Version 2.1

[2.1] 27-Nov-2024

Added

• New classes and methods: create the following new classes from a Python dictionary, a Pandas DataFrame, or a .csv file.
  • GasModel: information about gas-phase species. Methods available: add_species and remove_species.
  • EnergeticsModel: information about each cluster in the cluster expansion. Methods available: add_cluster, remove_cluster and write_energetics_input.
  • ReactionModel: information about each elementary step. Methods available: add_step, remove_steps and write_mechanism_input.
• Automatic neighboring structure generation: use a distance criteria between site to automatically create the neighboring structure for a custom lattice model.
• Use total pressure in heatmap axis: now total_pressure can be chosen for the x or y axis in a heatmap plot to create pressure vs temperature heatmaps.
• New tests: added a new test for continuous integration with GitHub Actions that generates all input files and compares them with reference files.
• New parameters:
  • added sig_figs_lattice parameter in KMCModel.create_job_dir to control the number of significant figures used when writing coordinates in lattice_input.dat.
  • added show_max parameter in plot_heatmap to display a green 'x' marker at the point with the highest TOF.

Changed

• Building a KMCModel: the KMCModel now is built from a GasModel, an EnergeticsModel, a ReactionModel and a LatticeModel.

Improved

• Parsing of output files: parse_general_output can now parse general_output.txt files generated by Zacros version 2.x.
• Validation of parameters: improved the parsing and validation of selected parameters for all modules to prevent errors.
• Docstrings: all docstrings have been updated using the Numpy format.
• Documentation: Improved the ZacrosTools Documentation.

Full details are available in the ZacrosTools CHANGELOG.