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# read by doxygen. +# +# Note the list of default checked file patterns might differ from the list of +# default file extension mappings. +# +# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp, +# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, +# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, +# *.m, *.markdown, *.md, *.mm, *.dox (to be provided as doxygen C comment), +# *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, *.f18, *.f, *.for, *.vhd, *.vhdl, +# *.ucf, *.qsf and *.ice. + +FILE_PATTERNS = *.F90 \ + *.f90 \ + *.f \ + *.F \ + *.h \ + *.c \ + *.md \ + *.inc + +# The RECURSIVE tag can be used to specify whether or not subdirectories should +# be searched for input files as well. +# The default value is: NO. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should be +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. +# +# Note that relative paths are relative to the directory from which doxygen is +# run. + +EXCLUDE = @abs_top_srcdir@/sorc + +# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or +# directories that are symbolic links (a Unix file system feature) are excluded +# from the input. +# The default value is: NO. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories use the pattern */test/* + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or directories +# that contain example code fragments that are included (see the \include +# command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and +# *.h) to filter out the source-files in the directories. If left blank all +# files are included. + +EXAMPLE_PATTERNS = + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude commands +# irrespective of the value of the RECURSIVE tag. +# The default value is: NO. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or directories +# that contain images that are to be included in the documentation (see the +# \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command: +# +# +# +# where is the value of the INPUT_FILTER tag, and is the +# name of an input file. Doxygen will then use the output that the filter +# program writes to standard output. If FILTER_PATTERNS is specified, this tag +# will be ignored. +# +# Note that the filter must not add or remove lines; it is applied before the +# code is scanned, but not when the output code is generated. If lines are added +# or removed, the anchors will not be placed correctly. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# properly processed by doxygen. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. The filters are a list of the form: pattern=filter +# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how +# filters are used. If the FILTER_PATTERNS tag is empty or if none of the +# patterns match the file name, INPUT_FILTER is applied. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# properly processed by doxygen. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will also be used to filter the input files that are used for +# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES). +# The default value is: NO. + +FILTER_SOURCE_FILES = NO + +# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file +# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and +# it is also possible to disable source filtering for a specific pattern using +# *.ext= (so without naming a filter). +# This tag requires that the tag FILTER_SOURCE_FILES is set to YES. + +FILTER_SOURCE_PATTERNS = + +# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that +# is part of the input, its contents will be placed on the main page +# (index.html). This can be useful if you have a project on for instance GitHub +# and want to reuse the introduction page also for the doxygen output. + +USE_MDFILE_AS_MAINPAGE = @abs_top_srcdir@/docs/sp_user_guide.md + +#--------------------------------------------------------------------------- +# Configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will be +# generated. Documented entities will be cross-referenced with these sources. +# +# Note: To get rid of all source code in the generated output, make sure that +# also VERBATIM_HEADERS is set to NO. +# The default value is: NO. + +SOURCE_BROWSER = YES + +# Setting the INLINE_SOURCES tag to YES will include the body of functions, +# classes and enums directly into the documentation. +# The default value is: NO. + +INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any +# special comment blocks from generated source code fragments. Normal C, C++ and +# Fortran comments will always remain visible. +# The default value is: YES. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES then for each documented +# entity all documented functions referencing it will be listed. +# The default value is: NO. + +REFERENCED_BY_RELATION = YES + +# If the REFERENCES_RELATION tag is set to YES then for each documented function +# all documented entities called/used by that function will be listed. +# The default value is: NO. + +REFERENCES_RELATION = YES + +# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set +# to YES then the hyperlinks from functions in REFERENCES_RELATION and +# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will +# link to the documentation. +# The default value is: YES. + +REFERENCES_LINK_SOURCE = YES + +# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the +# source code will show a tooltip with additional information such as prototype, +# brief description and links to the definition and documentation. Since this +# will make the HTML file larger and loading of large files a bit slower, you +# can opt to disable this feature. +# The default value is: YES. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +SOURCE_TOOLTIPS = YES + +# If the USE_HTAGS tag is set to YES then the references to source code will +# point to the HTML generated by the htags(1) tool instead of doxygen built-in +# source browser. The htags tool is part of GNU's global source tagging system +# (see https://www.gnu.org/software/global/global.html). You will need version +# 4.8.6 or higher. +# +# To use it do the following: +# - Install the latest version of global +# - Enable SOURCE_BROWSER and USE_HTAGS in the configuration file +# - Make sure the INPUT points to the root of the source tree +# - Run doxygen as normal +# +# Doxygen will invoke htags (and that will in turn invoke gtags), so these +# tools must be available from the command line (i.e. in the search path). +# +# The result: instead of the source browser generated by doxygen, the links to +# source code will now point to the output of htags. +# The default value is: NO. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a +# verbatim copy of the header file for each class for which an include is +# specified. Set to NO to disable this. +# See also: Section \class. +# The default value is: YES. + +VERBATIM_HEADERS = YES + +#--------------------------------------------------------------------------- +# Configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all +# compounds will be generated. Enable this if the project contains a lot of +# classes, structs, unions or interfaces. +# The default value is: YES. + +ALPHABETICAL_INDEX = NO + +# In case all classes in a project start with a common prefix, all classes will +# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag +# can be used to specify a prefix (or a list of prefixes) that should be ignored +# while generating the index headers. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output +# The default value is: YES. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each +# generated HTML page (for example: .htm, .php, .asp). +# The default value is: .html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a user-defined HTML header file for +# each generated HTML page. If the tag is left blank doxygen will generate a +# standard header. +# +# To get valid HTML the header file that includes any scripts and style sheets +# that doxygen needs, which is dependent on the configuration options used (e.g. +# the setting GENERATE_TREEVIEW). It is highly recommended to start with a +# default header using +# doxygen -w html new_header.html new_footer.html new_stylesheet.css +# YourConfigFile +# and then modify the file new_header.html. See also section "Doxygen usage" +# for information on how to generate the default header that doxygen normally +# uses. +# Note: The header is subject to change so you typically have to regenerate the +# default header when upgrading to a newer version of doxygen. For a description +# of the possible markers and block names see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each +# generated HTML page. If the tag is left blank doxygen will generate a standard +# footer. See HTML_HEADER for more information on how to generate a default +# footer and what special commands can be used inside the footer. See also +# section "Doxygen usage" for information on how to generate the default footer +# that doxygen normally uses. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style +# sheet that is used by each HTML page. It can be used to fine-tune the look of +# the HTML output. If left blank doxygen will generate a default style sheet. +# See also section "Doxygen usage" for information on how to generate the style +# sheet that doxygen normally uses. +# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as +# it is more robust and this tag (HTML_STYLESHEET) will in the future become +# obsolete. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_STYLESHEET = + +# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined +# cascading style sheets that are included after the standard style sheets +# created by doxygen. Using this option one can overrule certain style aspects. +# This is preferred over using HTML_STYLESHEET since it does not replace the +# standard style sheet and is therefore more robust against future updates. +# Doxygen will copy the style sheet files to the output directory. +# Note: The order of the extra style sheet files is of importance (e.g. the last +# style sheet in the list overrules the setting of the previous ones in the +# list). For an example see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_STYLESHEET = + +# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the HTML output directory. Note +# that these files will be copied to the base HTML output directory. Use the +# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these +# files. In the HTML_STYLESHEET file, use the file name only. Also note that the +# files will be copied as-is; there are no commands or markers available. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_FILES = + +# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen +# will adjust the colors in the style sheet and background images according to +# this color. Hue is specified as an angle on a colorwheel, see +# https://en.wikipedia.org/wiki/Hue for more information. For instance the value +# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300 +# purple, and 360 is red again. +# Minimum value: 0, maximum value: 359, default value: 220. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_HUE = 220 + +# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors +# in the HTML output. For a value of 0 the output will use grayscales only. A +# value of 255 will produce the most vivid colors. +# Minimum value: 0, maximum value: 255, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_SAT = 100 + +# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the +# luminance component of the colors in the HTML output. Values below 100 +# gradually make the output lighter, whereas values above 100 make the output +# darker. The value divided by 100 is the actual gamma applied, so 80 represents +# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not +# change the gamma. +# Minimum value: 40, maximum value: 240, default value: 80. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_GAMMA = 80 + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting this +# to YES can help to show when doxygen was last run and thus if the +# documentation is up to date. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_TIMESTAMP = NO + +# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML +# documentation will contain a main index with vertical navigation menus that +# are dynamically created via JavaScript. If disabled, the navigation index will +# consists of multiple levels of tabs that are statically embedded in every HTML +# page. Disable this option to support browsers that do not have JavaScript, +# like the Qt help browser. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_MENUS = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_SECTIONS = NO + +# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries +# shown in the various tree structured indices initially; the user can expand +# and collapse entries dynamically later on. Doxygen will expand the tree to +# such a level that at most the specified number of entries are visible (unless +# a fully collapsed tree already exceeds this amount). So setting the number of +# entries 1 will produce a full collapsed tree by default. 0 is a special value +# representing an infinite number of entries and will result in a full expanded +# tree by default. +# Minimum value: 0, maximum value: 9999, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_INDEX_NUM_ENTRIES = 100 + +# If the GENERATE_DOCSET tag is set to YES, additional index files will be +# generated that can be used as input for Apple's Xcode 3 integrated development +# environment (see: +# https://developer.apple.com/xcode/), introduced with OSX 10.5 (Leopard). To +# create a documentation set, doxygen will generate a Makefile in the HTML +# output directory. Running make will produce the docset in that directory and +# running make install will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at +# startup. See https://developer.apple.com/library/archive/featuredarticles/Doxy +# genXcode/_index.html for more information. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_DOCSET = NO + +# This tag determines the name of the docset feed. A documentation feed provides +# an umbrella under which multiple documentation sets from a single provider +# (such as a company or product suite) can be grouped. +# The default value is: Doxygen generated docs. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# This tag specifies a string that should uniquely identify the documentation +# set bundle. This should be a reverse domain-name style string, e.g. +# com.mycompany.MyDocSet. Doxygen will append .docset to the name. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify +# the documentation publisher. This should be a reverse domain-name style +# string, e.g. com.mycompany.MyDocSet.documentation. +# The default value is: org.doxygen.Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_ID = org.doxygen.Publisher + +# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher. +# The default value is: Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_NAME = Publisher + +# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three +# additional HTML index files: index.hhp, index.hhc, and index.hhk. The +# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop +# (see: +# https://www.microsoft.com/en-us/download/details.aspx?id=21138) on Windows. +# +# The HTML Help Workshop contains a compiler that can convert all HTML output +# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML +# files are now used as the Windows 98 help format, and will replace the old +# Windows help format (.hlp) on all Windows platforms in the future. Compressed +# HTML files also contain an index, a table of contents, and you can search for +# words in the documentation. The HTML workshop also contains a viewer for +# compressed HTML files. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_HTMLHELP = NO + +# The CHM_FILE tag can be used to specify the file name of the resulting .chm +# file. You can add a path in front of the file if the result should not be +# written to the html output directory. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_FILE = + +# The HHC_LOCATION tag can be used to specify the location (absolute path +# including file name) of the HTML help compiler (hhc.exe). If non-empty, +# doxygen will try to run the HTML help compiler on the generated index.hhp. +# The file has to be specified with full path. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +HHC_LOCATION = + +# The GENERATE_CHI flag controls if a separate .chi index file is generated +# (YES) or that it should be included in the main .chm file (NO). +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +GENERATE_CHI = NO + +# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc) +# and project file content. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_INDEX_ENCODING = + +# The BINARY_TOC flag controls whether a binary table of contents is generated +# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it +# enables the Previous and Next buttons. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members to +# the table of contents of the HTML help documentation and to the tree view. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and +# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that +# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help +# (.qch) of the generated HTML documentation. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify +# the file name of the resulting .qch file. The path specified is relative to +# the HTML output folder. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help +# Project output. For more information please see Qt Help Project / Namespace +# (see: +# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#namespace). +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt +# Help Project output. For more information please see Qt Help Project / Virtual +# Folders (see: +# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#virtual-folders). +# The default value is: doc. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_VIRTUAL_FOLDER = doc + +# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom +# filter to add. For more information please see Qt Help Project / Custom +# Filters (see: +# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the +# custom filter to add. For more information please see Qt Help Project / Custom +# Filters (see: +# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom-filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this +# project's filter section matches. Qt Help Project / Filter Attributes (see: +# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#filter-attributes). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_SECT_FILTER_ATTRS = + +# The QHG_LOCATION tag can be used to specify the location (absolute path +# including file name) of Qt's qhelpgenerator. If non-empty doxygen will try to +# run qhelpgenerator on the generated .qhp file. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be +# generated, together with the HTML files, they form an Eclipse help plugin. To +# install this plugin and make it available under the help contents menu in +# Eclipse, the contents of the directory containing the HTML and XML files needs +# to be copied into the plugins directory of eclipse. The name of the directory +# within the plugins directory should be the same as the ECLIPSE_DOC_ID value. +# After copying Eclipse needs to be restarted before the help appears. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the Eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have this +# name. Each documentation set should have its own identifier. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# If you want full control over the layout of the generated HTML pages it might +# be necessary to disable the index and replace it with your own. The +# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top +# of each HTML page. A value of NO enables the index and the value YES disables +# it. Since the tabs in the index contain the same information as the navigation +# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +DISABLE_INDEX = NO + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. If the tag +# value is set to YES, a side panel will be generated containing a tree-like +# index structure (just like the one that is generated for HTML Help). For this +# to work a browser that supports JavaScript, DHTML, CSS and frames is required +# (i.e. any modern browser). Windows users are probably better off using the +# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can +# further fine-tune the look of the index. As an example, the default style +# sheet generated by doxygen has an example that shows how to put an image at +# the root of the tree instead of the PROJECT_NAME. Since the tree basically has +# the same information as the tab index, you could consider setting +# DISABLE_INDEX to YES when enabling this option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_TREEVIEW = YES + +# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that +# doxygen will group on one line in the generated HTML documentation. +# +# Note that a value of 0 will completely suppress the enum values from appearing +# in the overview section. +# Minimum value: 0, maximum value: 20, default value: 4. +# This tag requires that the tag GENERATE_HTML is set to YES. + +ENUM_VALUES_PER_LINE = 4 + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used +# to set the initial width (in pixels) of the frame in which the tree is shown. +# Minimum value: 0, maximum value: 1500, default value: 250. +# This tag requires that the tag GENERATE_HTML is set to YES. + +TREEVIEW_WIDTH = 250 + +# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to +# external symbols imported via tag files in a separate window. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +EXT_LINKS_IN_WINDOW = NO + +# If the HTML_FORMULA_FORMAT option is set to svg, doxygen will use the pdf2svg +# tool (see https://github.com/dawbarton/pdf2svg) or inkscape (see +# https://inkscape.org) to generate formulas as SVG images instead of PNGs for +# the HTML output. These images will generally look nicer at scaled resolutions. +# Possible values are: png (the default) and svg (looks nicer but requires the +# pdf2svg or inkscape tool). +# The default value is: png. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FORMULA_FORMAT = png + +# Use this tag to change the font size of LaTeX formulas included as images in +# the HTML documentation. When you change the font size after a successful +# doxygen run you need to manually remove any form_*.png images from the HTML +# output directory to force them to be regenerated. +# Minimum value: 8, maximum value: 50, default value: 10. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_FONTSIZE = 10 + +# Use the FORMULA_TRANSPARENT tag to determine whether or not the images +# generated for formulas are transparent PNGs. Transparent PNGs are not +# supported properly for IE 6.0, but are supported on all modern browsers. +# +# Note that when changing this option you need to delete any form_*.png files in +# the HTML output directory before the changes have effect. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_TRANSPARENT = YES + +# The FORMULA_MACROFILE can contain LaTeX \newcommand and \renewcommand commands +# to create new LaTeX commands to be used in formulas as building blocks. See +# the section "Including formulas" for details. + +FORMULA_MACROFILE = + +# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see +# https://www.mathjax.org) which uses client side JavaScript for the rendering +# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX +# installed or if you want to formulas look prettier in the HTML output. When +# enabled you may also need to install MathJax separately and configure the path +# to it using the MATHJAX_RELPATH option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +USE_MATHJAX = NO + +# When MathJax is enabled you can set the default output format to be used for +# the MathJax output. See the MathJax site (see: +# http://docs.mathjax.org/en/v2.7-latest/output.html) for more details. +# Possible values are: HTML-CSS (which is slower, but has the best +# compatibility), NativeMML (i.e. MathML) and SVG. +# The default value is: HTML-CSS. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_FORMAT = HTML-CSS + +# When MathJax is enabled you need to specify the location relative to the HTML +# output directory using the MATHJAX_RELPATH option. The destination directory +# should contain the MathJax.js script. For instance, if the mathjax directory +# is located at the same level as the HTML output directory, then +# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax +# Content Delivery Network so you can quickly see the result without installing +# MathJax. However, it is strongly recommended to install a local copy of +# MathJax from https://www.mathjax.org before deployment. +# The default value is: https://cdn.jsdelivr.net/npm/mathjax@2. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_RELPATH = http://cdn.mathjax.org/mathjax/latest + +# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax +# extension names that should be enabled during MathJax rendering. For example +# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_EXTENSIONS = + +# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces +# of code that will be used on startup of the MathJax code. See the MathJax site +# (see: +# http://docs.mathjax.org/en/v2.7-latest/output.html) for more details. For an +# example see the documentation. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_CODEFILE = + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box for +# the HTML output. The underlying search engine uses javascript and DHTML and +# should work on any modern browser. Note that when using HTML help +# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) +# there is already a search function so this one should typically be disabled. +# For large projects the javascript based search engine can be slow, then +# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to +# search using the keyboard; to jump to the search box use + S +# (what the is depends on the OS and browser, but it is typically +# , /