Skip to content

Latest commit

 

History

History
92 lines (69 loc) · 5.3 KB

CHANGELOG.md

File metadata and controls

92 lines (69 loc) · 5.3 KB

Changelog

All notable changes to this project are documented in this file.

[2.2] 20-Dec-2024

Added

  • Plot event frequencies: introduced the ability to parse the event frequencies from procstat_output.txt using zacrostools.procstat_output and visualize them.
  • Plot stiffness coefficients: added functionality to parse stiffness coefficient information from general_output.txt using zacrostools.parse_general_output_file and generate corresponding plots.
  • Examples:
    • DRM_on_PtHfC: Demonstrates how to analyze hundreds of output files to generate heatmaps and plot the event frequencies and stiffness coefficients.
    • 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

[2.1] 27-Nov-2024

Added

  • New classes and methods: introduced the following classes, which can be instantiated 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.
  • Total pressure in heatmap axes: the total_pressure parameter can now be selected for either the x or y axis in heatmap plots, enabling the creation of pressure vs temperature heatmaps.
  • Continuous integration tests: added a new test for GitHub Actions that generates all input files and compares them against reference files to ensure consistency.
  • New parameters:
    • sig_figs_lattice: added to KMCModel.create_job_dir to control the number of significant figures used when writing coordinates in lattice_input.dat.
    • show_max: added to plot_heatmap to display a green 'x' marker at the point with the highest TOF.

Changed

  • Building a KMCModel: the KMCModel construction process now requires a GasModel, an EnergeticsModel, a ReactionModel, and a LatticeModel.

Improved

  • Output file parsing: enhanced parse_general_output to support parsing general_output.txt files generated by Zacros version 2.x.
  • Parameter validation: improved the parsing and validation of selected parameters across all modules to prevent errors.
  • Docstrings: updated all docstrings to adhere to the NumPy format for better clarity and consistency.
  • Documentation: Improved the ZacrosTools Documentation.

[1.3] 07-Nov-2024

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.
  • Documentation:
    • Updated README.md with detailed installation instructions, usage examples, badges, and contributor guidelines.

[1.2] 06-Nov-2024

Added

  • New parameters in KMCModel.create_job_dir: Introduced new parameters in anticipation of a future version of Zacros.

Changed

  • Parameter renaming in KMCModel.create_job_dir:
    • Renamed auto_scaling_steps to stiffness_scaling_steps.
    • Renamed auto_scaling_tags to stiffness_scaling_tags.

Fixed

  • Surface species list bug: Resolved an issue where, if only one surface species was declared, surf_specs_dent would be an integer instead of a list.
  • Total pressure format: Fixed a bug where the total pressure could be written as an integer, causing simulation crashes.

Improved

  • Keyword validation: Added checks to ensure that the keywords provided in stiffness_scaling_tags are allowed.
  • Documentation enhancements: Improved the ZacrosTools Documentation.

[1.1] 13-Oct-2024

Added

  • Data validation in plot_result.py: Implemented data validation and error handling to improve robustness.
  • Support for multidentate species: ZacrosTools now supports multidentate species.
  • Compatibility with default lattices: Added support for default lattice configurations.

Changed

  • detect_issues function:
    • Adjusted the function to consider only the specified analysis range.
    • Changed default analysis_range from [50, 100] to [30, 100].

Fixed

  • Vibrational energies bug: Fixed an issue where specifying vibrational energies of 0.0 could cause unexpected behavior.

Improved

[1.0] 06-Sep-2024

Initial Release

  • Launched ZacrosTools with core functionalities for preparing Zacros input files and parsing output data.