Merge branch 'merge-upstream' into 'main'

Merge latest version (v3.8.8) from upstream

Closes #1

See merge request naaice/iphreeqc!34

.github/subtrees.json

@@ -0,0 +1,30 @@
+[
+  {
+    "prefix": "src",
+    "repo": "usgs-coupled-subtrees/iphreeqc-src"
+  },
+  {
+    "prefix": "examples/c",
+    "repo": "usgs-coupled-subtrees/phreeqc-commanuscript-cgfinal-examples-c"
+  },
+  {
+    "prefix": "examples/com",
+    "repo": "usgs-coupled-subtrees/phreeqc-commanuscript-cgfinal-examples-com"
+  },
+  {
+    "prefix": "examples/fortran",
+    "repo": "usgs-coupled-subtrees/phreeqc-COMManuscript-CGfinal-examples-fortran"
+  },
+  {
+    "prefix": "database",
+    "repo": "usgs-coupled-subtrees/phreeqc3-database"
+  },
+  {
+    "prefix": "phreeqc3-doc",
+    "repo": "usgs-coupled-subtrees/phreeqc3-doc"
+  },
+  {
+    "prefix": "phreeqc3-examples",
+    "repo": "usgs-coupled-subtrees/phreeqc3-examples"
+  }
+]

.github/superprojects.json

@@ -0,0 +1,7 @@
+{
+  "usgs-coupled-subtrees/iphreeqc": {
+    "superprojects": [
+      "usgs-coupled-subtrees/webmod"
+    ]
+  }
+}

.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]

.github/workflows/lint-subtrees.yml

@@ -0,0 +1,19 @@
+name: Lint subtrees.json
+
+on:
+  pull_request:
+    paths:
+      - '.github/subtrees.json'
+  workflow_call:
+  workflow_dispatch:
+
+jobs:
+  lint-subtrees:
+    runs-on: ubuntu-latest
+    env:
+      CI_SERVER_HOST: github.com
+      GROUP: usgs-coupled
+    steps:
+      - uses: usgs-coupled-subtrees/sync-subtrees-action/lint-subtrees/@main
+        with:
+          ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}

.github/workflows/lint-superprojects.yml

@@ -0,0 +1,16 @@
+name: Lint superprojects.json
+
+on:
+  pull_request:
+    paths:
+      - '.github/superprojects.json'
+  workflow_call:
+  workflow_dispatch:
+
+jobs:
+  lint-superprojects:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: usgs-coupled-subtrees/sync-subtrees-action/lint-superprojects/@main
+        with:
+          ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}

.github/workflows/subtree.yml

@@ -0,0 +1,37 @@
+name: Sync Subtrees
+
+on:
+  push:
+    branches:
+      - master
+  workflow_dispatch:
+    inputs:
+      dryRun:
+        description: 'If true, don’t push any changes (for testing only).'
+        required: true
+        default: false
+        type: boolean
+      testMerge:
+        description: 'Run in test mode, pushing to a test branch.'
+        required: true
+        default: false
+        type: boolean
+
+jobs:
+  sync-subtrees:
+    if: startsWith(github.repository, 'usgs-coupled-subtrees/')
+    runs-on: ubuntu-latest
+    env:
+      CI_SERVER_HOST: github.com
+      GROUP: usgs-coupled
+      GH_TOKEN: ${{ secrets.WORKFLOW_PAT }}
+    steps:
+      - name: Run sync-subtrees-action
+        uses: usgs-coupled-subtrees/sync-subtrees-action@main
+        with:
+          dryRun: ${{ inputs.dryRun }}
+          testMerge: ${{ inputs.testMerge }}
+          repository_name: ${{ github.event.repository.name }}
+          default_branch: ${{ github.event.repository.default_branch }}
+          run_number: ${{ github.run_number }}
+          ssh_private_key: ${{ secrets.SSH_PRIVATE_KEY }}

.gitlab-ci.yml

@@ -6,6 +6,7 @@ before_script:
 
 stages:
     - test
+    - release
 
 test:
     stage: test
@@ -19,4 +20,21 @@ test:
         paths:
             - _build/test_results.xml
         reports:
-            junit: _build/test_results.xml
+            junit: _build/test_results.xml
+
+push:
+  stage: release
+  variables:
+    GITHUB_REPOSITORY: 'git@github.com:POET-Simulator/litephreeqc.git'
+    ORIGINAL_REPO_URL: 'https://git.gfz-potsdam.de/naaice/iphreeqc.git'
+    ORIGINAL_REPO_NAME: 'iphreeqc'
+  before_script:
+    - apt-get update -y && apt-get install -y git openssh-client
+    # I know that there is this file env variable in gitlab, but somehow it does not work for me (still complaining about white spaces ...)
+    # Therefore, the ssh key is stored as a base64 encoded string
+    - mkdir -p ~/.ssh && echo $GITHUB_SSH_PRIVATE_KEY | base64 -d > ~/.ssh/id_ed25519 && chmod 0600 ~/.ssh/id_ed25519
+    - ssh-keyscan github.com >> ~/.ssh/known_hosts
+  script:
+    - rm -rf $ORIGINAL_REPO_NAME.git
+    - git clone --mirror $ORIGINAL_REPO_URL "$ORIGINAL_REPO_NAME.git" && cd $ORIGINAL_REPO_NAME.git
+    - git push --mirror $GITHUB_REPOSITORY

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}>
   )
 
@@ -260,36 +226,8 @@ 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()
+# c++14
+target_compile_features(IPhreeqc PUBLIC cxx_std_14)
 
 set(IPhreeqc_Headers
   ${PROJECT_SOURCE_DIR}/src/IPhreeqc.h
@@ -319,158 +257,94 @@ 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)

IPhreeqc.makefile

@@ -42,7 +42,7 @@ ReleaseDll_Preprocessor_Definitions=-D NDEBUG -D GCC_BUILD -D _LIB
 Release_Preprocessor_Definitions=-D NDEBUG -D GCC_BUILD -D _LIB 
 Release_Preprocessor_Definitions=-D NDEBUG -D GCC_BUILD -D _LIB 
 
-# Implictly linked object files...
+# Implicitly linked object files...
 DebugDll_Implicitly_Linked_Objects=
 DebugDll_Implicitly_Linked_Objects=
 Debug_Implicitly_Linked_Objects=

R/CITATION

@@ -32,7 +32,7 @@ citEntry(entry="Article",
 	 journal      = "Computers & Geosciences",
          volume       = "37",
          pages        = "1653-1663",
-         url          = "http://dx.doi.org/10.1016/j.cageo.2011.02.005",
+         url          = "https://dx.doi.org/10.1016/j.cageo.2011.02.005",
          
 	 textVersion  =
          paste("Charlton, S.R., and Parkhurst, D.L, 2011, Modules based ",

R/DESCRIPTION.in

@@ -4,9 +4,35 @@ Version: @VERSION@
 License: GPL-3
 NeedsCompilation: yes
 Depends: R (>= 3.5.0)
-Author: S.R. Charlton [aut, cre], D.L. Parkhurst [aut], and C.A.J. Appelo [aut], with contributions
-    from D. Gillespie [ctb] for Chipmunk BASIC and S.D. Cohen [ctb], A.C. Hindmarsh [ctb],
-    R. Serban [ctb], D. Shumaker [ctb], and A.G. Taylor [ctb] for CVODE/SUNDIALS
+Authors@R:
+    c(person(given = "S.R.",
+             family = "Charlton",
+             role = c("aut", "cre"),
+             email = "charlton@usgs.gov"),
+      person(given = "D.L.",
+             family = "Parkhurst",
+             role = "aut"),
+      person(given = "C.A.J.",
+             family = "Appelo",
+             role = "aut"),
+      person(given = c("with", "contributions", "from", "D.", "Gillespie", "for", "Chipmunk"),
+             family = "BASIC",
+             role = "aut"),
+      person(given = "S.D.",
+             family = "Cohen",
+             role = "aut"),
+      person(given = "A.C.",
+             family = "Hindmarsh",
+             role = "aut"),
+      person(given = "R.",
+             family = "Serban",
+             role = "aut"),
+      person(given = "D.",
+             family = "Shumaker",
+             role = "aut"),
+      person(given = c("A.G.", "Taylor", "for"),
+             family = "CVODE/SUNDIALS",
+             role = "aut"))
 URL: https://www.usgs.gov/software/phreeqc-version-3
 Description: A geochemical modeling program developed by the US Geological
     Survey that is designed to perform a wide variety of aqueous geochemical

R/Makefile

@@ -42,6 +42,7 @@ DBS = \
 	phreeqc.ascii \
 	pitzer.ascii \
 	sit.ascii \
+	stimela.ascii \
 	Tipping_Hurley.ascii \
 	wateq4f.ascii
 
@@ -885,7 +886,7 @@ $(IDEST):
 $(DEST):
 	mkdir $(DEST)
 
-# Force directory creation everytime make is executed
+# Force directory creation every time make is executed
 # see https://www.cmcrossroads.com/article/making-directories-gnu-make
 
 $(shell mkdir -p $(TOPDIR)/R)

R/build-databases.R

@@ -25,6 +25,7 @@ phreeqc_rates.dat                     <- scan("phreeqc_rates.ascii",
 PHREEQC_ThermoddemV1.10_15Dec2020.dat <- scan("PHREEQC_ThermoddemV1.10_15Dec2020.ascii", what="", sep="\n")
 pitzer.dat                            <- scan("pitzer.ascii",                            what="", sep="\n")
 sit.dat                               <- scan("sit.ascii",                               what="", sep="\n")
+stimela.dat                           <- scan("stimela.ascii",                           what="", sep="\n")
 Tipping_Hurley.dat                    <- scan("Tipping_Hurley.ascii",                    what="", sep="\n")
 phreeqc.dat                           <- scan("phreeqc.ascii",                           what="", sep="\n")
 wateq4f.dat                           <- scan("wateq4f.ascii",                           what="", sep="\n")

R/phreeqc.R.in

@@ -32,7 +32,7 @@
 ##' # plot the results
 ##' attach(so$n1)
 ##' title  <- "Gypsum-Anhydrite Stability"
-##' xlabel <- "Temperature, in degrees celcius"
+##' xlabel <- "Temperature, in degrees celsius"
 ##' ylabel <- "Saturation index"
 ##' plot(temp.C., si_gypsum, main = title, xlab = xlabel, ylab = ylabel,
 ##'      col = "darkred", xlim = c(25, 75), ylim = c(-0.4, 0.0))
@@ -338,7 +338,7 @@ function() {
 ##' @useDynLib phreeqc, .registration = TRUE
 ##' @return TRUE if log messages are currently being stored as a character vector.
 ##' @family Log
-##' @references \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @references \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' 
 phrGetLogStringsOn <-
 function() {
@@ -1386,7 +1386,7 @@ function(nuser, value) {
 ##' @docType data
 ##' @family Databases
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @usage Amm.dat  # phrLoadDatabaseString(Amm.dat)
 ##' @keywords dataset
 NULL
@@ -1401,7 +1401,7 @@ NULL
 ##' The database has been reformatted for use by \code{\link{phrLoadDatabaseString}}.
 ##' @docType data
 ##' @family Databases
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @usage ColdChem.dat  # phrLoadDatabaseString(ColdChem.dat)
 ##' @keywords dataset
 NULL
@@ -1433,7 +1433,7 @@ NULL
 ##' @docType data
 ##' @family Databases
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @usage ex15.dat  # phrLoadDatabaseString(ex15.dat)
 ##' @keywords dataset
 NULL
@@ -1464,7 +1464,7 @@ NULL
 ##' @docType data
 ##' @family Databases
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @usage iso.dat  # phrLoadDatabaseString(iso.dat)
 ##' @keywords dataset
 NULL
@@ -1481,7 +1481,7 @@ NULL
 ##' @docType data
 ##' @family Databases
 ##' @references Hermanska et al. (2022, 2003) and Oelkers and Addassi (2024, in preparation).
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @usage Kinec_v3.dat  # phrLoadDatabaseString(Kinec_v3.dat)
 ##' @keywords dataset
 NULL
@@ -1498,7 +1498,7 @@ NULL
 ##' @docType data
 ##' @family Databases
 ##' @references Hermanska et al. (2022, 2003) and Oelkers and Addassi (2024, in preparation).
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @usage Kinec.v2.dat  # phrLoadDatabaseString(Kinec.v2.dat)
 ##' @keywords dataset
 NULL
@@ -1528,7 +1528,7 @@ NULL
 ##' @docType data
 ##' @family Databases
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @usage minteq.dat  # phrLoadDatabaseString(minteq.dat)
 ##' @keywords dataset
 NULL
@@ -1543,7 +1543,7 @@ NULL
 ##' @docType data
 ##' @family Databases
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @usage minteq.v4.dat  # phrLoadDatabaseString(minteq.v4.dat)
 ##' @keywords dataset
 NULL
@@ -1564,7 +1564,7 @@ NULL
 ##' @family Databases
 ##' @references Hermanska and others (2023), Palandri and Kharaka (2004),
 ##' and Sverdrup and others (2019).
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @usage phreeqc_rates.dat  # phrLoadDatabaseString(phreeqc_rates.dat)
 ##' @keywords dataset
 NULL
@@ -1577,7 +1577,7 @@ NULL
 ##' @docType data
 ##' @family Databases
 ##' @references \url{https://thermoddem.brgm.fr/}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @usage PHREEQC_ThermoddemV1.10_15Dec2020.dat
 ##' # phrLoadDatabaseString(PHREEQC_ThermoddemV1.10_15Dec2020.dat)
 NULL
@@ -1593,7 +1593,7 @@ NULL
 ##' @docType data
 ##' @family Databases
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @usage phreeqc.dat  # phrLoadDatabaseString(phreeqc.dat)
 ##' @keywords dataset
 NULL
@@ -1608,7 +1608,7 @@ NULL
 ##' @docType data
 ##' @family Databases
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @usage pitzer.dat  # phrLoadDatabaseString(pitzer.dat)
 ##' @keywords dataset
 NULL
@@ -1624,13 +1624,26 @@ NULL
 ##' @docType data
 ##' @family Databases
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @usage sit.dat  # phrLoadDatabaseString(sit.dat)
 ##' @keywords dataset
 NULL
 
 
 
+##' @name stimela.dat
+##' @title The stimela.dat database.
+##' @description stimela.dat is a database for use in drinking-water and waste-water
+##' treatment from Peter de Moel and Omnisys. The database has been reformatted
+##' for use by \code{\link{phrLoadDatabaseString}}.
+##' @docType data
+##' @family Databases
+##' @usage stimela.dat  # phrLoadDatabaseString(stimela.dat)
+##' @keywords dataset
+NULL
+
+
+
 ##' @name Tipping_Hurley.dat
 ##' @title The Tipping_Hurley.dat database
 ##' @description Tipping_Hurley.dat is a database for organic-ligand
@@ -1651,7 +1664,7 @@ NULL
 ##' @docType data
 ##' @family Databases
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @usage wateq4f.dat  # phrLoadDatabaseString(wateq4f.dat)
 ##' @keywords dataset
 NULL
@@ -1668,7 +1681,7 @@ NULL
 ##' @docType data
 ##' @family Examples
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @keywords dataset 
 ##' @examples
 ##' 
@@ -1689,7 +1702,7 @@ NULL
 ##' @docType data
 ##' @family Examples
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @keywords dataset 
 ##' @examples
 ##' 
@@ -1721,7 +1734,7 @@ NULL
 ##' @docType data
 ##' @family Examples
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @keywords dataset 
 ##' @examples
 ##' 
@@ -1753,7 +1766,7 @@ NULL
 ##' @docType data
 ##' @family Examples
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @keywords dataset 
 ##' @examples
 ##' 
@@ -1780,7 +1793,7 @@ NULL
 ##' @docType data
 ##' @family Examples
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @keywords dataset 
 ##' @examples
 ##' 
@@ -1806,7 +1819,7 @@ NULL
 ##' @docType data
 ##' @family Examples
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @keywords dataset 
 ##' @examples
 ##' 
@@ -1841,7 +1854,7 @@ NULL
 ##' @docType data
 ##' @family Examples
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @keywords dataset 
 ##' @examples
 ##' 
@@ -1866,7 +1879,7 @@ NULL
 ##' @docType data
 ##' @family Examples
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @keywords dataset 
 ##' @examples
 ##'
@@ -1905,7 +1918,7 @@ NULL
 ##' @docType data
 ##' @family Examples
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @keywords dataset 
 ##' @examples
 ##'
@@ -1933,7 +1946,7 @@ NULL
 ##' @docType data
 ##' @family Examples
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @keywords dataset 
 ##' @examples
 ##'
@@ -1960,7 +1973,7 @@ NULL
 ##' @docType data
 ##' @family Examples
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @keywords dataset 
 ##' @examples
 ##'
@@ -1995,7 +2008,7 @@ NULL
 ##' @docType data
 ##' @family Examples
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @keywords dataset 
 ##' @examples
 ##'
@@ -2025,7 +2038,7 @@ NULL
 ##' @docType data
 ##' @family Examples
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @keywords dataset 
 ##' @examples
 ##'
@@ -2058,7 +2071,7 @@ NULL
 ##' @docType data
 ##' @family Examples
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @keywords dataset 
 ##' @examples
 ##'
@@ -2088,7 +2101,7 @@ NULL
 ##' @docType data
 ##' @family Examples
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @keywords dataset 
 ##' @examples
 ##'
@@ -2121,7 +2134,7 @@ NULL
 ##' @docType data
 ##' @family Examples
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @keywords dataset 
 ##' @examples
 ##'
@@ -2153,7 +2166,7 @@ NULL
 ##' @docType data
 ##' @family Examples
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @keywords dataset 
 ##' @examples
 ##'
@@ -2195,7 +2208,7 @@ NULL
 ##' @docType data
 ##' @family Examples
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @keywords dataset 
 ##' @examples
 ##'
@@ -2223,7 +2236,7 @@ NULL
 ##' @docType data
 ##' @family Examples
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @keywords dataset 
 ##' @examples
 ##'
@@ -2259,7 +2272,7 @@ NULL
 ##' @docType data
 ##' @family Examples
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @keywords dataset 
 ##' @examples
 ##'
@@ -2291,7 +2304,7 @@ NULL
 ##' @docType data
 ##' @family Examples
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @keywords dataset 
 ##' @examples
 ##'
@@ -2324,7 +2337,7 @@ NULL
 ##' @docType data
 ##' @family Examples
 ##' @references \url{https://pubs.usgs.gov/tm/06/a43/pdf/tm6-A43.pdf}
-##' @source \url{http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc}
+##' @source \url{https://www.usgs.gov/software/phreeqc-version-3/}
 ##' @keywords dataset 
 ##' @examples
 ##'

R/valgrind.R

@@ -1606,7 +1606,7 @@ so <- phrGetSelectedOutput()
 # plot the results
 attach(so$n1)
 title  <- "Gypsum-Anhydrite Stability"
-xlabel <- "Temperature, in degrees celcius"
+xlabel <- "Temperature, in degrees celsius"
 ylabel <- "Saturation index"
 plot(temp.C., si_gypsum, main = title, xlab = xlabel, ylab = ylabel,
      col = "darkred", xlim = c(25, 75), ylim = c(-0.4, 0.0))

README.md

@@ -0,0 +1 @@
+# IPhreeqc ![workflow](https://github.com/usgs-coupled/iphreeqc/actions/workflows/cmake.yml/badge.svg)

database/.github/subtrees.json

@@ -0,0 +1 @@
+[]

database/.github/superprojects.json

@@ -0,0 +1,11 @@
+{
+  "usgs-coupled-subtrees/phreeqc3-database": {
+    "superprojects": [
+      "usgs-coupled-subtrees/iphreeqc",
+      "usgs-coupled-subtrees/iphreeqccom",
+      "usgs-coupled-subtrees/phreeqcrm",
+      "usgs-coupled-subtrees/phreeqc3",
+      "usgs-coupled-subtrees/wphast"
+    ]
+  }
+}

database/.github/workflows/lint-subtrees.yml

@@ -0,0 +1,19 @@
+name: Lint subtrees.json
+
+on:
+  pull_request:
+    paths:
+      - '.github/subtrees.json'
+  workflow_call:
+  workflow_dispatch:
+
+jobs:
+  lint-subtrees:
+    runs-on: ubuntu-latest
+    env:
+      CI_SERVER_HOST: github.com
+      GROUP: usgs-coupled
+    steps:
+      - uses: usgs-coupled-subtrees/sync-subtrees-action/lint-subtrees/@main
+        with:
+          ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}

database/.github/workflows/lint-superprojects.yml

@@ -0,0 +1,20 @@
+name: Lint superprojects.json
+
+on:
+  pull_request:
+    paths:
+      - '.github/superprojects.json'
+  workflow_call:
+  workflow_dispatch:
+
+jobs:
+  lint-superprojects:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: usgs-coupled-subtrees/sync-subtrees-action/lint-superprojects/@main
+        with:
+          ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}
+          # skip-repos: |
+          #   - usgs-coupled-subtrees/iphreeqccom
+          #   - usgs-coupled-subtrees/phreeqcrm-src
+

database/.github/workflows/subtree.yml

@@ -0,0 +1,37 @@
+name: Sync Subtrees
+
+on:
+  push:
+    branches:
+      - master
+  workflow_dispatch:
+    inputs:
+      dryRun:
+        description: 'If true, don’t push any changes (for testing only).'
+        required: true
+        default: false
+        type: boolean
+      testMerge:
+        description: 'Run in test mode, pushing to a test branch.'
+        required: true
+        default: false
+        type: boolean
+
+jobs:
+  sync-subtrees:
+    if: startsWith(github.repository, 'usgs-coupled-subtrees/')
+    runs-on: ubuntu-latest
+    env:
+      CI_SERVER_HOST: github.com
+      GROUP: usgs-coupled
+      GH_TOKEN: ${{ secrets.WORKFLOW_PAT }}
+    steps:
+      - name: Run sync-subtrees-action
+        uses: usgs-coupled-subtrees/sync-subtrees-action@main
+        with:
+          dryRun: ${{ inputs.dryRun }}
+          testMerge: ${{ inputs.testMerge }}
+          repository_name: ${{ github.event.repository.name }}
+          default_branch: ${{ github.event.repository.default_branch }}
+          run_number: ${{ github.run_number }}
+          ssh_private_key: ${{ secrets.SSH_PRIVATE_KEY }}

database/Amm.dat

@@ -1,8 +1,4 @@
-# File 1 = C:\GitPrograms\phreeqc3-1\database\Amm.dat, 22/05/2024  19:38, 1948 lines, 55817 bytes, md5=78b3659799b73ddca128328b6ee7533b
-# Created 22 May 2024 19:55:37
-# C:\3rdParty\lsp\lsp.exe -f2 -k=asis -ts Amm.dat
-
-# PHREEQC.DAT for calculating temperature and pressure dependence of reactions, and the specific conductance and viscosity of the solution. Based on:
+# Amm.dat for calculating temperature and pressure dependence of reactions, and the specific conductance and viscosity of the solution. Based on:
 #   diffusion coefficients and molal volumina of aqueous species, solubility and volume of minerals, and critical temperatures and pressures of gases in Peng-Robinson's EOS.
 # Details are given at the end of this file.
 
@@ -70,7 +66,7 @@ H+ = H+
 	-dw 9.31e-9 838 6.96 -2.285 0.206 24.01 0
 #	   Dw(25 C) dw_T a    a2    visc  a3    a_v_dif
 # Dw(TK) = 9.31e-9 * exp(838 / TK - 838 / 298.15) * viscos_0_25 / viscos_0_tc
-# a = DH ion size, a2 = exponent, visc = viscosity exponent, a3(H+) = 24.01 = new dw calculation from A.D. 2024, a_v_dif = exponent in (viscos_0_tc / viscos)^a_v_dif for tracer diffusion.
+# a = DH ion size (= 3.5 - 25), a2 = exponent (= 0 2.5), visc = viscosity exponent (= 0 2.5), a3 = switch [a3(H+) = 24.01 = new dw calculation from A.D. 2024], a_v_dif = exponent in (viscos_0_tc / viscos)^a_v_dif for tracer diffusion.
 
 # For SC, Dw(TK) *=  (viscos_0_tc / viscos)^visc (visc = 0.206 for H+)
 # a3 > 5 or a3 = 0 or not defined ? ka = DH_B * a * (1 + (vm - v0))^a2 * mu^0.5, in Onsager-Falkenhagen eqn. (For H+, the reference ion, vm = v0 = 0, a *= (1 + mu)^a2.)
@@ -80,7 +76,7 @@ H+ = H+
 # If a_v_dif <> 0, Dw(TK) *= (viscos_0_tc / viscos)^a_v_dif in TRANSPORT.
 e- = e-
 H2O = H2O
-	-dw 2.299e-9 -254
+	-dw 2.299e-9 -249 # Holz et al., Phys. Chem. Chem. Phys., 2000, 2, 4740. 
 # H2O + 0.01e- = H2O-0.01; -log_k -9 # aids convergence
 Li+ = Li+
 	-gamma 6 0 # The apparent volume parameters are defined in ref. 1 & 2
@@ -111,9 +107,9 @@ Ca+2 = Ca+2
 	-dw 0.792e-9 34 5.411 0 1.046
 Sr+2 = Sr+2
 	-gamma 5.26 0.121
-	-Vm -1.57e-2 -10.15 10.18 -2.36 0.86 5.26 0.859 -27 -4.1e-3 1.97
-	-viscosity 0.472 -0.252 5.51e-3 3.67e-3 0 1.876
-	-dw 0.794e-9 149 0.805 1.961 1e-9 0.7876
+	-Vm -5.6e-2 -10.15 9.90 -2.36 0.807 5.26 2.72 -82.7 -1.37e-2 0.956
+	-viscosity 0.493 -0.255 2.3e-3 4.2e-3 -3.8e-3 1.762
+	-dw 0.794e-9 18 0.681 2.069 0.965 0.271
 Ba+2 = Ba+2
 	-gamma 5 0
 	-gamma 4 0.153 # Barite solubility
@@ -147,10 +143,10 @@ CO3-2 = CO3-2
 	-viscosity -0.5 0.6521 5.44e-3 1.06e-3 -2.18e-2 1.208 -2.147
 	-dw 0.955e-9 -103 2.246 7.13e-2 0.3686
 SO4-2 = SO4-2
-	-gamma 5 -0.04
-	-Vm -7.77 43.17 176 -51.45 3.794 0 42.99 -541 -0.145 0.45 # with analytical_expressions for log K of NaSO4-, KSO4- & MgSO4, 0 - 200 oC
-	-viscosity -0.3 0.501 2.57e-3 0.195 3.14e-2 2.015 0.605
-	-dw 1.07e-9 -114 17 6.02e-2 4.94e-2
+	-gamma 5.0 -0.04
+	-Vm 5.36 10.69 33.566 -15.03 4.2582 25 0.341 153.8 1.089e-2 0.9224 # with Na2SO4 & better calculation of sulfates' solubilities in NaCl
+	-viscosity -0.5 0.521 4.2e-4 9.78e-3 1.24e-2 2.5 -4.94e-2
+	-dw 1.07e-9 -77.4 10.14 0.5 0.5549
 NO3- = NO3-
 	-gamma 3 0
 	-Vm 6.32 6.78 0 -3.06 0.346 0 0.93 0 -0.012 1
@@ -159,7 +155,7 @@ NO3- = NO3-
 AmmH+ = AmmH+
 	-gamma 2.5 0
 	-Vm 5.35 2.345 3.72 -2.88 1.55 2.5 -4.54 217 2.344e-2 0.569
-	-viscosity 9.9e-2 -0.159 1.36e-2 6.51e-3 3.21e-2 0.972
+	-viscosity 6.94e-2 -0.141 2.04e-2 9.4e-3 3.73e-2 0.898
 	-dw 1.98e-9 203 1.47 2.644 6.81e-2
 H3BO3 = H3BO3
 	-Vm 7.0643 8.8547 3.5844 -3.1451 -0.2 # supcrt
@@ -174,7 +170,7 @@ F- = F-
 	-viscosity 0 2.85e-2 1.35e-2 6.11e-2 4.38e-3 1.384 0.586
 	-dw 1.46e-9 -36 4.352
 Br- = Br-
-	-gamma 3 0
+	-gamma 3 0.045
 	-Vm 6.72 2.85 4.21 -3.14 1.38 0 -9.56e-2 7.08 -1.56e-3 1
 	-viscosity -6.98e-2 -0.141 1.78e-2 0.159 7.76e-3 6.25e-2 0.859
 	-dw 2.09e-9 208 3.5 0 0.5737
@@ -203,21 +199,21 @@ Mtg = Mtg # CH4
 	-Vm 9.01 -1.11 0 -1.85 -1.5 # Hnedkovsky et al., 1996, JCT 28, 125
 	-dw 1.85e-9
 Ntg = Ntg # N2
-	-Vm 7 # Pray et al., 1952, IEC 44 1146
+	-Vm 7 # Pray et al., 1952, IEC 44, 1146
 	-dw 1.96e-9 -90 # Cadogan et al. 2014, JCED 59, 519
 H2Sg = H2Sg # H2S
 	-Vm 1.39 28.3 0 -7.22 -0.59 # Hnedkovsky et al., 1996, JCT 28, 125
 	-dw 2.1e-9
 # aqueous species
 H2O = OH- + H+
-	-analytic 293.29227 0.1360833 -10576.913 -123.73158 0 -6.996455e-5
 	-gamma 3.5 0
+	-analytic 293.29227 0.1360833 -10576.913 -123.73158 0 -6.996455e-5
 	-Vm -9.66 28.5 80 -22.9 1.89 0 1.09 0 0 1
 	-viscosity -2.26e-2 0.106 2.184e-2  -3.2e-3 0 0.4082 -1.634 # < 5 M Li,Na,KOH
 	-dw 5.27e-9 478 0.8695
 2 H2O = O2 + 4 H+ + 4 e-
-	-log_k -86.08
-	-delta_h 134.79 kcal
+	-log_k -86.06; -delta_h 138.43 kcal
+	-analytic -1e3 -0.322 -5897.7 416.82 0 -1.88e-5
 	-Vm 5.7889 6.3536 3.2528 -3.0417 -0.3943 # supcrt
 	-dw 2.35e-9
 2 H+ + 2 e- = H2
@@ -308,7 +304,7 @@ NO3- + 2 H+ + 2 e- = NO2- + H2O
 #	  -delta_h -187.055	  kcal
 #	-gamma 2.5 0
 #	-Vm 5.35 2.345 3.72 -2.88 1.55 2.5 -4.54 217 2.344e-2 0.569
-#	-viscosity 9.9e-2 -0.159 1.36e-2 6.51e-3 3.21e-2 0.972
+#	-viscosity 6.94e-2 -0.141 2.04e-2 9.4e-3 3.73e-2 0.898
 #	-dw 1.98e-9 203 1.47 2.644 6.81e-2
 AmmH+ = Amm + H+
 #NH4+ = NH3 + H+
@@ -316,15 +312,15 @@ AmmH+ = Amm + H+
 	-delta_h 12.48 kcal
 	-analytic 0.6322 -0.001225 -2835.76
 	-Vm 6.69 2.8 3.58 -2.88 1.43
-	-viscosity 0.08 0 0 7.82e-3 -0.134 -0.986
+	-viscosity 0 -2.24e-2 0.101 8.66e-3 2.86e-2 -0.143 -0.769
 	-dw 2.28e-9
 AmmH+ + SO4-2 = AmmHSO4-
 #NH4+ + SO4-2 = NH4SO4-
-	-gamma 2.08 -0.0416
-	-log_k	1.211; -delta_h 8.56 kJ
-	-Vm -8.78 0 -36.09 0 -8.60 0 87.62 0 -0.3123 0.1172
-	-viscosity 0 0.116 -8.6e-3 0.159 -9.3e-3 0.522 0.627
-	-dw 0.9e-9 100 2.1 2 0
+	-gamma 3.64 -4.75e-2
+	-log_k 1.276; -delta_h -3.24 kcal
+	-Vm 6.64 8.5 -5.84 -3.1 2 0 19.24 0 -7.84e-2 0.289
+	-viscosity 0.267 -0.207 9.75e-2 6.18e-2 1.99e-2 1.166 0.61
+	-dw 1.56e-9 498 25 0.5 0.684
 H3BO3 = H2BO3- + H+
 	-log_k -9.24
 	-delta_h 3.224 kcal
@@ -376,13 +372,14 @@ Ca+2 + CO3-2 + H+ = CaHCO3+
 	-log_k 10.91; -delta_h 4.38 kcal
 	-analytic -6.009 3.377e-2 2044
 	-gamma 6 0
-	-Vm 30.19 .01 5.75 -2.78 .308 5.4
+	-Vm 3.19 .01 5.75 -2.78 .308 5.4
 	-dw 5.06e-10
 Ca+2 + SO4-2 = CaSO4
-	-log_k 2.25
-	-delta_h 1.325 kcal
-	-dw 4.71e-10
-	-Vm 2.791 -.9666 6.13 -2.739 -.001 # supcrt
+	-gamma 0 4.45e-2
+	-log_k 2.14; -delta_h 24.4
+	-analytical_expression 1.478 8.29e-3 -538.2
+	-vm 2.7 2 2 -3.7
+	-dw 4.71e-9
 Ca+2 + HSO4- = CaHSO4+
 	-log_k 1.08
 Ca+2 + PO4-3 = CaPO4-
@@ -419,19 +416,19 @@ Mg+2 + H+ + CO3-2 = MgHCO3+
 	-Vm 2.7171 -1.1469 6.2008 -2.7316 .5985 4 # supcrt
 	-dw 4.78e-10
 Mg+2 + SO4-2 = MgSO4
-	-gamma 0 0.2
-	-log_k 2.42; -delta_h 19 kJ
-	-analytical_expression 0 9.64e-3 -136 # mean salt gamma from Pitzer.dat and epsomite/hexahydrite/kieserite solubilities, 0 - 200 oC
-	-Vm 8.65 -10.21 29.58 -18.6 1.061
-	-viscosity 0.318 -5.4e-4 -3.42e-2 0.708 3.7e-3 0.696
+	-gamma 0 0.20
+	-log_k 2.42; -delta_h 19.0
+	-analytical_expression 0 9.64e-3 -136 # epsomite/hexahydrite/kieserite solubilities, 0 - 200 oC
+	-Vm 11.92 -27.758 29.752 -10.302 -0.1
+	-viscosity -0.799 1 2.2e-4 8.53e-2 -4.6e-3 1.35 -0.796
 	-dw 4.45e-10
 SO4-2 + MgSO4 = Mg(SO4)2-2
 	-gamma 7 0.047
-	-log_k 0.52; -delta_h -13.6 kJ
-	-analytical_expression 0 -1.51e-3 0 0 8.604e4 # mean salt gamma from Pitzer.dat and epsomite/hexahydrite/kieserite solubilities, 0 - 200 oC
-	-Vm -8.14 -62.2 -15.96 3.29 -3.01 0 150 0 0.153 3.79e-2
-	-viscosity -0.169 5e-4 -5.69e-2 0.11 2.03e-3 2.027 -1e-3
-	-dw 0.845e-9 -200 8 0 0.965
+	-log_k 0.52; -delta_h -13.6
+	-analytical_expression 0 -1.51e-3 0 0 8.604e4 # epsomite/hexahydrite/kieserite solubilities, 0 - 200 oC
+	-Vm 4.248 9.83 -7 -2.672 2 3.5 5 100 0.3359 9.518e-2
+	-viscosity 0.324 6.84e-2 -2.09e-2 0.104 6.19e-3 1.983 1e-3
+	-dw 1.11e-9 -500 3.5 0.5 0.731
 Mg+2 + PO4-3 = MgPO4-
 	-log_k 6.589
 	-delta_h 3.1 kcal
@@ -457,12 +454,19 @@ Na+ + HCO3- = NaHCO3
 	-viscosity -4e-2 -2.717 1.67e-5
 	-dw 6.73e-10
 Na+ + SO4-2 = NaSO4-
-	-gamma 5.5 0
-	-log_k 0.6; -delta_h -14.4 kJ
-	-analytical_expression 255.903 0.10057 0 -1.11138e2 -8.5983e5 # mirabilite/thenardite solubilities, 0 - 200 oC
-	-Vm 1.99 -10.78 21.88 -12.7 1.601 5 32.38 501 1.565e-2 0.2325
-	-viscosity 0.2 -5.93e-2 -4e-4 8.46e-3 1.78e-3 2.308 -0.208
-	-dw 1.13e-9 -23 8.5 0.392 0.521
+	-gamma 3.5 0.1072
+	-log_k 0.94; -delta_h 8.23
+	-analytical_expression -0.304 4.51e-3 -28.9 # mirabilite/thenardite solubilities, 0 - 200 oC
+	-Vm 8.523 -4.685 -8.61 0.106 2.7 25 3.634 13.4 3.738e-2 0.5476
+	-viscosity -1 0.33 0.128 1.143 7.7e-4 1.9e-2 -0.387
+	-dw 4e-10 -200 3.5 0.5 0.5
+2 Na+ + SO4-2 = Na2SO4
+	-gamma 0 8.85e-2
+	-log_k -2.37; -delta_h 82
+	-analytical_expression 15.432 -5.75e-3 -4796 # sulfates solubilities in NaCl
+	-Vm 9.405 -15.5 25 8.4 0.25
+	-viscosity -0.5 0.485 -1e-3 0.147 0 0.947 -0.175
+	-dw 0.8e-9
 Na+ + HPO4-2 = NaHPO4-
 	-log_k 0.29
 	-gamma 5.4 0
@@ -477,11 +481,11 @@ K+ + HCO3- = KHCO3
 	-viscosity 0.7 -1.289 9e-2
 K+ + SO4-2 = KSO4-
 	-gamma 5.4 0.19
-	-log_k 0.6; -delta_h -10.4 kJ
+	-log_k 1.18; -delta_h 3
 	-analytical_expression -3.0246 9.986e-3 0 0 1.093e5 # arcanite solubility, 0 - 200 oC
-	-Vm 13.48 -18.03 61.74 -19.6 2.046 5.4 -17.32 0 0.1522 1.919
-	-viscosity -1 1.06 1e-4 -0.464 3.78e-2 0.539 -0.69
-	-dw 0.9e-9 63 8.48 0 1.8
+	-Vm 3.443 5.04 13 -3.324 2.447 0 20 0 7.77e-3 0.3497
+	-viscosity 0.107 0.19 2.23e-2 -0.148 -4.91e-2 0.537 0.195
+	-dw 1.22e-9 100 25 0.5 2.5
 K+ + HPO4-2 = KHPO4-
 	-log_k 0.29
 	-gamma 5.4 0
@@ -501,9 +505,8 @@ Fe+2 + CO3-2 = FeCO3
 Fe+2 + HCO3- = FeHCO3+
 	-log_k 2
 Fe+2 + SO4-2 = FeSO4
-	-log_k 2.25
-	-delta_h 3.23 kcal
-	-Vm -13 0 123
+	-log_k 2.25; -delta_h 3.23 kcal
+	-Vm 5.8 6.5 3.7 -3 -0.09
 Fe+2 + HSO4- = FeHSO4+
 	-log_k 1.08
 Fe+2 + 2 HS- = Fe(HS)2
@@ -605,9 +608,9 @@ Mn+2 + HCO3- = MnHCO3+
 	-log_k 1.95
 	-gamma 5 0
 Mn+2 + SO4-2 = MnSO4
-	-log_k 2.25
-	-delta_h 3.37 kcal
-	-Vm -1.31 -1.83 62.3 -2.7
+	-gamma 0 -0.098
+	-log_k 1.408; -delta_h 21.55
+	-Vm 1.88 6.5 10 -3 0.1
 Mn+2 + 2 NO3- = Mn(NO3)2
 	-log_k 0.6
 	-delta_h -0.396 kcal
@@ -700,7 +703,8 @@ Ba+2 + HCO3- = BaHCO3+
 	-delta_h 5.56 kcal
 	-analytic -3.0938 0.013669
 Ba+2 + SO4-2 = BaSO4
-	-log_k 2.7
+	-log_k 3.457; -delta_h 26.15
+	-vm -6.25 24.66 -4.38 10.97 0.5
 Sr+2 + H2O = SrOH+ + H+
 	-log_k -13.29
 	-gamma 5 0
@@ -819,12 +823,13 @@ Zn+2 + 2 CO3-2 = Zn(CO3)2-2
 Zn+2 + HCO3- = ZnHCO3+
 	-log_k 2.1
 Zn+2 + SO4-2 = ZnSO4
-	-log_k 2.37
-	-delta_h 1.36 kcal
-	-Vm 2.51 0 18.8
+	-gamma 0 0.1
+	-log_k 2.26; -delta_h 16.15
+	-Vm 0.409 6.5 2 -3 0
 Zn+2 + 2 SO4-2 = Zn(SO4)2-2
-	-log_k 3.28
-	-Vm 10.9 0 -98.7 0 0 0 24 0 -0.236 1
+	-gamma 0.59 0.1
+	-log_k 1.15; -delta_h 17.52
+	-Vm 9.21 10.6 9 -3.2 3.8 25 0 100 -1e-3 0.256
 Zn+2 + Br- = ZnBr+
 	-log_k -0.58
 Zn+2 + 2 Br- = ZnBr2
@@ -870,12 +875,13 @@ Cd+2 + 2 CO3-2 = Cd(CO3)2-2
 Cd+2 + HCO3- = CdHCO3+
 	-log_k 1.5
 Cd+2 + SO4-2 = CdSO4
-	-log_k 2.46
-	-delta_h 1.08 kcal
-	-Vm 10.4 0 57.9
+	-gamma 0 0.1
+	-log_k 1.016; -delta_h 6.84
+	-Vm 2.11 6.5 10 -3 0.1
 Cd+2 + 2 SO4-2 = Cd(SO4)2-2
-	-log_k 3.5
-	-Vm -6.29 0 -93 0 9.5 7 0 0 0 1
+	-gamma 5.201 -0.1
+	-log_k 2.688; -delta_h 0.19
+	-Vm 9.14 10.6 -3.06 -3.2 3.8 7.44 1.27 0.32 -1e-3 2.5
 Cd+2 + Br- = CdBr+
 	-log_k 2.17
 	-delta_h -0.81 kcal
@@ -995,29 +1001,24 @@ Witherite
 	-Vm 46
 Gypsum
 	CaSO4:2H2O = Ca+2 + SO4-2 + 2 H2O
-	-log_k -4.58
-	-delta_h -0.109 kcal
-	-analytic 68.2401 0 -3221.51 -25.0627
-	-analytical_expression 93.7 5.99E-3 -4e3 -35.019 # better fits the appendix data of Appelo, 2015, AG 55, 62
-	-Vm 73.9 # 172.18 / 2.33 (Vm H2O = 13.9 cm3/mol)
+	-log_k -4.55; -delta_h -6.70
+	-analytical_expression 72.244 -1.474e-2 -4040 -23.7823 # fits the appendix data of Appelo, 2015, AG 55, 62
+	-Vm 73.9
 Anhydrite
 	CaSO4 = Ca+2 + SO4-2
-	-log_k -4.36
-	-delta_h -1.71 kcal
-	-analytic 84.9 0 -3135.12 -31.79 # 50 - 160oC, 1 - 1e3 atm, anhydrite dissolution, Blount and Dickson, 1973, Am. Mineral. 58, 323
+	log_k -4.25; -delta_h -22.4
+	-analytical_expression 5.725 -2.478e-2 -790.4 # 50 - 160oC, 1 - 1e3 atm, anhydrite dissolution, Blount and Dickson, 1973, Am. Mineral. 58, 323
 	-Vm 46.1 # 136.14 / 2.95
 Celestite
 	SrSO4 = Sr+2 + SO4-2
 	-log_k -6.63
 	-delta_h -4.037 kcal
-#	  -analytic	  -14805.9622	-2.4660924	 756968.533	 5436.3588	  -40553604.0
 	-analytic -7.14 6.11e-3 75 0 0 -1.79e-5 # Howell et al., 1992, JCED 37, 464
 	-Vm 46.4
 Barite
 	BaSO4 = Ba+2 + SO4-2
-	-log_k -9.97
-	-delta_h 6.35 kcal
-	-analytical_expression -282.43 -8.972e-2 5822 113.08 # Blount 1977; Templeton, 1960
+	-log_k -9.89; -delta_h 11.82
+	-analytical_expression -34.438 -3.316e-2 -1500 15.9485 # Blount 1977; Templeton, 1960
 	-Vm 52.9
 Arcanite
 	K2SO4 = SO4-2 + 2 K+
@@ -1027,12 +1028,14 @@ Arcanite
 	-Vm 65.5
 Mirabilite
 	Na2SO4:10H2O = SO4-2 + 2 Na+ + 10 H2O
-	-analytical_expression -301.9326 -0.16232 0 141.078 # ref. 3
+	-log_k -0.706; -delta_h 124
+	-analytical_expression -53.037 0.1242 4562 # ref. 3
 	Vm 216
 Thenardite
 	Na2SO4 = 2 Na+ + SO4-2
-	-analytical_expression 57.185 8.6024e-2 0 -30.8341 0 -7.6905e-5 # ref. 3
-	-Vm 52.9
+	-log_k 0.65; -delta_h -23.1
+	-analytical_expression 159.849 1.699e-2 -5000 -59.6073 # ref. 3
+	Vm 52.9
 Epsomite
 	MgSO4:7H2O = Mg+2 + SO4-2 + 7 H2O
 	log_k -1.74; -delta_h 10.57 kJ
@@ -1905,7 +1908,6 @@ Pyrolusite
 110 moles = 2e-3 * 6.98e-5 * (1 - sr_pl) * TIME
 200 SAVE moles * SOLN_VOL
   -end
-
 END
 # =============================================================================================
 #(a) means amorphous. (d) means disordered, or less crystalline.
@@ -1947,17 +1949,17 @@ END
 #   Av is the Debye-H<>ckel limiting slope (DH_AV in PHREEQC basic).
 #   a0 is the ion-size parameter in the extended Debye-H<>ckel equation:
 #	f(I^0.5) = I^0.5 / (1 + a0 * DH_B * I^0.5),
-#	a0 = -gamma	  x for cations, = 0 for anions.
-# For details, consult ref. 1.
+#	a0 = -gamma	  x for cations, = 0 for anions (or fitted).
+# For details, consult ref. 1 and subroutine calc_vm(tc, pa) in prep.cpp.
 # =============================================================================================
 # The viscosity is calculated with a (modified) Jones-Dole equation:
 #    viscos / viscos_0 = 1 + A * Sum(0.5 z_i m_i) + fan * Sum(B_i m_i + D_i m_i n_i)
 # Parameters are for calculating the B and D terms:
-#    -viscosity 9.35e-2 -8.31e-2 2.487e-2 4.49e-4 2.01e-2 1.570    0
-#    #	   b0	  b1	  b2	 d1	  d2	 d3	tan
+#    -viscosity 9.35e-2 -8.31e-2 2.487e-2 4.49e-4 2.01e-2 1.570 0
+#    #	        b0      b1	    b2	   d1	  d2	d3  tan
 #    z_i is absolute charge number, m_i is molality of i
 #    B_i = b0 + b1 exp(-b2 * tc)
-#    fan = (2 - tan V_i / V_Cl-), corrects for the volume of anions
+#    fan = (2 - tan V_i / V_Cl-), corrects for the volume of anions and neutral species
 #    D_i = d1 * exp(-d2 tc)
 #    n_i = (I^d3 * (1 + fI) + ((z_i^2 + z_i) / 2 <20> m_i)^d3) / (2 + fI), fI is an ionic strength term.
 # For details, consult ref. 4.

database/CMakeLists.txt

@@ -16,6 +16,7 @@ set(phreeqc_DATABASE
   phreeqc.dat
   pitzer.dat
   sit.dat
+  stimela.dat
   Tipping_Hurley.dat
   wateq4f.dat
 )

database/Kinec.v2.dat

@@ -1,4 +1,4 @@
-# KINEC.v2.dat - last edited April 18, 2024 by MA and EHO.
+# Kinec.v2.dat - last edited April 18, 2024 by MA and EHO.
 #
 # This database contains the parameters for calculating mineral dissolution rates for primary and secondary silicate minerals using the equations and parameters reported by Hermanska et al. (2022, 2023),
 # and dissolution rates for other non)-silicate mineral systems using the equations and parameters reported by Oelkers and Addassi (2024, in preparation).

database/Kinec_v3.dat

@@ -1,4 +1,4 @@
-# KINEC_v3.dat - last edited July 23, 2024 by MA and EHO.
+# Kinec_v3.dat - last edited July 23, 2024 by MA and EHO.
 #
 # This database contains the parameters for calculating mineral dissolution rates for primary and secondary silicate minerals using the equations and parameters reported by Hermanska et al. (2022, 2023),
 # and dissolution rates for other mineral systems using the equations and parameters reported by Oelkers and addassi (2024*).

database/Makefile.am

@@ -24,5 +24,6 @@ DATABASE=\
 	phreeqc.dat\
 	pitzer.dat\
 	sit.dat\
+	stimela.dat\
 	Tipping_Hurley.dat\
 	wateq4f.dat

database/OtherDatabases/CEMDATA18-31-03-2022-phaseVol.dat

@@ -24,7 +24,7 @@ SOLUTION_MASTER_SPECIES
 
 
 #
-#  elemen     species	alk   gfw_formula element_gfw atomic number
+# element     species	alk   gfw_formula element_gfw atomic number
 #
 
 

database/OtherDatabases/CEMDATA18.1-16-01-2019-phaseVol.dat

@@ -22,7 +22,7 @@ SOLUTION_MASTER_SPECIES
 
 
 #
-#  elemen     species	alk   gfw_formula element_gfw atomic number
+# element     species	alk   gfw_formula element_gfw atomic number
 #
 
 

database/OtherDatabases/CEMDATA18.dat

@@ -18,7 +18,7 @@ SOLUTION_MASTER_SPECIES
 
 
 #
-#  elemen     species	alk   gfw_formula element_gfw atomic number
+# element     species	alk   gfw_formula element_gfw atomic number
 #
 
 

database/OtherDatabases/PSINA_12_07_110615_DAV_s_win.dat

@@ -61,7 +61,7 @@ SOLUTION_MASTER_SPECIES
 #                                                                                                      
 #                                                                                                      
 #
-#  elemen     species        alk   gfw_formula element_gfw atomic Disposition           Source of data 
+# element     species        alk   gfw_formula element_gfw atomic Disposition           Source of data
 #                                                          number   PMATCHC    
 #
 H               H+          -1.0        H         1.008   #   1       Ele              NAGRA NTB 91-17   

database/Tipping_Hurley.dat

@@ -2,77 +2,76 @@
 # Created 17 May 2024 14:30:44
 # c:\3rdParty\lsp\lsp.exe  -f2 -k="asis" -ts "Tipping_Hurley.dat"
 
-#  $Id: wateq4f.dat 6895 2012-08-21 18:10:05Z dlpark $
 # Revised arsenic data from Archer and Nordstrom (2002)
 
 SOLUTION_MASTER_SPECIES
 
-Ag Ag+ 0 107.868 107.868
-Al Al+3 0 26.9815 26.9815
-Alkalinity CO3-2 1 50.05 50.05
-As H3AsO4 -1 74.9216 74.9216
-As(+3) H3AsO3 0 74.9216 74.9216
-As(+5) H3AsO4 -1 74.9216
-B H3BO3 0 10.81 10.81
-Ba Ba+2 0 137.34 137.34
-Br Br- 0 79.904 79.904
-C CO3-2 2 61.0173 12.0111
-C(+4) CO3-2 2 61.0173
-C(-4) CH4 0 16.042
-Ca Ca+2 0 40.08 40.08
-Cd Cd+2 0 112.4 112.4
-Cl Cl- 0 35.453 35.453
-Cs Cs+ 0 132.905 132.905
-Cu Cu+2 0 63.546 63.546
-Cu(+1) Cu+1 0 63.546
-Cu(+2) Cu+2 0 63.546
-E e- 1 0 0
-F F- 0 18.9984 18.9984
-Fe Fe+2 0 55.847 55.847
-Fe(+2) Fe+2 0 55.847
-Fe(+3) Fe+3 -2 55.847
-Fulvate Fulvate-2 0 650 650
-H H+ -1 1.008 1.008
-H(0) H2 0 1.008
-H(1) H+ -1 1.008
-Humate Humate-2 0 2000 2000
-I I- 0 126.9044 126.9044
-K K+ 0 39.102 39.102
-Li Li+ 0 6.939 6.939
-Mg Mg+2 0 24.312 24.312
-Mn Mn+2 0 54.938 54.938
-Mn(2) Mn+2 0 54.938
-Mn(3) Mn+3 0 54.938
-Mn(6) MnO4-2 0 54.938
-Mn(7) MnO4- 0 54.938
-N NO3- 0 14.0067 14.0067
-N(-3) NH4+ 0 14.0067
-N(0) N2 0 14.0067
-N(+3) NO2- 0 14.0067
-N(+5) NO3- 0 14.0067
-Na Na+ 0 22.9898 22.9898
-Ni Ni+2 0 58.71 58.71
-O H2O 0 16 16
-O(-2) H2O 0 18.016
-O(0) O2 0 16
-P PO4-3 2 30.9738 30.9738
-Pb Pb+2 0 207.19 207.19
-Rb Rb+ 0 85.47 85.47
-S SO4-2 0 96.0616 32.064
-S(-2) H2S 0 32.064
-S(6) SO4-2 0 96.0616
-Se SeO4-2 0 78.96 78.96
-Se(-2) HSe- 0 78.96
-Se(4) SeO3-2 0 78.96
-Se(6) SeO4-2 0 78.96
-Si H4SiO4 0 60.0843 28.0843
-Sr Sr+2 0 87.62 87.62
-Zn Zn+2 0 65.37 65.37
-U UO2+2 0 238.029 238.029
-U(3) U+3 0 238.029 238.029
-U(4) U+4 0 238.029 238.029
-U(5) UO2+ 0 238.029 238.029
-U(6) UO2+2 0 238.029 238.029
+Ag       Ag+            0.0     107.868         107.868
+Al       Al+3           0.0     26.9815         26.9815
+Alkalinity CO3-2        1.0     50.05           50.05
+As       H3AsO4        -1.0     74.9216         74.9216
+As(+3)   H3AsO3         0.0     74.9216         74.9216
+As(+5)   H3AsO4        -1.0     74.9216
+B        H3BO3          0.0     10.81           10.81
+Ba       Ba+2           0.0     137.34          137.34
+Br       Br-            0.0     79.904          79.904
+C        CO3-2          2.0     61.0173         12.0111
+C(+4)    CO3-2          2.0     61.0173
+C(-4)    CH4            0.0     16.042
+Ca       Ca+2           0.0     40.08           40.08
+Cd       Cd+2           0.0     112.4           112.4
+Cl       Cl-            0.0     35.453          35.453
+Cs       Cs+            0.0     132.905         132.905
+Cu       Cu+2           0.0     63.546          63.546
+Cu(+1)   Cu+1           0.0     63.546          
+Cu(+2)   Cu+2           0.0     63.546          
+E        e-             0.0     0.0             0.0
+F        F-             0.0     18.9984         18.9984
+Fe       Fe+2           0.0     55.847          55.847
+Fe(+2)   Fe+2           0.0     55.847
+Fe(+3)   Fe+3           -2.0    55.847
+Fulvate  Fulvate-2      0.0     650.            650.
+H        H+             -1.     1.008           1.008
+H(0)     H2             0.0     1.008
+H(1)     H+             -1.     1.008
+Humate   Humate-2       0.0     2000.           2000.
+I        I-             0.0     126.9044        126.9044
+K        K+             0.0     39.102          39.102
+Li       Li+            0.0     6.939           6.939
+Mg       Mg+2           0.0     24.312          24.312
+Mn       Mn+2           0.0     54.938          54.938
+Mn(2)    Mn+2           0.0     54.938
+Mn(3)    Mn+3           0.0     54.938
+Mn(6)    MnO4-2         0.0     54.938
+Mn(7)    MnO4-          0.0     54.938
+N        NO3-           0.0     14.0067         14.0067
+N(-3)    NH4+           0.0     14.0067
+N(0)     N2             0.0     14.0067
+N(+3)    NO2-           0.0     14.0067
+N(+5)    NO3-           0.0     14.0067
+Na       Na+            0.0     22.9898         22.9898
+Ni       Ni+2           0.0     58.71           58.71
+O        H2O            0.0     16.00           16.00
+O(-2)    H2O            0.0     18.016
+O(0)     O2             0.0     16.00
+P        PO4-3          2.0     30.9738         30.9738
+Pb       Pb+2           0.0     207.19          207.19
+Rb       Rb+            0.0     85.47           85.47
+S        SO4-2          0.0     96.0616         32.064
+S(-2)    H2S            0.0     32.064
+S(6)     SO4-2          0.0     96.0616
+Se       SeO4-2         0.0     78.96           78.96
+Se(-2)   HSe-           0.0     78.96
+Se(4)    SeO3-2         0.0     78.96
+Se(6)    SeO4-2         0.0     78.96
+Si       H4SiO4         0.0     60.0843         28.0843
+Sr       Sr+2           0.0     87.62           87.62
+Zn       Zn+2           0.0     65.37           65.37
+U        UO2+2          0.0     238.0290        238.0290
+U(3)     U+3            0.0     238.0290        238.0290
+U(4)     U+4            0.0     238.0290        238.0290
+U(5)     UO2+           0.0     238.0290        238.0290
+U(6)     UO2+2          0.0     238.0290        238.0290
 
 SOLUTION_SPECIES
 

database/iso.dat

@@ -3,38 +3,38 @@
 # c:\3rdParty\lsp\lsp.exe  -f2 -k="asis" -ts "iso.dat"
 
 SOLUTION_MASTER_SPECIES
-E e- 1 0 0
-H H3O+ -1 H 1.008
-H(0) H2 0 H
-H(1) H3O+ -1 H
-O H2O 0 O 16
-O(0) O2 0 O
-O(-2) H2O 0 O
-Ca Ca+2 0 Ca 40.08
-Mg Mg+2 0 Mg 24.312
-Na Na+ 0 Na 22.9898
-K K+ 0 K 39.102
-Fe Fe+2 0 Fe 55.847
-Fe(+2) Fe+2 0 Fe
-Fe(+3) Fe+3 -2 Fe
-Al Al+3 0 Al 26.9815
-Si H4SiO4 0 SiO2 28.0843
-Cl Cl- 0 Cl 35.453
-C CO2 0 HCO3 12.0111
-C(4) CO2 0 HCO3
-C(-4) CH4 0 CH4
-S SO4-2 0 S 31.972
-S(6) SO4-2 0 SO4
-S(-2) HS- 1 S
-N NO3- 0 N 14.0067
-N(+5) NO3- 0 N
-N(+3) NO2- 0 N
-N(0) N2 0 N
-N(-3) NH4+ 0 N
-P PO4-3 2 P 30.9738
-F F- 0 F 18.9984
-Br Br- 0 Br 79.904
-Alkalinity CO2 0 50.05 50.05
+E         e-        1         0         0
+H         H3O+      -1        H         1.008
+H(0)      H2        0         H
+H(1)      H3O+      -1        H
+O         H2O       0         O         16
+O(0)      O2        0         O
+O(-2)     H2O       0         O
+Ca        Ca+2      0         Ca        40.08
+Mg        Mg+2      0         Mg        24.312
+Na        Na+       0         Na        22.9898
+K         K+        0         K         39.102
+Fe        Fe+2      0         Fe        55.847
+Fe(+2)    Fe+2      0         Fe
+Fe(+3)    Fe+3      -2        Fe
+Al        Al+3      0         Al        26.9815
+Si        H4SiO4    0         SiO2      28.0843
+Cl        Cl-       0         Cl        35.453
+C         CO2       0         HCO3      12.0111
+C(4)      CO2       0         HCO3
+C(-4)     CH4       0         CH4
+S         SO4-2     0         S         31.972
+S(6)      SO4-2     0         SO4
+S(-2)     HS-       1         S
+N         NO3-      0         N         14.0067
+N(+5)     NO3-      0         N
+N(+3)     NO2-      0         N
+N(0)      N2        0         N
+N(-3)     NH4+      0         N
+P         PO4-3     2         P         30.9738
+F         F-        0         F         18.9984
+Br        Br-       0         Br        79.904
+Alkalinity CO2      0         50.05     50.05
 
 SOLUTION_SPECIES
 H3O+ = H3O+
@@ -639,11 +639,11 @@ CO2(g)
 
 O2(g)
      O2 = O2
-#	log_k	   -2.960
-#	delta_h -1.844  kcal
-	 # log K from llnl.dat  Dec 8, 2010
-	log_k -2.8983
-	-analytic -7.5001e+0 7.8981e-3 0e+0 0e+0 2.0027e+5
+#         log_k        -2.960
+#         delta_h -1.844  kcal
+           # log K from llnl.dat  Dec 8, 2010
+          log_k -2.8983
+          -analytic -7.5001e+0 7.8981e-3 0e+0 0e+0 2.0027e+5
 
 H2(g)
      H2 = H2
@@ -1122,8 +1122,8 @@ ISOTOPE_ALPHAS
 # N2(aq)
         Alpha_15N_N2(aq)/NO3- Log_alpha_15N_N2(aq)/NO3-
 # NH3(aq)
-	Alpha_D_NH3(aq)/H2O(l) Log_alpha_D_NH3(aq)/H2O(l)
-	Alpha_T_NH3(aq)/H2O(l) Log_alpha_T_NH3(aq)/H2O(l)
+          Alpha_D_NH3(aq)/H2O(l) Log_alpha_D_NH3(aq)/H2O(l)
+          Alpha_T_NH3(aq)/H2O(l) Log_alpha_T_NH3(aq)/H2O(l)
         Alpha_15N_NH3(aq)/NO3- Log_alpha_15N_NH3(aq)/NO3-
 # NH4+
         Alpha_D_NH4+/H2O(l) Log_alpha_D_NH4+/H2O(l)

database/minteq.dat

@@ -7,125 +7,125 @@ SOLUTION_MASTER_SPECIES
 #######################################################
 #               essential definitions
 #######################################################
-Alkalinity CO3-2 2 61.0173 61.0173
-E e- 1 0 0
-H H+ -1 1.008 1.008
-H(0) H2 0 1.008
-H(1) H+ -1 1.008
-O H2O 0 16 16
-O(-2) H2O 0 16 16
-O(0) O2 0 16 16
+Alkalinity CO3-2    2         61.0173   61.0173
+E         e-        1         0         0
+H         H+        -1        1.008     1.008
+H(0)      H2        0         1.008
+H(1)      H+        -1        1.008
+O         H2O       0         16        16
+O(-2)     H2O       0         16        16
+O(0)      O2        0         16        16
 #######################################################
-Ag Ag+ 0 107.868 107.868
-Al Al+3 0 26.9815 26.9815
-As H3AsO4 -1 74.9216 74.9216
-As(+3) H3AsO3 0 74.9216
-As(+5) H3AsO4 -1 74.9216
-B H3BO3 0 10.81 10.81
-Ba Ba+2 0 137.34 137.34
-Be Be+2 0 9.0122 9.0122
-Br Br- 0 79.904 79.904
-C CO3-2 2 61.0173 12.0111
-C(+4) CO3-2 2 61.0173
-#C(-4)          CH4		0.0     16.042
-Cyanide Cyanide- 0 26.018 26.018
-Cyanate Cyanate- 0 42.017 42.017
-#DOM            DOM-2.8		0       0               0
-#ClIG2          ClIG2		0       0               0
-Ca Ca+2 0 40.08 40.08
-Cd Cd+2 0 112.399 112.399
-Cl Cl- 0 35.453 35.453
-Cr CrO4-2 1 51.996 51.996
-Cr(2) Cr+2 0 51.996
-Cr(3) Cr(OH)2+ 1 51.996
-Cr(6) CrO4-2 1 51.996
-Cu Cu+2 0 63.546 63.546
-Cu(1) Cu+ 0 63.546
-Cu(2) Cu+2 0 63.546
-F F- 0 18.9984 18.9984
-Fe Fe+3 0 55.847 55.847
-Fe(+2) Fe+2 0 55.847
-Fe(+3) Fe+3 -2 55.847
-Hg Hg(OH)2 0 200.59 200.59
-Hg(2) Hg(OH)2 0 200.59
-Hg(1) Hg2+2 0 200.59
-Hg(0) Hg 0 200.59
-I I- 0 126.904 126.904
-K K+ 0 39.102 39.102
-Li Li+ 0 6.939 6.939
-Mg Mg+2 0 24.312 24.312
-Mn Mn+3 0 54.938 54.938
-Mn(2) Mn+2 0 54.938
-Mn(3) Mn+3 0 54.938
-Mn(6) MnO4-2 0 54.938
-Mn(7) MnO4- 0 54.938
-N NO3- 0 14.0067 14.0067
-N(-3) NH4+ 0 14.0067
-#N(0)           N2		0.0     14.0067
-N(+3) NO2- 0 14.0067
-N(+5) NO3- 0 14.0067
-Na Na+ 0 22.9898 22.9898
-Ni Ni+2 0 58.71 58.71
-P PO4-3 2 30.9738 30.9738
-Pb Pb+2 0 207.19 207.19
-Rb Rb+ 0 85.4699 85.4699
-S SO4-2 0 96.0616 32.064
-S(-2) HS- 1 32.064
-S(6) SO4-2 0 96.0616
-Sb Sb(OH)6- 0 Sb 121.75
-Sb(3) Sb(OH)3 0 Sb
-Sb(5) Sb(OH)6- 0 Sb
-Se SeO4-2 0 78.96 78.96
-Se(-2) HSe- 0 78.96
-Se(4) SeO3-2 0 78.96
-Se(6) SeO4-2 0 78.96
-Si H4SiO4 0 96.1155 28.0843
-Sr Sr+2 0 87.62 87.62
-Tl Tl(OH)3 0 204.37 204.37
-Tl(1) Tl+ 0 204.37
-Tl(3) Tl(OH)3 0 204.37
-U UO2+2 0 238.029 238.029
-U(3) U+3 0 238.029
-U(4) U+4 0 238.029
-U(5) UO2+ 0 238.029
-U(6) UO2+2 0 238.029
-V VO2+ -2 50.94 50.94
-V(2) V+2 0 50.94
-V(3) V+3 -3 50.94
-V(4) VO+2 0 50.94
-V(5) VO2+ -2 50.94
-Zn Zn+2 0 65.37 65.37
-Benzoate Benzoate- 0 121.12 121.12
-Para_acetate Para_acetate- 1 134.14 134.14
-Isophthalate Isophthalate-2 1 164.12 164.12
-Diethylamine Diethylamine 0 73 73
-Nbutylamine Nbutylamine 1 73 73
-Methylamine Methylamine 1 31.018 31.018
-Dimethylamine Dimethylamine 1 45.028 45.028
-Tributylphosphate Tributylphosphate 0 265.97 265.97
-Hexylamine Hexylamine 1 101 101
-Ethylenediamine Ethylenediamine 2 60.12 60.12
-Npropylamine Npropylamine 1 59.04 59.04
-Isopropylamine Isopropylamine 1 59.04 59.04
-Trimethylamine Trimethylamine 1 59.04 59.04
-Citrate Citrate-3 2 189.06 189.06
-Nta Nta-3 1 188.06 188.06
-Edta Edta-4 2 276 276
-Propanoate Propanoate- 1 73.032 73.032
-Butanoate Butanoate- 0 87.043 87.043
-Isobutyrate Isobutyrate- 1 87.043 87.043
-Two_methylpyridine Two_methylpyridine 1 94 94
-Three_methylpyridine Three_methylpyridine 1 94 94
-Four_methylpyridine Four_methylpyridine 1 94 94
-Formate Formate- 0 45.02 45.02
-Isovalerate Isovalerate- 1 101.13 101.13
-Valerate Valerate- 1 101.13 101.13
-Acetate Acetate- 1 59.05 59.05
-Tartrate Tartrate-2 0 148.09 148.09
-Glycine Glycine- 1 74.07 74.07
-Salicylate Salicylate-2 1 136.12 136.12
-Glutamate Glutamate-2 1 145.13 145.13
-Phthalate Phthalate-2 1 164.13 164.13
+Ag        Ag+       0         107.868   107.868
+Al        Al+3      0         26.9815   26.9815
+As        H3AsO4    -1        74.9216   74.9216
+As(+3)    H3AsO3    0         74.9216
+As(+5)    H3AsO4    -1        74.9216
+B         H3BO3     0         10.81     10.81
+Ba        Ba+2      0         137.34    137.34
+Be        Be+2      0         9.0122    9.0122
+Br        Br-       0         79.904    79.904
+C         CO3-2     2         61.0173   12.0111
+C(+4)     CO3-2     2         61.0173
+#C(-4)    CH4                 0.0       16.042
+Cyanide   Cyanide-  0         26.018    26.018
+Cyanate   Cyanate-  0         42.017    42.017
+#DOM      DOM-2.8             0         0         0
+#ClIG2    ClIG2               0         0         0
+Ca        Ca+2      0         40.08     40.08
+Cd        Cd+2      0         112.399   112.399
+Cl        Cl-       0         35.453    35.453
+Cr        CrO4-2    1         51.996    51.996
+Cr(2)     Cr+2      0         51.996
+Cr(3)     Cr(OH)2+  1         51.996
+Cr(6)     CrO4-2    1         51.996
+Cu        Cu+2      0         63.546    63.546
+Cu(1)     Cu+       0         63.546
+Cu(2)     Cu+2      0         63.546
+F         F-        0         18.9984   18.9984
+Fe        Fe+3      0         55.847    55.847
+Fe(+2)    Fe+2      0         55.847
+Fe(+3)    Fe+3      -2        55.847
+Hg        Hg(OH)2   0         200.59    200.59
+Hg(2)     Hg(OH)2   0         200.59
+Hg(1)     Hg2+2     0         200.59
+Hg(0)     Hg        0         200.59
+I         I-        0         126.904   126.904
+K         K+        0         39.102    39.102
+Li        Li+       0         6.939     6.939
+Mg        Mg+2      0         24.312    24.312
+Mn        Mn+3      0         54.938    54.938
+Mn(2)     Mn+2      0         54.938
+Mn(3)     Mn+3      0         54.938
+Mn(6)     MnO4-2    0         54.938
+Mn(7)     MnO4-     0         54.938
+N         NO3-      0         14.0067   14.0067
+N(-3)     NH4+      0         14.0067
+#N(0)     N2        0.0       14.0067
+N(+3)     NO2-      0         14.0067
+N(+5)     NO3-      0         14.0067
+Na        Na+       0         22.9898   22.9898
+Ni        Ni+2      0         58.71     58.71
+P         PO4-3     2         30.9738   30.9738
+Pb        Pb+2      0         207.19    207.19
+Rb        Rb+       0         85.4699   85.4699
+S         SO4-2     0         96.0616   32.064
+S(-2)     HS-       1         32.064
+S(6)      SO4-2     0         96.0616
+Sb        Sb(OH)6-  0         Sb        121.75
+Sb(3)     Sb(OH)3   0         Sb
+Sb(5)     Sb(OH)6-  0         Sb
+Se        SeO4-2    0         78.96     78.96
+Se(-2)    HSe-      0         78.96
+Se(4)     SeO3-2    0         78.96
+Se(6)     SeO4-2    0         78.96
+Si        H4SiO4    0         96.1155   28.0843
+Sr        Sr+2      0         87.62     87.62
+Tl        Tl(OH)3   0         204.37    204.37
+Tl(1)     Tl+       0         204.37
+Tl(3)     Tl(OH)3   0         204.37
+U         UO2+2     0         238.029   238.029
+U(3)      U+3       0         238.029
+U(4)      U+4       0         238.029
+U(5)      UO2+      0         238.029
+U(6)      UO2+2     0         238.029
+V         VO2+      -2        50.94     50.94
+V(2)      V+2       0         50.94
+V(3)      V+3       -3        50.94
+V(4)      VO+2      0         50.94
+V(5)      VO2+      -2        50.94
+Zn        Zn+2      0         65.37     65.37
+Benzoate  Benzoate- 0         121.12    121.12
+Para_acetate        Para_acetate-       1         134.14    134.14
+Isophthalate        Isophthalate-2      1         164.12    164.12
+Diethylamine        Diethylamine        0         73        73
+Nbutylamine         Nbutylamine         1         73        73
+Methylamine         Methylamine         1         31.018    31.018
+Dimethylamine       Dimethylamine       1         45.028    45.028
+Tributylphosphate   Tributylphosphate   0         265.97    265.97
+Hexylamine          Hexylamine          1         101       101
+Ethylenediamine     Ethylenediamine     2         60.12     60.12
+Npropylamine        Npropylamine        1         59.04     59.04
+Isopropylamine      Isopropylamine      1         59.04     59.04
+Trimethylamine      Trimethylamine      1         59.04     59.04
+Citrate   Citrate-3 2         189.06    189.06
+Nta       Nta-3     1         188.06    188.06
+Edta      Edta-4    2         276       276
+Propanoate          Propanoate-         1         73.032    73.032
+Butanoate Butanoate-          0         87.043    87.043
+Isobutyrate         Isobutyrate-        1         87.043    87.043
+Two_methylpyridine  Two_methylpyridine  1         94        94
+Three_methylpyridine          Three_methylpyridine          1         94        94
+Four_methylpyridine Four_methylpyridine 1         94        94
+Formate   Formate-  0         45.02     45.02
+Isovalerate         Isovalerate-        1         101.13    101.13
+Valerate  Valerate- 1         101.13    101.13
+Acetate   Acetate-  1         59.05     59.05
+Tartrate  Tartrate-2          0         148.09    148.09
+Glycine   Glycine-  1         74.07     74.07
+Salicylate          Salicylate-2        1         136.12    136.12
+Glutamate Glutamate-2         1         145.13    145.13
+Phthalate Phthalate-2         1         164.13    164.13
 SOLUTION_SPECIES
 #######################################################
 #             essential definitions
@@ -3691,12 +3691,12 @@ Greigite
         delta_h -0 kcal
 Gypsum
         CaSO4:2H2O = Ca+2 + SO4-2 + 2 H2O
-#	 	 	   # Log K gives too small a solubility < 10 mmol/L
-#			   # D. Parkhurst 7/13/09, Replacing log K with minteq version 4 log K
+#                                # Log K gives too small a solubility < 10 mmol/L
+#                                # D. Parkhurst 7/13/09, Replacing log K with minteq version 4 log K
 #        log_k   -4.848
 #        delta_h 0.261   kcal
-	log_k -4.61
-	delta_h 1 kJ
+          log_k -4.61
+          delta_h 1 kJ
 
 Halite
         NaCl = Na+ + Cl-

database/phreeqc.dat

@@ -1,8 +1,8 @@
-# File 1 = C:\GitPrograms\phreeqc3-1\database\Amm.dat, 22/05/2024  19:38, 1948 lines, 55817 bytes, md5=78b3659799b73ddca128328b6ee7533b
+# File 1 = C:\GitPrograms\phreeqc3-1\database\phreeqc.dat, 22/05/2024  19:38, 1948 lines, 55817 bytes, md5=78b3659799b73ddca128328b6ee7533b
 # Created 22 May 2024 19:55:37
-# C:\3rdParty\lsp\lsp.exe -f2 -k=asis -ts Amm.dat
+# C:\3rdParty\lsp\lsp.exe -f2 -k=asis -ts phreeqc.dat
 
-# PHREEQC.DAT for calculating temperature and pressure dependence of reactions, and the specific conductance and viscosity of the solution. Based on:
+# phreeqc.dat for calculating temperature and pressure dependence of reactions, and the specific conductance and viscosity of the solution. Based on:
 #   diffusion coefficients and molal volumina of aqueous species, solubility and volume of minerals, and critical temperatures and pressures of gases in Peng-Robinson's EOS.
 # Details are given at the end of this file.
 
@@ -70,7 +70,7 @@ H+ = H+
 	-dw 9.31e-9 838 6.96 -2.285 0.206 24.01 0
 #	   Dw(25 C) dw_T a    a2    visc  a3    a_v_dif
 # Dw(TK) = 9.31e-9 * exp(838 / TK - 838 / 298.15) * viscos_0_25 / viscos_0_tc
-# a = DH ion size, a2 = exponent, visc = viscosity exponent, a3(H+) = 24.01 = new dw calculation from A.D. 2024, a_v_dif = exponent in (viscos_0_tc / viscos)^a_v_dif for tracer diffusion.
+# a = DH ion size (= 3.5 - 25), a2 = exponent (= 0 2.5), visc = viscosity exponent (= 0 2.5), a3 = switch [a3(H+) = 24.01 = new dw calculation from A.D. 2024], a_v_dif = exponent in (viscos_0_tc / viscos)^a_v_dif for tracer diffusion.
 
 # For SC, Dw(TK) *=  (viscos_0_tc / viscos)^visc (visc = 0.206 for H+)
 # a3 > 5 or a3 = 0 or not defined ? ka = DH_B * a * (1 + (vm - v0))^a2 * mu^0.5, in Onsager-Falkenhagen eqn. (For H+, the reference ion, vm = v0 = 0, a *= (1 + mu)^a2.)
@@ -80,7 +80,7 @@ H+ = H+
 # If a_v_dif <> 0, Dw(TK) *= (viscos_0_tc / viscos)^a_v_dif in TRANSPORT.
 e- = e-
 H2O = H2O
-	-dw 2.299e-9 -254
+	-dw 2.299e-9 -249 # Holz et al., Phys. Chem. Chem. Phys., 2000, 2, 4740. 
 # H2O + 0.01e- = H2O-0.01; -log_k -9 # aids convergence
 Li+ = Li+
 	-gamma 6 0 # The apparent volume parameters are defined in ref. 1 & 2
@@ -111,9 +111,9 @@ Ca+2 = Ca+2
 	-dw 0.792e-9 34 5.411 0 1.046
 Sr+2 = Sr+2
 	-gamma 5.26 0.121
-	-Vm -1.57e-2 -10.15 10.18 -2.36 0.86 5.26 0.859 -27 -4.1e-3 1.97
-	-viscosity 0.472 -0.252 5.51e-3 3.67e-3 0 1.876
-	-dw 0.794e-9 149 0.805 1.961 1e-9 0.7876
+	-Vm -5.6e-2 -10.15 9.90 -2.36 0.807 5.26 2.72 -82.7 -1.37e-2 0.956
+	-viscosity 0.493 -0.255 2.3e-3 4.2e-3 -3.8e-3 1.762
+	-dw 0.794e-9 18 0.681 2.069 0.965 0.271
 Ba+2 = Ba+2
 	-gamma 5 0
 	-gamma 4 0.153 # Barite solubility
@@ -147,19 +147,19 @@ CO3-2 = CO3-2
 	-viscosity -0.5 0.6521 5.44e-3 1.06e-3 -2.18e-2 1.208 -2.147
 	-dw 0.955e-9 -103 2.246 7.13e-2 0.3686
 SO4-2 = SO4-2
-	-gamma 5 -0.04
-	-Vm -7.77 43.17 176 -51.45 3.794 0 42.99 -541 -0.145 0.45 # with analytical_expressions for log K of NaSO4-, KSO4- & MgSO4, 0 - 200 oC
-	-viscosity -0.3 0.501 2.57e-3 0.195 3.14e-2 2.015 0.605
-	-dw 1.07e-9 -114 17 6.02e-2 4.94e-2
+	-gamma 5.0 -0.04
+	-Vm 5.36 10.69 33.566 -15.03 4.2582 25 0.341 153.8 1.089e-2 0.9224 # with Na2SO4 & better calculation of sulfates' solubilities in NaCl
+	-viscosity -0.5 0.521 4.2e-4 9.78e-3 1.24e-2 2.5 -4.94e-2
+	-dw 1.07e-9 -77.4 10.14 0.5 0.5549
 NO3- = NO3-
 	-gamma 3 0
 	-Vm 6.32 6.78 0 -3.06 0.346 0 0.93 0 -0.012 1
 	-viscosity 8.37e-2 -0.458 1.54e-2 0.34 1.79e-2 5.02e-2 0.7381
 	-dw 1.9e-9 104 1.11
-# AmmH+ = AmmH+
+#AmmH+ = AmmH+
 #	-gamma 2.5 0
 #	-Vm 5.35 2.345 3.72 -2.88 1.55 2.5 -4.54 217 2.344e-2 0.569
-#	-viscosity 9.9e-2 -0.159 1.36e-2 6.51e-3 3.21e-2 0.972
+#	-viscosity 6.94e-2 -0.141 2.04e-2 9.4e-3 3.73e-2 0.898
 #	-dw 1.98e-9 203 1.47 2.644 6.81e-2
 H3BO3 = H3BO3
 	-Vm 7.0643 8.8547 3.5844 -3.1451 -0.2 # supcrt
@@ -174,7 +174,7 @@ F- = F-
 	-viscosity 0 2.85e-2 1.35e-2 6.11e-2 4.38e-3 1.384 0.586
 	-dw 1.46e-9 -36 4.352
 Br- = Br-
-	-gamma 3 0
+	-gamma 3 0.045
 	-Vm 6.72 2.85 4.21 -3.14 1.38 0 -9.56e-2 7.08 -1.56e-3 1
 	-viscosity -6.98e-2 -0.141 1.78e-2 0.159 7.76e-3 6.25e-2 0.859
 	-dw 2.09e-9 208 3.5 0 0.5737
@@ -203,21 +203,21 @@ Mtg = Mtg # CH4
 	-Vm 9.01 -1.11 0 -1.85 -1.5 # Hnedkovsky et al., 1996, JCT 28, 125
 	-dw 1.85e-9
 Ntg = Ntg # N2
-	-Vm 7 # Pray et al., 1952, IEC 44 1146
+	-Vm 7 # Pray et al., 1952, IEC 44, 1146
 	-dw 1.96e-9 -90 # Cadogan et al. 2014, JCED 59, 519
 H2Sg = H2Sg # H2S
 	-Vm 1.39 28.3 0 -7.22 -0.59 # Hnedkovsky et al., 1996, JCT 28, 125
 	-dw 2.1e-9
 # aqueous species
 H2O = OH- + H+
-	-analytic 293.29227 0.1360833 -10576.913 -123.73158 0 -6.996455e-5
 	-gamma 3.5 0
+	-analytic 293.29227 0.1360833 -10576.913 -123.73158 0 -6.996455e-5
 	-Vm -9.66 28.5 80 -22.9 1.89 0 1.09 0 0 1
 	-viscosity -2.26e-2 0.106 2.184e-2  -3.2e-3 0 0.4082 -1.634 # < 5 M Li,Na,KOH
 	-dw 5.27e-9 478 0.8695
 2 H2O = O2 + 4 H+ + 4 e-
-	-log_k -86.08
-	-delta_h 134.79 kcal
+	-log_k -86.06; -delta_h 138.43 kcal
+	-analytic -1e3 -0.322 -5897.7 416.82 0 -1.88e-5
 	-Vm 5.7889 6.3536 3.2528 -3.0417 -0.3943 # supcrt
 	-dw 2.35e-9
 2 H+ + 2 e- = H2
@@ -304,11 +304,11 @@ NO3- + 2 H+ + 2 e- = NO2- + H2O
 	-Vm 7 # Pray et al., 1952, IEC 44 1146
 	-dw 1.96e-9 -90 # Cadogan et al. 2014, JCED 59, 519
 NO3- + 10 H+ + 8 e- = NH4+ + 3 H2O
-	-log_k 119.077
-	-delta_h -187.055 kcal
+	  -log_k  119.077
+	  -delta_h -187.055	  kcal
 	-gamma 2.5 0
 	-Vm 5.35 2.345 3.72 -2.88 1.55 2.5 -4.54 217 2.344e-2 0.569
-	-viscosity 9.9e-2 -0.159 1.36e-2 6.51e-3 3.21e-2 0.972
+	-viscosity 6.94e-2 -0.141 2.04e-2 9.4e-3 3.73e-2 0.898
 	-dw 1.98e-9 203 1.47 2.644 6.81e-2
 #AmmH+ = Amm + H+
 NH4+ = NH3 + H+
@@ -316,15 +316,15 @@ NH4+ = NH3 + H+
 	-delta_h 12.48 kcal
 	-analytic 0.6322 -0.001225 -2835.76
 	-Vm 6.69 2.8 3.58 -2.88 1.43
-	-viscosity 0.08 0 0 7.82e-3 -0.134 -0.986
+	-viscosity 0 -2.24e-2 0.101 8.66e-3 2.86e-2 -0.143 -0.769
 	-dw 2.28e-9
 #AmmH+ + SO4-2 = AmmHSO4-
 NH4+ + SO4-2 = NH4SO4-
-	-gamma 2.08 -0.0416
-	-log_k	1.211; -delta_h 8.56 kJ
-	-Vm -8.78 0 -36.09 0 -8.60 0 87.62 0 -0.3123 0.1172
-	-viscosity 0 0.116 -8.6e-3 0.159 -9.3e-3 0.522 0.627
-	-dw 0.9e-9 100 2.1 2 0
+	-gamma 3.64 -4.75e-2
+	-log_k 1.276; -delta_h -3.24 kcal
+	-Vm 6.64 8.5 -5.84 -3.1 2 0 19.24 0 -7.84e-2 0.289
+	-viscosity 0.267 -0.207 9.75e-2 6.18e-2 1.99e-2 1.166 0.61
+	-dw 1.56e-9 498 25 0.5 0.684
 H3BO3 = H2BO3- + H+
 	-log_k -9.24
 	-delta_h 3.224 kcal
@@ -376,13 +376,14 @@ Ca+2 + CO3-2 + H+ = CaHCO3+
 	-log_k 10.91; -delta_h 4.38 kcal
 	-analytic -6.009 3.377e-2 2044
 	-gamma 6 0
-	-Vm 30.19 .01 5.75 -2.78 .308 5.4
+	-Vm 3.19 .01 5.75 -2.78 .308 5.4
 	-dw 5.06e-10
 Ca+2 + SO4-2 = CaSO4
-	-log_k 2.25
-	-delta_h 1.325 kcal
-	-dw 4.71e-10
-	-Vm 2.791 -.9666 6.13 -2.739 -.001 # supcrt
+	-gamma 0 4.45e-2
+	-log_k 2.14; -delta_h 24.4
+	-analytical_expression 1.478 8.29e-3 -538.2
+	-vm 2.7 2 2 -3.7
+	-dw 4.71e-9
 Ca+2 + HSO4- = CaHSO4+
 	-log_k 1.08
 Ca+2 + PO4-3 = CaPO4-
@@ -419,19 +420,19 @@ Mg+2 + H+ + CO3-2 = MgHCO3+
 	-Vm 2.7171 -1.1469 6.2008 -2.7316 .5985 4 # supcrt
 	-dw 4.78e-10
 Mg+2 + SO4-2 = MgSO4
-	-gamma 0 0.2
-	-log_k 2.42; -delta_h 19 kJ
-	-analytical_expression 0 9.64e-3 -136 # mean salt gamma from Pitzer.dat and epsomite/hexahydrite/kieserite solubilities, 0 - 200 oC
-	-Vm 8.65 -10.21 29.58 -18.6 1.061
-	-viscosity 0.318 -5.4e-4 -3.42e-2 0.708 3.7e-3 0.696
+	-gamma 0 0.20
+	-log_k 2.42; -delta_h 19.0
+	-analytical_expression 0 9.64e-3 -136 # epsomite/hexahydrite/kieserite solubilities, 0 - 200 oC
+	-Vm 11.92 -27.758 29.752 -10.302 -0.1
+	-viscosity -0.799 1 2.2e-4 8.53e-2 -4.6e-3 1.35 -0.796
 	-dw 4.45e-10
 SO4-2 + MgSO4 = Mg(SO4)2-2
 	-gamma 7 0.047
-	-log_k 0.52; -delta_h -13.6 kJ
-	-analytical_expression 0 -1.51e-3 0 0 8.604e4 # mean salt gamma from Pitzer.dat and epsomite/hexahydrite/kieserite solubilities, 0 - 200 oC
-	-Vm -8.14 -62.2 -15.96 3.29 -3.01 0 150 0 0.153 3.79e-2
-	-viscosity -0.169 5e-4 -5.69e-2 0.11 2.03e-3 2.027 -1e-3
-	-dw 0.845e-9 -200 8 0 0.965
+	-log_k 0.52; -delta_h -13.6
+	-analytical_expression 0 -1.51e-3 0 0 8.604e4 # epsomite/hexahydrite/kieserite solubilities, 0 - 200 oC
+	-Vm 4.248 9.83 -7 -2.672 2 3.5 5 100 0.3359 9.518e-2
+	-viscosity 0.324 6.84e-2 -2.09e-2 0.104 6.19e-3 1.983 1e-3
+	-dw 1.11e-9 -500 3.5 0.5 0.731
 Mg+2 + PO4-3 = MgPO4-
 	-log_k 6.589
 	-delta_h 3.1 kcal
@@ -457,12 +458,19 @@ Na+ + HCO3- = NaHCO3
 	-viscosity -4e-2 -2.717 1.67e-5
 	-dw 6.73e-10
 Na+ + SO4-2 = NaSO4-
-	-gamma 5.5 0
-	-log_k 0.6; -delta_h -14.4 kJ
-	-analytical_expression 255.903 0.10057 0 -1.11138e2 -8.5983e5 # mirabilite/thenardite solubilities, 0 - 200 oC
-	-Vm 1.99 -10.78 21.88 -12.7 1.601 5 32.38 501 1.565e-2 0.2325
-	-viscosity 0.2 -5.93e-2 -4e-4 8.46e-3 1.78e-3 2.308 -0.208
-	-dw 1.13e-9 -23 8.5 0.392 0.521
+	-gamma 3.5 0.1072
+	-log_k 0.94; -delta_h 8.23
+	-analytical_expression -0.304 4.51e-3 -28.9 # mirabilite/thenardite solubilities, 0 - 200 oC
+	-Vm 8.523 -4.685 -8.61 0.106 2.7 25 3.634 13.4 3.738e-2 0.5476
+	-viscosity -1 0.33 0.128 1.143 7.7e-4 1.9e-2 -0.387
+	-dw 4e-10 -200 3.5 0.5 0.5
+2 Na+ + SO4-2 = Na2SO4
+	-gamma 0 8.85e-2
+	-log_k -2.37; -delta_h 82
+	-analytical_expression 15.432 -5.75e-3 -4796 # sulfates solubilities in NaCl
+	-Vm 9.405 -15.5 25 8.4 0.25
+	-viscosity -0.5 0.485 -1e-3 0.147 0 0.947 -0.175
+	-dw 0.8e-9
 Na+ + HPO4-2 = NaHPO4-
 	-log_k 0.29
 	-gamma 5.4 0
@@ -477,11 +485,11 @@ K+ + HCO3- = KHCO3
 	-viscosity 0.7 -1.289 9e-2
 K+ + SO4-2 = KSO4-
 	-gamma 5.4 0.19
-	-log_k 0.6; -delta_h -10.4 kJ
+	-log_k 1.18; -delta_h 3
 	-analytical_expression -3.0246 9.986e-3 0 0 1.093e5 # arcanite solubility, 0 - 200 oC
-	-Vm 13.48 -18.03 61.74 -19.6 2.046 5.4 -17.32 0 0.1522 1.919
-	-viscosity -1 1.06 1e-4 -0.464 3.78e-2 0.539 -0.69
-	-dw 0.9e-9 63 8.48 0 1.8
+	-Vm 3.443 5.04 13 -3.324 2.447 0 20 0 7.77e-3 0.3497
+	-viscosity 0.107 0.19 2.23e-2 -0.148 -4.91e-2 0.537 0.195
+	-dw 1.22e-9 100 25 0.5 2.5
 K+ + HPO4-2 = KHPO4-
 	-log_k 0.29
 	-gamma 5.4 0
@@ -501,9 +509,8 @@ Fe+2 + CO3-2 = FeCO3
 Fe+2 + HCO3- = FeHCO3+
 	-log_k 2
 Fe+2 + SO4-2 = FeSO4
-	-log_k 2.25
-	-delta_h 3.23 kcal
-	-Vm -13 0 123
+	-log_k 2.25; -delta_h 3.23 kcal
+	-Vm 5.8 6.5 3.7 -3 -0.09
 Fe+2 + HSO4- = FeHSO4+
 	-log_k 1.08
 Fe+2 + 2 HS- = Fe(HS)2
@@ -605,9 +612,9 @@ Mn+2 + HCO3- = MnHCO3+
 	-log_k 1.95
 	-gamma 5 0
 Mn+2 + SO4-2 = MnSO4
-	-log_k 2.25
-	-delta_h 3.37 kcal
-	-Vm -1.31 -1.83 62.3 -2.7
+	-gamma 0 -0.098
+	-log_k 1.408; -delta_h 21.55
+	-Vm 1.88 6.5 10 -3 0.1
 Mn+2 + 2 NO3- = Mn(NO3)2
 	-log_k 0.6
 	-delta_h -0.396 kcal
@@ -700,7 +707,8 @@ Ba+2 + HCO3- = BaHCO3+
 	-delta_h 5.56 kcal
 	-analytic -3.0938 0.013669
 Ba+2 + SO4-2 = BaSO4
-	-log_k 2.7
+	-log_k 3.457; -delta_h 26.15
+	-vm -6.25 24.66 -4.38 10.97 0.5
 Sr+2 + H2O = SrOH+ + H+
 	-log_k -13.29
 	-gamma 5 0
@@ -819,12 +827,13 @@ Zn+2 + 2 CO3-2 = Zn(CO3)2-2
 Zn+2 + HCO3- = ZnHCO3+
 	-log_k 2.1
 Zn+2 + SO4-2 = ZnSO4
-	-log_k 2.37
-	-delta_h 1.36 kcal
-	-Vm 2.51 0 18.8
+	-gamma 0 0.1
+	-log_k 2.26; -delta_h 16.15
+	-Vm 0.409 6.5 2 -3 0
 Zn+2 + 2 SO4-2 = Zn(SO4)2-2
-	-log_k 3.28
-	-Vm 10.9 0 -98.7 0 0 0 24 0 -0.236 1
+	-gamma 0.59 0.1
+	-log_k 1.15; -delta_h 17.52
+	-Vm 9.21 10.6 9 -3.2 3.8 25 0 100 -1e-3 0.256
 Zn+2 + Br- = ZnBr+
 	-log_k -0.58
 Zn+2 + 2 Br- = ZnBr2
@@ -870,12 +879,13 @@ Cd+2 + 2 CO3-2 = Cd(CO3)2-2
 Cd+2 + HCO3- = CdHCO3+
 	-log_k 1.5
 Cd+2 + SO4-2 = CdSO4
-	-log_k 2.46
-	-delta_h 1.08 kcal
-	-Vm 10.4 0 57.9
+	-gamma 0 0.1
+	-log_k 1.016; -delta_h 6.84
+	-Vm 2.11 6.5 10 -3 0.1
 Cd+2 + 2 SO4-2 = Cd(SO4)2-2
-	-log_k 3.5
-	-Vm -6.29 0 -93 0 9.5 7 0 0 0 1
+	-gamma 5.201 -0.1
+	-log_k 2.688; -delta_h 0.19
+	-Vm 9.14 10.6 -3.06 -3.2 3.8 7.44 1.27 0.32 -1e-3 2.5
 Cd+2 + Br- = CdBr+
 	-log_k 2.17
 	-delta_h -0.81 kcal
@@ -995,29 +1005,24 @@ Witherite
 	-Vm 46
 Gypsum
 	CaSO4:2H2O = Ca+2 + SO4-2 + 2 H2O
-	-log_k -4.58
-	-delta_h -0.109 kcal
-	-analytic 68.2401 0 -3221.51 -25.0627
-	-analytical_expression 93.7 5.99E-3 -4e3 -35.019 # better fits the appendix data of Appelo, 2015, AG 55, 62
-	-Vm 73.9 # 172.18 / 2.33 (Vm H2O = 13.9 cm3/mol)
+	-log_k -4.55; -delta_h -6.70
+	-analytical_expression 72.244 -1.474e-2 -4040 -23.7823 # fits the appendix data of Appelo, 2015, AG 55, 62
+	-Vm 73.9
 Anhydrite
 	CaSO4 = Ca+2 + SO4-2
-	-log_k -4.36
-	-delta_h -1.71 kcal
-	-analytic 84.9 0 -3135.12 -31.79 # 50 - 160oC, 1 - 1e3 atm, anhydrite dissolution, Blount and Dickson, 1973, Am. Mineral. 58, 323
+	log_k -4.25; -delta_h -22.4
+	-analytical_expression 5.725 -2.478e-2 -790.4 # 50 - 160oC, 1 - 1e3 atm, anhydrite dissolution, Blount and Dickson, 1973, Am. Mineral. 58, 323
 	-Vm 46.1 # 136.14 / 2.95
 Celestite
 	SrSO4 = Sr+2 + SO4-2
 	-log_k -6.63
 	-delta_h -4.037 kcal
-#	  -analytic	  -14805.9622	-2.4660924	 756968.533	 5436.3588	  -40553604.0
 	-analytic -7.14 6.11e-3 75 0 0 -1.79e-5 # Howell et al., 1992, JCED 37, 464
 	-Vm 46.4
 Barite
 	BaSO4 = Ba+2 + SO4-2
-	-log_k -9.97
-	-delta_h 6.35 kcal
-	-analytical_expression -282.43 -8.972e-2 5822 113.08 # Blount 1977; Templeton, 1960
+	-log_k -9.89; -delta_h 11.82
+	-analytical_expression -34.438 -3.316e-2 -1500 15.9485 # Blount 1977; Templeton, 1960
 	-Vm 52.9
 Arcanite
 	K2SO4 = SO4-2 + 2 K+
@@ -1027,12 +1032,14 @@ Arcanite
 	-Vm 65.5
 Mirabilite
 	Na2SO4:10H2O = SO4-2 + 2 Na+ + 10 H2O
-	-analytical_expression -301.9326 -0.16232 0 141.078 # ref. 3
+	-log_k -0.706; -delta_h 124
+	-analytical_expression -53.037 0.1242 4562 # ref. 3
 	Vm 216
 Thenardite
 	Na2SO4 = 2 Na+ + SO4-2
-	-analytical_expression 57.185 8.6024e-2 0 -30.8341 0 -7.6905e-5 # ref. 3
-	-Vm 52.9
+	-log_k 0.65; -delta_h -23.1
+	-analytical_expression 159.849 1.699e-2 -5000 -59.6073 # ref. 3
+	Vm 52.9
 Epsomite
 	MgSO4:7H2O = Mg+2 + SO4-2 + 7 H2O
 	log_k -1.74; -delta_h 10.57 kJ
@@ -1905,7 +1912,6 @@ Pyrolusite
 110 moles = 2e-3 * 6.98e-5 * (1 - sr_pl) * TIME
 200 SAVE moles * SOLN_VOL
   -end
-
 END
 # =============================================================================================
 #(a) means amorphous. (d) means disordered, or less crystalline.
@@ -1947,17 +1953,17 @@ END
 #   Av is the Debye-H<>ckel limiting slope (DH_AV in PHREEQC basic).
 #   a0 is the ion-size parameter in the extended Debye-H<>ckel equation:
 #	f(I^0.5) = I^0.5 / (1 + a0 * DH_B * I^0.5),
-#	a0 = -gamma	  x for cations, = 0 for anions.
-# For details, consult ref. 1.
+#	a0 = -gamma	  x for cations, = 0 for anions (or fitted).
+# For details, consult ref. 1 and subroutine calc_vm(tc, pa) in prep.cpp.
 # =============================================================================================
 # The viscosity is calculated with a (modified) Jones-Dole equation:
 #    viscos / viscos_0 = 1 + A * Sum(0.5 z_i m_i) + fan * Sum(B_i m_i + D_i m_i n_i)
 # Parameters are for calculating the B and D terms:
-#    -viscosity 9.35e-2 -8.31e-2 2.487e-2 4.49e-4 2.01e-2 1.570    0
-#    #	   b0	  b1	  b2	 d1	  d2	 d3	tan
+#    -viscosity 9.35e-2 -8.31e-2 2.487e-2 4.49e-4 2.01e-2 1.570 0
+#    #	        b0      b1	    b2	   d1	  d2	d3  tan
 #    z_i is absolute charge number, m_i is molality of i
 #    B_i = b0 + b1 exp(-b2 * tc)
-#    fan = (2 - tan V_i / V_Cl-), corrects for the volume of anions
+#    fan = (2 - tan V_i / V_Cl-), corrects for the volume of anions and neutral species
 #    D_i = d1 * exp(-d2 tc)
 #    n_i = (I^d3 * (1 + fI) + ((z_i^2 + z_i) / 2 <20> m_i)^d3) / (2 + fI), fI is an ionic strength term.
 # For details, consult ref. 4.

database/phreeqc_rates.dat

@@ -1,10 +1,10 @@
-# PHREEQC.DAT for calculating temperature and pressure dependence of reactions, and the specific conductance and viscosity of the solution. Augmented with kinetic rates for minerals from compilations. Based on:
+# phreeqc_rates.dat for calculating temperature and pressure dependence of reactions, and the specific conductance and viscosity of the solution. Augmented with kinetic rates for minerals from compilations. Based on:
 #   diffusion coefficients and molal volumina of aqueous species, solubility and volume of minerals, and critical temperatures and pressures of gases in Peng-Robinson's EOS.
 # Details are given at the end of this file.
 
 SOLUTION_MASTER_SPECIES
 #
-#element  species	 alk	gfw_formula	element_gfw
+#element    species alk gfw_formula     element_gfw
 #
 H           H+      -1  H               1.008
 H(0)        H2      0   H
@@ -40,7 +40,7 @@ N(+5)       NO3-    0   N
 N(+3)       NO2-    0   N
 N(0)        N2      0   N
 N(-3)       NH4+    0   N               14.0067
-#Amm         AmmH+   0   AmmH           17.031
+#Amm        AmmH+   0   AmmH            17.031
 B           H3BO3   0   B               10.81
 P           PO4-3   2   P               30.9738
 F           F-      0   F               18.9984
@@ -66,7 +66,7 @@ H+ = H+
 	-dw 9.31e-9 838 6.96 -2.285 0.206 24.01 0
 #	   Dw(25 C) dw_T a    a2    visc  a3    a_v_dif
 # Dw(TK) = 9.31e-9 * exp(838 / TK - 838 / 298.15) * viscos_0_25 / viscos_0_tc
-# a = DH ion size, a2 = exponent, visc = viscosity exponent, a3(H+) = 24.01 = new dw calculation from A.D. 2024, a_v_dif = exponent in (viscos_0_tc / viscos)^a_v_dif for tracer diffusion.
+# a = DH ion size (= 3.5 - 25), a2 = exponent (= 0 2.5), visc = viscosity exponent (= 0 2.5), a3 = switch [a3(H+) = 24.01 = new dw calculation from A.D. 2024], a_v_dif = exponent in (viscos_0_tc / viscos)^a_v_dif for tracer diffusion.
 
 # For SC, Dw(TK) *=  (viscos_0_tc / viscos)^visc (visc = 0.206 for H+)
 # a3 > 5 or a3 = 0 or not defined ? ka = DH_B * a * (1 + (vm - v0))^a2 * mu^0.5, in Onsager-Falkenhagen eqn. (For H+, the reference ion, vm = v0 = 0, a *= (1 + mu)^a2.)
@@ -76,7 +76,7 @@ H+ = H+
 # If a_v_dif <> 0, Dw(TK) *= (viscos_0_tc / viscos)^a_v_dif in TRANSPORT.
 e- = e-
 H2O = H2O
-	-dw 2.299e-9 -254
+	-dw 2.299e-9 -249 # Holz et al., Phys. Chem. Chem. Phys., 2000, 2, 4740. 
 # H2O + 0.01e- = H2O-0.01; -log_k -9 # aids convergence
 Li+ = Li+
 	-gamma 6 0 # The apparent volume parameters are defined in ref. 1 & 2
@@ -107,9 +107,9 @@ Ca+2 = Ca+2
 	-dw 0.792e-9 34 5.411 0 1.046
 Sr+2 = Sr+2
 	-gamma 5.26 0.121
-	-Vm -1.57e-2 -10.15 10.18 -2.36 0.86 5.26 0.859 -27 -4.1e-3 1.97
-	-viscosity 0.472 -0.252 5.51e-3 3.67e-3 0 1.876
-	-dw 0.794e-9 149 0.805 1.961 1e-9 0.7876
+	-Vm -5.6e-2 -10.15 9.90 -2.36 0.807 5.26 2.72 -82.7 -1.37e-2 0.956
+	-viscosity 0.493 -0.255 2.3e-3 4.2e-3 -3.8e-3 1.762
+	-dw 0.794e-9 18 0.681 2.069 0.965 0.271
 Ba+2 = Ba+2
 	-gamma 5 0
 	-gamma 4 0.153 # Barite solubility
@@ -143,20 +143,20 @@ CO3-2 = CO3-2
 	-viscosity -0.5 0.6521 5.44e-3 1.06e-3 -2.18e-2 1.208 -2.147
 	-dw 0.955e-9 -103 2.246 7.13e-2 0.3686
 SO4-2 = SO4-2
-	-gamma 5 -0.04
-	-Vm -7.77 43.17 176 -51.45 3.794 0 42.99 -541 -0.145 0.45 # with analytical_expressions for log K of NaSO4-, KSO4- & MgSO4, 0 - 200 oC
-	-viscosity -0.3 0.501 2.57e-3 0.195 3.14e-2 2.015 0.605
-	-dw 1.07e-9 -114 17 6.02e-2 4.94e-2
+	-gamma 5.0 -0.04
+	-Vm 5.36 10.69 33.566 -15.03 4.2582 25 0.341 153.8 1.089e-2 0.9224 # with Na2SO4 & better calculation of sulfates' solubilities in NaCl
+	-viscosity -0.5 0.521 4.2e-4 9.78e-3 1.24e-2 2.5 -4.94e-2
+	-dw 1.07e-9 -77.4 10.14 0.5 0.5549
 NO3- = NO3-
 	-gamma 3 0
 	-Vm 6.32 6.78 0 -3.06 0.346 0 0.93 0 -0.012 1
 	-viscosity 8.37e-2 -0.458 1.54e-2 0.34 1.79e-2 5.02e-2 0.7381
 	-dw 1.9e-9 104 1.11
-# AmmH+ = AmmH+
-	# -gamma 2.50
-	# -Vm 5.35 2.345 3.72 -2.88 1.55 2.5 -4.54 217 2.344e-2 0.569
-	# -viscosity 9.9e-2 -0.159 1.36e-2 6.51e-3 3.21e-2 0.972
-	# -dw 1.98e-9 203 1.47 2.644 6.81e-2
+#AmmH+ = AmmH+
+#	-gamma 2.5 0
+#	-Vm 5.35 2.345 3.72 -2.88 1.55 2.5 -4.54 217 2.344e-2 0.569
+#	-viscosity 6.94e-2 -0.141 2.04e-2 9.4e-3 3.73e-2 0.898
+#	-dw 1.98e-9 203 1.47 2.644 6.81e-2
 H3BO3 = H3BO3
 	-Vm 7.0643 8.8547 3.5844 -3.1451 -0.2 # supcrt
 	-dw 1.1e-9
@@ -170,7 +170,7 @@ F- = F-
 	-viscosity 0 2.85e-2 1.35e-2 6.11e-2 4.38e-3 1.384 0.586
 	-dw 1.46e-9 -36 4.352
 Br- = Br-
-	-gamma 3 0
+	-gamma 3 0.045
 	-Vm 6.72 2.85 4.21 -3.14 1.38 0 -9.56e-2 7.08 -1.56e-3 1
 	-viscosity -6.98e-2 -0.141 1.78e-2 0.159 7.76e-3 6.25e-2 0.859
 	-dw 2.09e-9 208 3.5 0 0.5737
@@ -206,14 +206,14 @@ H2Sg = H2Sg # H2S
 	-dw 2.1e-9
 # aqueous species
 H2O = OH- + H+
-	-analytic 293.29227 0.1360833 -10576.913 -123.73158 0 -6.996455e-5
 	-gamma 3.5 0
+	-analytic 293.29227 0.1360833 -10576.913 -123.73158 0 -6.996455e-5
 	-Vm -9.66 28.5 80 -22.9 1.89 0 1.09 0 0 1
 	-viscosity -2.26e-2 0.106 2.184e-2  -3.2e-3 0 0.4082 -1.634 # < 5 M Li,Na,KOH
 	-dw 5.27e-9 478 0.8695
 2 H2O = O2 + 4 H+ + 4 e-
-	-log_k -86.08
-	-delta_h 134.79 kcal
+	-log_k -86.06; -delta_h 138.43 kcal
+	-analytic -1e3 -0.322 -5897.7 416.82 0 -1.88e-5
 	-Vm 5.7889 6.3536 3.2528 -3.0417 -0.3943 # supcrt
 	-dw 2.35e-9
 2 H+ + 2 e- = H2
@@ -300,11 +300,11 @@ NO3- + 2 H+ + 2 e- = NO2- + H2O
 	-Vm 7 # Pray et al., 1952, IEC 44 1146
 	-dw 1.96e-9 -90 # Cadogan et al. 2014, JCED 59, 519
 NO3- + 10 H+ + 8 e- = NH4+ + 3 H2O
-	-log_k 119.077
-	-delta_h -187.055 kcal
+	  -log_k  119.077
+	  -delta_h -187.055	  kcal
 	-gamma 2.5 0
 	-Vm 5.35 2.345 3.72 -2.88 1.55 2.5 -4.54 217 2.344e-2 0.569
-	-viscosity 9.9e-2 -0.159 1.36e-2 6.51e-3 3.21e-2 0.972
+	-viscosity 6.94e-2 -0.141 2.04e-2 9.4e-3 3.73e-2 0.898
 	-dw 1.98e-9 203 1.47 2.644 6.81e-2
 #AmmH+ = Amm + H+
 NH4+ = NH3 + H+
@@ -312,15 +312,15 @@ NH4+ = NH3 + H+
 	-delta_h 12.48 kcal
 	-analytic 0.6322 -0.001225 -2835.76
 	-Vm 6.69 2.8 3.58 -2.88 1.43
-	-viscosity 0.08 0 0 7.82e-3 -0.134 -0.986
+	-viscosity 0 -2.24e-2 0.101 8.66e-3 2.86e-2 -0.143 -0.769
 	-dw 2.28e-9
 #AmmH+ + SO4-2 = AmmHSO4-
 NH4+ + SO4-2 = NH4SO4-
-	-gamma 2.08 -0.0416
-	-log_k	1.211; -delta_h 8.56 kJ
-	-Vm -8.78 0 -36.09 0 -8.60 0 87.62 0 -0.3123 0.1172
-	-viscosity 0 0.116 -8.6e-3 0.159 -9.3e-3 0.522 0.627
-	-dw 0.9e-9 100 2.1 2 0
+	-gamma 3.64 -4.75e-2
+	-log_k 1.276; -delta_h -3.24 kcal
+	-Vm 6.64 8.5 -5.84 -3.1 2 0 19.24 0 -7.84e-2 0.289
+	-viscosity 0.267 -0.207 9.75e-2 6.18e-2 1.99e-2 1.166 0.61
+	-dw 1.56e-9 498 25 0.5 0.684
 H3BO3 = H2BO3- + H+
 	-log_k -9.24
 	-delta_h 3.224 kcal
@@ -372,13 +372,14 @@ Ca+2 + CO3-2 + H+ = CaHCO3+
 	-log_k 10.91; -delta_h 4.38 kcal
 	-analytic -6.009 3.377e-2 2044
 	-gamma 6 0
-	-Vm 30.19 .01 5.75 -2.78 .308 5.4
+	-Vm 3.19 .01 5.75 -2.78 .308 5.4
 	-dw 5.06e-10
 Ca+2 + SO4-2 = CaSO4
-	-log_k 2.25
-	-delta_h 1.325 kcal
-	-dw 4.71e-10
-	-Vm 2.791 -.9666 6.13 -2.739 -.001 # supcrt
+	-gamma 0 4.45e-2
+	-log_k 2.14; -delta_h 24.4
+	-analytical_expression 1.478 8.29e-3 -538.2
+	-vm 2.7 2 2 -3.7
+	-dw 4.71e-9
 Ca+2 + HSO4- = CaHSO4+
 	-log_k 1.08
 Ca+2 + PO4-3 = CaPO4-
@@ -415,19 +416,19 @@ Mg+2 + H+ + CO3-2 = MgHCO3+
 	-Vm 2.7171 -1.1469 6.2008 -2.7316 .5985 4 # supcrt
 	-dw 4.78e-10
 Mg+2 + SO4-2 = MgSO4
-	-gamma 0 0.2
-	-log_k 2.42; -delta_h 19 kJ
-	-analytical_expression 0 9.64e-3 -136 # mean salt gamma from Pitzer.dat and epsomite/hexahydrite/kieserite solubilities, 0 - 200 oC
-	-Vm 8.65 -10.21 29.58 -18.6 1.061
-	-viscosity 0.318 -5.4e-4 -3.42e-2 0.708 3.7e-3 0.696
+	-gamma 0 0.20
+	-log_k 2.42; -delta_h 19.0
+	-analytical_expression 0 9.64e-3 -136 # epsomite/hexahydrite/kieserite solubilities, 0 - 200 oC
+	-Vm 11.92 -27.758 29.752 -10.302 -0.1
+	-viscosity -0.799 1 2.2e-4 8.53e-2 -4.6e-3 1.35 -0.796
 	-dw 4.45e-10
 SO4-2 + MgSO4 = Mg(SO4)2-2
 	-gamma 7 0.047
-	-log_k 0.52; -delta_h -13.6 kJ
-	-analytical_expression 0 -1.51e-3 0 0 8.604e4 # mean salt gamma from Pitzer.dat and epsomite/hexahydrite/kieserite solubilities, 0 - 200 oC
-	-Vm -8.14 -62.2 -15.96 3.29 -3.01 0 150 0 0.153 3.79e-2
-	-viscosity -0.169 5e-4 -5.69e-2 0.11 2.03e-3 2.027 -1e-3
-	-dw 0.845e-9 -200 8 0 0.965
+	-log_k 0.52; -delta_h -13.6
+	-analytical_expression 0 -1.51e-3 0 0 8.604e4 # epsomite/hexahydrite/kieserite solubilities, 0 - 200 oC
+	-Vm 4.248 9.83 -7 -2.672 2 3.5 5 100 0.3359 9.518e-2
+	-viscosity 0.324 6.84e-2 -2.09e-2 0.104 6.19e-3 1.983 1e-3
+	-dw 1.11e-9 -500 3.5 0.5 0.731
 Mg+2 + PO4-3 = MgPO4-
 	-log_k 6.589
 	-delta_h 3.1 kcal
@@ -453,12 +454,19 @@ Na+ + HCO3- = NaHCO3
 	-viscosity -4e-2 -2.717 1.67e-5
 	-dw 6.73e-10
 Na+ + SO4-2 = NaSO4-
-	-gamma 5.5 0
-	-log_k 0.6; -delta_h -14.4 kJ
-	-analytical_expression 255.903 0.10057 0 -1.11138e2 -8.5983e5 # mirabilite/thenardite solubilities, 0 - 200 oC
-	-Vm 1.99 -10.78 21.88 -12.7 1.601 5 32.38 501 1.565e-2 0.2325
-	-viscosity 0.2 -5.93e-2 -4e-4 8.46e-3 1.78e-3 2.308 -0.208
-	-dw 1.13e-9 -23 8.5 0.392 0.521
+	-gamma 3.5 0.1072
+	-log_k 0.94; -delta_h 8.23
+	-analytical_expression -0.304 4.51e-3 -28.9 # mirabilite/thenardite solubilities, 0 - 200 oC
+	-Vm 8.523 -4.685 -8.61 0.106 2.7 25 3.634 13.4 3.738e-2 0.5476
+	-viscosity -1 0.33 0.128 1.143 7.7e-4 1.9e-2 -0.387
+	-dw 4e-10 -200 3.5 0.5 0.5
+2 Na+ + SO4-2 = Na2SO4
+	-gamma 0 8.85e-2
+	-log_k -2.37; -delta_h 82
+	-analytical_expression 15.432 -5.75e-3 -4796 # sulfates solubilities in NaCl
+	-Vm 9.405 -15.5 25 8.4 0.25
+	-viscosity -0.5 0.485 -1e-3 0.147 0 0.947 -0.175
+	-dw 0.8e-9
 Na+ + HPO4-2 = NaHPO4-
 	-log_k 0.29
 	-gamma 5.4 0
@@ -473,11 +481,11 @@ K+ + HCO3- = KHCO3
 	-viscosity 0.7 -1.289 9e-2
 K+ + SO4-2 = KSO4-
 	-gamma 5.4 0.19
-	-log_k 0.6; -delta_h -10.4 kJ
+	-log_k 1.18; -delta_h 3
 	-analytical_expression -3.0246 9.986e-3 0 0 1.093e5 # arcanite solubility, 0 - 200 oC
-	-Vm 13.48 -18.03 61.74 -19.6 2.046 5.4 -17.32 0 0.1522 1.919
-	-viscosity -1 1.06 1e-4 -0.464 3.78e-2 0.539 -0.69
-	-dw 0.9e-9 63 8.48 0 1.8
+	-Vm 3.443 5.04 13 -3.324 2.447 0 20 0 7.77e-3 0.3497
+	-viscosity 0.107 0.19 2.23e-2 -0.148 -4.91e-2 0.537 0.195
+	-dw 1.22e-9 100 25 0.5 2.5
 K+ + HPO4-2 = KHPO4-
 	-log_k 0.29
 	-gamma 5.4 0
@@ -497,9 +505,8 @@ Fe+2 + CO3-2 = FeCO3
 Fe+2 + HCO3- = FeHCO3+
 	-log_k 2
 Fe+2 + SO4-2 = FeSO4
-	-log_k 2.25
-	-delta_h 3.23 kcal
-	-Vm -13 0 123
+	-log_k 2.25; -delta_h 3.23 kcal
+	-Vm 5.8 6.5 3.7 -3 -0.09
 Fe+2 + HSO4- = FeHSO4+
 	-log_k 1.08
 Fe+2 + 2 HS- = Fe(HS)2
@@ -601,9 +608,9 @@ Mn+2 + HCO3- = MnHCO3+
 	-log_k 1.95
 	-gamma 5 0
 Mn+2 + SO4-2 = MnSO4
-	-log_k 2.25
-	-delta_h 3.37 kcal
-	-Vm -1.31 -1.83 62.3 -2.7
+	-gamma 0 -0.098
+	-log_k 1.408; -delta_h 21.55
+	-Vm 1.88 6.5 10 -3 0.1
 Mn+2 + 2 NO3- = Mn(NO3)2
 	-log_k 0.6
 	-delta_h -0.396 kcal
@@ -672,7 +679,7 @@ H4SiO4 = H3SiO4- + H+
 	-delta_h 6.12 kcal
 	-analytic -302.3724 -0.050698 15669.69 108.18466 -1119669
 	-gamma 4 0
-	-Vm 7.94 1.0881 5.3224 -2.824 1.4767 # supcrt  H2O in a1
+	-Vm 7.94 1.0881 5.3224 -2.824 1.4767 # supcrt + H2O in a1
 H4SiO4 = H2SiO4-2 + 2 H+
 	-log_k -23
 	-delta_h 17.6 kcal
@@ -696,7 +703,8 @@ Ba+2 + HCO3- = BaHCO3+
 	-delta_h 5.56 kcal
 	-analytic -3.0938 0.013669
 Ba+2 + SO4-2 = BaSO4
-	-log_k 2.7
+	-log_k 3.457; -delta_h 26.15
+	-vm -6.25 24.66 -4.38 10.97 0.5
 Sr+2 + H2O = SrOH+ + H+
 	-log_k -13.29
 	-gamma 5 0
@@ -815,12 +823,13 @@ Zn+2 + 2 CO3-2 = Zn(CO3)2-2
 Zn+2 + HCO3- = ZnHCO3+
 	-log_k 2.1
 Zn+2 + SO4-2 = ZnSO4
-	-log_k 2.37
-	-delta_h 1.36 kcal
-	-Vm 2.51 0 18.8
+	-gamma 0 0.1
+	-log_k 2.26; -delta_h 16.15
+	-Vm 0.409 6.5 2 -3 0
 Zn+2 + 2 SO4-2 = Zn(SO4)2-2
-	-log_k 3.28
-	-Vm 10.9 0 -98.7 0 0 0 24 0 -0.236 1
+	-gamma 0.59 0.1
+	-log_k 1.15; -delta_h 17.52
+	-Vm 9.21 10.6 9 -3.2 3.8 25 0 100 -1e-3 0.256
 Zn+2 + Br- = ZnBr+
 	-log_k -0.58
 Zn+2 + 2 Br- = ZnBr2
@@ -866,12 +875,13 @@ Cd+2 + 2 CO3-2 = Cd(CO3)2-2
 Cd+2 + HCO3- = CdHCO3+
 	-log_k 1.5
 Cd+2 + SO4-2 = CdSO4
-	-log_k 2.46
-	-delta_h 1.08 kcal
-	-Vm 10.4 0 57.9
+	-gamma 0 0.1
+	-log_k 1.016; -delta_h 6.84
+	-Vm 2.11 6.5 10 -3 0.1
 Cd+2 + 2 SO4-2 = Cd(SO4)2-2
-	-log_k 3.5
-	-Vm -6.29 0 -93 0 9.5 7 0 0 0 1
+	-gamma 5.201 -0.1
+	-log_k 2.688; -delta_h 0.19
+	-Vm 9.14 10.6 -3.06 -3.2 3.8 7.44 1.27 0.32 -1e-3 2.5
 Cd+2 + Br- = CdBr+
 	-log_k 2.17
 	-delta_h -0.81 kcal
@@ -991,29 +1001,24 @@ Witherite
 	-Vm 46
 Gypsum
 	CaSO4:2H2O = Ca+2 + SO4-2 + 2 H2O
-	-log_k -4.58
-	-delta_h -0.109 kcal
-	-analytic 68.2401 0 -3221.51 -25.0627
-	-analytical_expression 93.7 5.99E-3 -4e3 -35.019 # better fits the appendix data of Appelo, 2015, AG 55, 62
-	-Vm 73.9 # 172.18 / 2.33 (Vm H2O = 13.9 cm3/mol)
+	-log_k -4.55; -delta_h -6.70
+	-analytical_expression 72.244 -1.474e-2 -4040 -23.7823 # fits the appendix data of Appelo, 2015, AG 55, 62
+	-Vm 73.9
 Anhydrite
 	CaSO4 = Ca+2 + SO4-2
-	-log_k -4.36
-	-delta_h -1.71 kcal
-	-analytic 84.9 0 -3135.12 -31.79 # 50 - 160oC, 1 - 1e3 atm, anhydrite dissolution, Blount and Dickson, 1973, Am. Mineral. 58, 323
+	log_k -4.25; -delta_h -22.4
+	-analytical_expression 5.725 -2.478e-2 -790.4 # 50 - 160oC, 1 - 1e3 atm, anhydrite dissolution, Blount and Dickson, 1973, Am. Mineral. 58, 323
 	-Vm 46.1 # 136.14 / 2.95
 Celestite
 	SrSO4 = Sr+2 + SO4-2
 	-log_k -6.63
 	-delta_h -4.037 kcal
-#	  -analytic	  -14805.9622	-2.4660924	 756968.533	 5436.3588	  -40553604.0
 	-analytic -7.14 6.11e-3 75 0 0 -1.79e-5 # Howell et al., 1992, JCED 37, 464
 	-Vm 46.4
 Barite
 	BaSO4 = Ba+2 + SO4-2
-	-log_k -9.97
-	-delta_h 6.35 kcal
-	-analytical_expression -282.43 -8.972e-2 5822 113.08 # Blount 1977; Templeton, 1960
+	-log_k -9.89; -delta_h 11.82
+	-analytical_expression -34.438 -3.316e-2 -1500 15.9485 # Blount 1977; Templeton, 1960
 	-Vm 52.9
 Arcanite
 	K2SO4 = SO4-2 + 2 K+
@@ -1023,12 +1028,14 @@ Arcanite
 	-Vm 65.5
 Mirabilite
 	Na2SO4:10H2O = SO4-2 + 2 Na+ + 10 H2O
-	-analytical_expression -301.9326 -0.16232 0 141.078 # ref. 3
+	-log_k -0.706; -delta_h 124
+	-analytical_expression -53.037 0.1242 4562 # ref. 3
 	Vm 216
 Thenardite
 	Na2SO4 = 2 Na+ + SO4-2
-	-analytical_expression 57.185 8.6024e-2 0 -30.8341 0 -7.6905e-5 # ref. 3
-	-Vm 52.9
+	-log_k 0.65; -delta_h -23.1
+	-analytical_expression 159.849 1.699e-2 -5000 -59.6073 # ref. 3
+	Vm 52.9
 Epsomite
 	MgSO4:7H2O = Mg+2 + SO4-2 + 7 H2O
 	log_k -1.74; -delta_h 10.57 kJ
@@ -1240,7 +1247,7 @@ CH4(g)
 #Amm(g)
 #	Amm = Amm
 NH3(g)
-	NH3 = NH3
+	NH3 = NH3	
 	-log_k 1.7966
 	-analytic -18.758 3.367e-4 2.5113e3 4.8619 39.192
 	-T_c 405.6; -P_c 111.3; -Omega 0.25
@@ -3133,17 +3140,17 @@ Wollastonite    -6.97   700             56      0.4     0       0
 #   Av is the Debye-H<>ckel limiting slope (DH_AV in PHREEQC basic).
 #   a0 is the ion-size parameter in the extended Debye-H<>ckel equation:
 #	f(I^0.5) = I^0.5 / (1 + a0 * DH_B * I^0.5),
-#	a0 = -gamma	  x for cations, = 0 for anions.
-# For details, consult ref. 1.
+#	a0 = -gamma	  x for cations, = 0 for anions (or fitted).
+# For details, consult ref. 1 and subroutine calc_vm(tc, pa) in prep.cpp.
 # =============================================================================================
 # The viscosity is calculated with a (modified) Jones-Dole equation:
 #    viscos / viscos_0 = 1 + A * Sum(0.5 z_i m_i) + fan * Sum(B_i m_i + D_i m_i n_i)
 # Parameters are for calculating the B and D terms:
-#    -viscosity 9.35e-2 -8.31e-2 2.487e-2 4.49e-4 2.01e-2 1.570    0
-#    #	   b0	  b1	  b2	 d1	  d2	 d3	tan
+#    -viscosity 9.35e-2 -8.31e-2 2.487e-2 4.49e-4 2.01e-2 1.570 0
+#    #	        b0      b1	    b2	   d1	  d2	d3  tan
 #    z_i is absolute charge number, m_i is molality of i
 #    B_i = b0 + b1 exp(-b2 * tc)
-#    fan = (2 - tan V_i / V_Cl-), corrects for the volume of anions
+#    fan = (2 - tan V_i / V_Cl-), corrects for the volume of anions and neutral species
 #    D_i = d1 * exp(-d2 tc)
 #    n_i = (I^d3 * (1 + fI) + ((z_i^2 + z_i) / 2 <20> m_i)^d3) / (2 + fI), fI is an ionic strength term.
 # For details, consult ref. 4.

database/pitzer.dat

@@ -1,8 +1,4 @@
-# File 1 = C:\GitPrograms\phreeqc3-1\database\pitzer.dat, 22/05/2024  19:46, 1033 lines, 38088 bytes, md5=d70476773ed110a269ebbcaf334f1133
-# Created 22 May 2024 19:49:25
-# C:\3rdParty\lsp\lsp.exe -f2 -k=asis -ts pitzer.dat
-
-# Pitzer.DAT for calculating temperature and pressure dependence of reactions, and the specific conductance and viscosity of the solution, using
+# pitzer.dat for calculating temperature and pressure dependence of reactions, and the specific conductance and viscosity of the solution, using
 #   diffusion coefficients of species, molal volumina of aqueous species and minerals, and critical temperatures and pressures of gases used in Peng-Robinson's EOS.
 # Details are given at the end of this file.
 
@@ -73,13 +69,13 @@ Mg+2 = Mg+2
 	-viscosity 0.426 0 0 1.66e-3 4.32e-3 2.461
 	-dw 0.705e-9 -4 5.569 0 1.047
 Ca+2 = Ca+2
-	-Vm -0.3456 -7.252 6.149 -2.479 1.239 5 1.6 -57.1 -6.12e-3 1 # The apparent volume parameters are defined in ref. 1 & 2
+	-Vm -0.3456 -7.252 6.149 -2.479 1.239 5 1.6 -57.1 -6.12e-3 1
 	-viscosity 0.359 -0.158 4.2e-2 1.5e-3 8.04e-3 2.3 # ref. 4, CaCl2 < 6 M
 	-dw 0.792e-9 34 5.411 0 1.046
 Sr+2 = Sr+2
-	-Vm -1.57e-2 -10.15 10.18 -2.36 0.86 5.26 0.859 -27 -4.1e-3 1.97
-	-viscosity 0.472 -0.252 5.51e-3 3.67e-3 0 1.876
-	-dw 0.794e-9 149 0.805 1.961 1e-9 0.7876
+	-Vm -5.6e-2 -10.15 9.90 -2.36 0.807 5.26 2.72 -82.7 -1.37e-2 0.956
+	-viscosity 0.493 -0.255 2.3e-3 4.2e-3 -3.8e-3 1.762
+	-dw 0.794e-9 18 0.681 2.069 0.965 0.271
 Ba+2 = Ba+2
 	-Vm 2.063 -10.06 1.9534 -2.36 0.4218 5 1.58 -12.03 -8.35e-3 1
 	-viscosity 0.338 -0.227 1.39e-2 3.07e-2 0 0.768
@@ -217,11 +213,11 @@ Anthophyllite
 	log_k 66.8
 	-delta_H -483 kJ/mol
 	Vm 269
-Antigorite
-	Mg48Si34O85(OH)62 + 96 H+ = 34 H4SiO4 + 48 Mg+2 + 11 H2O # llnl.dat
-	log_k 477.19
-	-delta_H -3364 kJ/mol
-	Vm 1745
+# Antigorite
+	# Mg48Si34O85(OH)62 + 96 H+ = 34 H4SiO4 + 48 Mg+2 + 11 H2O # llnl.dat
+	# log_k 477.19 # seawater is impossibly supersaturated
+	# -delta_H -3364 kJ/mol
+	# Vm 1745
 Aragonite
 	CaCO3 = CO3-2 + Ca+2
 	log_k -8.336
@@ -1030,7 +1026,7 @@ END
 #    #	   b0	  b1	  b2	 d1	  d2	 d3	tan
 #    z_i is absolute charge number, m_i is molality of i
 #    B_i = b0 + b1 exp(-b2 * tc)
-#    fan = (2 - tan V_i / V_Cl-), corrects for the volume of anions
+#    fan = (2 - tan V_i / V_Cl-), corrects for the volume of anions and neutral species
 #    D_i = d1 * exp(-d2 tc)
 #    n_i = (I^d3 * (1 + fI) + ((z_i^2 + z_i) / 2 <20> m_i)^d3) / (2 + fI), fI is an ionic strength term.
 # For details, consult ref. 5.

database/sit.dat

@@ -6,153 +6,153 @@ SOLUTION_SPECIES
 # Name : ThermoChimie project
 # Database date: 22/08/2023 0:00:00
 # Generated by XCheck Tool v5.2.0
-# Comment: tidied with lsp.exe from https://phreeplot.org/lsp/lsp.html 
+# Comment: tidied with lsp.exe from https://phreeplot.org/lsp/lsp.html
 # Redox states modified by David Parkhurst May 18, 2024
 # GFW of S(6) and Si modified by David Parkhurst May 18, 2024
 SOLUTION_MASTER_SPECIES
-#element       species        alk            gfw_formula    element_gfw    
-E              e-             1              0              0        
-# DLP: Set Alkalinity to 1 to account for non-master species with e- in equations      
-Alkalinity     CO3-2          1              Ca0.5(CO3)0.5  50.0436        
-Adipate        Adipate-2      1              Adipate        144.0700       
-Acetate        Acetate-       1              Acetate        59.0100        
-Ag             Ag+            -2             Ag             107.8682       
-Al             Al+3           0              Al             26.9815        
-Am             Am+3           0              Am             243.0000       
-Am(+3)         Am+3           0              Am             243.0000       
-Am(+2)         Am+2           0              Am             243.0000       
-Am(+4)         Am+4           0              Am             243.0000       
-Am(+5)         AmO2+          0              Am             243.0000       
-Am(+6)         AmO2+2         0              Am             243.0000       
-As             AsO4-3         2              As             74.9216        
-As(+5)         AsO4-3         2              As             74.9216        
-As(+3)         H3(AsO3)       0              As             74.9216        
-B              B(OH)4-        1              B              10.8110        
-Ba             Ba+2           0              Ba             137.3270       
-Be             Be+2           0              Be             9.0122         
-Br             Br-            0              Br             79.9040        
-C              CO3-2          2              C              12.0110 
+#element       species        alk            gfw_formula    element_gfw
+E              e-             1              0              0
+# DLP: Set Alkalinity to 1 to account for non-master species with e- in equations
+Alkalinity     CO3-2          1              Ca0.5(CO3)0.5  50.0436
+Adipate        Adipate-2      1              Adipate        144.0700
+Acetate        Acetate-       1              Acetate        59.0100
+Ag             Ag+            -2             Ag             107.8682
+Al             Al+3           0              Al             26.9815
+Am             Am+3           0              Am             243.0000
+Am(+3)         Am+3           0              Am             243.0000
+Am(+2)         Am+2           0              Am             243.0000
+Am(+4)         Am+4           0              Am             243.0000
+Am(+5)         AmO2+          0              Am             243.0000
+Am(+6)         AmO2+2         0              Am             243.0000
+As             AsO4-3         2              As             74.9216
+As(+5)         AsO4-3         2              As             74.9216
+As(+3)         H3(AsO3)       0              As             74.9216
+B              B(OH)4-        1              B              10.8110
+Ba             Ba+2           0              Ba             137.3270
+Be             Be+2           0              Be             9.0122
+Br             Br-            0              Br             79.9040
+C              CO3-2          2              C              12.0110
 C(2)           CO             0              C       # DLP
-C(+4)          CO3-2          2              C              12.0110        
-C(-4)          CH4            0              C              12.0110        
-Ca             Ca+2           0              Ca             40.0780        
-Cd             Cd+2           -1             Cd             112.4110       
-Cit            Cit-3          1              Cit            189.1013       
-Cl             Cl-            0              Cl             35.4527   
+C(+4)          CO3-2          2              C              12.0110
+C(-4)          CH4            0              C              12.0110
+Ca             Ca+2           0              Ca             40.0780
+Cd             Cd+2           -1             Cd             112.4110
+Cit            Cit-3          1              Cit            189.1013
+Cl             Cl-            0              Cl             35.4527
 Cl(-1)         Cl-            0              Cl      # DLP
 Cl(0)          Cl2            0              Cl      # DLP
 Cl(7)          ClO4-          0              Cl      # DLP
-Cm             Cm+3           0              Cm             247.0000       
-Co             Co+2           0              Co             58.9332        
-Cr             CrO4-2         1              Cr             51.9961        
-Cr(+6)         CrO4-2         1              Cr             51.9961        
-Cr(+2)         Cr+2           -1             Cr             51.9961        
-Cr(+3)         Cr+3           2              Cr             51.9961        
-Cs             Cs+            0              Cs             132.9054       
-Cu             Cu+2           0              Cu             63.5460        
-Cu(+2)         Cu+2           0              Cu             63.5460        
-Cu(+1)         Cu+            -2             Cu             63.5460        
-Edta           Edta-4         2              Edta           288.2134       
-Eu             Eu+3           0              Eu             151.9650       
-Eu(+3)         Eu+3           0              Eu             151.9650       
-Eu(+2)         Eu+2           0              Eu             151.9650       
-F              F-             0              F              18.9984        
-Fe             Fe+2           0              Fe             55.8470        
-Fe(+2)         Fe+2           0              Fe             55.8470        
-Fe(+3)         Fe+3           -2             Fe             55.8470        
-Glu            HGlu-          0              Glu            194.1380       
-H              H+             -1             H              1.0079         
-H(+1)          H+             -1             H              1.0079         
-H(0)           H2             0              H              1.0079         
-Hf             Hf+4           -4             Hf             178.4900       
-Hg             Hg+2           -2             Hg             200.5900       
-Hg(+2)         Hg+2           -2             Hg             200.5900       
-Hg(+1)         Hg2+2          0              Hg             200.5900       
-Ho             Ho+3           0              Ho             164.9303       
-I              I-             0              I              126.9045       
-I(-1)          I-             0              I              126.9045  
-I(1)           IO-            0              I # DLP 
-I(+5)          IO3-           0              I              126.9045  
+Cm             Cm+3           0              Cm             247.0000
+Co             Co+2           0              Co             58.9332
+Cr             CrO4-2         1              Cr             51.9961
+Cr(+6)         CrO4-2         1              Cr             51.9961
+Cr(+2)         Cr+2           -1             Cr             51.9961
+Cr(+3)         Cr+3           2              Cr             51.9961
+Cs             Cs+            0              Cs             132.9054
+Cu             Cu+2           0              Cu             63.5460
+Cu(+2)         Cu+2           0              Cu             63.5460
+Cu(+1)         Cu+            -2             Cu             63.5460
+Edta           Edta-4         2              Edta           288.2134
+Eu             Eu+3           0              Eu             151.9650
+Eu(+3)         Eu+3           0              Eu             151.9650
+Eu(+2)         Eu+2           0              Eu             151.9650
+F              F-             0              F              18.9984
+Fe             Fe+2           0              Fe             55.8470
+Fe(+2)         Fe+2           0              Fe             55.8470
+Fe(+3)         Fe+3           -2             Fe             55.8470
+Glu            HGlu-          0              Glu            194.1380
+H              H+             -1             H              1.0079
+H(+1)          H+             -1             H              1.0079
+H(0)           H2             0              H              1.0079
+Hf             Hf+4           -4             Hf             178.4900
+Hg             Hg+2           -2             Hg             200.5900
+Hg(+2)         Hg+2           -2             Hg             200.5900
+Hg(+1)         Hg2+2          0              Hg             200.5900
+Ho             Ho+3           0              Ho             164.9303
+I              I-             0              I              126.9045
+I(-1)          I-             0              I              126.9045
+I(1)           IO-            0              I # DLP
+I(+5)          IO3-           0              I              126.9045
 I(7)           IO4-           0              I # DLP
-Isa            HIsa-          0              Isa            178.1421       
-K              K+             0              K              39.0983        
-Li             Li+            0              Li             6.9410         
-Malonate       Malonate-2     1              Malonate       102.0464       
-Mg             Mg+2           0              Mg             24.3050        
-Mn             Mn+2           0              Mn             54.9380 
+Isa            HIsa-          0              Isa            178.1421
+K              K+             0              K              39.0983
+Li             Li+            0              Li             6.9410
+Malonate       Malonate-2     1              Malonate       102.0464
+Mg             Mg+2           0              Mg             24.3050
+Mn             Mn+2           0              Mn             54.9380
 Mn(+2)         Mn+2           0              Mn # DLP
 Mn(+3)         Mn+3           0              Mn # DLP
 Mn(+5)         MnO4-3         0              Mn # DLP
 Mn(+6)         MnO4-2         0              Mn # DLP
-Mn(+7)         MnO4-          0              Mn # DLP 
-Mo             MoO4-2         0              Mo             95.9400 
+Mn(+7)         MnO4-          0              Mn # DLP
+Mo             MoO4-2         0              Mo             95.9400
 Mo(6)          MoO4-2         0              Mo # DLP
-Mo(3)          Mo+3           0              Mo # DLP       
-N              NO3-           0              N              14.0067        
-N(+5)          NO3-           0              N              14.0067        
-N(-3)          NH3            1              N              14.0067        
-Na             Na+            0              Na             22.9898        
-Nb             Nb(OH)6-       1              Nb             92.9064        
-Ni             Ni+2           0              Ni             58.6900        
-Np             NpO2+2         0              Np             237.0480       
-Np(+6)         NpO2+2         0              Np             237.0480       
-Np(+3)         Np+3           0              Np             237.0480       
-Np(+4)         Np+4           -3             Np             237.0480       
-Np(+5)         NpO2+          0              Np             237.0480       
-Nta            Nta-3          1              Nta            188.1165       
-O              H2O            0              O              15.9994        
-O(-2)          H2O            0              O              15.9994        
-O(0)           O2             0              O              15.9994        
-Ox             Ox-2           0              Ox             88.0196        
-P              H2(PO4)-       0              P              30.9738        
-Pa             Pa+4           -3             Pa             231.0359       
-Pa(+4)         Pa+4           -3             Pa             231.0359       
-Pa(+5)         PaO2+          0              Pa             231.0359       
-Pb             Pb+2           -1             Pb             207.2000       
-Pd             Pd+2           -4             Pd             106.4200       
-Phthalat       Phthalat-2     2              Phthalat       164.0840       
-Pu             PuO2+2         0              Pu             244.0000       
-Pu(+6)         PuO2+2         0              Pu             244.0000       
-Pu(+3)         Pu+3           0              Pu             244.0000       
-Pu(+4)         Pu+4           -3             Pu             244.0000       
-Pu(+5)         PuO2+          -1             Pu             244.0000       
-Pyrophos       Pyrophos-4     2              Pyrophos       173.9500       
-Ra             Ra+2           0              Ra             226.0250       
-Rb             Rb+            0              Rb             85.4678        
-S              SO4-2          0              S              32.0660        
-S(+6)          SO4-2          0              SO4            32.0660       # DLP  
-S(-2)          HS-            1              S              32.0660        
-S(+2)          S2O3-2         0              S              32.0660        
-S(+3)          S2O4-2         0              S              32.0660        
-S(+4)          SO3-2          1              S              32.0660 
+Mo(3)          Mo+3           0              Mo # DLP
+N              NO3-           0              N              14.0067
+N(+5)          NO3-           0              N              14.0067
+N(-3)          NH3            1              N              14.0067
+Na             Na+            0              Na             22.9898
+Nb             Nb(OH)6-       1              Nb             92.9064
+Ni             Ni+2           0              Ni             58.6900
+Np             NpO2+2         0              Np             237.0480
+Np(+6)         NpO2+2         0              Np             237.0480
+Np(+3)         Np+3           0              Np             237.0480
+Np(+4)         Np+4           -3             Np             237.0480
+Np(+5)         NpO2+          0              Np             237.0480
+Nta            Nta-3          1              Nta            188.1165
+O              H2O            0              O              15.9994
+O(-2)          H2O            0              O              15.9994
+O(0)           O2             0              O              15.9994
+Ox             Ox-2           0              Ox             88.0196
+P              H2(PO4)-       0              P              30.9738
+Pa             Pa+4           -3             Pa             231.0359
+Pa(+4)         Pa+4           -3             Pa             231.0359
+Pa(+5)         PaO2+          0              Pa             231.0359
+Pb             Pb+2           -1             Pb             207.2000
+Pd             Pd+2           -4             Pd             106.4200
+Phthalat       Phthalat-2     2              Phthalat       164.0840
+Pu             PuO2+2         0              Pu             244.0000
+Pu(+6)         PuO2+2         0              Pu             244.0000
+Pu(+3)         Pu+3           0              Pu             244.0000
+Pu(+4)         Pu+4           -3             Pu             244.0000
+Pu(+5)         PuO2+          -1             Pu             244.0000
+Pyrophos       Pyrophos-4     2              Pyrophos       173.9500
+Ra             Ra+2           0              Ra             226.0250
+Rb             Rb+            0              Rb             85.4678
+S              SO4-2          0              S              32.0660
+S(+6)          SO4-2          0              SO4            32.0660       # DLP
+S(-2)          HS-            1              S              32.0660
+S(+2)          S2O3-2         0              S              32.0660
+S(+3)          S2O4-2         0              S              32.0660
+S(+4)          SO3-2          1              S              32.0660
 S(8)           HSO5-          0              S # DLP
-Sb             Sb(OH)3        0              Sb             121.7600       
-Sb(+3)         Sb(OH)3        0              Sb             121.7600       
-Sb(+5)         Sb(OH)5        -6             Sb             121.7600       
-Se             SeO4-2         0              Se             78.9600        
-Se(+6)         SeO4-2         0              Se             78.9600        
-Se(-2)         HSe-           -1             Se             78.9600        
-Se(+4)         SeO3-2         1              Se             78.9600        
+Sb             Sb(OH)3        0              Sb             121.7600
+Sb(+3)         Sb(OH)3        0              Sb             121.7600
+Sb(+5)         Sb(OH)5        -6             Sb             121.7600
+Se             SeO4-2         0              Se             78.9600
+Se(+6)         SeO4-2         0              Se             78.9600
+Se(-2)         HSe-           -1             Se             78.9600
+Se(+4)         SeO3-2         1              Se             78.9600
 Si             H4(SiO4)       0              SiO2           28.0855        # DLP
-Sm             Sm+3           0              Sm             150.3600       
-Sn             Sn+2           -2             Sn             118.7100       
-Sn(+2)         Sn+2           -2             Sn             118.7100       
-Sn(+4)         Sn+4           -4             Sn             118.7100       
-Sr             Sr+2           0              Sr             87.6200        
-Succinat       Succinat-2     1              Succinat       116.0700       
-Suberate       Suberate-2     1              Suberate       172.1804       
-Tc             TcO(OH)2       0              Tc             98.0000        
-Tc(+4)         TcO(OH)2       0              Tc             98.0000        
-Tc(+7)         TcO4-          0              Tc             98.0000        
-Tc(+6)         TcO4-2         0              Tc             98.0000        
-Th             Th+4           0              Th             232.0381       
-U              UO2+2          0              U              238.0289       
-U(+6)          UO2+2          0              U              238.0289       
-U(+3)          U+3            0              U              238.0289       
-U(+4)          U+4            -3             U              238.0289       
-U(+5)          UO2+           0              U              238.0289       
-Zn             Zn+2           0              Zn             65.3900        
-Zr             Zr+4           -4             Zr             91.2200        
+Sm             Sm+3           0              Sm             150.3600
+Sn             Sn+2           -2             Sn             118.7100
+Sn(+2)         Sn+2           -2             Sn             118.7100
+Sn(+4)         Sn+4           -4             Sn             118.7100
+Sr             Sr+2           0              Sr             87.6200
+Succinat       Succinat-2     1              Succinat       116.0700
+Suberate       Suberate-2     1              Suberate       172.1804
+Tc             TcO(OH)2       0              Tc             98.0000
+Tc(+4)         TcO(OH)2       0              Tc             98.0000
+Tc(+7)         TcO4-          0              Tc             98.0000
+Tc(+6)         TcO4-2         0              Tc             98.0000
+Th             Th+4           0              Th             232.0381
+U              UO2+2          0              U              238.0289
+U(+6)          UO2+2          0              U              238.0289
+U(+3)          U+3            0              U              238.0289
+U(+4)          U+4            -3             U              238.0289
+U(+5)          UO2+           0              U              238.0289
+Zn             Zn+2           0              Zn             65.3900
+Zr             Zr+4           -4             Zr             91.2200
 
 SIT
 -epsilon
@@ -4547,12 +4547,12 @@ H+ + S2O4-2 = HS2O4-
       delta_h 118.877 #kJ/mol
 #     Enthalpy of formation: -51.463   kJ/mol  92JOH/OEL
       -analytic 26.56356E-1 00E+0 -62.09378E+2 00E+0 00E+0
-	  
+
 - 2 e- + 2 Cl- + I- = ICl2-
 # DLP: This species will be in the I(-1) and Cl(-1) mole balances
       log_k -26.8 #96FAL/REA
       -analytic -26.8E+0 00E+0 00E+0 00E+0 00E+0
-	  
+
 - 2 H+ - 2 e- + I- + H2O = IO-
       log_k -44 #96FAL/REA
       -analytic -44E+0 00E+0 00E+0 00E+0 00E+0
@@ -14345,4 +14345,3 @@ SO2 = 2 H+ + SO3-2 - H2O
       delta_h -48.42 #kJ/mol
 #     Enthalpy of formation: -296.810  kJ/mol  89COX/WAG
       -analytic -17.42282E+0 00E+0 25.29153E+2 00E+0 00E+0
-

database/wateq4f.dat

@@ -7,72 +7,72 @@
 
 SOLUTION_MASTER_SPECIES
 
-Ag Ag+ 0 107.868 107.868
-Al Al+3 0 26.9815 26.9815
-Alkalinity CO3-2 1 50.05 50.05
-As H3AsO4 -1 74.9216 74.9216
-As(+3) H3AsO3 0 74.9216 74.9216
-As(+5) H3AsO4 -1 74.9216
-B H3BO3 0 10.81 10.81
-Ba Ba+2 0 137.34 137.34
-Br Br- 0 79.904 79.904
-C CO3-2 2 61.0173 12.0111
-C(+4) CO3-2 2 61.0173
-C(-4) CH4 0 16.042
-Ca Ca+2 0 40.08 40.08
-Cd Cd+2 0 112.4 112.4
-Cl Cl- 0 35.453 35.453
-Cs Cs+ 0 132.905 132.905
-Cu Cu+2 0 63.546 63.546
-Cu(+1) Cu+1 0 63.546
-Cu(+2) Cu+2 0 63.546
-E e- 1 0 0
-F F- 0 18.9984 18.9984
-Fe Fe+2 0 55.847 55.847
-Fe(+2) Fe+2 0 55.847
-Fe(+3) Fe+3 -2 55.847
-Fulvate Fulvate-2 0 650 650
-H H+ -1 1.008 1.008
-H(0) H2 0 1.008
-H(1) H+ -1 1.008
-Humate Humate-2 0 2000 2000
-I I- 0 126.9044 126.9044
-K K+ 0 39.102 39.102
-Li Li+ 0 6.939 6.939
-Mg Mg+2 0 24.312 24.312
-Mn Mn+2 0 54.938 54.938
-Mn(2) Mn+2 0 54.938
-Mn(3) Mn+3 0 54.938
-Mn(6) MnO4-2 0 54.938
-Mn(7) MnO4- 0 54.938
-N NO3- 0 14.0067 14.0067
-N(-3) NH4+ 0 14.0067
-N(0) N2 0 14.0067
-N(+3) NO2- 0 14.0067
-N(+5) NO3- 0 14.0067
-Na Na+ 0 22.9898 22.9898
-Ni Ni+2 0 58.71 58.71
-O H2O 0 16 16
-O(-2) H2O 0 18.016
-O(0) O2 0 16
-P PO4-3 2 30.9738 30.9738
-Pb Pb+2 0 207.19 207.19
-Rb Rb+ 0 85.47 85.47
-S SO4-2 0 96.0616 32.064
-S(-2) H2S 0 32.064
-S(6) SO4-2 0 96.0616
-Se SeO4-2 0 78.96 78.96
-Se(-2) HSe- 0 78.96
-Se(4) SeO3-2 0 78.96
-Se(6) SeO4-2 0 78.96
-Si H4SiO4 0 60.0843 28.0843
-Sr Sr+2 0 87.62 87.62
-Zn Zn+2 0 65.37 65.37
-U UO2+2 0 238.029 238.029
-U(3) U+3 0 238.029 238.029
-U(4) U+4 0 238.029 238.029
-U(5) UO2+ 0 238.029 238.029
-U(6) UO2+2 0 238.029 238.029
+Ag        Ag+       0         107.868   107.868
+Al        Al+3      0         26.9815   26.9815
+Alkalinity CO3-2    1         50.05     50.05
+As        H3AsO4    -1        74.9216   74.9216
+As(+3)    H3AsO3    0         74.9216   74.9216
+As(+5)    H3AsO4    -1        74.9216
+B         H3BO3     0         10.81     10.81
+Ba        Ba+2      0         137.34    137.34
+Br        Br-       0         79.904    79.904
+C         CO3-2     2         61.0173   12.0111
+C(+4)     CO3-2     2         61.0173
+C(-4)     CH4       0         16.042
+Ca        Ca+2      0         40.08     40.08
+Cd        Cd+2      0         112.4     112.4
+Cl        Cl-       0         35.453    35.453
+Cs        Cs+       0         132.905   132.905
+Cu        Cu+2      0         63.546    63.546
+Cu(+1)    Cu+1      0         63.546
+Cu(+2)    Cu+2      0         63.546
+E         e-        1         0         0
+F         F-        0         18.9984   18.9984
+Fe        Fe+2      0         55.847    55.847
+Fe(+2)    Fe+2      0         55.847
+Fe(+3)    Fe+3      -2        55.847
+Fulvate   Fulvate-2 0         650       650
+H         H+        -1        1.008     1.008
+H(0)      H2        0         1.008
+H(1)      H+        -1        1.008
+Humate    Humate-2  0         2000      2000
+I         I-        0         126.9044  126.9044
+K         K+        0         39.102    39.102
+Li        Li+       0         6.939     6.939
+Mg        Mg+2      0         24.312    24.312
+Mn        Mn+2      0         54.938    54.938
+Mn(2)     Mn+2      0         54.938
+Mn(3)     Mn+3      0         54.938
+Mn(6)     MnO4-2    0         54.938
+Mn(7)     MnO4-     0         54.938
+N         NO3-      0         14.0067   14.0067
+N(-3)     NH4+      0         14.0067
+N(0)      N2        0         14.0067
+N(+3)     NO2-      0         14.0067
+N(+5)     NO3-      0         14.0067
+Na        Na+       0         22.9898   22.9898
+Ni        Ni+2      0         58.71     58.71
+O         H2O       0         16        16
+O(-2)     H2O       0         18.016
+O(0)      O2        0         16
+P         PO4-3     2         30.9738   30.9738
+Pb        Pb+2      0         207.19    207.19
+Rb        Rb+       0         85.47     85.47
+S         SO4-2     0         96.0616   32.064
+S(-2)     H2S       0         32.064
+S(6)      SO4-2     0         96.0616
+Se        SeO4-2    0         78.96     78.96
+Se(-2)    HSe-      0         78.96
+Se(4)     SeO3-2    0         78.96
+Se(6)     SeO4-2    0         78.96
+Si        H4SiO4    0         60.0843   28.0843
+Sr        Sr+2      0         87.62     87.62
+Zn        Zn+2      0         65.37     65.37
+U         UO2+2     0         238.029   238.029
+U(3)      U+3       0         238.029   238.029
+U(4)      U+4       0         238.029   238.029
+U(5)      UO2+      0         238.029   238.029
+U(6)      UO2+2     0         238.029   238.029
 
 SOLUTION_SPECIES
 
@@ -1345,53 +1345,53 @@ SOLUTION_SPECIES
         Fe+2 + 3 HS- = Fe(HS)3-
         log_k 10.987
 
-#H2AsO3- 		478	
-	H3AsO3 = H2AsO3- + H+
-	log_k -9.15
-	delta_h 27.54 kJ
+#H2AsO3-            478
+          H3AsO3 = H2AsO3- + H+
+          log_k -9.15
+          delta_h 27.54 kJ
 
-#HAsO3-2 		479	
-	H3AsO3 = HAsO3-2 + 2 H+
-	log_k -23.85
-	delta_h 59.41 kJ
+#HAsO3-2            479
+          H3AsO3 = HAsO3-2 + 2 H+
+          log_k -23.85
+          delta_h 59.41 kJ
 
-#AsO3-3 		480	
-	H3AsO3 = AsO3-3 + 3 H+
-	log_k -39.55
-	delta_h 84.73 kJ
+#AsO3-3             480
+          H3AsO3 = AsO3-3 + 3 H+
+          log_k -39.55
+          delta_h 84.73 kJ
 
 #H4AsO3+             481
   H3AsO3 + H+ = H4AsO3+
   log_k -0.305
 
-#H2AsO4- 		482	
-	H3AsO4 = H2AsO4- + H+
-	log_k -2.3
-	delta_h -7.066 kJ
+#H2AsO4-            482
+          H3AsO4 = H2AsO4- + H+
+          log_k -2.3
+          delta_h -7.066 kJ
 
-#HAsO4-2 		483	
-	H3AsO4 = HAsO4-2 + 2 H+
-	log_k -9.46
-	delta_h -3.846 kJ
+#HAsO4-2            483
+          H3AsO4 = HAsO4-2 + 2 H+
+          log_k -9.46
+          delta_h -3.846 kJ
 
-#AsO43- 		484	
-	H3AsO4 = AsO4-3 + 3 H+
-	log_k -21.11
-	delta_h 14.354 kJ
+#AsO43-             484
+          H3AsO4 = AsO4-3 + 3 H+
+          log_k -21.11
+          delta_h 14.354 kJ
 
 #As3  secondary master species   487
-	H3AsO4 + H2 = H3AsO3 + H2O
-	log_k 22.5
-	delta_h -117.480344 kJ
+          H3AsO4 + H2 = H3AsO3 + H2O
+          log_k 22.5
+          delta_h -117.480344 kJ
 
-#As3S4(HS)-2 		631	
-	3 H3AsO3 + 6 HS- + 5 H+ = As3S4(HS)2- + 9 H2O
-	log_k 72.314
+#As3S4(HS)-2                  631
+          3 H3AsO3 + 6 HS- + 5 H+ = As3S4(HS)2- + 9 H2O
+          log_k 72.314
         -gamma 5 0
 
-#AsS(OH)(HS)- 		637	
-	H3AsO3 + 2 HS- + H+ = AsS(OH)(HS)- + 2 H2O
-	log_k 18.038
+#AsS(OH)(HS)-                 637
+          H3AsO3 + 2 HS- + H+ = AsS(OH)(HS)- + 2 H2O
+          log_k 18.038
         -gamma 5 0
 
 #
@@ -3136,8 +3136,8 @@ Basaluminite 472
 
 As_native 557
         As + 3 H2O = H3AsO3 + 3 H+ + 3 e-
-	log_k -12.532
-	delta_h 115.131 kJ
+          log_k -12.532
+          delta_h 115.131 kJ
 
 As2O5(cr) 488
         As2O5 + 3 H2O = 2 H3AsO4
@@ -3180,17 +3180,17 @@ Arsenolite 497
 #        As4O6 + 6H2O = 4H3AsO3
 #        log_k           -2.801
 #        delta_h 14.330 kcal
-	As2O3 + 3 H2O = 2 H3AsO3	
-	log_k -1.38
-	delta_h 30.041 kJ
+          As2O3 + 3 H2O = 2 H3AsO3
+          log_k -1.38
+          delta_h 30.041 kJ
 
 Claudetite 498
 #        As4O6 + 6H2O = 4H3AsO3
 #        log_k           -3.065
 #        delta_h 13.290 kcal
-	As2O3 + 3 H2O = 2 H3AsO3
-	log_k -1.34
-	delta_h 28.443 kJ
+          As2O3 + 3 H2O = 2 H3AsO3
+          log_k -1.34
+          delta_h 28.443 kJ
 
 AsI3 499
         AsI3 + 3 H2O = H3AsO3 + 3 I- + 3 H+
@@ -3201,20 +3201,20 @@ Orpiment 500
         As2S3 + 6 H2O = 2 H3AsO3 + 3 HS- + 3 H+
 #        log_k           -60.971
 #        delta_h 82.890 kcal
-	log_k -46.3
-	delta_h 263.1 kJ
+          log_k -46.3
+          delta_h 263.1 kJ
 
 As2S3(am) 132
         As2S3 + 6 H2O = 2 H3AsO3 + 3 HS- + 3 H+
-	log_k -44.9
-	delta_h 244.2 kJ
+          log_k -44.9
+          delta_h 244.2 kJ
 
 Realgar 501
         AsS + 3 H2O = H3AsO3 + HS- + 2 H+ + e-
 #        log_k           -19.747
 #        delta_h 30.545 kcal
-	log_k -19.944
-	delta_h 129.2625 kJ
+          log_k -19.944
+          delta_h 129.2625 kJ
 
 BlaubleiI 533
         Cu0.9Cu0.2S + H+ = 0.9 Cu+2 + 0.2 Cu+ + HS-
@@ -3432,7 +3432,7 @@ O2(g)
         O2 = O2
 #        log_k           -2.960
 #        delta_h -1.844 kcal
-	 # log K from llnl.dat  Aug 23, 2005
+           # log K from llnl.dat  Aug 23, 2005
         log_k -2.8983
         -analytic -7.5001e+0 7.8981e-3 0e+0 0e+0 2.0027e+5
 
@@ -3727,9 +3727,9 @@ SURFACE_SPECIES
 #
 # Silicate: Swedlund, P.J. and Webster, J.G., 1999. Water Research, 33, 3413-3422.
 #
-	Hfo_wOH + H4SiO4 = Hfo_wH3SiO4 + H2O; log_K 4.28
-	Hfo_wOH + H4SiO4 = Hfo_wH2SiO4- + H+ + H2O; log_K -3.22
-	Hfo_wOH + H4SiO4 = Hfo_wHSiO4-2 + 2 H+ + H2O; log_K -11.69
+          Hfo_wOH + H4SiO4 = Hfo_wH3SiO4 + H2O; log_K 4.28
+          Hfo_wOH + H4SiO4 = Hfo_wH2SiO4- + H+ + H2O; log_K -3.22
+          Hfo_wOH + H4SiO4 = Hfo_wHSiO4-2 + 2 H+ + H2O; log_K -11.69
 
 RATES
 ###########
@@ -3738,12 +3738,12 @@ RATES
 #
 #######
 # Example of quartz kinetic rates block:
-#	KINETICS
-#	Quartz
-#		-m0  158.8	    # 90 % Qu
-#		-parms 0.146  1.5
-#		-step 3.1536e8 in 10
-#		-tol 1e-12
+#         KINETICS
+#         Quartz
+#                   -m0  158.8              # 90 % Qu
+#                   -parms 0.146  1.5
+#                   -step 3.1536e8 in 10
+#                   -tol 1e-12
 
 Quartz
   -start
@@ -3756,7 +3756,7 @@ Quartz
 10 dif_temp = 1/TK - 1/298
 20 pk_w = 13.7 + 4700.4 * dif_temp
 40 moles = PARM(1) * M0 * PARM(2) * (M/M0)^0.67 * 10^-pk_w * (1 - SR("Quartz"))
-#			 Integrate...
+#                              Integrate...
 50 SAVE moles * TIME
   -end
 
@@ -4033,4 +4033,3 @@ Pyrolusite
 200 SAVE moles * SOLN_VOL
   -end
 END
-

examples/c/.github/subtrees.json

@@ -0,0 +1 @@
+[]

examples/c/.github/superprojects.json

@@ -0,0 +1,9 @@
+{
+  "usgs-coupled-subtrees/phreeqc-commanuscript-cgfinal-examples-c": {
+    "superprojects": [
+      "usgs-coupled-subtrees/iphreeqc",
+      "usgs-coupled-subtrees/iphreeqccom",
+      "usgs-coupled-subtrees/phreeqc"
+    ]
+  }
+}

examples/c/.github/workflows/lint-subtrees.yml

@@ -0,0 +1,19 @@
+name: Lint subtrees.json
+
+on:
+  pull_request:
+    paths:
+      - '.github/subtrees.json'
+  workflow_call:
+  workflow_dispatch:
+
+jobs:
+  lint-subtrees:
+    runs-on: ubuntu-latest
+    env:
+      CI_SERVER_HOST: github.com
+      GROUP: usgs-coupled
+    steps:
+      - uses: usgs-coupled-subtrees/sync-subtrees-action/lint-subtrees/@main
+        with:
+          ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}

examples/c/.github/workflows/lint-superprojects.yml

@@ -0,0 +1,16 @@
+name: Lint superprojects.json
+
+on:
+  pull_request:
+    paths:
+      - '.github/superprojects.json'
+  workflow_call:
+  workflow_dispatch:
+
+jobs:
+  lint-superprojects:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: usgs-coupled-subtrees/sync-subtrees-action/lint-superprojects/@main
+        with:
+          ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}

examples/c/.github/workflows/subtree.yml

@@ -0,0 +1,37 @@
+name: Sync Subtrees
+
+on:
+  push:
+    branches:
+      - master
+  workflow_dispatch:
+    inputs:
+      dryRun:
+        description: 'If true, don’t push any changes (for testing only).'
+        required: true
+        default: false
+        type: boolean
+      testMerge:
+        description: 'Run in test mode, pushing to a test branch.'
+        required: true
+        default: false
+        type: boolean
+
+jobs:
+  sync-subtrees:
+    if: startsWith(github.repository, 'usgs-coupled-subtrees/')
+    runs-on: ubuntu-latest
+    env:
+      CI_SERVER_HOST: github.com
+      GROUP: usgs-coupled
+      GH_TOKEN: ${{ secrets.WORKFLOW_PAT }}
+    steps:
+      - name: Run sync-subtrees-action
+        uses: usgs-coupled-subtrees/sync-subtrees-action@main
+        with:
+          dryRun: ${{ inputs.dryRun }}
+          testMerge: ${{ inputs.testMerge }}
+          repository_name: ${{ github.event.repository.name }}
+          default_branch: ${{ github.event.repository.default_branch }}
+          run_number: ${{ github.run_number }}
+          ssh_private_key: ${{ secrets.SSH_PRIVATE_KEY }}

examples/com/.github/subtrees.json

@@ -0,0 +1 @@
+[]

examples/com/.github/superprojects.json

@@ -0,0 +1,9 @@
+{
+  "usgs-coupled-subtrees/phreeqc-commanuscript-cgfinal-examples-com": {
+    "superprojects": [
+      "usgs-coupled-subtrees/iphreeqc",
+      "usgs-coupled-subtrees/iphreeqccom",
+      "usgs-coupled-subtrees/phreeqc"
+    ]
+  }
+}

examples/com/.github/workflows/lint-subtrees.yml

@@ -0,0 +1,19 @@
+name: Lint subtrees.json
+
+on:
+  pull_request:
+    paths:
+      - '.github/subtrees.json'
+  workflow_call:
+  workflow_dispatch:
+
+jobs:
+  lint-subtrees:
+    runs-on: ubuntu-latest
+    env:
+      CI_SERVER_HOST: github.com
+      GROUP: usgs-coupled
+    steps:
+      - uses: usgs-coupled-subtrees/sync-subtrees-action/lint-subtrees/@main
+        with:
+          ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}

examples/com/.github/workflows/lint-superprojects.yml

@@ -0,0 +1,16 @@
+name: Lint superprojects.json
+
+on:
+  pull_request:
+    paths:
+      - '.github/superprojects.json'
+  workflow_call:
+  workflow_dispatch:
+
+jobs:
+  lint-superprojects:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: usgs-coupled-subtrees/sync-subtrees-action/lint-superprojects/@main
+        with:
+          ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}

examples/com/.github/workflows/subtree.yml

@@ -0,0 +1,37 @@
+name: Sync Subtrees
+
+on:
+  push:
+    branches:
+      - master
+  workflow_dispatch:
+    inputs:
+      dryRun:
+        description: 'If true, don’t push any changes (for testing only).'
+        required: true
+        default: false
+        type: boolean
+      testMerge:
+        description: 'Run in test mode, pushing to a test branch.'
+        required: true
+        default: false
+        type: boolean
+
+jobs:
+  sync-subtrees:
+    if: startsWith(github.repository, 'usgs-coupled-subtrees/')
+    runs-on: ubuntu-latest
+    env:
+      CI_SERVER_HOST: github.com
+      GROUP: usgs-coupled
+      GH_TOKEN: ${{ secrets.WORKFLOW_PAT }}
+    steps:
+      - name: Run sync-subtrees-action
+        uses: usgs-coupled-subtrees/sync-subtrees-action@main
+        with:
+          dryRun: ${{ inputs.dryRun }}
+          testMerge: ${{ inputs.testMerge }}
+          repository_name: ${{ github.event.repository.name }}
+          default_branch: ${{ github.event.repository.default_branch }}
+          run_number: ${{ github.run_number }}
+          ssh_private_key: ${{ secrets.SSH_PRIVATE_KEY }}

examples/com/python/parallel_advect.py

@@ -214,7 +214,7 @@ class ReactionModel(object):
 class PhreeqcCalculator(object):
     """All PHREEQC calculations happen here.
 
-    This is the only place where we interact wit IPhreeqc.
+    This is the only place where we interact with IPhreeqc.
     Each instance of this class might run in a different
     process using `multiprocessing`.
     """

examples/fortran/.github/subtrees.json

@@ -0,0 +1 @@
+[]

examples/fortran/.github/superprojects.json

@@ -0,0 +1,9 @@
+{
+  "usgs-coupled-subtrees/phreeqc-COMManuscript-CGfinal-examples-fortran": {
+    "superprojects": [
+      "usgs-coupled-subtrees/iphreeqc",
+      "usgs-coupled-subtrees/iphreeqccom",
+      "usgs-coupled-subtrees/phreeqc"
+    ]
+  }
+}

examples/fortran/.github/workflows/lint-subtrees.yml

@@ -0,0 +1,19 @@
+name: Lint subtrees.json
+
+on:
+  pull_request:
+    paths:
+      - '.github/subtrees.json'
+  workflow_call:
+  workflow_dispatch:
+
+jobs:
+  lint-subtrees:
+    runs-on: ubuntu-latest
+    env:
+      CI_SERVER_HOST: github.com
+      GROUP: usgs-coupled
+    steps:
+      - uses: usgs-coupled-subtrees/sync-subtrees-action/lint-subtrees/@main
+        with:
+          ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}

examples/fortran/.github/workflows/lint-superprojects.yml

@@ -0,0 +1,16 @@
+name: Lint superprojects.json
+
+on:
+  pull_request:
+    paths:
+      - '.github/superprojects.json'
+  workflow_call:
+  workflow_dispatch:
+
+jobs:
+  lint-superprojects:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: usgs-coupled-subtrees/sync-subtrees-action/lint-superprojects/@main
+        with:
+          ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}

examples/fortran/.github/workflows/subtree.yml

@@ -0,0 +1,37 @@
+name: Sync Subtrees
+
+on:
+  push:
+    branches:
+      - master
+  workflow_dispatch:
+    inputs:
+      dryRun:
+        description: 'If true, don’t push any changes (for testing only).'
+        required: true
+        default: false
+        type: boolean
+      testMerge:
+        description: 'Run in test mode, pushing to a test branch.'
+        required: true
+        default: false
+        type: boolean
+
+jobs:
+  sync-subtrees:
+    if: startsWith(github.repository, 'usgs-coupled-subtrees/')
+    runs-on: ubuntu-latest
+    env:
+      CI_SERVER_HOST: github.com
+      GROUP: usgs-coupled
+      GH_TOKEN: ${{ secrets.WORKFLOW_PAT }}
+    steps:
+      - name: Run sync-subtrees-action
+        uses: usgs-coupled-subtrees/sync-subtrees-action@main
+        with:
+          dryRun: ${{ inputs.dryRun }}
+          testMerge: ${{ inputs.testMerge }}
+          repository_name: ${{ github.event.repository.name }}
+          default_branch: ${{ github.event.repository.default_branch }}
+          run_number: ${{ github.run_number }}
+          ssh_private_key: ${{ secrets.SSH_PRIVATE_KEY }}

gtest/CMakeLists.txt

@@ -128,6 +128,12 @@ configure_file(
   COPYONLY
   )
 
+configure_file(
+  ../database/stimela.dat
+  stimela.dat
+  COPYONLY
+  )
+
 configure_file(
   ../database/ColdChem.dat
   ColdChem.dat

gtest/TestIPhreeqc.cpp

@@ -26,7 +26,7 @@ TEST(TestIPhreeqc, TestLoadDatabase)
 	std::string FILES[] = { "phreeqc.dat", "pitzer.dat", "wateq4f.dat",
 		"Amm.dat", "frezchem.dat", "iso.dat",
 		"llnl.dat", "minteq.dat", "minteq.v4.dat",
-		"sit.dat","ColdChem.dat","core10.dat",
+		"sit.dat", "stimela.dat" ,"ColdChem.dat","core10.dat", 
 		"Tipping_Hurley.dat"
 	};
 
@@ -283,7 +283,7 @@ TEST(TestIPhreeqc, TestSetErrorOn)
 	ASSERT_EQ(false, ::FileExists("missing.file"));
 
 	IPhreeqc obj;
-	ASSERT_EQ(true, obj.GetErrorOn());			// intial setting is true
+	ASSERT_EQ(true, obj.GetErrorOn());			// initial setting is true
 
 	obj.SetErrorOn(false);
 	ASSERT_EQ(false, obj.GetErrorOn());
@@ -314,7 +314,7 @@ TEST(TestIPhreeqc, TestSetErrorOn2)
 	obj.SetErrorFileOn(true);
 	obj.SetErrorFileName(ERR_FILENAME);
 
-	ASSERT_EQ(true, obj.GetErrorOn());			// intial setting is true
+	ASSERT_EQ(true, obj.GetErrorOn());			// initial setting is true
 
 	obj.SetErrorOn(false);
 	ASSERT_EQ(false, obj.GetErrorOn());
@@ -3829,7 +3829,7 @@ TEST(TestIPhreeqc, TestCErrorReporter)
 TEST(TestIPhreeqc, TestDelete)
 {
 	const char input[] =
-		"SOLUTION 1 # definition of intial condition 1\n"
+		"SOLUTION 1 # definition of initial condition 1\n"
 		"COPY cell 1 7405 # copy cell 1 to placeholder cell with index larger than the number of cells in the model domain\n"
 		"END\n"
 		"DELETE # delete initial condition 1 to allow for a redefinition of all reactions\n"

gtest/TestIPhreeqcLib.cpp

@@ -128,7 +128,7 @@ TEST(TestIPhreeqcLib, TestLoadDatabase)
 	std::string FILES[] = { "phreeqc.dat", "pitzer.dat", "wateq4f.dat",
 		"Amm.dat", "frezchem.dat", "iso.dat",
 		"llnl.dat", "minteq.dat", "minteq.v4.dat",
-		"sit.dat","ColdChem.dat","core10.dat",
+		"sit.dat", "stimela.dat", "ColdChem.dat","core10.dat",
 		"Tipping_Hurley.dat"
 	};
 
@@ -190,7 +190,7 @@ TEST(TestIPhreeqcLib, TestSetErrorOn)
 	int n = ::CreateIPhreeqc();
 	ASSERT_TRUE(n >= 0);
 
-	ASSERT_EQ(1, ::GetErrorOn(n));			// intial setting is true
+	ASSERT_EQ(1, ::GetErrorOn(n));			// initial setting is true
 	ASSERT_EQ(IPQ_OK, ::SetErrorOn(n, 0));
 	ASSERT_EQ(0, ::GetErrorOn(n));
 
@@ -4005,7 +4005,7 @@ TEST(TestIPhreeqcLib, TestIEEE)
 TEST(TestIPhreeqcLib, TestDelete)
 {
 	const char input[] =
-		"SOLUTION 1 # definition of intial condition 1\n"
+		"SOLUTION 1 # definition of initial condition 1\n"
 		"COPY cell 1 7405 # copy cell 1 to placeholder cell with index larger than the number of cells in the model domain\n"
 		"END\n"
 		"DELETE # delete initial condition 1 to allow for a redefinition of all reactions\n"

jenkins-dist.sh

@@ -17,7 +17,7 @@
 #   from the top-level of a branches/0.24.2 working copy will create
 #   the 0.24.2 release tarball.
 #
-#   When building a alpha, beta or rc tarballs pass the apppropriate flag
+#   When building a alpha, beta or rc tarballs pass the appropriate flag
 #   followed by the number for that release.  For example you'd do
 #   the following for a Beta 1 release:
 #      ./dist.sh -v 1.1.0 -r 10277 -pr branches/1.1.x -beta 1

litephreeqc/CMakeLists.txt

@@ -1,4 +1,5 @@
-set(POET_SOURCE_FILES
+
+set(LPQC_SOURCE_FILES
     src/Engine.cpp
     src/Runner.cpp 
     src/Knobs.cpp
@@ -20,19 +21,19 @@ set(POET_SOURCE_FILES
     src/PhreeqcMatrix/Misc.cpp
 )
 
-add_library(IPhreeqcPOET ${POET_SOURCE_FILES})
-target_link_libraries(IPhreeqcPOET PUBLIC IPhreeqc)
-target_include_directories(IPhreeqcPOET PUBLIC
+add_library(litephreeqc STATIC ${LPQC_SOURCE_FILES})
+target_link_libraries(litephreeqc PUBLIC IPhreeqc)
+target_include_directories(litephreeqc PUBLIC
     $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
     $<INSTALL_INTERFACE:include>)
 
 # Set C++20 standard
-target_compile_features(IPhreeqcPOET PUBLIC cxx_std_20)
+target_compile_features(litephreeqc PUBLIC cxx_std_20)
 
 if (BUILD_TESTING AND STANDALONE_BUILD)
     enable_testing()
 
-    set(POET_TEST_SOURCE_FILES
+    set(LPQC_TEST_SOURCE_FILES
         test/testPhreeqcEngine.cpp
         test/testPhreeqcMatrix.cpp
         test/testPhreeqcRunner.cpp
@@ -41,15 +42,15 @@ if (BUILD_TESTING AND STANDALONE_BUILD)
         test/IPhreeqcReader.cpp
     )
 
-    add_executable(poet_test ${POET_TEST_SOURCE_FILES})
+    add_executable(litephreeqc_test ${LPQC_TEST_SOURCE_FILES})
 
     target_link_libraries(
-        poet_test
-        IPhreeqcPOET
+        litephreeqc_test
+        litephreeqc
         GTest::gtest_main
     )
 
-    target_include_directories(poet_test PRIVATE ${CMAKE_CURRENT_BINARY_DIR})
+    target_include_directories(litephreeqc_test PRIVATE ${CMAKE_CURRENT_BINARY_DIR})
 
     # read file and store in variable
     file(REAL_PATH "${PROJECT_SOURCE_DIR}/database/phreeqc.dat" POET_PHREEQCDAT_DB)
@@ -59,11 +60,11 @@ if (BUILD_TESTING AND STANDALONE_BUILD)
     configure_file("${CMAKE_CURRENT_SOURCE_DIR}/test/testInput.hpp.in" "${CMAKE_CURRENT_BINARY_DIR}/testInput.hpp")
 
     include(GoogleTest)
-    gtest_discover_tests(poet_test)
+    gtest_discover_tests(litephreeqc_test)
 endif()
 
-add_executable(testGolemRunner test/testGolemRunner.cpp)
-target_link_libraries(testGolemRunner IPhreeqcPOET)
+add_executable(golemrunner test/testGolemRunner.cpp)
+target_link_libraries(golemrunner litephreeqc)
 
 add_executable(testGetters     test/testGetters.cpp)
-target_link_libraries(testGetters IPhreeqcPOET)
+target_link_libraries(testGetters litephreeqc)

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>

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>

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>

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"

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)

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>

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>

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"

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/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

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