max/iphreeqc
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Merge branch 'ml/project-name' into 'main'

Browse Source 
Change project name to `litephreeqc`

See merge request naaice/iphreeqc!32
This commit is contained in:
Max Lübke 2025-10-28 11:02:24 +01:00
commit cb44e26b69
51 changed files with 1177 additions and 850 deletions
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854
.github/workflows/cmake.yml vendored
View File

@ -1,296 +1,296 @@
name: CMake
on:
push:
pull_request:
branches:
- master
schedule:
- cron: '15 14 4,11,18,25 * *'
workflow_dispatch:
env:
# Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
BUILD_TYPE: Release
NAME: IPhreeqc
jobs:
init:
runs-on: ubuntu-latest
# Map step outputs to job outputs
outputs:
VER: ${{ steps.vars.outputs.VER }}
REL: ${{ steps.vars.outputs.REL }}
DATE: ${{ steps.vars.outputs.DATE }}
DATE_RFC_3339: ${{ steps.vars.outputs.DATE_RFC_3339 }}
steps:
- name: Setup vars
id: vars
run: |
echo VER=$(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) >> $GITHUB_OUTPUT
echo DATE=$(date "+%x") >> $GITHUB_OUTPUT
echo DATE_RFC_3339=$(date --rfc-3339=date) >> $GITHUB_OUTPUT
test:
strategy:
fail-fast: false
matrix:
os: [macos-latest, ubuntu-latest, windows-latest]
runs-on: ${{ matrix.os }}
env:
BUILD_DIR: _ctest # set in ctest.cmake
steps:
- uses: actions/checkout@v4
- name: Install ninja valgrind (Linux)
if: runner.os == 'Linux'
run: sudo apt-get update && sudo apt-get install -y ninja-build valgrind
- name: Install ninja (macOS)
if: runner.os == 'macOS'
run: brew install ninja
- name: Set up Visual Studio shell (Windows)
if: runner.os == 'Windows'
uses: egor-tensin/vs-shell@v2
with:
arch: x64
- name: CTest
run: ctest -S ctest.cmake -V --output-on-failure --timeout 900
- name: Upload results
uses: actions/upload-artifact@v4
with:
name: ${{ matrix.os }}-${{ github.job }}-results
path: ${{ github.workspace }}/${{ env.BUILD_DIR }}/Testing/
test-shared:
strategy:
fail-fast: false
matrix:
os: [macos-latest, ubuntu-latest, windows-latest]
runs-on: ${{ matrix.os }}
env:
BUILD_DIR: _ctest_shared # set in ctest-shared.cmake
steps:
- uses: actions/checkout@v4
- name: Install ninja valgrind (Linux)
if: runner.os == 'Linux'
run: sudo apt-get update && sudo apt-get install -y ninja-build valgrind
- name: Install ninja (macOS)
if: runner.os == 'macOS'
run: brew install ninja
- name: Set up Visual Studio shell (Windows)
if: runner.os == 'Windows'
uses: egor-tensin/vs-shell@v2
with:
arch: x64
- name: CTest
run: ctest -S ctest-shared.cmake -V --output-on-failure --timeout 900
- name: Upload results
uses: actions/upload-artifact@v4
with:
name: ${{ matrix.os }}-${{ github.job }}-results
path: ${{ github.workspace }}/${{ env.BUILD_DIR }}/Testing/
test-clang:
strategy:
fail-fast: false
matrix:
os: [macos-latest, ubuntu-latest, windows-latest]
shared_libs: [OFF, ON]
enable_module: [OFF, ON]
runs-on: ${{ matrix.os }}
env:
BUILD_DIR: _build
steps:
- uses: actions/checkout@v4
- name: Install ninja valgrind (Linux)
if: runner.os == 'Linux'
run: sudo apt-get update && sudo apt-get install -y ninja-build clang valgrind
- name: Install ninja (macOS)
if: runner.os == 'macOS'
run: brew install ninja
- name: Set up Visual Studio shell (Windows)
if: runner.os == 'Windows'
uses: egor-tensin/vs-shell@v2
with:
arch: x64
- name: CMake configure
if: runner.os == 'Linux'
run: CC=clang CXX=clang++ cmake -B ${{ env.BUILD_DIR }} -DBUILD_SHARED_LIBS=${{ matrix.shared_libs }} -DIPHREEQC_ENABLE_MODULE=${{ matrix.enable_module }} -DCMAKE_CXX_STANDARD=20 -DCMAKE_CXX_STANDARD_REQUIRED=ON
- name: CMake configure
if: runner.os == 'macOS'
run: CC=$(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
- name: CMake configure
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
- name: CMake build
run: cmake --build ${{ env.BUILD_DIR }}
- name: CTest
run: ctest --test-dir ${{ env.BUILD_DIR }}
- name: Upload results
uses: actions/upload-artifact@v4
with:
name: ${{ matrix.os }}-${{ github.job }}-SHARED=${{ matrix.shared_libs }}-MODULE=${{ matrix.enable_module }}-results
path: ${{ github.workspace }}/${{ env.BUILD_DIR }}/Testing/
chm:
runs-on: windows-latest
steps:
- name: Checkout phreeqc3-HTMLversion
uses: actions/checkout@v4
with:
repository: usgs-coupled-subtrees/phreeqc3-HTMLversion
ref: master
- name: cache htmlhelp
id: cache-htmlhelp
uses: actions/cache@v4
with:
path: "C:/Program Files (x86)/HTML Help Workshop"
key: ${{ runner.os }}-htmlhelp
- name: install htmlhelp
if: steps.cache-htmlhelp.outputs.cache-hit != 'true'
timeout-minutes: 5
run: |
curl -L -O --max-time 120 http://web.archive.org/web/20160201063255/http://download.microsoft.com/download/0/A/9/0A939EF6-E31C-430F-A3DF-DFAE7960D564/htmlhelp.exe
cmd /c start /wait .\htmlhelp.exe /q /c /t:$(Get-Location)\tmp
$file = "$(Get-Location)\tmp\htmlhelp.inf"
(Get-Content $file) | Foreach-Object { $_ `
-replace '^BeginPrompt', ';;BeginPrompt' `
-replace '^EndPrompt', ';;EndPrompt' `
-replace '^49000=CustomLDID49000, 1', '49000=CustomLDID49000, 5' `
-replace '^"hhupd.exe', ';;hhupd.exe' `
-replace '^DefaultInstallDir="C:\\Program Files\\HTML Help Workshop"', 'DefaultInstallDir="%ProgramFiles%\\HTML Help Workshop"'
} | Set-Content $file
cmd /c start /wait .\tmp\setup.exe
Remove-Item -Recurse -Force .\tmp
Remove-Item -Recurse -Force .\htmlhelp.exe
# the next line doesn't seem to work (supposed to set the path)
# echo 'C:\Program Files (x86)\HTML Help Workshop' >> $GITHUB_PATH
- name: compile chm
shell: bash
run: |
pushd HTML
bash fixup_html.bash
popd
# hhc returns 1 on success
set +e
'C:\Program Files (x86)\HTML Help Workshop\hhc' phreeqc3.hhp | tee hhc.out
status=${PIPESTATUS[0]}
set -e
if [ "$status" -eq 1 ]; then
echo "[OK]"
exit 0
else
echo "[FAILED]"
exit 1
fi
- uses: actions/upload-artifact@v4
with:
name: chm
path: ${{github.workspace}}/phreeqc3.chm
R-CMD-check:
needs: [init]
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
strategy:
fail-fast: false
matrix:
config:
- {os: macos-latest, r: 'release'}
- {os: windows-latest, r: 'release'}
- {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
- {os: ubuntu-latest, r: 'release'}
- {os: ubuntu-latest, r: 'oldrel-1'}
steps:
- uses: actions/checkout@v4
- name: versioning
run: ./jenkins-dist.sh -v ${{ needs.init.outputs.VER }} -r ${{ needs.init.outputs.REL }} -d ${{ needs.init.outputs.DATE }}
- name: Setup R
uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
http-user-agent: ${{ matrix.config.http-user-agent }}
use-public-rspm: true
- name: create source
working-directory: R
run: make VERSION=${{ needs.init.outputs.VER }} RELEASE_DATE=${{ needs.init.outputs.DATE_RFC_3339 }} source
- name: Install dependencies
uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::roxygen2, any::pkgbuild, any::rcmdcheck
needs: roxygen2, pkgbuild, check
working-directory: R/phreeqc
- name: Display sessionInfo()
run: sessionInfo()
working-directory: R/phreeqc
shell: Rscript {0}
- name: roxygen2::roxygenise()
run: roxygen2::roxygenise()
working-directory: R/phreeqc
shell: Rscript {0}
- name: Check
uses: r-lib/actions/check-r-package@v2
with:
working-directory: R/phreeqc
- name: List files
if: matrix.config.os == 'ubuntu-latest' && matrix.config.r == 'release'
run: |
pwd
ls -lR
find -name "*.tar.gz"
- uses: actions/upload-artifact@v4
if: matrix.config.os == 'ubuntu-latest' && matrix.config.r == 'release'
with:
name: cran
path: ${{ github.workspace }}/R/phreeqc/check/phreeqc_*.tar.gz
# name: CMake
#
# on:
# push:
#
# pull_request:
# branches:
# - master
#
# schedule:
# - cron: '15 14 4,11,18,25 * *'
#
# workflow_dispatch:
#
# env:
# # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
# BUILD_TYPE: Release
# NAME: IPhreeqc
#
# jobs:
#
# init:
# runs-on: ubuntu-latest
# # Map step outputs to job outputs
# outputs:
# VER: ${{ steps.vars.outputs.VER }}
# REL: ${{ steps.vars.outputs.REL }}
# DATE: ${{ steps.vars.outputs.DATE }}
# DATE_RFC_3339: ${{ steps.vars.outputs.DATE_RFC_3339 }}
# steps:
# - name: Setup vars
# id: vars
# run: |
# echo VER=$(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) >> $GITHUB_OUTPUT
# echo DATE=$(date "+%x") >> $GITHUB_OUTPUT
# echo DATE_RFC_3339=$(date --rfc-3339=date) >> $GITHUB_OUTPUT
#
#
# test:
# strategy:
# fail-fast: false
# matrix:
# os: [macos-latest, ubuntu-latest, windows-latest]
#
# runs-on: ${{ matrix.os }}
# env:
# BUILD_DIR: _ctest # set in ctest.cmake
#
# steps:
# - uses: actions/checkout@v4
#
# - name: Install ninja valgrind (Linux)
# if: runner.os == 'Linux'
# run: sudo apt-get update && sudo apt-get install -y ninja-build valgrind
#
# - name: Install ninja (macOS)
# if: runner.os == 'macOS'
# run: brew install ninja
#
# - name: Set up Visual Studio shell (Windows)
# if: runner.os == 'Windows'
# uses: egor-tensin/vs-shell@v2
# with:
# arch: x64
#
# - name: CTest
# run: ctest -S ctest.cmake -V --output-on-failure --timeout 900
#
# - name: Upload results
# uses: actions/upload-artifact@v4
# with:
# name: ${{ matrix.os }}-${{ github.job }}-results
# path: ${{ github.workspace }}/${{ env.BUILD_DIR }}/Testing/
#
# test-shared:
# strategy:
# fail-fast: false
# matrix:
# os: [macos-latest, ubuntu-latest, windows-latest]
#
# runs-on: ${{ matrix.os }}
# env:
# BUILD_DIR: _ctest_shared # set in ctest-shared.cmake
#
# steps:
# - uses: actions/checkout@v4
#
# - name: Install ninja valgrind (Linux)
# if: runner.os == 'Linux'
# run: sudo apt-get update && sudo apt-get install -y ninja-build valgrind
#
# - name: Install ninja (macOS)
# if: runner.os == 'macOS'
# run: brew install ninja
#
# - name: Set up Visual Studio shell (Windows)
# if: runner.os == 'Windows'
# uses: egor-tensin/vs-shell@v2
# with:
# arch: x64
#
# - name: CTest
# run: ctest -S ctest-shared.cmake -V --output-on-failure --timeout 900
#
# - name: Upload results
# uses: actions/upload-artifact@v4
# with:
# name: ${{ matrix.os }}-${{ github.job }}-results
# path: ${{ github.workspace }}/${{ env.BUILD_DIR }}/Testing/
#
# test-clang:
# strategy:
# fail-fast: false
# matrix:
# os: [macos-latest, ubuntu-latest, windows-latest]
# shared_libs: [OFF, ON]
# enable_module: [OFF, ON]
#
# runs-on: ${{ matrix.os }}
# env:
# BUILD_DIR: _build
#
# steps:
# - uses: actions/checkout@v4
#
# - name: Install ninja valgrind (Linux)
# if: runner.os == 'Linux'
# run: sudo apt-get update && sudo apt-get install -y ninja-build clang valgrind
#
# - name: Install ninja (macOS)
# if: runner.os == 'macOS'
# run: brew install ninja
#
# - name: Set up Visual Studio shell (Windows)
# if: runner.os == 'Windows'
# uses: egor-tensin/vs-shell@v2
# with:
# arch: x64
#
# - name: CMake configure
# if: runner.os == 'Linux'
# run: CC=clang CXX=clang++ cmake -B ${{ env.BUILD_DIR }} -DBUILD_SHARED_LIBS=${{ matrix.shared_libs }} -DIPHREEQC_ENABLE_MODULE=${{ matrix.enable_module }} -DCMAKE_CXX_STANDARD=20 -DCMAKE_CXX_STANDARD_REQUIRED=ON
#
# - name: CMake configure
# if: runner.os == 'macOS'
# run: CC=$(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
#
# - name: CMake configure
# 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
#
# - name: CMake build
# run: cmake --build ${{ env.BUILD_DIR }}
#
# - name: CTest
# run: ctest --test-dir ${{ env.BUILD_DIR }}
#
# - name: Upload results
# uses: actions/upload-artifact@v4
# with:
# name: ${{ matrix.os }}-${{ github.job }}-SHARED=${{ matrix.shared_libs }}-MODULE=${{ matrix.enable_module }}-results
# path: ${{ github.workspace }}/${{ env.BUILD_DIR }}/Testing/
#
# chm:
# runs-on: windows-latest
#
# steps:
# - name: Checkout phreeqc3-HTMLversion
# uses: actions/checkout@v4
# with:
# repository: usgs-coupled-subtrees/phreeqc3-HTMLversion
# ref: master
#
# - name: cache htmlhelp
# id: cache-htmlhelp
# uses: actions/cache@v4
# with:
# path: "C:/Program Files (x86)/HTML Help Workshop"
# key: ${{ runner.os }}-htmlhelp
#
# - name: install htmlhelp
# if: steps.cache-htmlhelp.outputs.cache-hit != 'true'
# timeout-minutes: 5
# run: |
# curl -L -O --max-time 120 http://web.archive.org/web/20160201063255/http://download.microsoft.com/download/0/A/9/0A939EF6-E31C-430F-A3DF-DFAE7960D564/htmlhelp.exe
# cmd /c start /wait .\htmlhelp.exe /q /c /t:$(Get-Location)\tmp
# $file = "$(Get-Location)\tmp\htmlhelp.inf"
# (Get-Content $file) | Foreach-Object { $_ `
# -replace '^BeginPrompt', ';;BeginPrompt' `
# -replace '^EndPrompt', ';;EndPrompt' `
# -replace '^49000=CustomLDID49000, 1', '49000=CustomLDID49000, 5' `
# -replace '^"hhupd.exe', ';;hhupd.exe' `
# -replace '^DefaultInstallDir="C:\\Program Files\\HTML Help Workshop"', 'DefaultInstallDir="%ProgramFiles%\\HTML Help Workshop"'
# } | Set-Content $file
# cmd /c start /wait .\tmp\setup.exe
# Remove-Item -Recurse -Force .\tmp
# Remove-Item -Recurse -Force .\htmlhelp.exe
# # the next line doesn't seem to work (supposed to set the path)
# # echo 'C:\Program Files (x86)\HTML Help Workshop' >> $GITHUB_PATH
#
# - name: compile chm
# shell: bash
# run: |
# pushd HTML
# bash fixup_html.bash
# popd
# # hhc returns 1 on success
# set +e
# 'C:\Program Files (x86)\HTML Help Workshop\hhc' phreeqc3.hhp | tee hhc.out
# status=${PIPESTATUS[0]}
# set -e
# if [ "$status" -eq 1 ]; then
# echo "[OK]"
# exit 0
# else
# echo "[FAILED]"
# exit 1
# fi
#
# - uses: actions/upload-artifact@v4
# with:
# name: chm
# path: ${{github.workspace}}/phreeqc3.chm
#
#
# R-CMD-check:
# needs: [init]
# runs-on: ${{ matrix.config.os }}
#
# name: ${{ matrix.config.os }} (${{ matrix.config.r }})
#
# strategy:
# fail-fast: false
# matrix:
# config:
# - {os: macos-latest, r: 'release'}
# - {os: windows-latest, r: 'release'}
# - {os: ubuntu-latest, r: 'devel', http-user-agent: 'release'}
# - {os: ubuntu-latest, r: 'release'}
# - {os: ubuntu-latest, r: 'oldrel-1'}
#
# steps:
# - uses: actions/checkout@v4
#
# - name: versioning
# run: ./jenkins-dist.sh -v ${{ needs.init.outputs.VER }} -r ${{ needs.init.outputs.REL }} -d ${{ needs.init.outputs.DATE }}
#
# - name: Setup R
# uses: r-lib/actions/setup-r@v2
# with:
# r-version: ${{ matrix.config.r }}
# http-user-agent: ${{ matrix.config.http-user-agent }}
# use-public-rspm: true
#
# - name: create source
# working-directory: R
# run: make VERSION=${{ needs.init.outputs.VER }} RELEASE_DATE=${{ needs.init.outputs.DATE_RFC_3339 }} source
#
# - name: Install dependencies
# uses: r-lib/actions/setup-r-dependencies@v2
# with:
# extra-packages: any::roxygen2, any::pkgbuild, any::rcmdcheck
# needs: roxygen2, pkgbuild, check
# working-directory: R/phreeqc
#
# - name: Display sessionInfo()
# run: sessionInfo()
# working-directory: R/phreeqc
# shell: Rscript {0}
#
# - name: roxygen2::roxygenise()
# run: roxygen2::roxygenise()
# working-directory: R/phreeqc
# shell: Rscript {0}
#
# - name: Check
# uses: r-lib/actions/check-r-package@v2
# with:
# working-directory: R/phreeqc
#
# - name: List files
# if: matrix.config.os == 'ubuntu-latest' && matrix.config.r == 'release'
# run: |
# pwd
# ls -lR
# find -name "*.tar.gz"
#
# - uses: actions/upload-artifact@v4
# if: matrix.config.os == 'ubuntu-latest' && matrix.config.r == 'release'
# with:
# name: cran
# path: ${{ github.workspace }}/R/phreeqc/check/phreeqc_*.tar.gz
# r-build:
@ -373,140 +373,140 @@ jobs:
# path: ${{github.workspace}}/R/valgrind.full.out
distcheck:
needs: [init, chm]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/download-artifact@v4
with:
name: chm
- name: mv chm
run: mv phreeqc3.chm doc/.
- name: versioning
run: ./jenkins-dist.sh -v ${{ needs.init.outputs.VER }} -r ${{ needs.init.outputs.REL }} -d ${{ needs.init.outputs.DATE }}
- name: doxygen
run: sudo apt-get install -y doxygen && cd doc && doxygen
- name: autoreconf
run: autoreconf -fvi
- name: mkdir
run: mkdir _build
- name: configure
working-directory: ${{github.workspace}}/_build
run: ../configure --prefix=$(pwd)/INSTALL
- name: make
working-directory: ${{github.workspace}}/_build
run: make -j2 distcheck
- name: convert
run: |
sudo apt install -y dos2unix
native="
doc/Makefile \
doc/examples/AccumulateLine.c \
doc/examples/CreateIPhreeqc.c \
doc/examples/F90ClearAccumulatedLines.f90 \
doc/examples/F90CreateIPhreeqc.f90 \
doc/examples/F90DestroyIPhreeqc.f90 \
doc/examples/F90GetComponent.f90 \
doc/examples/F90GetDumpStringLine.f90 \
doc/examples/F90GetSelectedOutputValue.f90 \
doc/examples/F90GetVersionString.f90 \
doc/examples/GetComponent.c \
doc/examples/GetDumpString.c \
doc/examples/GetSelectedOutputValue.c \
doc/examples/GetVersionString.c \
doc/examples/IPhreeqc.cpp \
doc/examples/Makefile \
doc/examples/phreeqc.dat \
src/CSelectedOutput.cpp \
src/CSelectedOutput.hxx \
src/CVar.hxx \
src/Debug.h \
src/ErrorReporter.hxx \
src/IPhreeqc.cpp \
src/IPhreeqc.f.inc \
src/IPhreeqc.f90.inc \
src/IPhreeqc.h \
src/IPhreeqc.hpp \
src/IPhreeqcCallbacks.h \
src/IPhreeqcF.f \
src/IPhreeqcLib.cpp \
src/IPhreeqc_interface.F90 \
src/IPhreeqc_interface_F.cpp \
src/IPhreeqc_interface_F.h \
src/Var.c \
src/Var.h \
src/Version.h \
src/fimpl.h \
src/fwrap.cpp \
src/fwrap.h \
src/fwrap1.cpp \
src/fwrap2.cpp \
src/fwrap3.cpp \
src/fwrap4.cpp \
src/fwrap5.cpp \
src/fwrap6.cpp \
src/fwrap7.cpp \
src/fwrap8.cpp \
src/pp_sys.cpp \
src/thread.h \
test/llnl.dat \
test/phreeqc.dat \
test2/Makefile \
test2/wateq4f.dat \
test5/Makefile \
test5/phreeqc.dat \
test5/test5.c \
tests/main_fortran.cxx \
tests/test_c.c \
tests/test_cxx.cxx \
tests/test_f90.F90 \
unit/TestCVar.cpp \
unit/TestCVar.h \
unit/TestInterface.cpp \
unit/TestInterface.h \
unit/TestSelectedOutput.cpp \
unit/TestSelectedOutput.h \
unit/TestVar.cpp \
unit/TestVar.h \
unit/llnl.dat.old \
unit/missing_e.dat \
unit/phreeqc.dat.old \
unit/unit.cpp"
for f in ${native}; do
unix2dos "${f}"
done
- name: dist-zip
working-directory: ${{github.workspace}}/_build
run: make dist-zip
- name: copy
run: cp doc/README IPhreeqc_ReadMe.txt
- uses: actions/upload-artifact@v4
with:
name: readme
path: ${{github.workspace}}/IPhreeqc_ReadMe.txt
- uses: actions/upload-artifact@v4
with:
name: tarball
path: ${{github.workspace}}/_build/*.tar.gz
- uses: actions/upload-artifact@v4
with:
name: zipball
path: ${{github.workspace}}/_build/*.zip
# distcheck:
# needs: [init, chm]
# runs-on: ubuntu-latest
# steps:
# - uses: actions/checkout@v4
#
# - uses: actions/download-artifact@v4
# with:
# name: chm
#
# - name: mv chm
# run: mv phreeqc3.chm doc/.
#
# - name: versioning
# run: ./jenkins-dist.sh -v ${{ needs.init.outputs.VER }} -r ${{ needs.init.outputs.REL }} -d ${{ needs.init.outputs.DATE }}
#
# - name: doxygen
# run: sudo apt-get install -y doxygen && cd doc && doxygen
#
# - name: autoreconf
# run: autoreconf -fvi
#
# - name: mkdir
# run: mkdir _build
#
# - name: configure
# working-directory: ${{github.workspace}}/_build
# run: ../configure --prefix=$(pwd)/INSTALL
#
# - name: make
# working-directory: ${{github.workspace}}/_build
# run: make -j2 distcheck
#
# - name: convert
# run: |
# sudo apt install -y dos2unix
# native="
# doc/Makefile \
# doc/examples/AccumulateLine.c \
# doc/examples/CreateIPhreeqc.c \
# doc/examples/F90ClearAccumulatedLines.f90 \
# doc/examples/F90CreateIPhreeqc.f90 \
# doc/examples/F90DestroyIPhreeqc.f90 \
# doc/examples/F90GetComponent.f90 \
# doc/examples/F90GetDumpStringLine.f90 \
# doc/examples/F90GetSelectedOutputValue.f90 \
# doc/examples/F90GetVersionString.f90 \
# doc/examples/GetComponent.c \
# doc/examples/GetDumpString.c \
# doc/examples/GetSelectedOutputValue.c \
# doc/examples/GetVersionString.c \
# doc/examples/IPhreeqc.cpp \
# doc/examples/Makefile \
# doc/examples/phreeqc.dat \
# src/CSelectedOutput.cpp \
# src/CSelectedOutput.hxx \
# src/CVar.hxx \
# src/Debug.h \
# src/ErrorReporter.hxx \
# src/IPhreeqc.cpp \
# src/IPhreeqc.f.inc \
# src/IPhreeqc.f90.inc \
# src/IPhreeqc.h \
# src/IPhreeqc.hpp \
# src/IPhreeqcCallbacks.h \
# src/IPhreeqcF.f \
# src/IPhreeqcLib.cpp \
# src/IPhreeqc_interface.F90 \
# src/IPhreeqc_interface_F.cpp \
# src/IPhreeqc_interface_F.h \
# src/Var.c \
# src/Var.h \
# src/Version.h \
# src/fimpl.h \
# src/fwrap.cpp \
# src/fwrap.h \
# src/fwrap1.cpp \
# src/fwrap2.cpp \
# src/fwrap3.cpp \
# src/fwrap4.cpp \
# src/fwrap5.cpp \
# src/fwrap6.cpp \
# src/fwrap7.cpp \
# src/fwrap8.cpp \
# src/pp_sys.cpp \
# src/thread.h \
# test/llnl.dat \
# test/phreeqc.dat \
# test2/Makefile \
# test2/wateq4f.dat \
# test5/Makefile \
# test5/phreeqc.dat \
# test5/test5.c \
# tests/main_fortran.cxx \
# tests/test_c.c \
# tests/test_cxx.cxx \
# tests/test_f90.F90 \
# unit/TestCVar.cpp \
# unit/TestCVar.h \
# unit/TestInterface.cpp \
# unit/TestInterface.h \
# unit/TestSelectedOutput.cpp \
# unit/TestSelectedOutput.h \
# unit/TestVar.cpp \
# unit/TestVar.h \
# unit/llnl.dat.old \
# unit/missing_e.dat \
# unit/phreeqc.dat.old \
# unit/unit.cpp"
# for f in ${native}; do
# unix2dos "${f}"
# done
#
# - name: dist-zip
# working-directory: ${{github.workspace}}/_build
# run: make dist-zip
#
# - name: copy
# run: cp doc/README IPhreeqc_ReadMe.txt
#
# - uses: actions/upload-artifact@v4
# with:
# name: readme
# path: ${{github.workspace}}/IPhreeqc_ReadMe.txt
#
# - uses: actions/upload-artifact@v4
# with:
# name: tarball
# path: ${{github.workspace}}/_build/*.tar.gz
#
# - uses: actions/upload-artifact@v4
# with:
# name: zipball
# path: ${{github.workspace}}/_build/*.zip
# build:
# needs: [init]

307
CMakeLists.txt
View File

@ -2,47 +2,28 @@
cmake_minimum_required(VERSION 3.20)
project (
IPhreeqc
litephreeqc
VERSION 3.8.5
LANGUAGES CXX C
)
# check if this is the root project
if (CMAKE_PROJECT_NAME STREQUAL PROJECT_NAME)
set(STANDALONE_BUILD 1)
else()
set(STANDALONE_BUILD 0)
if (WIN32)
message(FATAL_ERROR "litephreeqc cannot be built on Windows systems.")
endif()
if (STANDALONE_BUILD)
# Set a default build type if none was specified
set(default_build_type "Release")
if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
set(CMAKE_BUILD_TYPE "${default_build_type}" CACHE
STRING "Choose the type of build." FORCE)
# Set the possible values of build type for cmake-gui
set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS
"Debug" "Release" "MinSizeRel" "RelWithDebInfo")
endif()
endif()
# overide docdir on windows
if (WIN32 AND NOT CMAKE_INSTALL_DOCDIR)
set(CMAKE_INSTALL_DOCDIR "" CACHE PATH "documentation root (doc)")
set(CMAKE_INSTALL_DOCDIR "doc")
# Set a default build type if none was specified
set(default_build_type "Release")
if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
set(CMAKE_BUILD_TYPE "${default_build_type}" CACHE
STRING "Choose the type of build." FORCE)
# Set the possible values of build type for cmake-gui
set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS
"Debug" "Release" "MinSizeRel" "RelWithDebInfo")
endif()
# set standard directory locations
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
option (IPHREEQC_ENABLE_MODULE "Enable Fortran module" ON)
if (STANDALONE_BUILD)
@ -60,22 +41,7 @@ endif()
# compile Var.c as c++
set_source_files_properties(src/Var.c PROPERTIES LANGUAGE CXX)
if (STANDALONE_BUILD)
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)
add_library(IPhreeqc STATIC src/IPhreeqc.cpp)
target_sources(IPhreeqc
PRIVATE
@ -220,7 +186,7 @@ target_sources(IPhreeqc
src/phreeqcpp/UserPunch.cpp
src/phreeqcpp/UserPunch.h
src/phreeqcpp/utilities.cpp
src/phreeqcpp/GFZ.cpp
src/phreeqcpp/litephreeqc_funcs.cpp
src/thread.h
src/Var.c
src/Var.h
@ -229,10 +195,10 @@ target_sources(IPhreeqc
target_include_directories(IPhreeqc
PUBLIC
$<BUILD_INTERFACE:${IPhreeqc_SOURCE_DIR}/src>
$<BUILD_INTERFACE:${IPhreeqc_SOURCE_DIR}/src/phreeqcpp>
$<BUILD_INTERFACE:${IPhreeqc_SOURCE_DIR}/src/phreeqcpp/common>
$<BUILD_INTERFACE:${IPhreeqc_SOURCE_DIR}/src/phreeqcpp/PhreeqcKeywords>
$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/src>
$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/src/phreeqcpp>
$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/src/phreeqcpp/common>
$<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/src/phreeqcpp/PhreeqcKeywords>
$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
)
@ -260,37 +226,6 @@ if (NOT IPHREEQC_ENABLE_MODULE)
)
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
${PROJECT_SOURCE_DIR}/src/IPhreeqc.h
${PROJECT_SOURCE_DIR}/src/IPhreeqc.hpp
@ -319,158 +254,94 @@ else()
)
endif()
# Setup references for /CLR
if (MSVC AND BUILD_SHARED_LIBS AND BUILD_CLR_LIBS)
if (MSVC_VERSION LESS 1600)
message(FATAL_ERROR "CLR options must be set manually for versions prior to Visual Studio 2010")
endif()
set_target_properties(IPhreeqc PROPERTIES VS_DOTNET_REFERENCES "System;System.Drawing;System.Windows.Forms;${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
VERSION "${IPhreeqc_VERSION}"
SOVERSION "${IPhreeqc_VERSION_MAJOR}"
)
# install
if (STANDALONE_BUILD)
include(CMakePackageConfigHelpers)
include(CMakePackageConfigHelpers)
configure_package_config_file(IPhreeqcConfig.cmake.in
${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
configure_package_config_file(IPhreeqcConfig.cmake.in
${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()
include (CTest)
if (STANDALONE_BUILD)
# add_subdirectory(database)
# add_subdirectory(doc)
# add_subdirectory(examples)
add_subdirectory(database)
add_subdirectory(doc)
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()
if (BUILD_TESTING)
add_subdirectory(tests)
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)
# list (SORT _variableNames)

29
poet/CMakeLists.txt → litephreeqc/CMakeLists.txt
View File

@ -1,4 +1,5 @@
set(POET_SOURCE_FILES
set(LPQC_SOURCE_FILES
src/Engine.cpp
src/Runner.cpp
src/Knobs.cpp
@ -20,19 +21,19 @@ set(POET_SOURCE_FILES
src/PhreeqcMatrix/Misc.cpp
)
add_library(IPhreeqcPOET ${POET_SOURCE_FILES})
target_link_libraries(IPhreeqcPOET PUBLIC IPhreeqc)
target_include_directories(IPhreeqcPOET PUBLIC
add_library(litephreeqc STATIC ${LPQC_SOURCE_FILES})
target_link_libraries(litephreeqc PUBLIC IPhreeqc)
target_include_directories(litephreeqc PUBLIC
$<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
$<INSTALL_INTERFACE:include>)
# 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)
enable_testing()
set(POET_TEST_SOURCE_FILES
set(LPQC_TEST_SOURCE_FILES
test/testPhreeqcEngine.cpp
test/testPhreeqcMatrix.cpp
test/testPhreeqcRunner.cpp
@ -41,15 +42,15 @@ if (BUILD_TESTING AND STANDALONE_BUILD)
test/IPhreeqcReader.cpp
)
add_executable(poet_test ${POET_TEST_SOURCE_FILES})
add_executable(litephreeqc_test ${LPQC_TEST_SOURCE_FILES})
target_link_libraries(
poet_test
IPhreeqcPOET
litephreeqc_test
litephreeqc
GTest::gtest_main
)
target_include_directories(poet_test PRIVATE ${CMAKE_CURRENT_BINARY_DIR})
target_include_directories(litephreeqc_test PRIVATE ${CMAKE_CURRENT_BINARY_DIR})
# read file and store in variable
file(REAL_PATH "${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")
include(GoogleTest)
gtest_discover_tests(poet_test)
gtest_discover_tests(litephreeqc_test)
endif()
add_executable(testGolemRunner test/testGolemRunner.cpp)
target_link_libraries(testGolemRunner IPhreeqcPOET)
add_executable(golemrunner test/testGolemRunner.cpp)
target_link_libraries(golemrunner litephreeqc)
add_executable(testGetters test/testGetters.cpp)
target_link_libraries(testGetters IPhreeqcPOET)
target_link_libraries(testGetters litephreeqc)

10
litephreeqc/LICENSE.txt Normal file
View 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

13
poet/include/PhreeqcEngine.hpp → litephreeqc/include/PhreeqcEngine.hpp
View File

@ -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
#include "PhreeqcMatrix.hpp"

13
poet/include/PhreeqcKnobs.hpp → litephreeqc/include/PhreeqcKnobs.hpp
View File

@ -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
#include <cstdint>

13
poet/include/PhreeqcMatrix.hpp → litephreeqc/include/PhreeqcMatrix.hpp
View File

@ -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
#include <map>

13
poet/include/PhreeqcRunner.hpp → litephreeqc/include/PhreeqcRunner.hpp
View File

@ -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
#include "PhreeqcEngine.hpp"

13
poet/src/Engine.cpp → litephreeqc/src/Engine.cpp
View File

@ -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 <cstddef>
#include <iomanip>

13
poet/src/Knobs.cpp → litephreeqc/src/Knobs.cpp
View File

@ -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 <Phreeqc.h>

13
poet/src/PhreeqcMatrix/Access.cpp → litephreeqc/src/PhreeqcMatrix/Access.cpp
View File

@ -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 <algorithm>
#include <cstddef>

13
poet/src/PhreeqcMatrix/Ctor.cpp → litephreeqc/src/PhreeqcMatrix/Ctor.cpp
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@ -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 "PhreeqcKnobs.hpp"
#include "PhreeqcMatrix.hpp"

13
poet/src/PhreeqcMatrix/Init.cpp → litephreeqc/src/PhreeqcMatrix/Init.cpp
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@ -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 "../Wrapper/EquilibriumWrapper.hpp"

13
poet/src/PhreeqcMatrix/Misc.cpp → litephreeqc/src/PhreeqcMatrix/Misc.cpp
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@ -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 <IPhreeqc.hpp>

13
poet/src/Runner.cpp → litephreeqc/src/Runner.cpp
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@ -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 "PhreeqcMatrix.hpp"
#include "PhreeqcRunner.hpp"

13
poet/src/Wrapper/EquilibriumCompWrapper.cpp → litephreeqc/src/Wrapper/EquilibriumCompWrapper.cpp
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@ -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"
EquilibriumWrapper::EquilibriumCompWrapper::EquilibriumCompWrapper(

13
poet/src/Wrapper/EquilibriumWrapper.cpp → litephreeqc/src/Wrapper/EquilibriumWrapper.cpp
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@ -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 <algorithm>

13
poet/src/Wrapper/EquilibriumWrapper.hpp → litephreeqc/src/Wrapper/EquilibriumWrapper.hpp
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@ -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
#include "PPassemblage.h"

13
poet/src/Wrapper/ExchangeCompWrapper.cpp → litephreeqc/src/Wrapper/ExchangeCompWrapper.cpp
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@ -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"
ExchangeWrapper::ExchangeCompWrapper::ExchangeCompWrapper(cxxExchComp &comp)

59
poet/src/Wrapper/ExchangeWrapper.cpp → litephreeqc/src/Wrapper/ExchangeWrapper.cpp
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@ -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"
ExchangeWrapper::ExchangeWrapper(cxxExchange *exch,
@ -21,36 +34,36 @@ ExchangeWrapper::ExchangeWrapper(cxxExchange *exch,
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() &&
// exchange_comps.size() < defined_comps) {
// const std::string formular = *header_it;
// while (header_it != remaining_field_header.end() &&
// exchange_comps.size() < defined_comps) {
// const std::string formular = *header_it;
// auto it = std::find_if(exchange->Get_exchange_comps().begin(),
// exchange->Get_exchange_comps().end(),
// [&](const cxxExchComp &comp) {
// return comp.Get_formula() == formular;
// });
// auto it = std::find_if(exchange->Get_exchange_comps().begin(),
// exchange->Get_exchange_comps().end(),
// [&](const cxxExchComp &comp) {
// return comp.Get_formula() == formular;
// });
// if (it != exchange->Get_exchange_comps().end()) {
// const size_t i = this->exchange_comps.size();
// if (it != exchange->Get_exchange_comps().end()) {
// const size_t i = this->exchange_comps.size();
// exchange_comps.push_back(std::make_unique<ExchangeCompWrapper>(*it));
// header_it += this->exchange_comps[i]->size();
// num_elements += this->exchange_comps[i]->size();
// continue;
// }
// exchange_comps.push_back(std::make_unique<ExchangeCompWrapper>(*it));
// header_it += this->exchange_comps[i]->size();
// num_elements += this->exchange_comps[i]->size();
// continue;
// }
// header_it++;
// }
// header_it++;
// }
// if (exchange_comps.size() != defined_comps) {
// throw std::runtime_error(
// "Not all exchange components found in Phreeqc variables");
// }
// if (exchange_comps.size() != defined_comps) {
// throw std::runtime_error(
// "Not all exchange components found in Phreeqc variables");
// }
}
void ExchangeWrapper::get(std::span<LDBLE> &exchange) const {

13
poet/src/Wrapper/ExchangeWrapper.hpp → litephreeqc/src/Wrapper/ExchangeWrapper.hpp
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@ -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
#include "ExchComp.h"

13
poet/src/Wrapper/KineticCompWrapper.cpp → litephreeqc/src/Wrapper/KineticCompWrapper.cpp
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@ -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 <cstddef>
#include <string>

13
poet/src/Wrapper/KineticWrapper.cpp → litephreeqc/src/Wrapper/KineticWrapper.cpp
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@ -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 <vector>

13
poet/src/Wrapper/KineticWrapper.hpp → litephreeqc/src/Wrapper/KineticWrapper.hpp
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@ -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
#include "KineticsComp.h"

13
poet/src/Wrapper/SolutionWrapper.cpp → litephreeqc/src/Wrapper/SolutionWrapper.cpp
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@ -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 "NameDouble.h"
#include <set>

13
poet/src/Wrapper/SolutionWrapper.hpp → litephreeqc/src/Wrapper/SolutionWrapper.hpp
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@ -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
#include "Solution.h"

13
poet/src/Wrapper/SurfaceChargeWrapper.cpp → litephreeqc/src/Wrapper/SurfaceChargeWrapper.cpp
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@ -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"
SurfaceWrapper::SurfaceChargeWrapper::SurfaceChargeWrapper(

13
poet/src/Wrapper/SurfaceCompWrapper.cpp → litephreeqc/src/Wrapper/SurfaceCompWrapper.cpp
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@ -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"
SurfaceWrapper::SurfaceCompWrapper::SurfaceCompWrapper(cxxSurfaceComp &comp)

13
poet/src/Wrapper/SurfaceWrapper.cpp → litephreeqc/src/Wrapper/SurfaceWrapper.cpp
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@ -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 "SurfaceComp.h"

13
poet/src/Wrapper/SurfaceWrapper.hpp → litephreeqc/src/Wrapper/SurfaceWrapper.hpp
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@ -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
#include "Surface.h"

31
litephreeqc/src/Wrapper/WrapperBase.hpp Normal file
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@ -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;
};

0
poet/test/IPhreeqcReader.cpp → litephreeqc/test/IPhreeqcReader.cpp
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0
poet/test/IPhreeqcReader.hpp → litephreeqc/test/IPhreeqcReader.hpp
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0
poet/test/barite_db.dat → litephreeqc/test/barite_db.dat
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0
poet/test/barite_het.pqi → litephreeqc/test/barite_het.pqi
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0
poet/test/dolo.pqi → litephreeqc/test/dolo.pqi
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0
poet/test/phreeqc_kin.dat → litephreeqc/test/phreeqc_kin.dat
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0
poet/test/run_kin_cor_end2.pqi → litephreeqc/test/run_kin_cor_end2.pqi
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0
poet/test/testGetters.cpp → litephreeqc/test/testGetters.cpp
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147
litephreeqc/test/testGolemRunner.cpp Normal file
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@ -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

2
poet/test/testInput.hpp.in → litephreeqc/test/testInput.hpp.in
View File

@ -6,7 +6,7 @@
#include <gtest/gtest.h>
#define POET_TEST(name) TEST(TestPOET, name)
#define POET_TEST(name) TEST(litephreeqc, name)
namespace base_test {
const std::string script = R"(SOLUTION 1

13
poet/test/testPhreeqcEngine.cpp → litephreeqc/test/testPhreeqcEngine.cpp
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@ -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 <testInput.hpp>

13
poet/test/testPhreeqcKnobs.cpp → litephreeqc/test/testPhreeqcKnobs.cpp
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@ -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 <testInput.hpp>

13
poet/test/testPhreeqcMatrix.cpp → litephreeqc/test/testPhreeqcMatrix.cpp
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@ -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 <gtest/gtest.h>
#include <string>

13
poet/test/testPhreeqcRunner.cpp → litephreeqc/test/testPhreeqcRunner.cpp
View File

@ -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 "utils.hpp"

13
poet/test/utils.cpp → litephreeqc/test/utils.cpp
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@ -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 <fstream>

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litephreeqc/test/utils.hpp Normal file
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@ -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);

18
poet/src/Wrapper/WrapperBase.hpp
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@ -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;
};

144
poet/test/testGolemRunner.cpp
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@ -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

5
poet/test/utils.hpp
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#pragma once
#include <string>
std::string readFile(const std::string &path);

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src/phreeqcpp/GFZ.cpp → src/phreeqcpp/litephreeqc_funcs.cpp
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/*
* 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 <set>