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hprats committed Nov 27, 2024
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20 changes: 11 additions & 9 deletions CHANGELOG.md
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Expand Up @@ -5,26 +5,28 @@ All notable changes to this project will be documented in this file.
## [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.
- **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.
- **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.
- **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**:
- 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.
- `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` now is built from a `GasModel`, an `EnergeticsModel`, a `ReactionModel` and a `LatticeModel`.
- **Building a `KMCModel`**: the `KMCModel` construction process now requires 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.
- **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](https://zacrostools.readthedocs.io/en/latest/).

Full details are available in the [ZacrosTools CHANGELOG](https://github.com/hprats/ZacrosTools/blob/main/CHANGELOG.md).

## [1.3] 07-Nov-2024

### Added
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18 changes: 9 additions & 9 deletions docs/source/index.md
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Expand Up @@ -76,24 +76,24 @@ The ZacrosTools documentation is organized into the following sections:
### [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.
- **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.
- **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.
- **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**:
- 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.
- `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` now is built from a `GasModel`, an `EnergeticsModel`, a `ReactionModel` and a `LatticeModel`.
- **Building a `KMCModel`**: the `KMCModel` construction process now requires 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.
- **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](https://zacrostools.readthedocs.io/en/latest/).

Full details are available in the [ZacrosTools CHANGELOG](https://github.com/hprats/ZacrosTools/blob/main/CHANGELOG.md).
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