build(cmake): disable database, doc, examples subdirs

refactor: Rename 'poet' directory to 'litephreeqc'

.github/workflows/cmake.yml

@@ -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]

CMakeLists.txt

@@ -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)

litephreeqc/CMakeLists.txt

@@ -1,4 +1,5 @@
-set(POET_SOURCE_FILES
+
+set(LPQC_SOURCE_FILES
     src/Engine.cpp
     src/Runner.cpp 
     src/Knobs.cpp
@@ -20,35 +21,36 @@ 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
         test/testPhreeqcKnobs.cpp
         test/utils.cpp
+        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 "${PROJECT_SOURCE_DIR}/database/phreeqc.dat" POET_PHREEQCDAT_DB)
@@ -58,8 +60,11 @@ if (BUILD_TESTING AND STANDALONE_BUILD)
     configure_file("${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(golemrunner test/testGolemRunner.cpp)
-target_link_libraries(golemrunner IPhreeqcPOET)
+target_link_libraries(golemrunner litephreeqc)
+
+add_executable(testGetters     test/testGetters.cpp)
+target_link_libraries(testGetters litephreeqc)

litephreeqc/LICENSE.txt

@@ -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
+

litephreeqc/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
+ *
+ */
+
 #pragma once
 
 #include "PhreeqcMatrix.hpp"

litephreeqc/include/PhreeqcKnobs.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
 
 #include <cstdint>

litephreeqc/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
 
 #include <map>
@@ -313,6 +326,48 @@ public:
    */
   bool withRedox() const { return _m_with_redox; }
 
+  // MDL
+  /**
+   * @brief Returns all column names of the Matrix pertaining to KINETICS
+   *
+   * This function returns a string vector.
+   *
+   * @return std::vector<std::string> Whole vector of names. Empty if no KINETICS
+   * is defined
+   */
+   std::vector<std::string> getMatrixKinetics() const;
+   
+  /**
+   * @brief Returns all column names of the Matrix pertaining to EQUILIBRIUM
+   *
+   * This function returns a string vector.
+   *
+   * @return std::vector<std::string> Whole vector of names. Empty if no EQUILIBRIUM
+   * is defined
+   */
+   std::vector<std::string> getMatrixEquilibrium() const;
+
+      
+   /*
+   
+   @brief Returns all column names of the Matrix pertaining to
+   quantities that must be transported
+   
+   @return std::vector<std::string> vector of names
+
+   */
+   std::vector<std::string> getMatrixTransported() const;
+
+   /*
+
+   @brief Returns all column names of the Matrix pertaining to
+   quantities that must NOT be transported but have to be included in
+   the output
+   
+   @return std::vector<std::string> vector of names
+   */
+   std::vector<std::string> getMatrixOutOnly() const;
+
 private:
   std::map<int, std::vector<element>> _m_map;
   std::map<int, std::vector<base_names>> _m_internal_names;
@@ -330,4 +385,4 @@ private:
 
   bool _m_with_h0_o0;
   bool _m_with_redox;
-};
+};

litephreeqc/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
+ *
+ */
+
 #pragma once
 
 #include "PhreeqcEngine.hpp"

litephreeqc/src/Engine.cpp

@@ -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>
@@ -130,6 +143,12 @@ void PhreeqcEngine::Impl::run(double time_step) {
   const std::string runs_string =
       "RUN_CELLS\n -cells 1\n -time_step " + time_ss.str() + "\nEND\n";
   this->RunString(runs_string.c_str());
+
+  if (this->GetErrorStringLineCount() > 0) {
+    std::cerr << ":: Error in Phreeqc script: " << this->GetErrorString()
+              << "\n";
+    throw std::runtime_error("Phreeqc script error");
+  }
 }
 
 void PhreeqcEngine::Impl::init_wrappers(const InitCell &cell) {
@@ -242,4 +261,4 @@ void PhreeqcEngine::Impl::set_essential_values(const std::span<double> &data) {
         data.subspan(offset, this->surfaceWrapperPtr->size())};
     this->surfaceWrapperPtr->set(surf_span);
   }
-}
+}

litephreeqc/src/Knobs.cpp

@@ -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>

litephreeqc/src/PhreeqcMatrix/Access.cpp

@@ -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>
@@ -119,6 +132,7 @@ PhreeqcMatrix::STLExport PhreeqcMatrix::get(VectorExportType type,
     for (; column_index < result.names.size(); column_index++) {
       for (const auto &[_, elements] : _m_map) {
         double value_to_add = std::numeric_limits<double>::quiet_NaN();
+        // double value_to_add;
         for (const auto &curr_element : elements) {
           const std::string &curr_element_name = curr_element.name;
 
@@ -238,4 +252,81 @@ double PhreeqcMatrix::operator()(int cell_id, const std::string &name) const {
   }
 
   return it->value;
-}
+}
+
+
+// MDL
+std::vector<std::string> PhreeqcMatrix::getMatrixKinetics() const {
+    std::vector<std::string> names;
+    
+    auto n = this->getIds().size();
+    for (auto i = 0; i<n; ++i) {
+	auto pqc_kinnames = this->getKineticsNames(i);
+	for (auto nam : pqc_kinnames ) {
+	    for (auto mat_name : this->get().names){
+		if (mat_name.starts_with(nam)) {
+		    // check if we already have this mat_name
+		    if (std::find(names.begin(), names.end(), mat_name) == names.end()) {
+			names.push_back(mat_name);
+		    }
+		}
+	    }
+	}
+    }
+    return names;
+}
+
+
+// MDL
+std::vector<std::string> PhreeqcMatrix::getMatrixEquilibrium() const {
+
+    std::vector<std::string> names;
+    std::vector<std::string> mat_names = this->get().names;
+    auto n = this->getIds().size();
+    for (auto i = 0; i<n; ++i) {
+	auto pqc_eqnames = this->getEquilibriumNames(i);
+	for (auto nam : pqc_eqnames ) {
+	    for (auto mat_name : mat_names){
+		if (mat_name.starts_with(nam)) {
+		    // check if we already have this mat_name
+		    if (std::find(names.begin(), names.end(), mat_name) == names.end()) {
+			names.push_back(mat_name);
+		    }
+		}
+	    }
+	}
+    }
+    return names;
+}
+
+// MDL
+std::vector<std::string> PhreeqcMatrix::getMatrixTransported() const {
+    std::vector<std::string> names;
+    
+    const std::vector<std::string> to_remove = {
+	"tc", "patm", "SolVol", "pH", "pe"
+    };
+
+    // sols contains all solutes; we must remove { tc, patm, SolVol, pH, pe }
+    auto sols = this->getSolutionNames();
+    for (auto name : sols) {
+	if (std::find(to_remove.begin(), to_remove.end(), name) == to_remove.end()) {
+	    names.push_back(name);
+	}
+    }
+    
+    return names;
+}
+
+// MDL
+std::vector<std::string> PhreeqcMatrix::getMatrixOutOnly() const {
+    // MDL we must append here selected_output / user_punch
+    std::vector<std::string> defaultnames = {
+	"tc", "patm", "SolVol", "pH", "pe"
+    };
+    std::vector<std::string> ret;
+    for (auto nm : defaultnames) {
+	ret.push_back(nm);
+    }
+    return ret;
+}

litephreeqc/src/PhreeqcMatrix/Ctor.cpp

@@ -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"
@@ -18,6 +31,12 @@ PhreeqcMatrix::PhreeqcMatrix(const std::string &database,
   this->_m_pqc->LoadDatabaseString(database.c_str());
   this->_m_pqc->RunString(input_script.c_str());
 
+  if (this->_m_pqc->GetErrorStringLineCount() > 0) {
+    std::cerr << ":: Error in Phreeqc script: "
+              << this->_m_pqc->GetErrorString() << "\n";
+    throw std::runtime_error("Phreeqc script error");
+  }
+
   this->_m_knobs =
       std::make_shared<PhreeqcKnobs>(this->_m_pqc.get()->GetPhreeqcPtr());
 
@@ -52,4 +71,4 @@ PhreeqcMatrix::PhreeqcMatrix(const std::string &database,
 //   _m_database = other._m_database;
 
 //   return *this;
-// }
+// }

litephreeqc/src/PhreeqcMatrix/Init.cpp

@@ -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"

litephreeqc/src/PhreeqcMatrix/Misc.cpp

@@ -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>

litephreeqc/src/Runner.cpp

@@ -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"

litephreeqc/src/Wrapper/EquilibriumCompWrapper.cpp

@@ -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(

litephreeqc/src/Wrapper/EquilibriumWrapper.cpp

@@ -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>

litephreeqc/src/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
+ *
+ */
+
 #pragma once
 
 #include "PPassemblage.h"

litephreeqc/src/Wrapper/ExchangeCompWrapper.cpp

@@ -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)
@@ -8,6 +21,9 @@ ExchangeWrapper::ExchangeCompWrapper::ExchangeCompWrapper(cxxExchComp &comp)
 
 void ExchangeWrapper::ExchangeCompWrapper::get(
     std::span<LDBLE> &exchange) const {
+
+  std::size_t exch_index = this->NUM_NOT_TOTALS;
+
   exchange[0] = exch_comp.Get_totals().find(exch_comp.Get_formula())->second;
   exchange[1] = exch_comp.Get_charge_balance();
   exchange[2] = exch_comp.Get_la();
@@ -16,15 +32,16 @@ void ExchangeWrapper::ExchangeCompWrapper::get(
 
   for (const auto &[name, value] : exch_comp.Get_totals()) {
     if (name != exch_comp.Get_formula()) {
-      exchange[NUM_NOT_TOTALS +
-               std::distance(exch_comp.Get_totals().begin(),
-                             exch_comp.Get_totals().find(name))] = value;
+      exchange[exch_index++] = value;
     }
   }
 }
 
 void ExchangeWrapper::ExchangeCompWrapper::set(
     const std::span<LDBLE> &exchange) {
+
+  std::size_t exch_index = this->NUM_NOT_TOTALS;
+
   exch_comp.Get_totals().find(exch_comp.Get_formula())->second = exchange[0];
   exch_comp.Set_charge_balance(exchange[1]);
   exch_comp.Set_la(exchange[2]);
@@ -33,9 +50,7 @@ void ExchangeWrapper::ExchangeCompWrapper::set(
 
   for (auto &[name, value] : exch_comp.Get_totals()) {
     if (name != exch_comp.Get_formula()) {
-      value = exchange[NUM_NOT_TOTALS +
-                       std::distance(exch_comp.Get_totals().begin(),
-                                     exch_comp.Get_totals().find(name))];
+      value = exchange[exch_index++];
     }
   }
-}
+}

litephreeqc/src/Wrapper/ExchangeWrapper.cpp

@@ -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 {

litephreeqc/src/Wrapper/ExchangeWrapper.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
 
 #include "ExchComp.h"

litephreeqc/src/Wrapper/KineticCompWrapper.cpp

@@ -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>
@@ -30,11 +43,11 @@ KineticWrapper::KineticCompWrapper::names(const cxxKineticsComp &comp) {
   std::vector<std::string> names;
 
   const std::string &comp_name = comp.Get_rate_name();
-  names.push_back(comp_name);
+  names.push_back(comp_name + "_kin");
 
   for (std::size_t i = 0; i < comp.Get_d_params().size(); i++) {
     names.push_back(comp_name + "_p" + std::to_string(i + 1));
   }
 
   return names;
-}
+}

litephreeqc/src/Wrapper/KineticWrapper.cpp

@@ -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>
 

litephreeqc/src/Wrapper/KineticWrapper.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
 
 #include "KineticsComp.h"

litephreeqc/src/Wrapper/SolutionWrapper.cpp

@@ -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>
@@ -18,6 +31,11 @@ void SolutionWrapper::get(std::span<LDBLE> &data) const {
   data[0] = solution->Get_total_h();
   data[1] = solution->Get_total_o();
   data[2] = solution->Get_cb();
+  data[3] = solution->Get_tc();
+  data[4] = solution->Get_patm();
+  data[5] = solution->Get_soln_vol();
+  data[6] = solution->Get_ph();
+  data[7] = solution->Get_pe();
 
   const cxxNameDouble &totals =
       (_with_redox ? solution->Get_totals()
@@ -41,6 +59,8 @@ void SolutionWrapper::set(const std::span<LDBLE> &data) {
   const double &total_h = data[0];
   const double &total_o = data[1];
   const double &cb = data[2];
+  const double &tc = data[3];
+  const double &patm = data[4];
 
   for (const auto &tot_name : solution_order) {
     const double value = data[i++];
@@ -51,7 +71,7 @@ void SolutionWrapper::set(const std::span<LDBLE> &data) {
     new_totals[tot_name] = value;
   }
 
-  this->solution->Update(total_h, total_o, cb,
+  this->solution->Update(total_h, total_o, cb, tc, patm,
                          _with_redox ? new_totals
                                      : new_totals.Simplify_redox());
 }
@@ -85,4 +105,4 @@ SolutionWrapper::names(cxxSolution *solution, bool include_h0_o0,
 
   names.insert(names.end(), names_set.begin(), names_set.end());
   return names;
-}
+}

litephreeqc/src/Wrapper/SolutionWrapper.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
 
 #include "Solution.h"
@@ -27,10 +40,12 @@ private:
   cxxSolution *solution;
   const std::vector<std::string> solution_order;
 
-  static constexpr std::array<const char *, 3> ESSENTIALS = {"H", "O",
-                                                             "Charge"};
+  static constexpr std::array<const char *, 8> ESSENTIALS = {
+      "H",      "O",  "Charge", "tc", "patm",
+
+      "SolVol", "pH", "pe"}; // MDL; ML: only output
 
   static constexpr std::size_t NUM_ESSENTIALS = ESSENTIALS.size();
 
   const bool _with_redox;
-};
+};

litephreeqc/src/Wrapper/SurfaceChargeWrapper.cpp

@@ -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(

litephreeqc/src/Wrapper/SurfaceCompWrapper.cpp

@@ -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)

litephreeqc/src/Wrapper/SurfaceWrapper.cpp

@@ -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"
 

litephreeqc/src/Wrapper/SurfaceWrapper.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
 
 #include "Surface.h"

litephreeqc/src/Wrapper/WrapperBase.hpp

@@ -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;
+};

litephreeqc/test/IPhreeqcReader.cpp

@@ -0,0 +1,139 @@
+#include "IPhreeqcReader.hpp"
+
+#include <cstdint>
+#include <iostream>
+#include <limits>
+#include <map>
+#include <memory>
+#include <regex>
+#include <stdexcept>
+#include <string>
+
+IPhreeqcReader::IPhreeqcReader(const std::string &database,
+                               const std::string &script) {
+
+  _m_pqc = std::make_unique<IPhreeqc>();
+
+  _m_pqc->LoadDatabaseString(database.c_str());
+  _m_pqc->RunString(script.c_str());
+
+  if (_m_pqc->GetErrorStringLineCount() > 0) {
+    std::cerr << ":: Error in Phreeqc script: " << _m_pqc->GetErrorString()
+              << "\n";
+    throw std::runtime_error("Phreeqc script error");
+  }
+}
+
+void IPhreeqcReader::setOutputID(std::uint32_t cell_id) {
+
+  _m_pqc->SetDumpStringOn(true);
+
+  const std::string call_string =
+      "DUMP\n -cells " + std::to_string(cell_id) + "\nEND\n";
+
+  _m_pqc->RunString(call_string.c_str());
+
+  if (_m_pqc->GetErrorStringLineCount() > 0) {
+    std::cerr << ":: Error in Phreeqc script: " << _m_pqc->GetErrorString()
+              << "\n";
+    throw std::runtime_error("Possibly invalid cell ID: " +
+                             std::to_string(cell_id));
+  }
+
+  _m_raw_output = _m_pqc->GetDumpString();
+
+  _m_pqc->SetDumpStringOn(false);
+}
+
+double IPhreeqcReader::operator[](const std::string &name) const {
+  if (_m_raw_output.empty()) {
+    throw std::runtime_error("No output set. Call setOutputID first.");
+  }
+
+  std::size_t pos;
+
+  auto it = _m_rename_map.find(name);
+
+  if (it != _m_rename_map.end()) {
+    pos = _m_raw_output.find(it->second);
+
+    if (pos == std::string::npos) {
+      throw std::runtime_error("Renamed name not found in output: " +
+                               it->second);
+    }
+
+  } else if (name.ends_with("_eq") || name.ends_with("_si")) {
+    // remove the suffix and check for the base name
+    std::string base_name(name, 0, name.size() - 3); // remove "_eq"
+
+    pos = _m_raw_output.find(base_name);
+
+    if (pos == std::string::npos) {
+      return std::numeric_limits<double>::quiet_NaN();
+    }
+
+    if (name.ends_with("_eq")) {
+      // if it ends with '_eq', we need to find '-moles'
+      pos = _m_raw_output.find("-moles", pos);
+    } else {
+      // if it ends with '_si', we need to find '-si'
+      pos = _m_raw_output.find("-si", pos);
+    }
+  } else {
+    // if not, we first need to find '-totals'
+    pos = _m_raw_output.find("-totals");
+    if (pos == std::string::npos) {
+      throw std::runtime_error("Name not found in output: " + name);
+    }
+
+    std::size_t next_field_pos = _m_raw_output.find(" -", pos);
+
+    // Then, find the name in the output
+    pos = _m_raw_output.find(name, pos);
+
+    if (pos >= next_field_pos) {
+      return 0;
+    }
+  }
+
+  std::size_t end_pos = _m_raw_output.find('\n', pos);
+
+  if (end_pos == std::string::npos) {
+    throw std::runtime_error("End of line not found in output for name: " +
+                             name);
+  }
+
+  std::regex fp_regex(
+      R"( +([+-]?(?=\.\d|\d)(?:\d+)?(?:\.?\d*))(?:[Ee]([+-]?\d+))?)");
+  std::smatch match;
+
+  const std::string line_to_parse = _m_raw_output.substr(pos, end_pos - pos);
+
+  if (!std::regex_search(line_to_parse, match, fp_regex)) {
+    throw std::runtime_error("No floating point number found in line: " +
+                             line_to_parse);
+  }
+
+  return std::stod(match[0].str());
+}
+
+void IPhreeqcReader::run(double dt, std::vector<std::uint32_t> &&cell_ids) {
+  std::string run_string =
+      "RUN_CELLS\n -time_step " + std::to_string(dt) + "\n -cells ";
+
+  for (const auto &cell_id : cell_ids) {
+    run_string += std::to_string(cell_id) + " ";
+  }
+
+  run_string += "\nEND\n";
+
+  _m_pqc->RunString(run_string.c_str());
+
+  if (_m_pqc->GetErrorStringLineCount() > 0) {
+    std::cerr << ":: Error in Phreeqc script: " << _m_pqc->GetErrorString()
+              << "\n";
+    throw std::runtime_error("Phreeqc run error");
+  }
+
+  _m_raw_output.clear();
+}

litephreeqc/test/IPhreeqcReader.hpp

@@ -0,0 +1,28 @@
+#pragma once
+
+#include "IPhreeqc.hpp"
+
+#include <cstdint>
+#include <map>
+#include <memory>
+#include <string>
+
+class IPhreeqcReader {
+public:
+  IPhreeqcReader(const std::string &database, const std::string &script);
+
+  void setOutputID(std::uint32_t cell_id);
+  double operator[](const std::string &name) const;
+
+  void run(double dt, std::vector<std::uint32_t> &&cell_ids);
+
+private:
+  std::unique_ptr<IPhreeqc> _m_pqc;
+
+  std::string _m_raw_output = "";
+
+  const std::map<std::string, std::string> _m_rename_map = {
+      {"H", "-total_h"}, {"O", "-total_o"},     {"Charge", "-cb"},
+      {"tc", "-temp"},   {"patm", "-pressure"}, {"SolVol", "-soln_vol"},
+      {"pH", "-pH"},     {"pe", "-pe"}};
+};

litephreeqc/test/run_kin_cor_end2.pqi

@@ -0,0 +1,110 @@
+SOLUTION  1
+units	mol/kgw
+temp	35
+pH      7
+pe      4 
+Cl      0.003 charge
+Na      0.003
+PURE  1
+Calcite 0.0  10
+
+SOLUTION 2
+units   mol/kgw
+pH     6.921 
+pe    -1.258
+water  1
+temp  17
+Na   1e-15
+Cl   1e-15 charge
+Ca   1e-15
+C    1e-15
+Fe   1e-15
+S    1e-15
+Al   1e-15
+Si   7.963e-5
+
+PURE  2
+Pyrite  0.0  2.1e-4
+
+KINETICS  2
+Quartz
+  -m         2.2e-4
+  -parms     0.01  1
+
+SOLUTION 3
+units   mol/kgw
+pH     9.963
+pe    -6.769 
+temp 17
+Na   1e-15
+Cl   1e-15 
+Ca   1.345e-4
+C    1.345e-4
+Fe   1.433e-8
+S    2.866e-8
+Al   2.692e-5
+Si   2.692e-5
+
+PURE  3
+Pyrite         0 2e-4
+Calcite        0 1e-4
+
+KINETICS  3
+Kaolinite
+  -m          1.4e-3
+  -parms      0.6 1000
+Siderite
+  -m          1.2e-12
+  -parms      1.2 10
+
+SOLUTION  4 
+units	mol/kgw
+temp	17
+pH      5.576
+pe      4      O2(g) -1
+Cl      0.0003 charge
+Na      0.0003
+C       1e-15 CO2(g) -3.38
+Ca	1e-15
+Fe      1e-15
+S       1e-15
+Al      1e-15
+Si      1e-15
+
+
+SOLUTION 5 
+ units   mol/kgw
+ pH    6.653
+ pe    -3.167
+ water  1
+ temp  17
+ Na   1e-15
+ Cl   1e-15 charge
+ Ca   1e-15
+ C    1e-15
+ Fe   4.386e-9
+ S    8.772e-9
+ Al   5.031e-7
+ Si   5.031e-7
+
+PURE  5
+Pyrite  0.0  2.5e-4
+
+KINETICS 5
+Kaolinite
+  -m       1.5e-4 
+  -parms   0.6 100000
+
+SOLUTION  6
+units	mol/kgw
+temp	35
+pH      7
+pe      4 
+Cl      0.003 charge
+Na      0.003
+PURE  6
+Calcite 0.0  10
+
+RUN_CELLS
+ -cells 1 2 3 4 5 6
+END

litephreeqc/test/testGetters.cpp

@@ -0,0 +1,104 @@
+//  Time-stamp: "Last modified 2025-07-28 20:14:08 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
+    std::cout << ":: Creating a PhreeqcMatrix with valence states and H(0)/O(0) \n";
+    PhreeqcMatrix pqc_mat1(db, script, true, true);
+    
+    // How many different SOLUTIONS ("CELLS") are defined in the script?
+    const auto ids = pqc_mat1.getIds();
+    
+    int n = ids.size();
+    
+    std::cout << ":: Found " << n << " distinct PHREEQC problems \n";
+
+    std::cout << ":: getSolutionsNames(): the common solutes across all problems: \n";
+    const auto solutes1  = pqc_mat1.getSolutionNames();
+    std::cout << solutes1 << "\n";
+
+    // auto expmat = pqc_mat1.get();
+    auto allvars = pqc_mat1.get().names;
+    std::cout << ":: pqc_mat1.get().names (all names in the PhreeqcMatrix): \n";
+    std::cout << allvars << "\n\n";
+
+    std::cout << "\n-- Now the new getMatrix*() --\n\n";
+    
+    auto transported = pqc_mat1.getMatrixTransported(); 
+    std::cout << ":: pqc_mat1.getMatrixTransported(): \n";
+    std::cout << transported << "\n\n";
+
+    auto MatNamesKin = pqc_mat1.getMatrixKinetics(); 
+    std::cout << ":: pqc_mat1.getMatrixKinetics(): \n";
+    std::cout << MatNamesKin << "\n\n";
+    
+    auto MatNamesEqui = pqc_mat1.getMatrixEquilibrium(); 
+    std::cout << ":: pqc_mat1.getMatrixEquilibrium(): \n";
+    std::cout << MatNamesEqui << "\n\n";
+
+    auto outonly = pqc_mat1.getMatrixOutOnly(); 
+    std::cout << ":: pqc_mat1.getMatrixOutOnly(): \n";
+    std::cout << outonly << "\n\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

litephreeqc/test/testGolemRunner.cpp

@@ -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

litephreeqc/test/testInput.hpp.in

@@ -0,0 +1,101 @@
+#pragma once
+
+#include <limits>
+#include <string>
+#include <vector>
+
+#include <gtest/gtest.h>
+
+#define POET_TEST(name) TEST(litephreeqc, name)
+
+namespace base_test {
+const std::string script = R"(SOLUTION 1
+units mol/kgw
+temp 25
+Ca 0.1
+Mg 0.1
+Cl 0.5 charge
+Na 0.1
+PURE 1
+Calcite  0.0 1
+Dolomite 0.0 0
+RUN_CELLS
+ -cells 1
+END)";
+
+const std::vector<std::string> expected_names = {
+    "ID",         "H",          "O",           "Charge",     "tc",
+    "patm",       "SolVol",     "pH",          "pe",         "C(-4)",
+    "C(4)",       "Ca",         "Cl",          "Mg",         "Na",
+    "Calcite_eq", "Calcite_si", "Dolomite_eq", "Dolomite_si"};
+
+const std::string phreeqc_database = R"database(@POET_PHREEQCDAT_DB@)database";
+} // namespace base_test
+
+namespace barite_test {
+const std::string script = R"barite(@POET_BARITE_PQI@)barite";
+const std::string database = R"barite(@POET_BARITE_DB@)barite";
+
+const std::vector<std::string> expected_names = {"ID",
+                                                 "H",
+                                                 "O",
+                                                 "Charge",
+                                                 "tc",
+                                                 "patm",
+                                                 "SolVol",
+                                                 "pH",
+                                                 "pe",
+                                                 "Ba",
+                                                 "Cl",
+                                                 "S(-2)",
+                                                 "S(6)",
+                                                 "Sr",
+                                                 "Barite_kin",
+                                                 "Barite_p1",
+                                                 "Celestite_kin",
+                                                 "Celestite_p1",
+                                                 "Celestite_eq",
+                                                 "Celestite_si"};
+
+const std::vector<std::string> expected_names_erased = {"ID",
+                                                        "H",
+                                                        "O",
+                                                        "Charge",
+                                                        "tc",
+                                                        "patm",
+                                                        "SolVol",
+                                                        "pH",
+                                                        "pe",
+                                                        "Ba",
+                                                        "Cl",
+                                                        "S(-2)",
+                                                        "S(6)",
+                                                        "Sr",
+                                                        "Barite_kin",
+                                                        "Barite_p1",
+                                                        "Celestite_kin",
+                                                        "Celestite_p1"};
+
+const std::vector<std::string> expected_names_subset = {
+    "ID", "H",  "O",  "Charge", "tc",   "patm", "SolVol",       "pH",
+    "pe", "Ba", "Cl", "S(-2)",  "S(6)", "Sr",   "Celestite_eq", "Celestite_si"};
+} // namespace barite_test
+
+namespace test_engine {
+const std::string script = R"(SOLUTION 1
+  units mol/kgw
+  temp 25
+  Ca 0.1
+  Mg 0.1
+  Cl 0.5 charge
+  Na 0.1
+  PURE 1
+  Calcite  0.0 1
+  Dolomite 0.0 0
+  ## RUN_CELLS
+  ##  -cells 1
+  END)";
+
+const std::string phreeqc_database = R"database(@POET_PHREEQCDAT_DB@)database";
+
+} // namespace test_engine

litephreeqc/test/testPhreeqcEngine.cpp

@@ -0,0 +1,65 @@
+/*
+ * 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>
+
+#include <gtest/gtest.h>
+
+#include "IPhreeqcReader.hpp"
+#include "PhreeqcEngine.hpp"
+#include "PhreeqcMatrix.hpp"
+#include "utils.hpp"
+
+const std::string test_database = readFile(base_test::phreeqc_database);
+
+POET_TEST(PhreeqcEngineConstructor) {
+
+  PhreeqcMatrix pqc_mat(test_database, base_test::script);
+
+  EXPECT_NO_THROW(PhreeqcEngine(pqc_mat, 1));
+  EXPECT_THROW(PhreeqcEngine(pqc_mat, 2), std::invalid_argument);
+}
+
+POET_TEST(PhreeqcEngineStep) {
+  PhreeqcMatrix pqc_mat(test_database, base_test::script);
+
+  PhreeqcEngine engine(pqc_mat, 1);
+
+  IPhreeqcReader pqc_compare(test_database, base_test::script);
+
+  std::vector<double> cell_values = pqc_mat.get().values;
+  std::vector<std::string> cell_names = pqc_mat.get().names;
+  cell_values.erase(cell_values.begin(), cell_values.begin() + 1);
+  cell_names.erase(cell_names.begin(), cell_names.begin() + 1);
+
+  EXPECT_NO_THROW(engine.runCell(cell_values, 0));
+  EXPECT_NO_THROW(engine.runCell(cell_values, 100));
+
+  pqc_compare.run(0, {1});
+  pqc_compare.run(100, {1});
+
+  pqc_compare.setOutputID(1);
+
+  for (std::size_t i = 0; i < cell_names.size(); ++i) {
+    // Somehow 'pe' will not result in a expected near value, therefore we skip
+    // it
+    if (cell_names[i] == "pe") {
+      continue;
+    }
+    EXPECT_NEAR(cell_values[i], pqc_compare[cell_names[i]], 1e-6);
+  }
+
+  EXPECT_THROW(engine.runCell(cell_values, -1), std::invalid_argument);
+}

litephreeqc/test/testPhreeqcKnobs.cpp

@@ -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>
 

litephreeqc/test/testPhreeqcMatrix.cpp

@@ -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>
@@ -5,6 +18,7 @@
 
 #include <testInput.hpp>
 
+#include "IPhreeqcReader.hpp"
 #include "PhreeqcMatrix.hpp"
 #include "utils.hpp"
 
@@ -25,12 +39,18 @@ POET_TEST(PhreeqcMatrixOneSolution) {
 
   PhreeqcMatrix::STLExport exported_init = pqc_mat.get();
   // ID + H,O,Charge + 6 Solutions + 4 Equil incl. params
-  EXPECT_EQ(exported_init.names.size(), 14);
+  EXPECT_EQ(exported_init.names.size(), 19);
+
+  IPhreeqcReader pqc_compare(base_db, base_test::script);
+  pqc_compare.setOutputID(1);
 
   EXPECT_EQ(exported_init.names, base_test::expected_names);
-  for (std::size_t i = 0; i < exported_init.values.size(); ++i) {
-    EXPECT_NEAR(exported_init.values[i], base_test::expected_values[i],
-                base_test::expected_errors[i]);
+  EXPECT_EQ(exported_init.values[0], 1);
+  for (std::size_t i = 1; i < exported_init.values.size(); ++i) {
+    EXPECT_NEAR(exported_init.values[i], pqc_compare[exported_init.names[i]],
+                1e-7);
+    // EXPECT_NEAR(exported_init.values[i], base_test::expected_values[i],
+    //             base_test::expected_errors[i]);
   }
 
   auto dumps = pqc_mat.getDumpStringsPQI();
@@ -50,9 +70,12 @@ POET_TEST(PhreeqcMatrixOneSolution) {
 
 POET_TEST(PhreeqcMatrixBracketOperator) {
   PhreeqcMatrix pqc_mat(base_db, base_test::script);
+  IPhreeqcReader pqc_compare(base_db, base_test::script);
+
+  pqc_compare.setOutputID(1);
 
   EXPECT_NO_THROW(pqc_mat(1, "H"));
-  EXPECT_NEAR(pqc_mat(1, "H"), base_test::expected_values[1], 1e-5);
+  EXPECT_NEAR(pqc_mat(1, "H"), pqc_compare["H"], 1e-7);
   EXPECT_ANY_THROW(pqc_mat(1, "J"));
   EXPECT_ANY_THROW(pqc_mat(2, "H"));
 }
@@ -63,6 +86,8 @@ const std::string barite_script = readFile(barite_test::script);
 POET_TEST(PhreeqcMatrixMultiSolution) {
   PhreeqcMatrix pqc_mat(barite_db, barite_script);
 
+  IPhreeqcReader pqc_compare(barite_db, barite_script);
+
   const auto ids = pqc_mat.getIds();
   EXPECT_EQ(ids.size(), 4);
   EXPECT_EQ(ids[0], 1);
@@ -73,13 +98,17 @@ POET_TEST(PhreeqcMatrixMultiSolution) {
   PhreeqcMatrix::STLExport exported = pqc_mat.get();
 
   EXPECT_EQ(exported.names, barite_test::expected_names);
-  for (std::size_t i = 0; i < exported.names.size(); i++) {
-    if (i > 8 && i < 13) {
+
+  pqc_compare.setOutputID(1);
+
+  for (std::size_t i = 1; i < exported.names.size(); i++) {
+    if (i > 13 && i < 18) {
       EXPECT_TRUE(std::isnan(exported.values[i]));
       continue;
     }
-    EXPECT_NEAR(exported.values[i], barite_test::expected_values_line_one[i],
-                barite_test::expected_errors[i]);
+    EXPECT_NEAR(exported.values[i], pqc_compare[exported.names[i]], 1e-7);
+    // EXPECT_NEAR(exported.values[i], barite_test::expected_values_line_one[i],
+    //             barite_test::expected_errors[i]);
   }
 
   auto dumps = pqc_mat.getDumpStringsPQI();
@@ -114,6 +143,8 @@ POET_TEST(PhreeqcMatrixCtor) {
   PhreeqcMatrix pqc_mat_copy(pqc_mat);
   PhreeqcMatrix pqc_mat_move(std::move(pqc_mat_copy));
 
+  IPhreeqcReader pqc_compare(barite_db, barite_script);
+
   const auto ids = pqc_mat_move.getIds();
   EXPECT_EQ(ids.size(), 4);
   EXPECT_EQ(ids[0], 1);
@@ -124,13 +155,17 @@ POET_TEST(PhreeqcMatrixCtor) {
   PhreeqcMatrix::STLExport exported = pqc_mat_move.get();
 
   EXPECT_EQ(exported.names, barite_test::expected_names);
-  for (std::size_t i = 0; i < exported.names.size(); i++) {
-    if (i > 8 && i < 13) {
+
+  pqc_compare.setOutputID(1);
+
+  for (std::size_t i = 1; i < exported.names.size(); i++) {
+    if (i > 13 && i < 18) {
       EXPECT_TRUE(std::isnan(exported.values[i]));
       continue;
     }
-    EXPECT_NEAR(exported.values[i], barite_test::expected_values_line_one[i],
-                barite_test::expected_errors[i]);
+    EXPECT_NEAR(exported.values[i], pqc_compare[exported.names[i]], 1e-7);
+    // EXPECT_NEAR(exported.values[i], barite_test::expected_values_line_one[i],
+    //             barite_test::expected_errors[i]);
   }
 }
 
@@ -138,6 +173,8 @@ POET_TEST(PhreeqcMatrixOperator) {
   PhreeqcMatrix pqc_mat(barite_db, barite_script);
   PhreeqcMatrix pqc_mat_copy = pqc_mat;
 
+  IPhreeqcReader pqc_compare(barite_db, barite_script);
+
   const auto ids = pqc_mat_copy.getIds();
 
   EXPECT_EQ(ids.size(), 4);
@@ -149,13 +186,17 @@ POET_TEST(PhreeqcMatrixOperator) {
   PhreeqcMatrix::STLExport exported = pqc_mat_copy.get();
 
   EXPECT_EQ(exported.names, barite_test::expected_names);
-  for (std::size_t i = 0; i < exported.names.size(); i++) {
-    if (i > 8 && i < 13) {
+
+  pqc_compare.setOutputID(1);
+
+  for (std::size_t i = 1; i < exported.names.size(); i++) {
+    if (i > 13 && i < 18) {
       EXPECT_TRUE(std::isnan(exported.values[i]));
       continue;
     }
-    EXPECT_NEAR(exported.values[i], barite_test::expected_values_line_one[i],
-                barite_test::expected_errors[i]);
+    EXPECT_NEAR(exported.values[i], pqc_compare[exported.names[i]], 1e-7);
+    // EXPECT_NEAR(exported.values[i], barite_test::expected_values_line_one[i],
+    //             barite_test::expected_errors[i]);
   }
 }
 
@@ -214,8 +255,9 @@ POET_TEST(PhreeqcMatrixWithoutRedoxAndH0O0) {
   PhreeqcMatrix pqc_mat(barite_db, barite_script, false, false);
 
   const std::vector<std::string> expected_names_without_redox = {
-      "H", "O", "Charge", "Ba", "Cl", "S", "Sr",
+      "H",  "O",  "Charge", "tc", "patm", "SolVol",
+      "pH", "pe", "Ba",     "Cl", "S",    "Sr",
   };
 
   EXPECT_EQ(expected_names_without_redox, pqc_mat.getSolutionNames());
-}
+}

litephreeqc/test/testPhreeqcRunner.cpp

@@ -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"
 
@@ -48,10 +61,10 @@ POET_TEST(PhreeqcRunnerSimulation) {
     const bool is_first_half = cell_index < half_cells;
     if (is_first_half) {
       EXPECT_EQ(simulationInOut[cell_index][0], expected_value_first_half);
-      EXPECT_TRUE(std::isnan(simulationInOut[cell_index][9]));
+      EXPECT_TRUE(std::isnan(simulationInOut[cell_index][14]));
     } else {
       EXPECT_EQ(simulationInOut[cell_index][0], expected_value_second_half);
-      EXPECT_FALSE(std::isnan(simulationInOut[cell_index][9]));
+      EXPECT_FALSE(std::isnan(simulationInOut[cell_index][14]));
     }
 
     EXPECT_NEAR(simulationInOut[cell_index][1], 111, 1);
@@ -94,4 +107,4 @@ POET_TEST(PhreeqcRunnerSimulationWithIgnoredCells) {
   for (std::size_t i = 0; i < num_columns; ++i) {
     EXPECT_DOUBLE_EQ(simulationInOut[0][i], second_line[i]);
   }
-}
+}

litephreeqc/test/utils.cpp

@@ -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>

litephreeqc/test/utils.hpp

@@ -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);

poet/src/Wrapper/WrapperBase.hpp

@@ -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;
-};

poet/test/testGolemRunner.cpp

@@ -1,161 +0,0 @@
-//  Time-stamp: "Last modified 2024-12-02 17:37:08 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);
-    
-    // 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";
-
-    // std::cout << exported_mat.names  << "\n";
-    // std::cout << cell_values << "\n";
-    // END INIT
-
-
-    
-    //// 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;
-
-    // grid cells
-    const std::size_t num_cells = 10;
-    const std::size_t half_cells = 5;
-
-    // copy the values to the InOut vector. We replicate cell 1 
-    for (std::size_t index = 0; index < num_cells; ++index) {
-	if (index < half_cells) {
-	    simulationInOut.push_back(std::vector<double>(
-            matrix_values.begin(), matrix_values.begin() + num_columns));
-	} else {
-	    simulationInOut.push_back(std::vector<double>(
-            matrix_values.begin() + num_columns, matrix_values.end()));
-	}
-    }
-
-    const double timestep = 100.;
-
-    // compute 1 timestep
-    runner.run(simulationInOut, timestep);
-
-    for (std::size_t cell_index = 0; cell_index < simulationInOut.size(); ++cell_index) {
-	const bool is_first_half = cell_index < half_cells;
-	if (is_first_half) {
-	    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

poet/test/testInput.hpp.in

@@ -1,131 +0,0 @@
-#pragma once
-
-#include <limits>
-#include <string>
-#include <vector>
-
-#include <gtest/gtest.h>
-
-#define POET_TEST(name) TEST(TestPOET, name)
-
-namespace base_test {
-const std::string script = R"(SOLUTION 1
-units mol/kgw
-temp 25
-Ca 0.1
-Mg 0.1
-Cl 0.5 charge
-Na 0.1
-PURE 1
-Calcite  0.0 1
-Dolomite 0.0 0
-RUN_CELLS
- -cells 1
-END)";
-
-const std::vector<std::string> expected_names = {
-    "ID", "H",  "O",  "Charge",     "C(-4)",      "C(4)",        "Ca",
-    "Cl", "Mg", "Na", "Calcite_eq", "Calcite_si", "Dolomite_eq", "Dolomite_si"};
-
-const std::vector<double> expected_values = {1,
-                                             111.01243522078478,
-                                             55.506323405120348,
-                                             -4.7919630342304069e-13,
-                                             0,
-                                             3.500625006800175e-05,
-                                             0.12131244646561848,
-                                             0.49999844804496646,
-                                             0.078722559784449683,
-                                             0.099999999999999978,
-                                             0.95741011331883141,
-                                             0,
-                                             0.021277440215550378,
-                                             0};
-
-const std::vector<double> expected_errors = {
-    0, 1e-3, 1e-3, 1e-15, 1e-5, 1e-5, 1e-5, 1e-5, 1e-5, 1e-5, 1e-5, 0, 1e-5, 0};
-
-const std::string phreeqc_database = R"database(@POET_PHREEQCDAT_DB@)database";
-} // namespace base_test
-
-namespace barite_test {
-const std::string script = R"barite(@POET_BARITE_PQI@)barite";
-const std::string database = R"barite(@POET_BARITE_DB@)barite";
-
-const std::vector<std::string> expected_names = {"ID",
-                                                 "H",
-                                                 "O",
-                                                 "Charge",
-                                                 "Ba",
-                                                 "Cl",
-                                                 "S(-2)",
-                                                 "S(6)",
-                                                 "Sr",
-                                                 "Barite",
-                                                 "Barite_p1",
-                                                 "Celestite",
-                                                 "Celestite_p1",
-                                                 "Celestite_eq",
-                                                 "Celestite_si"};
-
-const std::vector<double> expected_values_line_one = {
-    1,
-    111.01243359383071,
-    55.508698688362124,
-    -1.2153078399577636e-09,
-    1.0000001848805677e-12,
-    1.0000000116187218e-12,
-    0,
-    0.00062047270964839664,
-    0.00062047270964840271,
-    std::numeric_limits<double>::quiet_NaN(),
-    std::numeric_limits<double>::quiet_NaN(),
-    std::numeric_limits<double>::quiet_NaN(),
-    std::numeric_limits<double>::quiet_NaN(),
-    0.99937952729135193,
-    0};
-
-const std::vector<double> expected_errors = {
-    0,
-    1e-3,
-    1e-3,
-    1e-15,
-    1e-5,
-    1e-5,
-    1e-5,
-    1e-5,
-    1e-5,
-    std::numeric_limits<double>::quiet_NaN(),
-    std::numeric_limits<double>::quiet_NaN(),
-    std::numeric_limits<double>::quiet_NaN(),
-    std::numeric_limits<double>::quiet_NaN(),
-    1e-5,
-    0};
-
-const std::vector<std::string> expected_names_erased = {
-    "ID",   "H",  "O",      "Charge",    "Ba",        "Cl",          "S(-2)",
-    "S(6)", "Sr", "Barite", "Barite_p1", "Celestite", "Celestite_p1"};
-
-const std::vector<std::string> expected_names_subset = {
-    "ID",    "H",    "O",  "Charge",       "Ba",          "Cl",
-    "S(-2)", "S(6)", "Sr", "Celestite_eq", "Celestite_si"};
-} // namespace barite_test
-
-namespace test_engine {
-const std::string script = R"(SOLUTION 1
-  units mol/kgw
-  temp 25
-  Ca 0.1
-  Mg 0.1
-  Cl 0.5 charge
-  Na 0.1
-  PURE 1
-  Calcite  0.0 1
-  Dolomite 0.0 0
-  ## RUN_CELLS
-  ##  -cells 1
-  END)";
-
-const std::string phreeqc_database = R"database(@POET_PHREEQCDAT_DB@)database";
-
-} // namespace test_engine

poet/test/testPhreeqcEngine.cpp

@@ -1,42 +0,0 @@
-#include <stdexcept>
-
-#include <testInput.hpp>
-
-#include <gtest/gtest.h>
-
-#include "PhreeqcEngine.hpp"
-#include "PhreeqcMatrix.hpp"
-#include "utils.hpp"
-
-const std::string test_database = readFile(base_test::phreeqc_database);
-
-POET_TEST(PhreeqcEngineConstructor) {
-
-  PhreeqcMatrix pqc_mat(test_database, base_test::script);
-
-  EXPECT_NO_THROW(PhreeqcEngine(pqc_mat, 1));
-  EXPECT_THROW(PhreeqcEngine(pqc_mat, 2), std::invalid_argument);
-}
-
-POET_TEST(PhreeqcEngineStep) {
-  PhreeqcMatrix pqc_mat(test_database, base_test::script);
-
-  PhreeqcEngine engine(pqc_mat, 1);
-
-  std::vector<double> cell_values = pqc_mat.get().values;
-  cell_values.erase(cell_values.begin(), cell_values.begin() + 1);
-
-  EXPECT_NO_THROW(engine.runCell(cell_values, 0));
-  EXPECT_NO_THROW(engine.runCell(cell_values, 100));
-
-  for (std::size_t i = 0; i < cell_values.size(); ++i) {
-    // skip Charge, H(0) and O(0)
-    if (i >= 2 && i <= 4) {
-      continue;
-    }
-    EXPECT_NEAR(cell_values[i], base_test::expected_values[i + 1],
-                base_test::expected_errors[i + 1]);
-  }
-
-  EXPECT_THROW(engine.runCell(cell_values, -1), std::invalid_argument);
-}

poet/test/utils.hpp

@@ -1,5 +0,0 @@
-#pragma once
-
-#include <string>
-
-std::string readFile(const std::string &path);

src/phreeqcpp/Solution.cxx

@@ -1061,26 +1061,26 @@ void cxxSolution::read_raw(CParser &parser, bool check) {
   return;
 }
 
-void cxxSolution::Update(LDBLE h_tot, LDBLE o_tot, LDBLE charge,
+void cxxSolution::Update(LDBLE h_tot, LDBLE o_tot, LDBLE charge, LDBLE tc, LDBLE patm,
                          const cxxNameDouble &const_nd) {
   this->new_def = false;
-  this->patm = 1.0;
-  this->potV = 0.0;
-  this->tc = 25.0;
-  this->ph = 7.0;
-  this->pe = 4.0;
-  this->mu = 1e-7;
-  this->ah2o = 1.0;
+  this->patm = patm;
+  // this->potV = 0.0;
+  this->tc = tc;
+  // this->ph = 7.0;
+  // this->pe = 4.0;
+  // this->mu = 1e-7;
+  // this->ah2o = 1.0;
   // H, O, charge, totals, and activities of solution are updated
   this->total_h = h_tot;
   this->total_o = o_tot;
   this->cb = charge;
   this->mass_water = o_tot / 55.55;
 
-  this->density = 1.0;
-  this->viscosity = 1.0;
-  this->soln_vol = 1.0;
-  this->total_alkalinity = 0.0;
+  // this->density = 1.0;
+  // this->viscosity = 1.0;
+  // this->soln_vol = 1.0;
+  // this->total_alkalinity = 0.0;
 
   this->master_activity.clear();
   this->species_gamma.clear();

src/phreeqcpp/Solution.h

@@ -123,7 +123,7 @@ public:
   // void modify_activities(const cxxSolution & original);
   // void Simplify_totals();
   void Update(const cxxNameDouble &nd);
-  void Update(LDBLE h_tot, LDBLE o_tot, LDBLE charge, const cxxNameDouble &nd);
+  void Update(LDBLE h_tot, LDBLE o_tot, LDBLE charge, LDBLE tc, LDBLE patm, const cxxNameDouble &nd);
   void Update_activities(const cxxNameDouble &original_tot);
   void Serialize(Dictionary &dictionary, std::vector<int> &ints,
                  std::vector<double> &doubles);

src/phreeqcpp/litephreeqc_funcs.cpp

@@ -1,7 +1,21 @@
+/*
+ * 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>
 
-const std::set<std::string> to_ignore = {"H", "O", "Charge", "H(0)", "O(0)"};
+const std::set<std::string> to_ignore = {
+    "H", "O", "Charge", "tc", "patm", "SolVol", "pH", "pe", "H(0)", "O(0)"};
 
 std::vector<std::string> Phreeqc::find_all_valence_states(
     const std::vector<std::string> &solution_names) {
@@ -85,4 +99,4 @@ std::vector<std::string> Phreeqc::find_all_valence_states(
   }
 
   return solution_with_valences;
-}
+}