Merge branch 'main' into compute_thermo

ReactionMechanismGenerator · Nov 10, 2023 · 9d359fc · 9d359fc
2 parents d3cd2de + cf69799
commit 9d359fc
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diff --git a/.github/workflows/cont_int.yml b/.github/workflows/cont_int.yml
@@ -17,6 +17,17 @@ jobs:
         - name: Checkout T3
           uses: actions/checkout@v3
 
+        - name: Clean Ubuntu Image
+          uses: kfir4444/free-disk-space@main
+          with:
+            # This may remove tools actually needed - currently does not
+            tool-cache: true
+            android: true
+            dotnet: true
+            haskell: true
+            large-packages: true
+            swap-storage: true
+
         - name: Cache RMG
           id: cache-rmg
           uses: actions/cache@v2
@@ -97,7 +108,7 @@ jobs:
               conda-${{ runner.os }}--${{ runner.arch }}-rmgpyenv-${{ env.CACHE_NUMBER}}
           env:
             # Increase this value to reset cache if etc/example-environment.yml has not changed
-            CACHE_NUMBER: 0
+            CACHE_NUMBER: 1
           id: cache-rmgpy-env
         - name: Update environment
           run: mamba env update -n rmg_env -f RMG-Py/environment.yml
@@ -107,6 +118,7 @@ jobs:
           run: |
             cd RMG-Py
             conda activate rmg_env
+            make clean
             make
             echo "PYTHONPATH=$(pwd):$PYTHONPATH" >> $GITHUB_ENV
             echo "PATH=$(pwd):$PATH" >> $GITHUB_ENV
@@ -115,9 +127,7 @@ jobs:
             echo "PATH=$(pwd):$PATH" >> ~/.bashrc
             echo "export rmgpy_path=$(pwd)" >> ~/.bashrc
         
-        - name: Install PyCall RMG_ENV
-          run: python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
-
+
         - name: Cache RMS
           id: cache-rms
           uses: actions/cache@v2
@@ -133,12 +143,10 @@ jobs:
                 ${{ runner.os }}-julia-${{ env.CACHE_NUMBER }}-rms
 
         - name: Install RMS Julia
-          run: julia -e 'using Pkg; Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main"));using ReactionMechanismSimulator'
+          run: julia -e 'using Pkg; Pkg.add(PackageSpec(name="PyCall",rev="master"));Pkg.build("PyCall");Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator;'
 
-        - name: Link Python-JL
-          run: |
-            ln -sfn $(which python-jl) $(which python)
-            cd .. 
+        - name: Install PyCall RMG_ENV
+          run: python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"
 
         - name: Install ARC ENV
           run: |

diff --git a/.github/workflows/docker_build.yml b/.github/workflows/docker_build.yml
@@ -1,14 +1,16 @@
 name: Docker Image Build and Push
 
 on:
+  schedule:
+    - cron: "0 0 */7 * *" # every 7 days
   push:
     branches:
         - main
   pull_request:
     branches:
         - main
     paths:
-        - 'devtools/Dockerfile'
+        - './Dockerfile'
 jobs:
   ci-check:
     if: github.event_name == 'pull_request'
@@ -27,7 +29,7 @@ jobs:
         uses: docker/build-push-action@v2
         with:
           context: .
-          file: ./devtools/Dockerfile
+          file: ./Dockerfile
           push: false
 
   build-and-push:
@@ -54,7 +56,7 @@ jobs:
       uses: docker/build-push-action@v2
       with:
         context: .
-        file: ./devtools/Dockerfile
+        file: ./Dockerfile
         push: true
         tags: ${{ secrets.DOCKERHUB_USERNAME }}/thetandemtool-t3:latest
 
diff --git a/devtools/Dockerfile → Dockerfile b/devtools/Dockerfile → Dockerfile
@@ -61,7 +61,10 @@ RUN micromamba create -y -f environment.yml && \
 # Add alias to bashrc - rmge to activate the environment
 # These commands are not necessary for the Docker image to run, but they are useful for the user
 RUN echo "alias arce='micromamba activate arc_env'" >> ~/.bashrc \
+    && echo "export PYTHONPATH=/home/rmguser/Code/ARC:$PYTHONPATH" >> ~/.bashrc \
+    && echo "export PYTHONPATH=\"${PYTHONPATH}:/home/rmguser/Code/AutoTST\"" >> ~/.bashrc \
     && echo "alias arc='python /home/rmguser/Code/ARC/ARC.py input.yml'" >> ~/.bashrc \
+    && echo "export PYTHONPATH=\"${PYTHONPATH}:/home/rmguser/Code/TS-GCN\"" >> ~/.bashrc \
     && echo "alias deact='micromamba deactivate'" >> ~/.bashrc \
     && echo "export arc_path='/home/rmguser/Code/ARC/'" >> ~/.bashrc \
     && echo "export t3_path='/home/rmguser/Code/T3/'" >> ~/.bashrc \

diff --git a/README.md b/README.md
@@ -2,7 +2,7 @@
   <a href="https://reactionmechanismgenerator.github.io/T3/"><img src="https://github.com/ReactionMechanismGenerator/T3/blob/main/grf/T3_logo_small.gif" alt="T3"></a>
 </p>
 
-# The Tandem Tool (T3) for automated kinetic model generation and refinement
+# The Tandem Tool (T3) for automated chemical kinetic model development
 
 ![Release](https://img.shields.io/badge/version-0.1.0-blue.svg)
 ![Build Status](https://github.com/ReactionMechanismGenerator/T3/actions/workflows/cont_int.yml/badge.svg)

diff --git a/devtools/Dockerfile_rmgpy b/devtools/Dockerfile_rmgpy
@@ -16,8 +16,6 @@ RUN usermod "--login=${NEW_MAMBA_USER}" "--home=/home/${NEW_MAMBA_USER}" \
         --move-home "-u ${NEW_MAMBA_USER_ID}" "${MAMBA_USER}" && \
     groupmod "--new-name=${NEW_MAMBA_USER}" \
              "-g ${NEW_MAMBA_USER_GID}" "${MAMBA_USER}" && \
-    # Update the expected value of MAMBA_USER for the
-    # _entrypoint.sh consistency check.
     echo "${NEW_MAMBA_USER}" > "/etc/arg_mamba_user" && \
     :
 
@@ -41,11 +39,12 @@ RUN apt-get update && apt-get install -y \
     make \
     libgomp1\
     libxrender1 \
+    sudo \
     && apt-get clean \
     && apt-get autoclean \
     && apt-get autoremove -y \
-    && rm -rf /var/lib/apt/lists/*
-
+    && rm -rf /var/lib/apt/lists/*\
+    && echo "${NEW_MAMBA_USER} ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
 # Change user to the non-root user
 USER $MAMBA_USER
 
@@ -64,6 +63,7 @@ WORKDIR /home/rmguser/Code/RMG-Py
 
 # Install RMG-Py and then clean up the micromamba cache
 RUN micromamba create -y -f environment.yml && \
+    micromamba install -n rmg_env -c conda-forge conda && \
     micromamba clean --all -f -y
 
 # Activate the RMG environment
@@ -88,7 +88,7 @@ RUN make \
 # The extra arguments are required to install PyCall and RMS in this Dockerfile. Will not work without them.
 # Final command is to compile the RMS during Docker build - This will reduce the time it takes to run RMS for the first time
 RUN touch /opt/conda/envs/rmg_env/condarc-julia.yml
-RUN CONDA_JL_CONDA_EXE=/bin/micromamba julia -e 'using Pkg;Pkg.add(PackageSpec(name="PyCall", rev="master")); Pkg.build("PyCall"); Pkg.add(PackageSpec(name="ReactionMechanismSimulator", rev="main"))' \
+RUN CONDA_JL_CONDA_EXE=/bin/micromamba julia -e 'ENV["CONDA_JL_CONDA_EXE"]="/opt/conda/envs/rmg_env/bin/conda";using Pkg;Pkg.add(PackageSpec(name="PyCall", rev="master")); Pkg.build("PyCall"); Pkg.add(PackageSpec(name="ReactionMechanismSimulator", rev="main"))' \
     && python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()" \
     && python-jl -c "from pyrms import rms"
 

diff --git a/docs/cite.md b/docs/cite.md
@@ -2,15 +2,15 @@
 
 Text form:
 
-    A. Grinberg Dana, K.A. Spiekermann, W.H. Green, 
-    The Tandem Tool (T3) for automated kinetic model generation and refinement, 
+    C. Pieters, K. Kaplan, K.A. Spiekermann, W.H. Green, A. Grinberg Dana,
+    The Tandem Tool (T3) for automated chemical kinetic model development, 
     version 0.1.0, source code: https://github.com/ReactionMechanismGenerator/T3
 
 LaTeX form:
 
     @misc{T3,
-      author = {A. Grinberg Dana, K.A. Spiekermann, W.H. Green},
-      title = {The Tandem Tool (T3) for automated kinetic model generation and refinement. https://github.com/ReactionMechanismGenerator/T3, Version 0.1.0},
-      year = {2020},
+      author = {C. Pieters, K. Kaplan, K.A. Spiekermann, W.H. Green, A. Grinberg Dana,},
+      title = {The Tandem Tool (T3) for automated chemical kinetic model development. https://github.com/ReactionMechanismGenerator/T3, Version 0.1.0},
+      year = {2023},
       howpublished = {\url{https://github.com/ReactionMechanismGenerator/T3}},
     }
diff --git a/docs/index.md b/docs/index.md
@@ -3,7 +3,7 @@
   <img src="T3_logo_small.gif" alt="T3"></a>
 </p>
 <p align="center">
-    <em>The Tandem Tool for automated kinetic model generation and refinement</em>
+    <em>The Tandem Tool for automated chemical kinetic model development</em>
 </p>
 <p align="center">
 <a href="https://github.com/ReactionMechanismGenerator/T3/releases" target="_blank">

diff --git a/environment.yml b/environment.yml
@@ -3,6 +3,7 @@ channels:
   - conda-forge
 dependencies:
   - python=3.7
+  - pydot
   - cantera=2.6
   - ca-certificates
   - openssl

diff --git a/ipython/flux_diagram/Generate Flux Diagram.ipynb b/ipython/flux_diagram/Generate Flux Diagram.ipynb
diff --git a/ipython/flux_diagram/HOCHO_flux_diagrams/bar_ROPs/H(3)_2.0_s.png b/ipython/flux_diagram/HOCHO_flux_diagrams/bar_ROPs/H(3)_2.0_s.png
diff --git a/ipython/flux_diagram/HOCHO_flux_diagrams/bar_ROPs/HOCHO(1)_2.0_s.png b/ipython/flux_diagram/HOCHO_flux_diagrams/bar_ROPs/HOCHO(1)_2.0_s.png
diff --git a/ipython/flux_diagram/HOCHO_flux_diagrams/bar_ROPs/HOCO(10)_2.0_s.png b/ipython/flux_diagram/HOCHO_flux_diagrams/bar_ROPs/HOCO(10)_2.0_s.png
diff --git a/ipython/flux_diagram/HOCHO_flux_diagrams/flux_diagrams/H(3)/flux_diagram_2.0_s.dot b/ipython/flux_diagram/HOCHO_flux_diagrams/flux_diagrams/H(3)/flux_diagram_2.0_s.dot
@@ -0,0 +1,36 @@
+digraph G {
+label="Flux diagram at 2.0 s, ROP range: [8.01e-17, 1.51e-02] mol/cm³/s)";
+"H(3)" [fillcolor="#DCE5F4", fontsize=8, penwidth=1.7530392047540462, style=filled, xlabel="2.80e-11"];
+"CO(8)" [fontsize=8, penwidth=3.999999999999999, xlabel="4.68e-05"];
+"H2(4)" [fontsize=8, penwidth=3.927639860174137, xlabel="2.95e-05"];
+"OH(5)" [fontsize=8, penwidth=1.6100755035270433, xlabel="1.12e-11"];
+"H(3)" -> "CO(8)"  [arrowhead=vee, fontsize=8, label="0.9\n+ HOCHO(1)\n- H2(4) - OH(5)", penwidth=3.984676425213845];
+"H(3)" -> "H2(4)"  [arrowhead=vee, fontsize=8, label="0.9\n+ HOCHO(1)\n- CO(8) - OH(5)", penwidth=3.984676425213845];
+"H(3)" -> "OH(5)"  [arrowhead=vee, fontsize=8, label="0.9\n+ HOCHO(1)\n- CO(8) - H2(4)", penwidth=3.984676425213845];
+"HOCO(10)" [fontsize=8, penwidth=0.5383397186827532, xlabel="1.21e-14"];
+"H(3)" -> "H2(4)"  [arrowhead=vee, fontsize=8, label="0.2\n+ HOCHO(1)\n- HOCO(10)", penwidth=3.7536269933534743];
+"H(3)" -> "HOCO(10)"  [arrowhead=vee, fontsize=8, label="0.2\n+ HOCHO(1)\n- H2(4)", penwidth=3.7536269933534743];
+"HOCO(10)" -> "CO(8)"  [arrowhead=vee, fontsize=8, label="1.0\n- OH(5)", penwidth=3.997757463516357];
+"HOCO(10)" -> "OH(5)"  [arrowhead=vee, fontsize=8, label="1.0\n- CO(8)", penwidth=3.997757463516357];
+"CO2(9)" [fontsize=8, penwidth=3.927639907930275, xlabel="2.95e-05"];
+"H2O(17)" [fontsize=8, penwidth=3.9999999645295996, xlabel="4.68e-05"];
+"OH(5)" -> "CO2(9)"  [arrowhead=vee, fontsize=8, label="1.0\n+ HOCHO(1)\n- H(3) - H2O(17)", penwidth=4.0];
+"OH(5)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="1.0\n+ HOCHO(1)\n- CO2(9) - H2O(17)", penwidth=4.0];
+"OH(5)" -> "H2O(17)"  [arrowhead=vee, fontsize=8, label="1.0\n+ HOCHO(1)\n- CO2(9) - H(3)", penwidth=4.0];
+"OH(5)" -> "H2O(17)"  [arrowhead=vee, fontsize=8, label="0.8\n+ HOCHO(1)\n- HOCO(10)", penwidth=3.9539926576457947];
+"OH(5)" -> "HOCO(10)"  [arrowhead=vee, fontsize=8, label="0.8\n+ HOCHO(1)\n- H2O(17)", penwidth=3.9539926576457947];
+"OCHO(11)" [fontsize=8, penwidth=0.19999999999999937, xlabel="1.40e-15"];
+"OH(5)" -> "H2O(17)"  [arrowhead=vee, fontsize=8, label="0.1\n+ HOCHO(1)\n- OCHO(11)", penwidth=3.67123391780574];
+"OH(5)" -> "OCHO(11)"  [arrowhead=vee, fontsize=8, label="0.1\n+ HOCHO(1)\n- H2O(17)", penwidth=3.67123391780574];
+"OCHO(11)" -> "CO2(9)"  [arrowhead=vee, fontsize=8, label="0.1\n- H(3)", penwidth=3.676279894902382];
+"OCHO(11)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="0.1\n- CO2(9)", penwidth=3.676279894902382];
+"H2O(17)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="4.3e-10\n- OH(5)", penwidth=0.43016435137560394];
+"H2O(17)" -> "OH(5)"  [arrowhead=vee, fontsize=8, label="4.3e-10\n- H(3)", penwidth=0.43016435137560394];
+"H2O(17)" -> "CO2(9)"  [arrowhead=vee, fontsize=8, label="1.1e-10\n+ CO(8)\n- H2(4)", penwidth=0.20000000000000034];
+"H2O(17)" -> "H2(4)"  [arrowhead=vee, fontsize=8, label="1.1e-10\n+ CO(8)\n- CO2(9)", penwidth=0.20000000000000034];
+"CO2(9)" -> "HOCO(10)"  [arrowhead=vee, fontsize=8, label="3.6e-08\n+ HOCHO(1)", penwidth=1.4627966491004998];
+"H2(4)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="1.0e-04\n+ OH(5)\n- H2O(17)", penwidth=2.483741242797586];
+"H2(4)" -> "H2O(17)"  [arrowhead=vee, fontsize=8, label="1.0e-04\n+ OH(5)\n- H(3)", penwidth=2.483741242797586];
+"CO(8)" -> "CO2(9)"  [arrowhead=vee, fontsize=8, label="2.0e-03\n+ OH(5)\n- H(3)", penwidth=2.9739529963274607];
+"CO(8)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="2.0e-03\n+ OH(5)\n- CO2(9)", penwidth=2.9739529963274607];
+}
diff --git a/ipython/flux_diagram/HOCHO_flux_diagrams/flux_diagrams/H(3)/flux_diagram_2.0_s.png b/ipython/flux_diagram/HOCHO_flux_diagrams/flux_diagrams/H(3)/flux_diagram_2.0_s.png
diff --git a/ipython/flux_diagram/HOCHO_flux_diagrams/flux_diagrams/HOCHO(1)/flux_diagram_2.0_s.dot b/ipython/flux_diagram/HOCHO_flux_diagrams/flux_diagrams/HOCHO(1)/flux_diagram_2.0_s.dot
@@ -0,0 +1,24 @@
+digraph G {
+label="Flux diagram at 2.0 s, ROP range: [8.01e-17, 1.51e-02] mol/cm³/s)";
+"HOCHO(1)" [fillcolor="#DCE5F4", fontsize=8, penwidth=4.0, style=filled, xlabel="1.69e-01"];
+"CO(8)" [fontsize=8, penwidth=2.6712938924744143, xlabel="4.68e-05"];
+"H2O(17)" [fontsize=8, penwidth=2.671293855796359, xlabel="4.68e-05"];
+"HOCHO(1)" -> "CO(8)"  [arrowhead=vee, fontsize=8, label="1.0\n- H2O(17)", penwidth=4.0];
+"HOCHO(1)" -> "H2O(17)"  [arrowhead=vee, fontsize=8, label="1.0\n- CO(8)", penwidth=4.0];
+"CO2(9)" [fontsize=8, penwidth=2.596470167350586, xlabel="2.95e-05"];
+"H2(4)" [fontsize=8, penwidth=2.5964701179685017, xlabel="2.95e-05"];
+"HOCHO(1)" -> "CO2(9)"  [arrowhead=vee, fontsize=8, label="0.6\n- H2(4)", penwidth=3.9466405710292745];
+"HOCHO(1)" -> "H2(4)"  [arrowhead=vee, fontsize=8, label="0.6\n- CO2(9)", penwidth=3.9466405710292745];
+"H(3)" [fontsize=8, penwidth=0.34783116462852137, xlabel="2.80e-11"];
+"H2(4)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="5.2e-09\n+ OH(5)\n- H2O(17)", penwidth=1.7955577099046087];
+"H2(4)" -> "H2O(17)"  [arrowhead=vee, fontsize=8, label="5.2e-09\n+ OH(5)\n- H(3)", penwidth=1.7955577099046087];
+"HOCO(10)" [fontsize=8, penwidth=0.7324480422152477, xlabel="1.21e-14"];
+"CO2(9)" -> "HOCO(10)"  [arrowhead=vee, fontsize=8, label="1.8e-12\n+ HOCHO(1)", penwidth=1.1729774870268643];
+"OH(5)" [fontsize=8, penwidth=0.2000000000000002, xlabel="1.12e-11"];
+"H2O(17)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="2.1e-14\n- OH(5)", penwidth=0.3608065303110556];
+"H2O(17)" -> "OH(5)"  [arrowhead=vee, fontsize=8, label="2.1e-14\n- H(3)", penwidth=0.3608065303110556];
+"H2O(17)" -> "CO2(9)"  [arrowhead=vee, fontsize=8, label="5.3e-15\n+ CO(8)\n- H2(4)", penwidth=0.2];
+"H2O(17)" -> "H2(4)"  [arrowhead=vee, fontsize=8, label="5.3e-15\n+ CO(8)\n- CO2(9)", penwidth=0.2];
+"CO(8)" -> "CO2(9)"  [arrowhead=vee, fontsize=8, label="1.0e-07\n+ OH(5)\n- H(3)", penwidth=2.138048850394896];
+"CO(8)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="1.0e-07\n+ OH(5)\n- CO2(9)", penwidth=2.138048850394896];
+}
diff --git a/.../flux_diagram/HOCHO_flux_diagrams/flux_diagrams/HOCHO(1)/flux_diagram_2.0_s.png b/.../flux_diagram/HOCHO_flux_diagrams/flux_diagrams/HOCHO(1)/flux_diagram_2.0_s.png
diff --git a/ipython/flux_diagram/HOCHO_flux_diagrams/flux_diagrams/HOCO(10)/flux_diagram_2.0_s.dot b/ipython/flux_diagram/HOCHO_flux_diagrams/flux_diagrams/HOCO(10)/flux_diagram_2.0_s.dot
@@ -0,0 +1,34 @@
+digraph G {
+label="Flux diagram at 2.0 s, ROP range: [8.01e-17, 1.51e-02] mol/cm³/s)";
+"HOCO(10)" [fillcolor="#DCE5F4", fontsize=8, penwidth=0.5383397186827532, style=filled, xlabel="1.21e-14"];
+"CO(8)" [fontsize=8, penwidth=3.999999999999999, xlabel="4.68e-05"];
+"OH(5)" [fontsize=8, penwidth=1.6100755035270433, xlabel="1.12e-11"];
+"HOCO(10)" -> "CO(8)"  [arrowhead=vee, fontsize=8, label="1.0\n- OH(5)", penwidth=3.997757463516357];
+"HOCO(10)" -> "OH(5)"  [arrowhead=vee, fontsize=8, label="1.0\n- CO(8)", penwidth=3.997757463516357];
+"CO2(9)" [fontsize=8, penwidth=3.927639907930275, xlabel="2.95e-05"];
+"H(3)" [fontsize=8, penwidth=1.7530392047540462, xlabel="2.80e-11"];
+"H2O(17)" [fontsize=8, penwidth=3.9999999645295996, xlabel="4.68e-05"];
+"OH(5)" -> "CO2(9)"  [arrowhead=vee, fontsize=8, label="1.0\n+ HOCHO(1)\n- H(3) - H2O(17)", penwidth=4.0];
+"OH(5)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="1.0\n+ HOCHO(1)\n- CO2(9) - H2O(17)", penwidth=4.0];
+"OH(5)" -> "H2O(17)"  [arrowhead=vee, fontsize=8, label="1.0\n+ HOCHO(1)\n- CO2(9) - H(3)", penwidth=4.0];
+"OH(5)" -> "H2O(17)"  [arrowhead=vee, fontsize=8, label="0.8\n+ HOCHO(1)\n- HOCO(10)", penwidth=3.9539926576457947];
+"OH(5)" -> "HOCO(10)"  [arrowhead=vee, fontsize=8, label="0.8\n+ HOCHO(1)\n- H2O(17)", penwidth=3.9539926576457947];
+"OCHO(11)" [fontsize=8, penwidth=0.19999999999999937, xlabel="1.40e-15"];
+"OH(5)" -> "H2O(17)"  [arrowhead=vee, fontsize=8, label="0.1\n+ HOCHO(1)\n- OCHO(11)", penwidth=3.67123391780574];
+"OH(5)" -> "OCHO(11)"  [arrowhead=vee, fontsize=8, label="0.1\n+ HOCHO(1)\n- H2O(17)", penwidth=3.67123391780574];
+"OCHO(11)" -> "CO2(9)"  [arrowhead=vee, fontsize=8, label="0.1\n- H(3)", penwidth=3.676279894902382];
+"OCHO(11)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="0.1\n- CO2(9)", penwidth=3.676279894902382];
+"H2O(17)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="4.3e-10\n- OH(5)", penwidth=0.43016435137560394];
+"H2O(17)" -> "OH(5)"  [arrowhead=vee, fontsize=8, label="4.3e-10\n- H(3)", penwidth=0.43016435137560394];
+"H2(4)" [fontsize=8, penwidth=3.927639860174137, xlabel="2.95e-05"];
+"H2O(17)" -> "CO2(9)"  [arrowhead=vee, fontsize=8, label="1.1e-10\n+ CO(8)\n- H2(4)", penwidth=0.20000000000000034];
+"H2O(17)" -> "H2(4)"  [arrowhead=vee, fontsize=8, label="1.1e-10\n+ CO(8)\n- CO2(9)", penwidth=0.20000000000000034];
+"H(3)" -> "CO(8)"  [arrowhead=vee, fontsize=8, label="0.9\n+ HOCHO(1)\n- H2(4) - OH(5)", penwidth=3.984676425213845];
+"H(3)" -> "H2(4)"  [arrowhead=vee, fontsize=8, label="0.9\n+ HOCHO(1)\n- CO(8) - OH(5)", penwidth=3.984676425213845];
+"H(3)" -> "OH(5)"  [arrowhead=vee, fontsize=8, label="0.9\n+ HOCHO(1)\n- CO(8) - H2(4)", penwidth=3.984676425213845];
+"H(3)" -> "H2(4)"  [arrowhead=vee, fontsize=8, label="0.2\n+ HOCHO(1)\n- HOCO(10)", penwidth=3.7536269933534743];
+"H(3)" -> "HOCO(10)"  [arrowhead=vee, fontsize=8, label="0.2\n+ HOCHO(1)\n- H2(4)", penwidth=3.7536269933534743];
+"CO2(9)" -> "HOCO(10)"  [arrowhead=vee, fontsize=8, label="3.6e-08\n+ HOCHO(1)", penwidth=1.4627966491004998];
+"CO(8)" -> "CO2(9)"  [arrowhead=vee, fontsize=8, label="2.0e-03\n+ OH(5)\n- H(3)", penwidth=2.9739529963274607];
+"CO(8)" -> "H(3)"  [arrowhead=vee, fontsize=8, label="2.0e-03\n+ OH(5)\n- CO2(9)", penwidth=2.9739529963274607];
+}
diff --git a/.../flux_diagram/HOCHO_flux_diagrams/flux_diagrams/HOCO(10)/flux_diagram_2.0_s.png b/.../flux_diagram/HOCHO_flux_diagrams/flux_diagrams/HOCO(10)/flux_diagram_2.0_s.png
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -1,6 +1,6 @@
 # Project information
 site_name: T3
-site_description: The Tandem Tool for automated kinetic model generation and refinement
+site_description: The Tandem Tool for automated chemical kinetic model development
 site_author: Alon Grinberg Dana
 site_url: https://reactionmechanismgenerator.github.io/T3/
 

diff --git a/t3/common.py b/t3/common.py
@@ -17,6 +17,7 @@
 DATA_BASE_PATH = os.path.join(t3_path, 'tests', 'data')
 SIMULATE_DATA_BASE_PATH = os.path.join(t3_path, 'tests', 'test_simulate_adapters', 'data')
 EXAMPLES_BASE_PATH = os.path.join(t3_path, 'examples')
+SCRATCH_BASE_PATH = os.path.join(t3_path, 'tests', 'scratch')
 IPYTHON_SIMULATOR_EXAMPLES_PATH = os.path.join(t3_path, 'ipython', 'simulator_adapter_examples')
 PROJECTS_BASE_PATH = os.path.join(t3_path, 'Projects')
 VALID_CHARS = "-_=.,%s%s" % (string.ascii_letters, string.digits)

diff --git a/t3/logger.py b/t3/logger.py
@@ -123,7 +123,7 @@ def log_header(self):
                  f'################################################################\n'
                  f'#                                                              #\n'
                  f'#                  The   Tandem   Tool   (T3)                  #\n'
-                 f'#      Automated kinetic model generation and refinement       #\n'
+                 f'#       for automated chemical kinetic model development       #\n'
                  f'#                                                              #\n'
                  f'#                        Version: {VERSION}{" " * (10 - len(VERSION))}                   #\n'
                  f'#                                                              #\n'