mirror of
https://git.gfz-potsdam.de/naaice/iphreeqc.git
synced 2025-12-15 16:18:22 +01:00
Merge branch 'ml/project-name' into 'main'
Change project name to `litephreeqc` See merge request naaice/iphreeqc!32
This commit is contained in:
Max Lübke
commit
cb44e26b69
854
.github/workflows/cmake.yml
vendored
854
.github/workflows/cmake.yml
vendored
@ -1,296 +1,296 @@
|
|||||||
name: CMake
|
# name: CMake
|
||||||
|
#
|
||||||
on:
|
# on:
|
||||||
push:
|
# push:
|
||||||
|
#
|
||||||
pull_request:
|
# pull_request:
|
||||||
branches:
|
# branches:
|
||||||
- master
|
# - master
|
||||||
|
#
|
||||||
schedule:
|
# schedule:
|
||||||
- cron: '15 14 4,11,18,25 * *'
|
# - cron: '15 14 4,11,18,25 * *'
|
||||||
|
#
|
||||||
workflow_dispatch:
|
# workflow_dispatch:
|
||||||
|
#
|
||||||
env:
|
# env:
|
||||||
# Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
|
# # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
|
||||||
BUILD_TYPE: Release
|
# BUILD_TYPE: Release
|
||||||
NAME: IPhreeqc
|
# NAME: IPhreeqc
|
||||||
|
#
|
||||||
jobs:
|
# jobs:
|
||||||
|
#
|
||||||
init:
|
# init:
|
||||||
runs-on: ubuntu-latest
|
# runs-on: ubuntu-latest
|
||||||
# Map step outputs to job outputs
|
# # Map step outputs to job outputs
|
||||||
outputs:
|
# outputs:
|
||||||
VER: ${{ steps.vars.outputs.VER }}
|
# VER: ${{ steps.vars.outputs.VER }}
|
||||||
REL: ${{ steps.vars.outputs.REL }}
|
# REL: ${{ steps.vars.outputs.REL }}
|
||||||
DATE: ${{ steps.vars.outputs.DATE }}
|
# DATE: ${{ steps.vars.outputs.DATE }}
|
||||||
DATE_RFC_3339: ${{ steps.vars.outputs.DATE_RFC_3339 }}
|
# DATE_RFC_3339: ${{ steps.vars.outputs.DATE_RFC_3339 }}
|
||||||
steps:
|
# steps:
|
||||||
- name: Setup vars
|
# - name: Setup vars
|
||||||
id: vars
|
# id: vars
|
||||||
run: |
|
# run: |
|
||||||
echo VER=$(curl -sS https://raw.githubusercontent.com/usgs-coupled/phreeqc-version/main/next_ver.sh | sh) >> $GITHUB_OUTPUT
|
# echo VER=$(curl -sS https://raw.githubusercontent.com/usgs-coupled/phreeqc-version/main/next_ver.sh | sh) >> $GITHUB_OUTPUT
|
||||||
echo REL=$(curl -sS https://raw.githubusercontent.com/usgs-coupled/phreeqc-version/main/rel.py | python3) >> $GITHUB_OUTPUT
|
# echo REL=$(curl -sS https://raw.githubusercontent.com/usgs-coupled/phreeqc-version/main/rel.py | python3) >> $GITHUB_OUTPUT
|
||||||
echo DATE=$(date "+%x") >> $GITHUB_OUTPUT
|
# echo DATE=$(date "+%x") >> $GITHUB_OUTPUT
|
||||||
echo DATE_RFC_3339=$(date --rfc-3339=date) >> $GITHUB_OUTPUT
|
# echo DATE_RFC_3339=$(date --rfc-3339=date) >> $GITHUB_OUTPUT
|
||||||
|
#
|
||||||
|
#
|
||||||
test:
|
# test:
|
||||||
strategy:
|
# strategy:
|
||||||
fail-fast: false
|
# fail-fast: false
|
||||||
matrix:
|
# matrix:
|
||||||
os: [macos-latest, ubuntu-latest, windows-latest]
|
# os: [macos-latest, ubuntu-latest, windows-latest]
|
||||||
|
#
|
||||||
runs-on: ${{ matrix.os }}
|
# runs-on: ${{ matrix.os }}
|
||||||
env:
|
# env:
|
||||||
BUILD_DIR: _ctest # set in ctest.cmake
|
# BUILD_DIR: _ctest # set in ctest.cmake
|
||||||
|
#
|
||||||
steps:
|
# steps:
|
||||||
- uses: actions/checkout@v4
|
# - uses: actions/checkout@v4
|
||||||
|
#
|
||||||
- name: Install ninja valgrind (Linux)
|
# - name: Install ninja valgrind (Linux)
|
||||||
if: runner.os == 'Linux'
|
# if: runner.os == 'Linux'
|
||||||
run: sudo apt-get update && sudo apt-get install -y ninja-build valgrind
|
# run: sudo apt-get update && sudo apt-get install -y ninja-build valgrind
|
||||||
|
#
|
||||||
- name: Install ninja (macOS)
|
# - name: Install ninja (macOS)
|
||||||
if: runner.os == 'macOS'
|
# if: runner.os == 'macOS'
|
||||||
run: brew install ninja
|
# run: brew install ninja
|
||||||
|
#
|
||||||
- name: Set up Visual Studio shell (Windows)
|
# - name: Set up Visual Studio shell (Windows)
|
||||||
if: runner.os == 'Windows'
|
# if: runner.os == 'Windows'
|
||||||
uses: egor-tensin/vs-shell@v2
|
# uses: egor-tensin/vs-shell@v2
|
||||||
with:
|
# with:
|
||||||
arch: x64
|
# arch: x64
|
||||||
|
#
|
||||||
- name: CTest
|
# - name: CTest
|
||||||
run: ctest -S ctest.cmake -V --output-on-failure --timeout 900
|
# run: ctest -S ctest.cmake -V --output-on-failure --timeout 900
|
||||||
|
#
|
||||||
- name: Upload results
|
# - name: Upload results
|
||||||
uses: actions/upload-artifact@v4
|
# uses: actions/upload-artifact@v4
|
||||||
with:
|
# with:
|
||||||
name: ${{ matrix.os }}-${{ github.job }}-results
|
# name: ${{ matrix.os }}-${{ github.job }}-results
|
||||||
path: ${{ github.workspace }}/${{ env.BUILD_DIR }}/Testing/
|
# path: ${{ github.workspace }}/${{ env.BUILD_DIR }}/Testing/
|
||||||
|
#
|
||||||
test-shared:
|
# test-shared:
|
||||||
strategy:
|
# strategy:
|
||||||
fail-fast: false
|
# fail-fast: false
|
||||||
matrix:
|
# matrix:
|
||||||
os: [macos-latest, ubuntu-latest, windows-latest]
|
# os: [macos-latest, ubuntu-latest, windows-latest]
|
||||||
|
#
|
||||||
runs-on: ${{ matrix.os }}
|
# runs-on: ${{ matrix.os }}
|
||||||
env:
|
# env:
|
||||||
BUILD_DIR: _ctest_shared # set in ctest-shared.cmake
|
# BUILD_DIR: _ctest_shared # set in ctest-shared.cmake
|
||||||
|
#
|
||||||
steps:
|
# steps:
|
||||||
- uses: actions/checkout@v4
|
# - uses: actions/checkout@v4
|
||||||
|
#
|
||||||
- name: Install ninja valgrind (Linux)
|
# - name: Install ninja valgrind (Linux)
|
||||||
if: runner.os == 'Linux'
|
# if: runner.os == 'Linux'
|
||||||
run: sudo apt-get update && sudo apt-get install -y ninja-build valgrind
|
# run: sudo apt-get update && sudo apt-get install -y ninja-build valgrind
|
||||||
|
#
|
||||||
- name: Install ninja (macOS)
|
# - name: Install ninja (macOS)
|
||||||
if: runner.os == 'macOS'
|
# if: runner.os == 'macOS'
|
||||||
run: brew install ninja
|
# run: brew install ninja
|
||||||
|
#
|
||||||
- name: Set up Visual Studio shell (Windows)
|
# - name: Set up Visual Studio shell (Windows)
|
||||||
if: runner.os == 'Windows'
|
# if: runner.os == 'Windows'
|
||||||
uses: egor-tensin/vs-shell@v2
|
# uses: egor-tensin/vs-shell@v2
|
||||||
with:
|
# with:
|
||||||
arch: x64
|
# arch: x64
|
||||||
|
#
|
||||||
- name: CTest
|
# - name: CTest
|
||||||
run: ctest -S ctest-shared.cmake -V --output-on-failure --timeout 900
|
# run: ctest -S ctest-shared.cmake -V --output-on-failure --timeout 900
|
||||||
|
#
|
||||||
- name: Upload results
|
# - name: Upload results
|
||||||
uses: actions/upload-artifact@v4
|
# uses: actions/upload-artifact@v4
|
||||||
with:
|
# with:
|
||||||
name: ${{ matrix.os }}-${{ github.job }}-results
|
# name: ${{ matrix.os }}-${{ github.job }}-results
|
||||||
path: ${{ github.workspace }}/${{ env.BUILD_DIR }}/Testing/
|
# path: ${{ github.workspace }}/${{ env.BUILD_DIR }}/Testing/
|
||||||
|
#
|
||||||
test-clang:
|
# test-clang:
|
||||||
strategy:
|
# strategy:
|
||||||
fail-fast: false
|
# fail-fast: false
|
||||||
matrix:
|
# matrix:
|
||||||
os: [macos-latest, ubuntu-latest, windows-latest]
|
# os: [macos-latest, ubuntu-latest, windows-latest]
|
||||||
shared_libs: [OFF, ON]
|
# shared_libs: [OFF, ON]
|
||||||
enable_module: [OFF, ON]
|
# enable_module: [OFF, ON]
|
||||||
|
#
|
||||||
runs-on: ${{ matrix.os }}
|
# runs-on: ${{ matrix.os }}
|
||||||
env:
|
# env:
|
||||||
BUILD_DIR: _build
|
# BUILD_DIR: _build
|
||||||
|
#
|
||||||
steps:
|
# steps:
|
||||||
- uses: actions/checkout@v4
|
# - uses: actions/checkout@v4
|
||||||
|
#
|
||||||
- name: Install ninja valgrind (Linux)
|
# - name: Install ninja valgrind (Linux)
|
||||||
if: runner.os == 'Linux'
|
# if: runner.os == 'Linux'
|
||||||
run: sudo apt-get update && sudo apt-get install -y ninja-build clang valgrind
|
# run: sudo apt-get update && sudo apt-get install -y ninja-build clang valgrind
|
||||||
|
#
|
||||||
- name: Install ninja (macOS)
|
# - name: Install ninja (macOS)
|
||||||
if: runner.os == 'macOS'
|
# if: runner.os == 'macOS'
|
||||||
run: brew install ninja
|
# run: brew install ninja
|
||||||
|
#
|
||||||
- name: Set up Visual Studio shell (Windows)
|
# - name: Set up Visual Studio shell (Windows)
|
||||||
if: runner.os == 'Windows'
|
# if: runner.os == 'Windows'
|
||||||
uses: egor-tensin/vs-shell@v2
|
# uses: egor-tensin/vs-shell@v2
|
||||||
with:
|
# with:
|
||||||
arch: x64
|
# arch: x64
|
||||||
|
#
|
||||||
- name: CMake configure
|
# - name: CMake configure
|
||||||
if: runner.os == 'Linux'
|
# if: runner.os == 'Linux'
|
||||||
run: CC=clang CXX=clang++ cmake -B ${{ env.BUILD_DIR }} -DBUILD_SHARED_LIBS=${{ matrix.shared_libs }} -DIPHREEQC_ENABLE_MODULE=${{ matrix.enable_module }} -DCMAKE_CXX_STANDARD=20 -DCMAKE_CXX_STANDARD_REQUIRED=ON
|
# run: CC=clang CXX=clang++ cmake -B ${{ env.BUILD_DIR }} -DBUILD_SHARED_LIBS=${{ matrix.shared_libs }} -DIPHREEQC_ENABLE_MODULE=${{ matrix.enable_module }} -DCMAKE_CXX_STANDARD=20 -DCMAKE_CXX_STANDARD_REQUIRED=ON
|
||||||
|
#
|
||||||
- name: CMake configure
|
# - name: CMake configure
|
||||||
if: runner.os == 'macOS'
|
# if: runner.os == 'macOS'
|
||||||
run: CC=$(brew --prefix llvm@15)/bin/clang CXX=$(brew --prefix llvm@15)/bin/clang++ cmake -B ${{ env.BUILD_DIR }} -DBUILD_SHARED_LIBS=${{ matrix.shared_libs }} -DIPHREEQC_ENABLE_MODULE=${{ matrix.enable_module }} -DCMAKE_CXX_STANDARD=20 -DCMAKE_CXX_STANDARD_REQUIRED=ON
|
# run: CC=$(brew --prefix llvm@15)/bin/clang CXX=$(brew --prefix llvm@15)/bin/clang++ cmake -B ${{ env.BUILD_DIR }} -DBUILD_SHARED_LIBS=${{ matrix.shared_libs }} -DIPHREEQC_ENABLE_MODULE=${{ matrix.enable_module }} -DCMAKE_CXX_STANDARD=20 -DCMAKE_CXX_STANDARD_REQUIRED=ON
|
||||||
|
#
|
||||||
- name: CMake configure
|
# - name: CMake configure
|
||||||
if: runner.os == 'Windows'
|
# if: runner.os == 'Windows'
|
||||||
run: cmake -B ${{ env.BUILD_DIR }} -A x64 -T "ClangCL" -DBUILD_SHARED_LIBS=${{ matrix.shared_libs }} -DIPHREEQC_ENABLE_MODULE=${{ matrix.enable_module }} -DCMAKE_CXX_STANDARD=20 -DCMAKE_CXX_STANDARD_REQUIRED=ON
|
# run: cmake -B ${{ env.BUILD_DIR }} -A x64 -T "ClangCL" -DBUILD_SHARED_LIBS=${{ matrix.shared_libs }} -DIPHREEQC_ENABLE_MODULE=${{ matrix.enable_module }} -DCMAKE_CXX_STANDARD=20 -DCMAKE_CXX_STANDARD_REQUIRED=ON
|
||||||
|
#
|
||||||
- name: CMake build
|
# - name: CMake build
|
||||||
run: cmake --build ${{ env.BUILD_DIR }}
|
# run: cmake --build ${{ env.BUILD_DIR }}
|
||||||
|
#
|
||||||
- name: CTest
|
# - name: CTest
|
||||||
run: ctest --test-dir ${{ env.BUILD_DIR }}
|
# run: ctest --test-dir ${{ env.BUILD_DIR }}
|
||||||
|
#
|
||||||
- name: Upload results
|
# - name: Upload results
|
||||||
uses: actions/upload-artifact@v4
|
# uses: actions/upload-artifact@v4
|
||||||
with:
|
# with:
|
||||||
name: ${{ matrix.os }}-${{ github.job }}-SHARED=${{ matrix.shared_libs }}-MODULE=${{ matrix.enable_module }}-results
|
# name: ${{ matrix.os }}-${{ github.job }}-SHARED=${{ matrix.shared_libs }}-MODULE=${{ matrix.enable_module }}-results
|
||||||
path: ${{ github.workspace }}/${{ env.BUILD_DIR }}/Testing/
|
# path: ${{ github.workspace }}/${{ env.BUILD_DIR }}/Testing/
|
||||||
|
#
|
||||||
chm:
|
# chm:
|
||||||
runs-on: windows-latest
|
# runs-on: windows-latest
|
||||||
|
#
|
||||||
steps:
|
# steps:
|
||||||
- name: Checkout phreeqc3-HTMLversion
|
# - name: Checkout phreeqc3-HTMLversion
|
||||||
uses: actions/checkout@v4
|
# uses: actions/checkout@v4
|
||||||
with:
|
# with:
|
||||||
repository: usgs-coupled-subtrees/phreeqc3-HTMLversion
|
# repository: usgs-coupled-subtrees/phreeqc3-HTMLversion
|
||||||
ref: master
|
# ref: master
|
||||||
|
#
|
||||||
- name: cache htmlhelp
|
# - name: cache htmlhelp
|
||||||
id: cache-htmlhelp
|
# id: cache-htmlhelp
|
||||||
uses: actions/cache@v4
|
# uses: actions/cache@v4
|
||||||
with:
|
# with:
|
||||||
path: "C:/Program Files (x86)/HTML Help Workshop"
|
# path: "C:/Program Files (x86)/HTML Help Workshop"
|
||||||
key: ${{ runner.os }}-htmlhelp
|
# key: ${{ runner.os }}-htmlhelp
|
||||||
|
#
|
||||||
- name: install htmlhelp
|
# - name: install htmlhelp
|
||||||
if: steps.cache-htmlhelp.outputs.cache-hit != 'true'
|
# if: steps.cache-htmlhelp.outputs.cache-hit != 'true'
|
||||||
timeout-minutes: 5
|
# timeout-minutes: 5
|
||||||
run: |
|
# run: |
|
||||||
curl -L -O --max-time 120 http://web.archive.org/web/20160201063255/http://download.microsoft.com/download/0/A/9/0A939EF6-E31C-430F-A3DF-DFAE7960D564/htmlhelp.exe
|
# curl -L -O --max-time 120 http://web.archive.org/web/20160201063255/http://download.microsoft.com/download/0/A/9/0A939EF6-E31C-430F-A3DF-DFAE7960D564/htmlhelp.exe
|
||||||
cmd /c start /wait .\htmlhelp.exe /q /c /t:$(Get-Location)\tmp
|
# cmd /c start /wait .\htmlhelp.exe /q /c /t:$(Get-Location)\tmp
|
||||||
$file = "$(Get-Location)\tmp\htmlhelp.inf"
|
# $file = "$(Get-Location)\tmp\htmlhelp.inf"
|
||||||
(Get-Content $file) | Foreach-Object { $_ `
|
# (Get-Content $file) | Foreach-Object { $_ `
|
||||||
-replace '^BeginPrompt', ';;BeginPrompt' `
|
# -replace '^BeginPrompt', ';;BeginPrompt' `
|
||||||
-replace '^EndPrompt', ';;EndPrompt' `
|
# -replace '^EndPrompt', ';;EndPrompt' `
|
||||||
-replace '^49000=CustomLDID49000, 1', '49000=CustomLDID49000, 5' `
|
# -replace '^49000=CustomLDID49000, 1', '49000=CustomLDID49000, 5' `
|
||||||
-replace '^"hhupd.exe', ';;hhupd.exe' `
|
# -replace '^"hhupd.exe', ';;hhupd.exe' `
|
||||||
-replace '^DefaultInstallDir="C:\\Program Files\\HTML Help Workshop"', 'DefaultInstallDir="%ProgramFiles%\\HTML Help Workshop"'
|
# -replace '^DefaultInstallDir="C:\\Program Files\\HTML Help Workshop"', 'DefaultInstallDir="%ProgramFiles%\\HTML Help Workshop"'
|
||||||
} | Set-Content $file
|
# } | Set-Content $file
|
||||||
cmd /c start /wait .\tmp\setup.exe
|
# cmd /c start /wait .\tmp\setup.exe
|
||||||
Remove-Item -Recurse -Force .\tmp
|
# Remove-Item -Recurse -Force .\tmp
|
||||||
Remove-Item -Recurse -Force .\htmlhelp.exe
|
# Remove-Item -Recurse -Force .\htmlhelp.exe
|
||||||
# the next line doesn't seem to work (supposed to set the path)
|
# # the next line doesn't seem to work (supposed to set the path)
|
||||||
# echo 'C:\Program Files (x86)\HTML Help Workshop' >> $GITHUB_PATH
|
# # echo 'C:\Program Files (x86)\HTML Help Workshop' >> $GITHUB_PATH
|
||||||
|
#
|
||||||
- name: compile chm
|
# - name: compile chm
|
||||||
shell: bash
|
# shell: bash
|
||||||
run: |
|
# run: |
|
||||||
pushd HTML
|
# pushd HTML
|
||||||
bash fixup_html.bash
|
# bash fixup_html.bash
|
||||||
popd
|
# popd
|
||||||
# hhc returns 1 on success
|
# # hhc returns 1 on success
|
||||||
set +e
|
# set +e
|
||||||
'C:\Program Files (x86)\HTML Help Workshop\hhc' phreeqc3.hhp | tee hhc.out
|
# 'C:\Program Files (x86)\HTML Help Workshop\hhc' phreeqc3.hhp | tee hhc.out
|
||||||
status=${PIPESTATUS[0]}
|
# status=${PIPESTATUS[0]}
|
||||||
set -e
|
# set -e
|
||||||
if [ "$status" -eq 1 ]; then
|
# if [ "$status" -eq 1 ]; then
|
||||||
echo "[OK]"
|
# echo "[OK]"
|
||||||
exit 0
|
# exit 0
|
||||||
else
|
# else
|
||||||
echo "[FAILED]"
|
# echo "[FAILED]"
|
||||||
exit 1
|
# exit 1
|
||||||
fi
|
# fi
|
||||||
|
#
|
||||||
- uses: actions/upload-artifact@v4
|
# - uses: actions/upload-artifact@v4
|
||||||
with:
|
# with:
|
||||||
name: chm
|
# name: chm
|
||||||
path: ${{github.workspace}}/phreeqc3.chm
|
# path: ${{github.workspace}}/phreeqc3.chm
|
||||||
|
#
|
||||||
|
#
|
||||||
R-CMD-check:
|
# R-CMD-check:
|
||||||
needs: [init]
|
# needs: [init]
|
||||||
runs-on: ${{ matrix.config.os }}
|
# runs-on: ${{ matrix.config.os }}
|
||||||
|
#
|
||||||
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
|
# name: ${{ matrix.config.os }} (${{ matrix.config.r }})
|
||||||
|
#
|
||||||
strategy:
|
# strategy:
|
||||||
fail-fast: false
|
# fail-fast: false
|
||||||
matrix:
|
# matrix:
|
||||||
config:
|
# config:
|
||||||
- {os: macos-latest, r: 'release'}
|
# - {os: macos-latest, r: 'release'}
|
||||||
- {os: windows-latest, r: 'release'}
|
# - {os: windows-latest, r: 'release'}
|
||||||
- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
|
# - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
|
||||||
- {os: ubuntu-latest, r: 'release'}
|
# - {os: ubuntu-latest, r: 'release'}
|
||||||
- {os: ubuntu-latest, r: 'oldrel-1'}
|
# - {os: ubuntu-latest, r: 'oldrel-1'}
|
||||||
|
#
|
||||||
steps:
|
# steps:
|
||||||
- uses: actions/checkout@v4
|
# - uses: actions/checkout@v4
|
||||||
|
#
|
||||||
- name: versioning
|
# - name: versioning
|
||||||
run: ./jenkins-dist.sh -v ${{ needs.init.outputs.VER }} -r ${{ needs.init.outputs.REL }} -d ${{ needs.init.outputs.DATE }}
|
# run: ./jenkins-dist.sh -v ${{ needs.init.outputs.VER }} -r ${{ needs.init.outputs.REL }} -d ${{ needs.init.outputs.DATE }}
|
||||||
|
#
|
||||||
- name: Setup R
|
# - name: Setup R
|
||||||
uses: r-lib/actions/setup-r@v2
|
# uses: r-lib/actions/setup-r@v2
|
||||||
with:
|
# with:
|
||||||
r-version: ${{ matrix.config.r }}
|
# r-version: ${{ matrix.config.r }}
|
||||||
http-user-agent: ${{ matrix.config.http-user-agent }}
|
# http-user-agent: ${{ matrix.config.http-user-agent }}
|
||||||
use-public-rspm: true
|
# use-public-rspm: true
|
||||||
|
#
|
||||||
- name: create source
|
# - name: create source
|
||||||
working-directory: R
|
# working-directory: R
|
||||||
run: make VERSION=${{ needs.init.outputs.VER }} RELEASE_DATE=${{ needs.init.outputs.DATE_RFC_3339 }} source
|
# run: make VERSION=${{ needs.init.outputs.VER }} RELEASE_DATE=${{ needs.init.outputs.DATE_RFC_3339 }} source
|
||||||
|
#
|
||||||
- name: Install dependencies
|
# - name: Install dependencies
|
||||||
uses: r-lib/actions/setup-r-dependencies@v2
|
# uses: r-lib/actions/setup-r-dependencies@v2
|
||||||
with:
|
# with:
|
||||||
extra-packages: any::roxygen2, any::pkgbuild, any::rcmdcheck
|
# extra-packages: any::roxygen2, any::pkgbuild, any::rcmdcheck
|
||||||
needs: roxygen2, pkgbuild, check
|
# needs: roxygen2, pkgbuild, check
|
||||||
working-directory: R/phreeqc
|
# working-directory: R/phreeqc
|
||||||
|
#
|
||||||
- name: Display sessionInfo()
|
# - name: Display sessionInfo()
|
||||||
run: sessionInfo()
|
# run: sessionInfo()
|
||||||
working-directory: R/phreeqc
|
# working-directory: R/phreeqc
|
||||||
shell: Rscript {0}
|
# shell: Rscript {0}
|
||||||
|
#
|
||||||
- name: roxygen2::roxygenise()
|
# - name: roxygen2::roxygenise()
|
||||||
run: roxygen2::roxygenise()
|
# run: roxygen2::roxygenise()
|
||||||
working-directory: R/phreeqc
|
# working-directory: R/phreeqc
|
||||||
shell: Rscript {0}
|
# shell: Rscript {0}
|
||||||
|
#
|
||||||
- name: Check
|
# - name: Check
|
||||||
uses: r-lib/actions/check-r-package@v2
|
# uses: r-lib/actions/check-r-package@v2
|
||||||
with:
|
# with:
|
||||||
working-directory: R/phreeqc
|
# working-directory: R/phreeqc
|
||||||
|
#
|
||||||
- name: List files
|
# - name: List files
|
||||||
if: matrix.config.os == 'ubuntu-latest' && matrix.config.r == 'release'
|
# if: matrix.config.os == 'ubuntu-latest' && matrix.config.r == 'release'
|
||||||
run: |
|
# run: |
|
||||||
pwd
|
# pwd
|
||||||
ls -lR
|
# ls -lR
|
||||||
find -name "*.tar.gz"
|
# find -name "*.tar.gz"
|
||||||
|
#
|
||||||
- uses: actions/upload-artifact@v4
|
# - uses: actions/upload-artifact@v4
|
||||||
if: matrix.config.os == 'ubuntu-latest' && matrix.config.r == 'release'
|
# if: matrix.config.os == 'ubuntu-latest' && matrix.config.r == 'release'
|
||||||
with:
|
# with:
|
||||||
name: cran
|
# name: cran
|
||||||
path: ${{ github.workspace }}/R/phreeqc/check/phreeqc_*.tar.gz
|
# path: ${{ github.workspace }}/R/phreeqc/check/phreeqc_*.tar.gz
|
||||||
|
|
||||||
|
|
||||||
# r-build:
|
# r-build:
|
||||||
@ -373,140 +373,140 @@ jobs:
|
|||||||
# path: ${{github.workspace}}/R/valgrind.full.out
|
# path: ${{github.workspace}}/R/valgrind.full.out
|
||||||
|
|
||||||
|
|
||||||
distcheck:
|
# distcheck:
|
||||||
needs: [init, chm]
|
# needs: [init, chm]
|
||||||
runs-on: ubuntu-latest
|
# runs-on: ubuntu-latest
|
||||||
steps:
|
# steps:
|
||||||
- uses: actions/checkout@v4
|
# - uses: actions/checkout@v4
|
||||||
|
#
|
||||||
- uses: actions/download-artifact@v4
|
# - uses: actions/download-artifact@v4
|
||||||
with:
|
# with:
|
||||||
name: chm
|
# name: chm
|
||||||
|
#
|
||||||
- name: mv chm
|
# - name: mv chm
|
||||||
run: mv phreeqc3.chm doc/.
|
# run: mv phreeqc3.chm doc/.
|
||||||
|
#
|
||||||
- name: versioning
|
# - name: versioning
|
||||||
run: ./jenkins-dist.sh -v ${{ needs.init.outputs.VER }} -r ${{ needs.init.outputs.REL }} -d ${{ needs.init.outputs.DATE }}
|
# run: ./jenkins-dist.sh -v ${{ needs.init.outputs.VER }} -r ${{ needs.init.outputs.REL }} -d ${{ needs.init.outputs.DATE }}
|
||||||
|
#
|
||||||
- name: doxygen
|
# - name: doxygen
|
||||||
run: sudo apt-get install -y doxygen && cd doc && doxygen
|
# run: sudo apt-get install -y doxygen && cd doc && doxygen
|
||||||
|
#
|
||||||
- name: autoreconf
|
# - name: autoreconf
|
||||||
run: autoreconf -fvi
|
# run: autoreconf -fvi
|
||||||
|
#
|
||||||
- name: mkdir
|
# - name: mkdir
|
||||||
run: mkdir _build
|
# run: mkdir _build
|
||||||
|
#
|
||||||
- name: configure
|
# - name: configure
|
||||||
working-directory: ${{github.workspace}}/_build
|
# working-directory: ${{github.workspace}}/_build
|
||||||
run: ../configure --prefix=$(pwd)/INSTALL
|
# run: ../configure --prefix=$(pwd)/INSTALL
|
||||||
|
#
|
||||||
- name: make
|
# - name: make
|
||||||
working-directory: ${{github.workspace}}/_build
|
# working-directory: ${{github.workspace}}/_build
|
||||||
run: make -j2 distcheck
|
# run: make -j2 distcheck
|
||||||
|
#
|
||||||
- name: convert
|
# - name: convert
|
||||||
run: |
|
# run: |
|
||||||
sudo apt install -y dos2unix
|
# sudo apt install -y dos2unix
|
||||||
native="
|
# native="
|
||||||
doc/Makefile \
|
# doc/Makefile \
|
||||||
doc/examples/AccumulateLine.c \
|
# doc/examples/AccumulateLine.c \
|
||||||
doc/examples/CreateIPhreeqc.c \
|
# doc/examples/CreateIPhreeqc.c \
|
||||||
doc/examples/F90ClearAccumulatedLines.f90 \
|
# doc/examples/F90ClearAccumulatedLines.f90 \
|
||||||
doc/examples/F90CreateIPhreeqc.f90 \
|
# doc/examples/F90CreateIPhreeqc.f90 \
|
||||||
doc/examples/F90DestroyIPhreeqc.f90 \
|
# doc/examples/F90DestroyIPhreeqc.f90 \
|
||||||
doc/examples/F90GetComponent.f90 \
|
# doc/examples/F90GetComponent.f90 \
|
||||||
doc/examples/F90GetDumpStringLine.f90 \
|
# doc/examples/F90GetDumpStringLine.f90 \
|
||||||
doc/examples/F90GetSelectedOutputValue.f90 \
|
# doc/examples/F90GetSelectedOutputValue.f90 \
|
||||||
doc/examples/F90GetVersionString.f90 \
|
# doc/examples/F90GetVersionString.f90 \
|
||||||
doc/examples/GetComponent.c \
|
# doc/examples/GetComponent.c \
|
||||||
doc/examples/GetDumpString.c \
|
# doc/examples/GetDumpString.c \
|
||||||
doc/examples/GetSelectedOutputValue.c \
|
# doc/examples/GetSelectedOutputValue.c \
|
||||||
doc/examples/GetVersionString.c \
|
# doc/examples/GetVersionString.c \
|
||||||
doc/examples/IPhreeqc.cpp \
|
# doc/examples/IPhreeqc.cpp \
|
||||||
doc/examples/Makefile \
|
# doc/examples/Makefile \
|
||||||
doc/examples/phreeqc.dat \
|
# doc/examples/phreeqc.dat \
|
||||||
src/CSelectedOutput.cpp \
|
# src/CSelectedOutput.cpp \
|
||||||
src/CSelectedOutput.hxx \
|
# src/CSelectedOutput.hxx \
|
||||||
src/CVar.hxx \
|
# src/CVar.hxx \
|
||||||
src/Debug.h \
|
# src/Debug.h \
|
||||||
src/ErrorReporter.hxx \
|
# src/ErrorReporter.hxx \
|
||||||
src/IPhreeqc.cpp \
|
# src/IPhreeqc.cpp \
|
||||||
src/IPhreeqc.f.inc \
|
# src/IPhreeqc.f.inc \
|
||||||
src/IPhreeqc.f90.inc \
|
# src/IPhreeqc.f90.inc \
|
||||||
src/IPhreeqc.h \
|
# src/IPhreeqc.h \
|
||||||
src/IPhreeqc.hpp \
|
# src/IPhreeqc.hpp \
|
||||||
src/IPhreeqcCallbacks.h \
|
# src/IPhreeqcCallbacks.h \
|
||||||
src/IPhreeqcF.f \
|
# src/IPhreeqcF.f \
|
||||||
src/IPhreeqcLib.cpp \
|
# src/IPhreeqcLib.cpp \
|
||||||
src/IPhreeqc_interface.F90 \
|
# src/IPhreeqc_interface.F90 \
|
||||||
src/IPhreeqc_interface_F.cpp \
|
# src/IPhreeqc_interface_F.cpp \
|
||||||
src/IPhreeqc_interface_F.h \
|
# src/IPhreeqc_interface_F.h \
|
||||||
src/Var.c \
|
# src/Var.c \
|
||||||
src/Var.h \
|
# src/Var.h \
|
||||||
src/Version.h \
|
# src/Version.h \
|
||||||
src/fimpl.h \
|
# src/fimpl.h \
|
||||||
src/fwrap.cpp \
|
# src/fwrap.cpp \
|
||||||
src/fwrap.h \
|
# src/fwrap.h \
|
||||||
src/fwrap1.cpp \
|
# src/fwrap1.cpp \
|
||||||
src/fwrap2.cpp \
|
# src/fwrap2.cpp \
|
||||||
src/fwrap3.cpp \
|
# src/fwrap3.cpp \
|
||||||
src/fwrap4.cpp \
|
# src/fwrap4.cpp \
|
||||||
src/fwrap5.cpp \
|
# src/fwrap5.cpp \
|
||||||
src/fwrap6.cpp \
|
# src/fwrap6.cpp \
|
||||||
src/fwrap7.cpp \
|
# src/fwrap7.cpp \
|
||||||
src/fwrap8.cpp \
|
# src/fwrap8.cpp \
|
||||||
src/pp_sys.cpp \
|
# src/pp_sys.cpp \
|
||||||
src/thread.h \
|
# src/thread.h \
|
||||||
test/llnl.dat \
|
# test/llnl.dat \
|
||||||
test/phreeqc.dat \
|
# test/phreeqc.dat \
|
||||||
test2/Makefile \
|
# test2/Makefile \
|
||||||
test2/wateq4f.dat \
|
# test2/wateq4f.dat \
|
||||||
test5/Makefile \
|
# test5/Makefile \
|
||||||
test5/phreeqc.dat \
|
# test5/phreeqc.dat \
|
||||||
test5/test5.c \
|
# test5/test5.c \
|
||||||
tests/main_fortran.cxx \
|
# tests/main_fortran.cxx \
|
||||||
tests/test_c.c \
|
# tests/test_c.c \
|
||||||
tests/test_cxx.cxx \
|
# tests/test_cxx.cxx \
|
||||||
tests/test_f90.F90 \
|
# tests/test_f90.F90 \
|
||||||
unit/TestCVar.cpp \
|
# unit/TestCVar.cpp \
|
||||||
unit/TestCVar.h \
|
# unit/TestCVar.h \
|
||||||
unit/TestInterface.cpp \
|
# unit/TestInterface.cpp \
|
||||||
unit/TestInterface.h \
|
# unit/TestInterface.h \
|
||||||
unit/TestSelectedOutput.cpp \
|
# unit/TestSelectedOutput.cpp \
|
||||||
unit/TestSelectedOutput.h \
|
# unit/TestSelectedOutput.h \
|
||||||
unit/TestVar.cpp \
|
# unit/TestVar.cpp \
|
||||||
unit/TestVar.h \
|
# unit/TestVar.h \
|
||||||
unit/llnl.dat.old \
|
# unit/llnl.dat.old \
|
||||||
unit/missing_e.dat \
|
# unit/missing_e.dat \
|
||||||
unit/phreeqc.dat.old \
|
# unit/phreeqc.dat.old \
|
||||||
unit/unit.cpp"
|
# unit/unit.cpp"
|
||||||
for f in ${native}; do
|
# for f in ${native}; do
|
||||||
unix2dos "${f}"
|
# unix2dos "${f}"
|
||||||
done
|
# done
|
||||||
|
#
|
||||||
- name: dist-zip
|
# - name: dist-zip
|
||||||
working-directory: ${{github.workspace}}/_build
|
# working-directory: ${{github.workspace}}/_build
|
||||||
run: make dist-zip
|
# run: make dist-zip
|
||||||
|
#
|
||||||
- name: copy
|
# - name: copy
|
||||||
run: cp doc/README IPhreeqc_ReadMe.txt
|
# run: cp doc/README IPhreeqc_ReadMe.txt
|
||||||
|
#
|
||||||
- uses: actions/upload-artifact@v4
|
# - uses: actions/upload-artifact@v4
|
||||||
with:
|
# with:
|
||||||
name: readme
|
# name: readme
|
||||||
path: ${{github.workspace}}/IPhreeqc_ReadMe.txt
|
# path: ${{github.workspace}}/IPhreeqc_ReadMe.txt
|
||||||
|
#
|
||||||
- uses: actions/upload-artifact@v4
|
# - uses: actions/upload-artifact@v4
|
||||||
with:
|
# with:
|
||||||
name: tarball
|
# name: tarball
|
||||||
path: ${{github.workspace}}/_build/*.tar.gz
|
# path: ${{github.workspace}}/_build/*.tar.gz
|
||||||
|
#
|
||||||
- uses: actions/upload-artifact@v4
|
# - uses: actions/upload-artifact@v4
|
||||||
with:
|
# with:
|
||||||
name: zipball
|
# name: zipball
|
||||||
path: ${{github.workspace}}/_build/*.zip
|
# path: ${{github.workspace}}/_build/*.zip
|
||||||
|
|
||||||
# build:
|
# build:
|
||||||
# needs: [init]
|
# needs: [init]
|
||||||
|
|||||||
307
CMakeLists.txt
307
CMakeLists.txt
@ -2,47 +2,28 @@
|
|||||||
cmake_minimum_required(VERSION 3.20)
|
cmake_minimum_required(VERSION 3.20)
|
||||||
|
|
||||||
project (
|
project (
|
||||||
IPhreeqc
|
litephreeqc
|
||||||
VERSION 3.8.5
|
VERSION 3.8.5
|
||||||
LANGUAGES CXX C
|
LANGUAGES CXX C
|
||||||
)
|
)
|
||||||
|
|
||||||
# check if this is the root project
|
if (WIN32)
|
||||||
if (CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
|
message(FATAL_ERROR "litephreeqc cannot be built on Windows systems.")
|
||||||
set(STANDALONE_BUILD 1)
|
|
||||||
else()
|
|
||||||
set(STANDALONE_BUILD 0)
|
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
if (STANDALONE_BUILD)
|
# Set a default build type if none was specified
|
||||||
# Set a default build type if none was specified
|
set(default_build_type "Release")
|
||||||
set(default_build_type "Release")
|
if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
|
||||||
if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
|
set(CMAKE_BUILD_TYPE "${default_build_type}" CACHE
|
||||||
set(CMAKE_BUILD_TYPE "${default_build_type}" CACHE
|
STRING "Choose the type of build." FORCE)
|
||||||
STRING "Choose the type of build." FORCE)
|
# Set the possible values of build type for cmake-gui
|
||||||
# Set the possible values of build type for cmake-gui
|
set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS
|
||||||
set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS
|
"Debug" "Release" "MinSizeRel" "RelWithDebInfo")
|
||||||
"Debug" "Release" "MinSizeRel" "RelWithDebInfo")
|
|
||||||
endif()
|
|
||||||
endif()
|
|
||||||
|
|
||||||
# overide docdir on windows
|
|
||||||
if (WIN32 AND NOT CMAKE_INSTALL_DOCDIR)
|
|
||||||
set(CMAKE_INSTALL_DOCDIR "" CACHE PATH "documentation root (doc)")
|
|
||||||
set(CMAKE_INSTALL_DOCDIR "doc")
|
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
# set standard directory locations
|
# set standard directory locations
|
||||||
include(GNUInstallDirs)
|
include(GNUInstallDirs)
|
||||||
|
|
||||||
if (STANDALONE_BUILD AND MSVC)
|
|
||||||
option (IPHREEQC_STATIC_RUNTIME "Build with a static runtime" OFF)
|
|
||||||
if (IPHREEQC_STATIC_RUNTIME)
|
|
||||||
# compile with static runtime
|
|
||||||
set(CMAKE_MSVC_RUNTIME_LIBRARY "MultiThreaded$<$<CONFIG:Debug>:Debug>")
|
|
||||||
endif()
|
|
||||||
endif()
|
|
||||||
|
|
||||||
# Fortran
|
# Fortran
|
||||||
option (IPHREEQC_ENABLE_MODULE "Enable Fortran module" ON)
|
option (IPHREEQC_ENABLE_MODULE "Enable Fortran module" ON)
|
||||||
if (STANDALONE_BUILD)
|
if (STANDALONE_BUILD)
|
||||||
@ -60,22 +41,7 @@ endif()
|
|||||||
# compile Var.c as c++
|
# compile Var.c as c++
|
||||||
set_source_files_properties(src/Var.c PROPERTIES LANGUAGE CXX)
|
set_source_files_properties(src/Var.c PROPERTIES LANGUAGE CXX)
|
||||||
|
|
||||||
if (STANDALONE_BUILD)
|
add_library(IPhreeqc STATIC src/IPhreeqc.cpp)
|
||||||
option(BUILD_SHARED_LIBS "Build Shared Libraries" OFF)
|
|
||||||
set(LIB_TYPE STATIC)
|
|
||||||
endif()
|
|
||||||
|
|
||||||
if (STANDALONE_BUILD)
|
|
||||||
if (MSVC)
|
|
||||||
option(BUILD_CLR_LIBS "Build CLR Libraries" OFF)
|
|
||||||
endif()
|
|
||||||
endif()
|
|
||||||
|
|
||||||
if (BUILD_SHARED_LIBS)
|
|
||||||
set(LIB_TYPE SHARED)
|
|
||||||
endif()
|
|
||||||
|
|
||||||
add_library(IPhreeqc ${LIB_TYPE} src/IPhreeqc.cpp)
|
|
||||||
|
|
||||||
target_sources(IPhreeqc
|
target_sources(IPhreeqc
|
||||||
PRIVATE
|
PRIVATE
|
||||||
@ -220,7 +186,7 @@ target_sources(IPhreeqc
|
|||||||
src/phreeqcpp/UserPunch.cpp
|
src/phreeqcpp/UserPunch.cpp
|
||||||
src/phreeqcpp/UserPunch.h
|
src/phreeqcpp/UserPunch.h
|
||||||
src/phreeqcpp/utilities.cpp
|
src/phreeqcpp/utilities.cpp
|
||||||
src/phreeqcpp/GFZ.cpp
|
src/phreeqcpp/litephreeqc_funcs.cpp
|
||||||
src/thread.h
|
src/thread.h
|
||||||
src/Var.c
|
src/Var.c
|
||||||
src/Var.h
|
src/Var.h
|
||||||
@ -229,10 +195,10 @@ target_sources(IPhreeqc
|
|||||||
|
|
||||||
target_include_directories(IPhreeqc
|
target_include_directories(IPhreeqc
|
||||||
PUBLIC
|
PUBLIC
|
||||||
$<BUILD_INTERFACE:${IPhreeqc_SOURCE_DIR}/src>
|
$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/src>
|
||||||
$<BUILD_INTERFACE:${IPhreeqc_SOURCE_DIR}/src/phreeqcpp>
|
$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/src/phreeqcpp>
|
||||||
$<BUILD_INTERFACE:${IPhreeqc_SOURCE_DIR}/src/phreeqcpp/common>
|
$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/src/phreeqcpp/common>
|
||||||
$<BUILD_INTERFACE:${IPhreeqc_SOURCE_DIR}/src/phreeqcpp/PhreeqcKeywords>
|
$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/src/phreeqcpp/PhreeqcKeywords>
|
||||||
$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
|
$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
|
||||||
)
|
)
|
||||||
|
|
||||||
@ -260,37 +226,6 @@ if (NOT IPHREEQC_ENABLE_MODULE)
|
|||||||
)
|
)
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
if (${CMAKE_CXX_COMPILER_ID} STREQUAL MSVC)
|
|
||||||
target_compile_options(IPhreeqc PRIVATE /wd4251 /wd4275 /wd4793)
|
|
||||||
endif()
|
|
||||||
|
|
||||||
# Disable deprecation warnings for standard C and STL functions in VS2005
|
|
||||||
# and later
|
|
||||||
if (MSVC_VERSION EQUAL 1400 OR MSVC_VERSION GREATER 1400)
|
|
||||||
target_compile_definitions(IPhreeqc PUBLIC _CRT_SECURE_NO_DEPRECATE)
|
|
||||||
target_compile_definitions(IPhreeqc PUBLIC _SCL_SECURE_NO_WARNINGS)
|
|
||||||
endif()
|
|
||||||
|
|
||||||
if (WIN32 AND BUILD_SHARED_LIBS)
|
|
||||||
# Required to build IMPLIB
|
|
||||||
# (Seems to be automatically set when using Visual Studio as the generator)
|
|
||||||
target_compile_definitions(IPhreeqc PRIVATE _WINDLL)
|
|
||||||
endif()
|
|
||||||
|
|
||||||
# Allow user to override POSTFIX properties (but mandate them so that
|
|
||||||
# all builds can be installed to the same directory)
|
|
||||||
if (NOT CMAKE_DEBUG_POSTFIX)
|
|
||||||
set_target_properties(IPhreeqc PROPERTIES DEBUG_POSTFIX "d")
|
|
||||||
endif()
|
|
||||||
|
|
||||||
if (NOT CMAKE_MINSIZEREL_POSTFIX)
|
|
||||||
set_target_properties(IPhreeqc PROPERTIES MINSIZEREL_POSTFIX "msr")
|
|
||||||
endif()
|
|
||||||
|
|
||||||
if (NOT CMAKE_RELWITHDEBINFO_POSTFIX)
|
|
||||||
set_target_properties(IPhreeqc PROPERTIES RELWITHDEBINFO_POSTFIX "rwd")
|
|
||||||
endif()
|
|
||||||
|
|
||||||
set(IPhreeqc_Headers
|
set(IPhreeqc_Headers
|
||||||
${PROJECT_SOURCE_DIR}/src/IPhreeqc.h
|
${PROJECT_SOURCE_DIR}/src/IPhreeqc.h
|
||||||
${PROJECT_SOURCE_DIR}/src/IPhreeqc.hpp
|
${PROJECT_SOURCE_DIR}/src/IPhreeqc.hpp
|
||||||
@ -319,158 +254,94 @@ else()
|
|||||||
)
|
)
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
# Setup references for /CLR
|
|
||||||
if (MSVC AND BUILD_SHARED_LIBS AND BUILD_CLR_LIBS)
|
|
||||||
if (MSVC_VERSION LESS 1600)
|
|
||||||
message(FATAL_ERROR "CLR options must be set manually for versions prior to Visual Studio 2010")
|
|
||||||
endif()
|
|
||||||
set_target_properties(IPhreeqc PROPERTIES VS_DOTNET_REFERENCES "System;System.Drawing;System.Windows.Forms;${CMAKE_CURRENT_SOURCE_DIR}/src/phreeqcpp/ZedGraph.dll")
|
|
||||||
set_target_properties(IPhreeqc PROPERTIES COMMON_LANGUAGE_RUNTIME "")
|
|
||||||
target_compile_definitions(IPhreeqc PRIVATE "MULTICHART")
|
|
||||||
endif()
|
|
||||||
|
|
||||||
set_target_properties(IPhreeqc PROPERTIES
|
set_target_properties(IPhreeqc PROPERTIES
|
||||||
VERSION "${IPhreeqc_VERSION}"
|
VERSION "${IPhreeqc_VERSION}"
|
||||||
SOVERSION "${IPhreeqc_VERSION_MAJOR}"
|
SOVERSION "${IPhreeqc_VERSION_MAJOR}"
|
||||||
)
|
)
|
||||||
|
|
||||||
# install
|
# install
|
||||||
if (STANDALONE_BUILD)
|
include(CMakePackageConfigHelpers)
|
||||||
|
|
||||||
include(CMakePackageConfigHelpers)
|
configure_package_config_file(IPhreeqcConfig.cmake.in
|
||||||
|
${CMAKE_CURRENT_BINARY_DIR}/IPhreeqcConfig.cmake
|
||||||
configure_package_config_file(IPhreeqcConfig.cmake.in
|
INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/IPhreeqc
|
||||||
${CMAKE_CURRENT_BINARY_DIR}/IPhreeqcConfig.cmake
|
|
||||||
INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/IPhreeqc
|
|
||||||
)
|
|
||||||
|
|
||||||
write_basic_package_version_file("IPhreeqcConfigVersion.cmake"
|
|
||||||
VERSION ${IPhreeqc_VERSION}
|
|
||||||
COMPATIBILITY SameMajorVersion
|
|
||||||
)
|
|
||||||
|
|
||||||
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/IPhreeqcConfig.cmake ${CMAKE_CURRENT_BINARY_DIR}/IPhreeqcConfigVersion.cmake
|
|
||||||
DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/IPhreeqc
|
|
||||||
)
|
|
||||||
|
|
||||||
install(TARGETS IPhreeqc
|
|
||||||
EXPORT IPhreeqcTargets
|
|
||||||
LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
|
|
||||||
ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
|
|
||||||
RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
|
|
||||||
INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
|
|
||||||
)
|
|
||||||
install(EXPORT IPhreeqcTargets
|
|
||||||
FILE IPhreeqcTargets.cmake
|
|
||||||
NAMESPACE IPhreeqc::
|
|
||||||
DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/IPhreeqc
|
|
||||||
)
|
|
||||||
|
|
||||||
install(FILES ${IPhreeqc_Headers} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
|
|
||||||
if (WIN32)
|
|
||||||
install(FILES ${IPhreeqc_SRC} DESTINATION src)
|
|
||||||
else()
|
|
||||||
install(FILES ${IPhreeqc_SRC} DESTINATION ${CMAKE_INSTALL_DOCDIR}/src)
|
|
||||||
endif()
|
|
||||||
if (BUILD_CLR_LIBS)
|
|
||||||
install(FILES "${PROJECT_SOURCE_DIR}/src/phreeqcpp/ZedGraph.dll" DESTINATION ${CMAKE_INSTALL_BINDIR})
|
|
||||||
endif()
|
|
||||||
endif()
|
|
||||||
|
|
||||||
if (BUILD_CLR_LIBS)
|
|
||||||
if (NOT BUILD_SHARED_LIBS)
|
|
||||||
message(FATAL_ERROR "BUILD_CLR_LIBS requires that BUILD_SHARED_LIBS be set")
|
|
||||||
endif()
|
|
||||||
|
|
||||||
if (IPHREEQC_STATIC_RUNTIME)
|
|
||||||
message(FATAL_ERROR "BUILD_CLR_LIBS and IPHREEQC_STATIC_RUNTIME are mutually exclusive")
|
|
||||||
endif()
|
|
||||||
|
|
||||||
# CLR files
|
|
||||||
target_sources(IPhreeqc
|
|
||||||
PRIVATE
|
|
||||||
src/phreeqcpp/ChartHandler.cpp
|
|
||||||
src/phreeqcpp/ChartHandler.h
|
|
||||||
src/phreeqcpp/ChartObject.cpp
|
|
||||||
src/phreeqcpp/ChartObject.h
|
|
||||||
src/phreeqcpp/CurveObject.cpp
|
|
||||||
src/phreeqcpp/CurveObject.h
|
|
||||||
)
|
)
|
||||||
|
|
||||||
|
write_basic_package_version_file("IPhreeqcConfigVersion.cmake"
|
||||||
|
VERSION ${IPhreeqc_VERSION}
|
||||||
|
COMPATIBILITY SameMajorVersion
|
||||||
|
)
|
||||||
|
|
||||||
|
install(FILES ${CMAKE_CURRENT_BINARY_DIR}/IPhreeqcConfig.cmake ${CMAKE_CURRENT_BINARY_DIR}/IPhreeqcConfigVersion.cmake
|
||||||
|
DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/IPhreeqc
|
||||||
|
)
|
||||||
|
|
||||||
|
install(TARGETS IPhreeqc
|
||||||
|
EXPORT IPhreeqcTargets
|
||||||
|
LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
|
||||||
|
ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
|
||||||
|
RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
|
||||||
|
INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
|
||||||
|
)
|
||||||
|
install(EXPORT IPhreeqcTargets
|
||||||
|
FILE IPhreeqcTargets.cmake
|
||||||
|
NAMESPACE IPhreeqc::
|
||||||
|
DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/IPhreeqc
|
||||||
|
)
|
||||||
|
|
||||||
|
install(FILES ${IPhreeqc_Headers} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
|
||||||
|
if (WIN32)
|
||||||
|
install(FILES ${IPhreeqc_SRC} DESTINATION src)
|
||||||
|
else()
|
||||||
|
install(FILES ${IPhreeqc_SRC} DESTINATION ${CMAKE_INSTALL_DOCDIR}/src)
|
||||||
endif()
|
endif()
|
||||||
|
if (BUILD_CLR_LIBS)
|
||||||
|
install(FILES "${PROJECT_SOURCE_DIR}/src/phreeqcpp/ZedGraph.dll" DESTINATION ${CMAKE_INSTALL_BINDIR})
|
||||||
|
endif()
|
||||||
|
|
||||||
|
|
||||||
include (CTest)
|
include (CTest)
|
||||||
|
|
||||||
if (STANDALONE_BUILD)
|
# add_subdirectory(database)
|
||||||
|
# add_subdirectory(doc)
|
||||||
|
# add_subdirectory(examples)
|
||||||
|
|
||||||
add_subdirectory(database)
|
if (BUILD_TESTING)
|
||||||
add_subdirectory(doc)
|
add_subdirectory(tests)
|
||||||
add_subdirectory(examples)
|
|
||||||
|
|
||||||
if (BUILD_TESTING)
|
|
||||||
add_subdirectory(tests)
|
|
||||||
endif()
|
|
||||||
|
|
||||||
|
|
||||||
if (BUILD_TESTING) # may need to add MSVC version check
|
|
||||||
include(FetchContent)
|
|
||||||
|
|
||||||
# Avoid warning about DOWNLOAD_EXTRACT_TIMESTAMP in CMake 3.24:
|
|
||||||
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.24.0")
|
|
||||||
cmake_policy(SET CMP0135 NEW)
|
|
||||||
endif()
|
|
||||||
|
|
||||||
FetchContent_Declare(
|
|
||||||
googletest
|
|
||||||
URL https://github.com/google/googletest/archive/release-1.12.1.tar.gz
|
|
||||||
)
|
|
||||||
|
|
||||||
mark_as_advanced(
|
|
||||||
FETCHCONTENT_BASE_DIR
|
|
||||||
FETCHCONTENT_FULLY_DISCONNECTED
|
|
||||||
FETCHCONTENT_QUIET
|
|
||||||
FETCHCONTENT_SOURCE_DIR_GOOGLETEST
|
|
||||||
FETCHCONTENT_UPDATES_DISCONNECTED
|
|
||||||
FETCHCONTENT_UPDATES_DISCONNECTED_GOOGLETEST
|
|
||||||
)
|
|
||||||
|
|
||||||
# Prevent GoogleTest from overriding our compiler/linker options
|
|
||||||
# when building with Visual Studio
|
|
||||||
set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
|
|
||||||
|
|
||||||
set(BUILD_GTEST ON CACHE BOOL "" FORCE)
|
|
||||||
set(BUILD_GMOCK ON CACHE BOOL "" FORCE)
|
|
||||||
|
|
||||||
set(INSTALL_GTEST OFF CACHE BOOL "" FORCE)
|
|
||||||
set(INSTALL_GMOCK OFF CACHE BOOL "" FORCE)
|
|
||||||
|
|
||||||
mark_as_advanced(
|
|
||||||
BUILD_GTEST
|
|
||||||
BUILD_GMOCK
|
|
||||||
INSTALL_GTEST
|
|
||||||
INSTALL_GMOCK
|
|
||||||
gmock_build_tests
|
|
||||||
gtest_build_tests
|
|
||||||
gtest_build_samples
|
|
||||||
gtest_disable_pthreads
|
|
||||||
gtest_force_shared_crt
|
|
||||||
gtest_hide_internal_symbols
|
|
||||||
)
|
|
||||||
|
|
||||||
FetchContent_MakeAvailable(googletest)
|
|
||||||
if (NOT googletest_POPULATED)
|
|
||||||
# Always build googletest static
|
|
||||||
set(SAVE_BUILD_SHARED_LIBS ${BUILD_SHARED_LIBS})
|
|
||||||
set(BUILD_SHARED_LIBS OFF)
|
|
||||||
FetchContent_MakeAvailable(googletest)
|
|
||||||
set(BUILD_SHARED_LIBS ${SAVE_BUILD_SHARED_LIBS})
|
|
||||||
endif()
|
|
||||||
|
|
||||||
add_subdirectory(gtest)
|
|
||||||
endif()
|
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
add_subdirectory(poet)
|
|
||||||
|
if (BUILD_TESTING) # may need to add MSVC version check
|
||||||
|
include(FetchContent)
|
||||||
|
|
||||||
|
# Avoid warning about DOWNLOAD_EXTRACT_TIMESTAMP in CMake 3.24:
|
||||||
|
if (CMAKE_VERSION VERSION_GREATER_EQUAL "3.24.0")
|
||||||
|
cmake_policy(SET CMP0135 NEW)
|
||||||
|
endif()
|
||||||
|
|
||||||
|
FetchContent_Declare(
|
||||||
|
googletest
|
||||||
|
GIT_REPOSITORY https://github.com/google/googletest.git
|
||||||
|
GIT_TAG v1.17.0
|
||||||
|
)
|
||||||
|
|
||||||
|
# Prevent GoogleTest from overriding our compiler/linker options
|
||||||
|
# when building with Visual Studio
|
||||||
|
set(gtest_force_shared_crt ON CACHE BOOL "" FORCE)
|
||||||
|
|
||||||
|
FetchContent_MakeAvailable(googletest)
|
||||||
|
if (NOT googletest_POPULATED)
|
||||||
|
# Always build googletest static
|
||||||
|
set(SAVE_BUILD_SHARED_LIBS ${BUILD_SHARED_LIBS})
|
||||||
|
set(BUILD_SHARED_LIBS OFF)
|
||||||
|
FetchContent_MakeAvailable(googletest)
|
||||||
|
set(BUILD_SHARED_LIBS ${SAVE_BUILD_SHARED_LIBS})
|
||||||
|
endif()
|
||||||
|
|
||||||
|
add_subdirectory(gtest)
|
||||||
|
endif()
|
||||||
|
|
||||||
|
add_subdirectory(litephreeqc)
|
||||||
|
|
||||||
# get_cmake_property(_variableNames VARIABLES)
|
# get_cmake_property(_variableNames VARIABLES)
|
||||||
# list (SORT _variableNames)
|
# list (SORT _variableNames)
|
||||||
|
|||||||
@ -1,4 +1,5 @@
|
|||||||
set(POET_SOURCE_FILES
|
|
||||||
|
set(LPQC_SOURCE_FILES
|
||||||
src/Engine.cpp
|
src/Engine.cpp
|
||||||
src/Runner.cpp
|
src/Runner.cpp
|
||||||
src/Knobs.cpp
|
src/Knobs.cpp
|
||||||
@ -20,19 +21,19 @@ set(POET_SOURCE_FILES
|
|||||||
src/PhreeqcMatrix/Misc.cpp
|
src/PhreeqcMatrix/Misc.cpp
|
||||||
)
|
)
|
||||||
|
|
||||||
add_library(IPhreeqcPOET ${POET_SOURCE_FILES})
|
add_library(litephreeqc STATIC ${LPQC_SOURCE_FILES})
|
||||||
target_link_libraries(IPhreeqcPOET PUBLIC IPhreeqc)
|
target_link_libraries(litephreeqc PUBLIC IPhreeqc)
|
||||||
target_include_directories(IPhreeqcPOET PUBLIC
|
target_include_directories(litephreeqc PUBLIC
|
||||||
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
|
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
|
||||||
$<INSTALL_INTERFACE:include>)
|
$<INSTALL_INTERFACE:include>)
|
||||||
|
|
||||||
# Set C++20 standard
|
# Set C++20 standard
|
||||||
target_compile_features(IPhreeqcPOET PUBLIC cxx_std_20)
|
target_compile_features(litephreeqc PUBLIC cxx_std_20)
|
||||||
|
|
||||||
if (BUILD_TESTING AND STANDALONE_BUILD)
|
if (BUILD_TESTING AND STANDALONE_BUILD)
|
||||||
enable_testing()
|
enable_testing()
|
||||||
|
|
||||||
set(POET_TEST_SOURCE_FILES
|
set(LPQC_TEST_SOURCE_FILES
|
||||||
test/testPhreeqcEngine.cpp
|
test/testPhreeqcEngine.cpp
|
||||||
test/testPhreeqcMatrix.cpp
|
test/testPhreeqcMatrix.cpp
|
||||||
test/testPhreeqcRunner.cpp
|
test/testPhreeqcRunner.cpp
|
||||||
@ -41,15 +42,15 @@ if (BUILD_TESTING AND STANDALONE_BUILD)
|
|||||||
test/IPhreeqcReader.cpp
|
test/IPhreeqcReader.cpp
|
||||||
)
|
)
|
||||||
|
|
||||||
add_executable(poet_test ${POET_TEST_SOURCE_FILES})
|
add_executable(litephreeqc_test ${LPQC_TEST_SOURCE_FILES})
|
||||||
|
|
||||||
target_link_libraries(
|
target_link_libraries(
|
||||||
poet_test
|
litephreeqc_test
|
||||||
IPhreeqcPOET
|
litephreeqc
|
||||||
GTest::gtest_main
|
GTest::gtest_main
|
||||||
)
|
)
|
||||||
|
|
||||||
target_include_directories(poet_test PRIVATE ${CMAKE_CURRENT_BINARY_DIR})
|
target_include_directories(litephreeqc_test PRIVATE ${CMAKE_CURRENT_BINARY_DIR})
|
||||||
|
|
||||||
# read file and store in variable
|
# read file and store in variable
|
||||||
file(REAL_PATH "${PROJECT_SOURCE_DIR}/database/phreeqc.dat" POET_PHREEQCDAT_DB)
|
file(REAL_PATH "${PROJECT_SOURCE_DIR}/database/phreeqc.dat" POET_PHREEQCDAT_DB)
|
||||||
@ -59,11 +60,11 @@ if (BUILD_TESTING AND STANDALONE_BUILD)
|
|||||||
configure_file("${CMAKE_CURRENT_SOURCE_DIR}/test/testInput.hpp.in" "${CMAKE_CURRENT_BINARY_DIR}/testInput.hpp")
|
configure_file("${CMAKE_CURRENT_SOURCE_DIR}/test/testInput.hpp.in" "${CMAKE_CURRENT_BINARY_DIR}/testInput.hpp")
|
||||||
|
|
||||||
include(GoogleTest)
|
include(GoogleTest)
|
||||||
gtest_discover_tests(poet_test)
|
gtest_discover_tests(litephreeqc_test)
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
add_executable(testGolemRunner test/testGolemRunner.cpp)
|
add_executable(golemrunner test/testGolemRunner.cpp)
|
||||||
target_link_libraries(testGolemRunner IPhreeqcPOET)
|
target_link_libraries(golemrunner litephreeqc)
|
||||||
|
|
||||||
add_executable(testGetters test/testGetters.cpp)
|
add_executable(testGetters test/testGetters.cpp)
|
||||||
target_link_libraries(testGetters IPhreeqcPOET)
|
target_link_libraries(testGetters litephreeqc)
|
||||||
10
litephreeqc/LICENSE.txt
Normal file
10
litephreeqc/LICENSE.txt
Normal file
@ -0,0 +1,10 @@
|
|||||||
|
This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
|
||||||
|
It adds a C++ interface on top of the original PHREEQC code, with small changes
|
||||||
|
to the original code base.
|
||||||
|
|
||||||
|
Authors of Modifications:
|
||||||
|
- Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
- Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#pragma once
|
#pragma once
|
||||||
|
|
||||||
#include "PhreeqcMatrix.hpp"
|
#include "PhreeqcMatrix.hpp"
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#pragma once
|
#pragma once
|
||||||
|
|
||||||
#include <cstdint>
|
#include <cstdint>
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#pragma once
|
#pragma once
|
||||||
|
|
||||||
#include <map>
|
#include <map>
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#pragma once
|
#pragma once
|
||||||
|
|
||||||
#include "PhreeqcEngine.hpp"
|
#include "PhreeqcEngine.hpp"
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include "PhreeqcEngine.hpp"
|
#include "PhreeqcEngine.hpp"
|
||||||
#include <cstddef>
|
#include <cstddef>
|
||||||
#include <iomanip>
|
#include <iomanip>
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include "PhreeqcKnobs.hpp"
|
#include "PhreeqcKnobs.hpp"
|
||||||
|
|
||||||
#include <Phreeqc.h>
|
#include <Phreeqc.h>
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include <PhreeqcMatrix.hpp>
|
#include <PhreeqcMatrix.hpp>
|
||||||
#include <algorithm>
|
#include <algorithm>
|
||||||
#include <cstddef>
|
#include <cstddef>
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include "IPhreeqc.hpp"
|
#include "IPhreeqc.hpp"
|
||||||
#include "PhreeqcKnobs.hpp"
|
#include "PhreeqcKnobs.hpp"
|
||||||
#include "PhreeqcMatrix.hpp"
|
#include "PhreeqcMatrix.hpp"
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include "PhreeqcMatrix.hpp"
|
#include "PhreeqcMatrix.hpp"
|
||||||
|
|
||||||
#include "../Wrapper/EquilibriumWrapper.hpp"
|
#include "../Wrapper/EquilibriumWrapper.hpp"
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include "PhreeqcMatrix.hpp"
|
#include "PhreeqcMatrix.hpp"
|
||||||
|
|
||||||
#include <IPhreeqc.hpp>
|
#include <IPhreeqc.hpp>
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include "PhreeqcEngine.hpp"
|
#include "PhreeqcEngine.hpp"
|
||||||
#include "PhreeqcMatrix.hpp"
|
#include "PhreeqcMatrix.hpp"
|
||||||
#include "PhreeqcRunner.hpp"
|
#include "PhreeqcRunner.hpp"
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include "EquilibriumWrapper.hpp"
|
#include "EquilibriumWrapper.hpp"
|
||||||
|
|
||||||
EquilibriumWrapper::EquilibriumCompWrapper::EquilibriumCompWrapper(
|
EquilibriumWrapper::EquilibriumCompWrapper::EquilibriumCompWrapper(
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include "EquilibriumWrapper.hpp"
|
#include "EquilibriumWrapper.hpp"
|
||||||
|
|
||||||
#include <algorithm>
|
#include <algorithm>
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#pragma once
|
#pragma once
|
||||||
|
|
||||||
#include "PPassemblage.h"
|
#include "PPassemblage.h"
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include "ExchangeWrapper.hpp"
|
#include "ExchangeWrapper.hpp"
|
||||||
|
|
||||||
ExchangeWrapper::ExchangeCompWrapper::ExchangeCompWrapper(cxxExchComp &comp)
|
ExchangeWrapper::ExchangeCompWrapper::ExchangeCompWrapper(cxxExchComp &comp)
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include "ExchangeWrapper.hpp"
|
#include "ExchangeWrapper.hpp"
|
||||||
|
|
||||||
ExchangeWrapper::ExchangeWrapper(cxxExchange *exch,
|
ExchangeWrapper::ExchangeWrapper(cxxExchange *exch,
|
||||||
@ -21,36 +34,36 @@ ExchangeWrapper::ExchangeWrapper(cxxExchange *exch,
|
|||||||
num_elements += exchange_comps.back()->size();
|
num_elements += exchange_comps.back()->size();
|
||||||
}
|
}
|
||||||
|
|
||||||
// const std::size_t defined_comps = exchange->Get_exchange_comps().size();
|
// const std::size_t defined_comps = exchange->Get_exchange_comps().size();
|
||||||
|
|
||||||
// auto header_it = remaining_field_header.begin();
|
// auto header_it = remaining_field_header.begin();
|
||||||
|
|
||||||
// while (header_it != remaining_field_header.end() &&
|
// while (header_it != remaining_field_header.end() &&
|
||||||
// exchange_comps.size() < defined_comps) {
|
// exchange_comps.size() < defined_comps) {
|
||||||
// const std::string formular = *header_it;
|
// const std::string formular = *header_it;
|
||||||
|
|
||||||
// auto it = std::find_if(exchange->Get_exchange_comps().begin(),
|
// auto it = std::find_if(exchange->Get_exchange_comps().begin(),
|
||||||
// exchange->Get_exchange_comps().end(),
|
// exchange->Get_exchange_comps().end(),
|
||||||
// [&](const cxxExchComp &comp) {
|
// [&](const cxxExchComp &comp) {
|
||||||
// return comp.Get_formula() == formular;
|
// return comp.Get_formula() == formular;
|
||||||
// });
|
// });
|
||||||
|
|
||||||
// if (it != exchange->Get_exchange_comps().end()) {
|
// if (it != exchange->Get_exchange_comps().end()) {
|
||||||
// const size_t i = this->exchange_comps.size();
|
// const size_t i = this->exchange_comps.size();
|
||||||
|
|
||||||
// exchange_comps.push_back(std::make_unique<ExchangeCompWrapper>(*it));
|
// exchange_comps.push_back(std::make_unique<ExchangeCompWrapper>(*it));
|
||||||
// header_it += this->exchange_comps[i]->size();
|
// header_it += this->exchange_comps[i]->size();
|
||||||
// num_elements += this->exchange_comps[i]->size();
|
// num_elements += this->exchange_comps[i]->size();
|
||||||
// continue;
|
// continue;
|
||||||
// }
|
// }
|
||||||
|
|
||||||
// header_it++;
|
// header_it++;
|
||||||
// }
|
// }
|
||||||
|
|
||||||
// if (exchange_comps.size() != defined_comps) {
|
// if (exchange_comps.size() != defined_comps) {
|
||||||
// throw std::runtime_error(
|
// throw std::runtime_error(
|
||||||
// "Not all exchange components found in Phreeqc variables");
|
// "Not all exchange components found in Phreeqc variables");
|
||||||
// }
|
// }
|
||||||
}
|
}
|
||||||
|
|
||||||
void ExchangeWrapper::get(std::span<LDBLE> &exchange) const {
|
void ExchangeWrapper::get(std::span<LDBLE> &exchange) const {
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#pragma once
|
#pragma once
|
||||||
|
|
||||||
#include "ExchComp.h"
|
#include "ExchComp.h"
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include "KineticWrapper.hpp"
|
#include "KineticWrapper.hpp"
|
||||||
#include <cstddef>
|
#include <cstddef>
|
||||||
#include <string>
|
#include <string>
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include "KineticWrapper.hpp"
|
#include "KineticWrapper.hpp"
|
||||||
#include <vector>
|
#include <vector>
|
||||||
|
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#pragma once
|
#pragma once
|
||||||
|
|
||||||
#include "KineticsComp.h"
|
#include "KineticsComp.h"
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include "SolutionWrapper.hpp"
|
#include "SolutionWrapper.hpp"
|
||||||
#include "NameDouble.h"
|
#include "NameDouble.h"
|
||||||
#include <set>
|
#include <set>
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#pragma once
|
#pragma once
|
||||||
|
|
||||||
#include "Solution.h"
|
#include "Solution.h"
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include "SurfaceWrapper.hpp"
|
#include "SurfaceWrapper.hpp"
|
||||||
|
|
||||||
SurfaceWrapper::SurfaceChargeWrapper::SurfaceChargeWrapper(
|
SurfaceWrapper::SurfaceChargeWrapper::SurfaceChargeWrapper(
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include "SurfaceWrapper.hpp"
|
#include "SurfaceWrapper.hpp"
|
||||||
|
|
||||||
SurfaceWrapper::SurfaceCompWrapper::SurfaceCompWrapper(cxxSurfaceComp &comp)
|
SurfaceWrapper::SurfaceCompWrapper::SurfaceCompWrapper(cxxSurfaceComp &comp)
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include "SurfaceWrapper.hpp"
|
#include "SurfaceWrapper.hpp"
|
||||||
#include "SurfaceComp.h"
|
#include "SurfaceComp.h"
|
||||||
|
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#pragma once
|
#pragma once
|
||||||
|
|
||||||
#include "Surface.h"
|
#include "Surface.h"
|
||||||
31
litephreeqc/src/Wrapper/WrapperBase.hpp
Normal file
31
litephreeqc/src/Wrapper/WrapperBase.hpp
Normal file
@ -0,0 +1,31 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
|
#pragma once
|
||||||
|
|
||||||
|
#include <phrqtype.h>
|
||||||
|
#include <span>
|
||||||
|
|
||||||
|
class WrapperBase {
|
||||||
|
public:
|
||||||
|
virtual ~WrapperBase() = default;
|
||||||
|
|
||||||
|
std::size_t size() const { return this->num_elements; };
|
||||||
|
|
||||||
|
virtual void get(std::span<LDBLE> &data) const = 0;
|
||||||
|
|
||||||
|
virtual void set(const std::span<LDBLE> &data) = 0;
|
||||||
|
|
||||||
|
protected:
|
||||||
|
std::size_t num_elements = 0;
|
||||||
|
};
|
||||||
147
litephreeqc/test/testGolemRunner.cpp
Normal file
147
litephreeqc/test/testGolemRunner.cpp
Normal file
@ -0,0 +1,147 @@
|
|||||||
|
// Time-stamp: "Last modified 2025-07-28 13:03:01 delucia"
|
||||||
|
#include <algorithm>
|
||||||
|
#include <cmath>
|
||||||
|
#include <fstream>
|
||||||
|
#include <iomanip>
|
||||||
|
#include <iostream>
|
||||||
|
#include <iterator>
|
||||||
|
#include <linux/limits.h>
|
||||||
|
#include <memory>
|
||||||
|
#include <sstream>
|
||||||
|
#include <string>
|
||||||
|
#include <vector>
|
||||||
|
|
||||||
|
#include "PhreeqcEngine.hpp"
|
||||||
|
#include "PhreeqcMatrix.hpp"
|
||||||
|
#include "PhreeqcRunner.hpp"
|
||||||
|
|
||||||
|
std::string readFile(const std::string &path) {
|
||||||
|
std::string string_rpath(PATH_MAX, '\0');
|
||||||
|
|
||||||
|
if (realpath(path.c_str(), string_rpath.data()) == nullptr) {
|
||||||
|
throw std::runtime_error(":: Failed to resolve the realpath to file " +
|
||||||
|
path);
|
||||||
|
}
|
||||||
|
|
||||||
|
std::ifstream file(string_rpath);
|
||||||
|
|
||||||
|
if (!file.is_open()) {
|
||||||
|
throw std::runtime_error(":: Failed to open file: " + path);
|
||||||
|
}
|
||||||
|
|
||||||
|
std::stringstream buffer;
|
||||||
|
buffer << file.rdbuf();
|
||||||
|
|
||||||
|
return buffer.str();
|
||||||
|
}
|
||||||
|
|
||||||
|
// pretty print a vector, standard implementation from stackoverflow
|
||||||
|
template <typename T>
|
||||||
|
std::ostream &operator<<(std::ostream &os, std::vector<T> vec) {
|
||||||
|
os << "{ ";
|
||||||
|
std::copy(vec.begin(), vec.end(), std::ostream_iterator<T>(os, ", "));
|
||||||
|
os << " }";
|
||||||
|
return os;
|
||||||
|
}
|
||||||
|
|
||||||
|
int main(int argc, char *argv[]) {
|
||||||
|
|
||||||
|
if (argc < 3) {
|
||||||
|
std::cout << "::" << argv[0] << ": two args needed, script and database\n";
|
||||||
|
return 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
////// INITIALISATION
|
||||||
|
// read Script and Database and put it in a std::string
|
||||||
|
auto script = readFile(argv[1]);
|
||||||
|
auto db = readFile(argv[2]);
|
||||||
|
|
||||||
|
// Create the matrix directly from database and init script
|
||||||
|
PhreeqcMatrix pqc_mat(db, script, true, true);
|
||||||
|
|
||||||
|
// How many different SOLUTIONS ("CELLS") are defined in the script?
|
||||||
|
const auto ids = pqc_mat.getIds();
|
||||||
|
|
||||||
|
int n = ids.size();
|
||||||
|
|
||||||
|
std::cout << ":: Found " << n << " distinct PHREEQC problems \n";
|
||||||
|
std::cout << ids << "\n";
|
||||||
|
|
||||||
|
const auto solutes = pqc_mat.getSolutionNames();
|
||||||
|
std::cout << ":: These are the common solutes across all the " << n
|
||||||
|
<< " problems: \n";
|
||||||
|
std::cout << solutes << "\n";
|
||||||
|
|
||||||
|
// iterate on the ids (THEY start at 1!!)
|
||||||
|
for (const auto &i : ids) {
|
||||||
|
auto pphases = pqc_mat.getEquilibriumNames(i);
|
||||||
|
if (!pphases.empty()) {
|
||||||
|
std::cout << ":: Equilibrium phases [" << (int)i << "]: \n";
|
||||||
|
std::cout << pphases << "\n";
|
||||||
|
}
|
||||||
|
|
||||||
|
auto kinetics = pqc_mat.getKineticsNames(i);
|
||||||
|
if (!kinetics.empty()) {
|
||||||
|
std::cout << ":: Kinetics [" << i << "]: \n";
|
||||||
|
std::cout << kinetics << "\n";
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// The exported data type holds the matrix in a "STL format" with
|
||||||
|
// a "header" of names and their accompanying values. The values
|
||||||
|
// are stored in a row-major order per default.
|
||||||
|
auto exported_mat = pqc_mat.get();
|
||||||
|
// Get the total number of solutes
|
||||||
|
const int len = exported_mat.names.size();
|
||||||
|
// Get the values as reference to modify them in place
|
||||||
|
std::vector<double> &cell_values = exported_mat.values;
|
||||||
|
|
||||||
|
std::cout << ":: Values in the PhreeqcMatrix: \n";
|
||||||
|
|
||||||
|
//// Phreeqc RUN through the new Runner class
|
||||||
|
|
||||||
|
// optional SUBSET the matrix (i.e., the unique ids defined in
|
||||||
|
// golem map as input)
|
||||||
|
// const auto subsetted_pqc_mat = pqc_mat.subset({1, 2});
|
||||||
|
PhreeqcRunner runner(pqc_mat);
|
||||||
|
|
||||||
|
const auto stl_mat = pqc_mat.get();
|
||||||
|
const auto matrix_values = stl_mat.values;
|
||||||
|
const auto num_columns = stl_mat.names.size();
|
||||||
|
const auto spec_names = stl_mat.names;
|
||||||
|
|
||||||
|
// container to pass in/out
|
||||||
|
std::vector<std::vector<double>> simulationInOut;
|
||||||
|
|
||||||
|
// copy the values to the InOut vector. We replicate cell 1
|
||||||
|
for (std::size_t index = 0; index < n; ++index) {
|
||||||
|
simulationInOut.push_back(
|
||||||
|
std::vector<double>(matrix_values.begin() + num_columns * index,
|
||||||
|
matrix_values.begin() + num_columns * (index + 1)));
|
||||||
|
}
|
||||||
|
|
||||||
|
const double timestep = 100.;
|
||||||
|
|
||||||
|
// compute 1 timestep
|
||||||
|
runner.run(simulationInOut, timestep);
|
||||||
|
|
||||||
|
for (std::size_t cell_index = 0; cell_index < simulationInOut.size();
|
||||||
|
++cell_index) {
|
||||||
|
|
||||||
|
std::cout << "Grid element: " << cell_index << " \n";
|
||||||
|
for (std::size_t spec = 0; spec < num_columns; ++spec) {
|
||||||
|
std::cout << ":" << spec_names[spec] << "="
|
||||||
|
<< simulationInOut[cell_index][spec];
|
||||||
|
}
|
||||||
|
std::cout << "\n";
|
||||||
|
}
|
||||||
|
|
||||||
|
return 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
// Oneliner for rz-vm278 relative to iphreeqc/poet/test!!
|
||||||
|
|
||||||
|
// g++ testGolemRunner.cpp -o testG -Wall -I../../poet/include -I../../src
|
||||||
|
// -I../../src/phreeqcpp -I../../src/phreeqcpp/common
|
||||||
|
// -I../../src/phreeqcpp/PhreeqcKeywords -lIPhreeqc -lIPhreeqcPOET
|
||||||
|
// -L../../bbuild/ -L../../bbuild/poet
|
||||||
@ -6,7 +6,7 @@
|
|||||||
|
|
||||||
#include <gtest/gtest.h>
|
#include <gtest/gtest.h>
|
||||||
|
|
||||||
#define POET_TEST(name) TEST(TestPOET, name)
|
#define POET_TEST(name) TEST(litephreeqc, name)
|
||||||
|
|
||||||
namespace base_test {
|
namespace base_test {
|
||||||
const std::string script = R"(SOLUTION 1
|
const std::string script = R"(SOLUTION 1
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include <stdexcept>
|
#include <stdexcept>
|
||||||
|
|
||||||
#include <testInput.hpp>
|
#include <testInput.hpp>
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include <gtest/gtest.h>
|
#include <gtest/gtest.h>
|
||||||
#include <testInput.hpp>
|
#include <testInput.hpp>
|
||||||
|
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include <cmath>
|
#include <cmath>
|
||||||
#include <gtest/gtest.h>
|
#include <gtest/gtest.h>
|
||||||
#include <string>
|
#include <string>
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include "PhreeqcRunner.hpp"
|
#include "PhreeqcRunner.hpp"
|
||||||
#include "utils.hpp"
|
#include "utils.hpp"
|
||||||
|
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include "utils.hpp"
|
#include "utils.hpp"
|
||||||
|
|
||||||
#include <fstream>
|
#include <fstream>
|
||||||
18
litephreeqc/test/utils.hpp
Normal file
18
litephreeqc/test/utils.hpp
Normal file
@ -0,0 +1,18 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
|
#pragma once
|
||||||
|
|
||||||
|
#include <string>
|
||||||
|
|
||||||
|
std::string readFile(const std::string &path);
|
||||||
@ -1,18 +0,0 @@
|
|||||||
#pragma once
|
|
||||||
|
|
||||||
#include <phrqtype.h>
|
|
||||||
#include <span>
|
|
||||||
|
|
||||||
class WrapperBase {
|
|
||||||
public:
|
|
||||||
virtual ~WrapperBase() = default;
|
|
||||||
|
|
||||||
std::size_t size() const { return this->num_elements; };
|
|
||||||
|
|
||||||
virtual void get(std::span<LDBLE> &data) const = 0;
|
|
||||||
|
|
||||||
virtual void set(const std::span<LDBLE> &data) = 0;
|
|
||||||
|
|
||||||
protected:
|
|
||||||
std::size_t num_elements = 0;
|
|
||||||
};
|
|
||||||
@ -1,144 +0,0 @@
|
|||||||
// Time-stamp: "Last modified 2025-07-28 13:03:01 delucia"
|
|
||||||
#include <iostream>
|
|
||||||
#include <iomanip>
|
|
||||||
#include <linux/limits.h>
|
|
||||||
#include <sstream>
|
|
||||||
#include <fstream>
|
|
||||||
#include <algorithm>
|
|
||||||
#include <iterator>
|
|
||||||
#include <vector>
|
|
||||||
#include <string>
|
|
||||||
#include <memory>
|
|
||||||
#include <cmath>
|
|
||||||
|
|
||||||
#include "PhreeqcMatrix.hpp"
|
|
||||||
#include "PhreeqcEngine.hpp"
|
|
||||||
#include "PhreeqcRunner.hpp"
|
|
||||||
|
|
||||||
|
|
||||||
std::string readFile(const std::string &path) {
|
|
||||||
std::string string_rpath(PATH_MAX, '\0');
|
|
||||||
|
|
||||||
if (realpath(path.c_str(), string_rpath.data()) == nullptr) {
|
|
||||||
throw std::runtime_error(":: Failed to resolve the realpath to file " + path);
|
|
||||||
}
|
|
||||||
|
|
||||||
std::ifstream file(string_rpath);
|
|
||||||
|
|
||||||
if (!file.is_open()) {
|
|
||||||
throw std::runtime_error(":: Failed to open file: " + path);
|
|
||||||
}
|
|
||||||
|
|
||||||
std::stringstream buffer;
|
|
||||||
buffer << file.rdbuf();
|
|
||||||
|
|
||||||
return buffer.str();
|
|
||||||
}
|
|
||||||
|
|
||||||
// pretty print a vector, standard implementation from stackoverflow
|
|
||||||
template<typename T>
|
|
||||||
std::ostream & operator<<(std::ostream & os, std::vector<T> vec)
|
|
||||||
{
|
|
||||||
os << "{ ";
|
|
||||||
std::copy(vec.begin(), vec.end(), std::ostream_iterator<T>(os, ", "));
|
|
||||||
os << " }";
|
|
||||||
return os;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
int main(int argc, char *argv[]) {
|
|
||||||
|
|
||||||
if (argc < 3) {
|
|
||||||
std::cout << "::" << argv[0] << ": two args needed, script and database\n";
|
|
||||||
return 1;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
////// INITIALISATION
|
|
||||||
// read Script and Database and put it in a std::string
|
|
||||||
auto script = readFile(argv[1]);
|
|
||||||
auto db = readFile(argv[2]);
|
|
||||||
|
|
||||||
// Create the matrix directly from database and init script
|
|
||||||
PhreeqcMatrix pqc_mat(db, script, true, true);
|
|
||||||
|
|
||||||
// How many different SOLUTIONS ("CELLS") are defined in the script?
|
|
||||||
const auto ids = pqc_mat.getIds();
|
|
||||||
|
|
||||||
int n = ids.size();
|
|
||||||
|
|
||||||
std::cout << ":: Found " << n << " distinct PHREEQC problems \n";
|
|
||||||
std::cout << ids << "\n";
|
|
||||||
|
|
||||||
const auto solutes = pqc_mat.getSolutionNames();
|
|
||||||
std::cout << ":: These are the common solutes across all the " << n << " problems: \n";
|
|
||||||
std::cout << solutes << "\n";
|
|
||||||
|
|
||||||
// iterate on the ids (THEY start at 1!!)
|
|
||||||
for (const auto & i : ids) {
|
|
||||||
auto pphases = pqc_mat.getEquilibriumNames(i);
|
|
||||||
if (!pphases.empty()) {
|
|
||||||
std::cout << ":: Equilibrium phases [" << (int) i << "]: \n";
|
|
||||||
std::cout << pphases << "\n";
|
|
||||||
}
|
|
||||||
|
|
||||||
auto kinetics = pqc_mat.getKineticsNames(i);
|
|
||||||
if (!kinetics.empty()) {
|
|
||||||
std::cout << ":: Kinetics [" << i << "]: \n";
|
|
||||||
std::cout << kinetics << "\n";
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
// The exported data type holds the matrix in a "STL format" with
|
|
||||||
// a "header" of names and their accompanying values. The values
|
|
||||||
// are stored in a row-major order per default.
|
|
||||||
auto exported_mat = pqc_mat.get();
|
|
||||||
// Get the total number of solutes
|
|
||||||
const int len = exported_mat.names.size();
|
|
||||||
// Get the values as reference to modify them in place
|
|
||||||
std::vector<double> &cell_values = exported_mat.values;
|
|
||||||
|
|
||||||
std::cout << ":: Values in the PhreeqcMatrix: \n";
|
|
||||||
|
|
||||||
//// Phreeqc RUN through the new Runner class
|
|
||||||
|
|
||||||
// optional SUBSET the matrix (i.e., the unique ids defined in
|
|
||||||
// golem map as input)
|
|
||||||
// const auto subsetted_pqc_mat = pqc_mat.subset({1, 2});
|
|
||||||
PhreeqcRunner runner(pqc_mat);
|
|
||||||
|
|
||||||
const auto stl_mat = pqc_mat.get();
|
|
||||||
const auto matrix_values = stl_mat.values;
|
|
||||||
const auto num_columns = stl_mat.names.size();
|
|
||||||
const auto spec_names = stl_mat.names;
|
|
||||||
|
|
||||||
// container to pass in/out
|
|
||||||
std::vector<std::vector<double>> simulationInOut;
|
|
||||||
|
|
||||||
// copy the values to the InOut vector. We replicate cell 1
|
|
||||||
for (std::size_t index = 0; index < n; ++index) {
|
|
||||||
simulationInOut.push_back(std::vector<double>(
|
|
||||||
matrix_values.begin() + num_columns*index, matrix_values.begin() + num_columns*(index +1)));
|
|
||||||
}
|
|
||||||
|
|
||||||
const double timestep = 100.;
|
|
||||||
|
|
||||||
// compute 1 timestep
|
|
||||||
runner.run(simulationInOut, timestep);
|
|
||||||
|
|
||||||
for (std::size_t cell_index = 0; cell_index < simulationInOut.size(); ++cell_index) {
|
|
||||||
|
|
||||||
std::cout << "Grid element: " << cell_index << " \n";
|
|
||||||
for (std::size_t spec = 0; spec < num_columns; ++spec) {
|
|
||||||
std::cout << ":" << spec_names[spec] << "=" << simulationInOut[cell_index][spec];
|
|
||||||
}
|
|
||||||
std::cout << "\n";
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
return 0;
|
|
||||||
}
|
|
||||||
|
|
||||||
// Oneliner for rz-vm278 relative to iphreeqc/poet/test!!
|
|
||||||
|
|
||||||
// g++ testGolemRunner.cpp -o testG -Wall -I../../poet/include -I../../src -I../../src/phreeqcpp -I../../src/phreeqcpp/common -I../../src/phreeqcpp/PhreeqcKeywords -lIPhreeqc -lIPhreeqcPOET -L../../bbuild/ -L../../bbuild/poet
|
|
||||||
@ -1,5 +0,0 @@
|
|||||||
#pragma once
|
|
||||||
|
|
||||||
#include <string>
|
|
||||||
|
|
||||||
std::string readFile(const std::string &path);
|
|
||||||
@ -1,3 +1,16 @@
|
|||||||
|
/*
|
||||||
|
* This project is subject to the original PHREEQC license. `litephreeqc` is a
|
||||||
|
* version of the PHREEQC code that has been modified to be used as a library.
|
||||||
|
*
|
||||||
|
* It adds a C++ interface on top of the original PHREEQC code, with small
|
||||||
|
* changes to the original code base.
|
||||||
|
*
|
||||||
|
* Authors of Modifications:
|
||||||
|
* - Max Luebke (mluebke@uni-potsdam.de) - University of Potsdam
|
||||||
|
* - Marco De Lucia (delucia@gfz.de) - GFZ Helmholz Centre for Geosciences
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
|
||||||
#include "Phreeqc.h"
|
#include "Phreeqc.h"
|
||||||
#include <set>
|
#include <set>
|
||||||
|
|
||||||
Loading…
x
Reference in New Issue
Block a user