Version 2.2

[2.2] 20-Dec-2024

Added

• Stiffness coefficients parsing: added to ability to parse stiffness coefficient information from general_output.txt using zacrostools.parse_general_output_file.
• Examples:
  • DRM_on_PtHfC: Demonstrates how to analyze hundreds of output files to generate heatmaps.
  • custom_lattice_models: Illustrates how to create custom lattice models for Zacros simulations..

Changed

• Analysis of output files:
  • Renamed window_percent to analysis_range
  • Renamed window_type to range_type

Improved

• Documentation: Improved the ZacrosTools Documentation.

Full details are available in the ZacrosTools CHANGELOG.

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.

Version 1.3

Added

• Comprehensive Test Suite with Pytest: Implemented a suite of tests using Pytest to ensure code reliability and facilitate future development.
• Continuous Integration with GitHub Actions: Set up CI workflows to automatically run tests on every push and pull request, enhancing code quality and preventing regressions.
• Enhanced Documentation:
  • Updated README.md with detailed installation instructions, usage examples, badges, and contributor guidelines.

Version 1.02

Added

• Added new parameters in KMCModel.create_job_dir in anticipation of a future version of Zacros.

Changed

• In KMCModel.create_job_dir method, parameter auto_scaling_steps has been renamed to stiffness_scaling_stepsand
  parameter auto_scaling_tags has been renamed to stiffness_scaling_tags.

Fixed

• Fixed bug where, if only one surface species was declared, surf_specs_dent would be an integer instead of a list.
• Fixed bug where the total pressure could be written as an integer, and then the simulation will crash.

Improved

• Now, ZacrosTools checks if the keywords provided in stiffness_scaling_tags are allowed.
• Improved the ZacrosTools Documentation.

Version 1.01

Added

• Added data validation and error handling in plot_result.py.
• ZacrosTools is now compatible with multidentate species.
• ZacrosTools is now compatible with default lattices.

Changed

• The detect_issues function now only considers the specified window percent.
• Default window_percent for detect_issues changed from [50, 100] to [30, 100].

Fixed

• Bug fix for cases where vibrational energies of 0.0 are specified in the reaction model.

Improved

• Improved the ZacrosTools Documentation.

Version 1.0.0

[1.0.0] - 2024-09-06

I am excited to announce the first stable release of ZacrosTools! This version marks a significant milestone as it transitions from beta to stable, incorporating user feedback and ensuring reliability and performance.

Getting Started:

To get started with ZacrosTools, please visit the Documentation.

Contributions:

We welcome contributions and feedback! If you find any issues or have suggestions for improvements, please open an issue or submit a pull request.

Acknowledgments:

I would like to thank Sharath Yadavalli and Zeyu Wu who have tested this library and provided feedback.