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uclchem-tools

This repository can be used to efficiently interact with UCLCHEM in scenarios where you need to interact with UCLCHEM in a reproducible way between development versions or if you need to convert large amounts of data originally stored in csv into efficient HDF storage, and later load it.

List of tools:

  • scripts/new_uclchem.sh tool to generate new uclchem python environments given one root uclchem clone using the git worktree command. Example: bash script/new_uclchem.sh directory_with_patch commitish_of_patch
  • scripts/run_grid_converter.py Useful converter that can convert a grid of generated csv files into one large hdf5 file for space saving and efficient loading. See the documentation to see how you can generate a grid. Save
  • src/uclchem_tools/run/main.py Run UCLCHEM based on a configuration file as shown in configs/phase1-test.yaml. This is especially useful for development and comparison across different branches created by the command above, as you can specify which virtual environment should be used.
  • src/io/io.py File that takes csv outputs from a grid or uclchem run and converts it to HDF storage. This includes loaders to later load the data into memory again.