Global Sensitivity analysis and conversion of all notebooks to jupytext #3
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First:
conda install jupytext
Then run this:
grep -rl '"language": "julia"' . --include="*.ipynb" \
| while read -r nb; do
echo "Pairing $nb"
jupytext --set-formats ipynb,jl "$nb"
done
grep -rl '"language": "julia"' . --include="*.ipynb" \
| while read -r nb; do
# Normalize to repo-relative path without leading "./"
nb_clean=$(realpath --relative-to="$(git rev-parse --show-toplevel)" "$nb")
# Append to .gitignore if not already present
if ! grep -qx "$nb_clean" .gitignore 2>/dev/null; then
echo "$nb_clean" >> .gitignore
echo "Added $nb_clean to .gitignore"
fi
# Remove from git index without deleting it locally
git rm --cached "$nb"
echo "Untracked $nb_clean from git"
done
When adding Volmer and Heyrovsky, it was not able to solve until I changed the boundary layer thickness from 1mm to 1 um. also changed some plots
Adjusted the Morris GSA and it converged
The GlobalSensitivity has results but require more probe to conclude the findings
added the exact code used in the Morris GlobalSensitivity.jl doc
You still need to manually sync sometimes. Try: jupytext --sync */*.jl
Nothing major yet.
Open
But think I broke something
Trying to make a Project.toml
this tells Julia Pkg thing what to install
This explicitly shows that ReactionMechanismSimulator is being loaded from your local path. This makes it crystal clear when you (or collaborators) look at the file that it's a development version, not the official package. Presumes it's alongside the current project
Presumably this is better (or at least more stable)
Changed the Pkg to activate the current project. ALso swapped to Cu mechanism. BUT DIDN"T CHANGE ANY FIGURE LABELS or anything else
It should help you get started from the project.toml
Volmer and Heyrosky Ea and A were added from BEP paper for Ag
Volmer and Heyrovsky mechanism with their Ea and A values were added fro BEP paper
the delete was an error
Volmer and Heyrovsky Ea and A values were added for Cu
Morris method for the Cu and Ag but Sobol method still needs accuracy for capturing the error
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This has Torrie01's global sensitivity analysis branch rebased into it, but I also converted everything to .jl files from .ipynb using jupytext, before rebasing and fixing conflicts.
You need to
conda install jupytextinto your conda environment.You can manually
jupytext --sync *.jlto make syncronize between your .ipynb and .jl files.In VSCode I am using https://marketplace.visualstudio.com/items?itemName=caenrigen.jupytext-sync to automatically sync.
But you might need to point it to a newer conda environment than is compatible with RMG-Py, just to get a recent enough version of jupytext.