reaxkit 1.0.0__tar.gz

reaxkit-1.0.0/AUTHORS.md

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+#  Authors and Acknowledgments
+
+**ReaxKit** was primarily developed by:
+
+- **Ali Mohammadi Dinani** – Project lead; design, and architecture; developing handlers, analyzers, and workflows
+- **Adri van Duin** - Supervision and support for ReaxKit; developing `xtob.f` and `place2.f` fortran codes used in `geo_generator.py`; developing ReaxFF
+
+### Code Contributions and Collaborations 
+
+
+Parts of this codebase were inspired by or adapted from work contributed by:
+
+- **[Yun Kyung Shin]** – developed the `elastic_energy.f` and `elastic_geo.f` fortran codes used in `trainset_generator.py`
+- **[Alireza Sepehrinezhad]** – developed the initial version of `make_eregime_sinusoidal` used in `eregime_generator.py` and `dipole_analyzer.py` code used in the `electrostatics_analyzers.py`
+
+Their original contributions have been modified and integrated with permission.
+
+---
+
+If you believe your contributions or ideas are reflected here and you’re not yet listed, please contact the maintainer.

reaxkit-1.0.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Ali Mohammadi Dinani
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the “Software”), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

reaxkit-1.0.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: reaxkit
+Version: 1.0.0
+Summary: A toolkit for parsing, analyzing, and visualizing ReaxFF simulation data.
+Author-email: Ali Mohammadi <alimohammadi2265@gmail.com>, Adri van Duin <acv13@psu.edu>, Yun Kyung Shin <yks2@psu.edu>, Alireza Sepehrinezhad <alireza.sepehri@psu.edu>
+License: MIT
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+License-File: AUTHORS.md
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: matplotlib
+Requires-Dist: seaborn
+Requires-Dist: scipy
+Requires-Dist: tqdm
+Requires-Dist: rich
+Requires-Dist: freud-analysis
+Requires-Dist: ovito
+Requires-Dist: tabulate
+Requires-Dist: ase
+Requires-Dist: imageio
+Requires-Dist: mp_api
+Requires-Dist: PyYAML
+Requires-Dist: rapidfuzz
+Dynamic: license-file
+
+# ReaxKit
+
+**ReaxKit** is a modular, extensible Python toolkit for **pre‑processing, post‑processing, and analysis of ReaxFF** molecular dynamics simulations.
+It provides a clean separation between file parsing, analysis routines, and reproducible workflows, with both **Python APIs** and a **CLI interface**.
+
+ReaxKit is designed for researchers who want a transparent, scriptable bridge between raw ReaxFF files and quantitative, publication‑ready results.
+
+---
+
+## Key Capabilities
+
+### File IO (Parsing & Generation)
+- Robust handlers for ReaxFF input and output files:
+  - `xmolout`, `fort.7`, `fort.13`, `molfra`, and more
+- Input file generators:
+  - `control`, `geo`, `eregime`, `tregime`, and more
+- Unified handler interface for consistent data access
+
+### Analysis
+- Per‑file analyzers (one analyzer per ReaxFF file type)
+- Composed analyzers that combine multiple data sources:
+  - Coordination numbers
+  - Connectivity graphs
+  - Electrostatics and dipoles
+  - Radial distribution functions (RDF)
+- Numerical utilities for smoothing, extrema detection, and signal processing
+
+### Workflows
+- Reproducible, CLI‑driven workflows for:
+  - Single‑file analysis
+  - Multi‑file composed analysis
+  - Plotting and media generation
+- Designed to automate common ReaxFF post‑processing tasks
+
+### Visualization & Media
+- Publication‑ready plotting utilities (2D, dual‑axis, tornado plots, 3D scatter, heatmaps)
+- Trajectory and plot video generation
+
+See the full documentation (API reference, tutorials, examples) on [ReaxKit Site](https://ali-m-dinani.github.io/reaxkit/).
+
+---
+
+## Project Layout
+
+```
+src/reaxkit/
+├── analysis/        # Analysis routines (per-file and composed)
+├── io/              # File handlers and generators
+├── utils/           # Shared utilities (aliases, units, constants, numerics)
+├── workflows/       # CLI and automation workflows
+├── help/            # Introspection and help system
+└── cli.py           # Command-line entry point
+```
+
+Additional resources:
+
+- [Installation notes](docs/installation.md) — Full installation instructions (requires **Python ≥ 3.9**).
+- [Quickstart](docs/quickstart.md) — Get up and running with core ReaxKit workflows in minutes.
+- [Tutorials notes](docs/tutorials/index.md) and [source files](https://ali-m-dinani.github.io/reaxkit/tutorials/) — Step-by-step guides for common ReaxKit workflows and use cases.
+- [Examples](docs/examples/README.md) and [source files](https://ali-m-dinani.github.io/reaxkit/examples/) — Minimal, runnable Python examples using public APIs.
+- [ReaxFF Reference](docs/reaxff_reference/index.md) — Reference documentation for ReaxFF input and output files.
+- [Contributing](docs/contributing.md) — Guidelines for contributing to ReaxKit.
+- [File Templates](docs/file_templates/index.md) and [Docstring Conventions](docs/file_templates/docstrings.md) — Development guidelines and code templates.
+- [AUTHORS.md](AUTHORS.md) —  Full credits and acknowledgments.
+- [LICENSE](LICENSE) — Full license terms under the **MIT License**
+
+---
+
+##  Testing
+
+Run unit tests with:
+
+```bash
+pytest -s tests/
+```
+
+to test the package and get the timing for their execution.
+
+---
+
+## Citation
+
+If you use ReaxKit in your work, please cite:
+
+```text
+Dinani, A. M., van Duin, A., Shin, Y. K., & Sepehrinezhad, A. (2025).
+ReaxKit: A modular Python toolkit for ReaxFF simulation analysis.
+Zenodo. https://doi.org/10.5281/zenodo.18485384
+
+Source code: https://github.com/ali-m-dinani/reaxkit
+```
+
+---
+
+## Future Directions
+
+* Add support for other analyzers including autocorrelation functions, thermodynamic properties calculations, etc.
+* Develop GUI dashboard for interactive ReaxFF data inspection
+* Implement ML-based trend prediction for simulation outputs
+
+If you have any feature request, you can submit it through the ReaxKit's GitHub page, or directly sending an email to `Dinani@psu.edu`.

reaxkit-1.0.0/README.md

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+# ReaxKit
+
+**ReaxKit** is a modular, extensible Python toolkit for **pre‑processing, post‑processing, and analysis of ReaxFF** molecular dynamics simulations.
+It provides a clean separation between file parsing, analysis routines, and reproducible workflows, with both **Python APIs** and a **CLI interface**.
+
+ReaxKit is designed for researchers who want a transparent, scriptable bridge between raw ReaxFF files and quantitative, publication‑ready results.
+
+---
+
+## Key Capabilities
+
+### File IO (Parsing & Generation)
+- Robust handlers for ReaxFF input and output files:
+  - `xmolout`, `fort.7`, `fort.13`, `molfra`, and more
+- Input file generators:
+  - `control`, `geo`, `eregime`, `tregime`, and more
+- Unified handler interface for consistent data access
+
+### Analysis
+- Per‑file analyzers (one analyzer per ReaxFF file type)
+- Composed analyzers that combine multiple data sources:
+  - Coordination numbers
+  - Connectivity graphs
+  - Electrostatics and dipoles
+  - Radial distribution functions (RDF)
+- Numerical utilities for smoothing, extrema detection, and signal processing
+
+### Workflows
+- Reproducible, CLI‑driven workflows for:
+  - Single‑file analysis
+  - Multi‑file composed analysis
+  - Plotting and media generation
+- Designed to automate common ReaxFF post‑processing tasks
+
+### Visualization & Media
+- Publication‑ready plotting utilities (2D, dual‑axis, tornado plots, 3D scatter, heatmaps)
+- Trajectory and plot video generation
+
+See the full documentation (API reference, tutorials, examples) on [ReaxKit Site](https://ali-m-dinani.github.io/reaxkit/).
+
+---
+
+## Project Layout
+
+```
+src/reaxkit/
+├── analysis/        # Analysis routines (per-file and composed)
+├── io/              # File handlers and generators
+├── utils/           # Shared utilities (aliases, units, constants, numerics)
+├── workflows/       # CLI and automation workflows
+├── help/            # Introspection and help system
+└── cli.py           # Command-line entry point
+```
+
+Additional resources:
+
+- [Installation notes](docs/installation.md) — Full installation instructions (requires **Python ≥ 3.9**).
+- [Quickstart](docs/quickstart.md) — Get up and running with core ReaxKit workflows in minutes.
+- [Tutorials notes](docs/tutorials/index.md) and [source files](https://ali-m-dinani.github.io/reaxkit/tutorials/) — Step-by-step guides for common ReaxKit workflows and use cases.
+- [Examples](docs/examples/README.md) and [source files](https://ali-m-dinani.github.io/reaxkit/examples/) — Minimal, runnable Python examples using public APIs.
+- [ReaxFF Reference](docs/reaxff_reference/index.md) — Reference documentation for ReaxFF input and output files.
+- [Contributing](docs/contributing.md) — Guidelines for contributing to ReaxKit.
+- [File Templates](docs/file_templates/index.md) and [Docstring Conventions](docs/file_templates/docstrings.md) — Development guidelines and code templates.
+- [AUTHORS.md](AUTHORS.md) —  Full credits and acknowledgments.
+- [LICENSE](LICENSE) — Full license terms under the **MIT License**
+
+---
+
+##  Testing
+
+Run unit tests with:
+
+```bash
+pytest -s tests/
+```
+
+to test the package and get the timing for their execution.
+
+---
+
+## Citation
+
+If you use ReaxKit in your work, please cite:
+
+```text
+Dinani, A. M., van Duin, A., Shin, Y. K., & Sepehrinezhad, A. (2025).
+ReaxKit: A modular Python toolkit for ReaxFF simulation analysis.
+Zenodo. https://doi.org/10.5281/zenodo.18485384
+
+Source code: https://github.com/ali-m-dinani/reaxkit
+```
+
+---
+
+## Future Directions
+
+* Add support for other analyzers including autocorrelation functions, thermodynamic properties calculations, etc.
+* Develop GUI dashboard for interactive ReaxFF data inspection
+* Implement ML-based trend prediction for simulation outputs
+
+If you have any feature request, you can submit it through the ReaxKit's GitHub page, or directly sending an email to `Dinani@psu.edu`.

reaxkit-1.0.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "reaxkit"
+version = "1.0.0"
+description = "A toolkit for parsing, analyzing, and visualizing ReaxFF simulation data."
+authors = [
+  { name = "Ali Mohammadi", email = "alimohammadi2265@gmail.com" },
+  { name = "Adri van Duin", email = "acv13@psu.edu" },
+  { name = "Yun Kyung Shin", email = "yks2@psu.edu" },
+  { name = "Alireza Sepehrinezhad", email = "alireza.sepehri@psu.edu" },
+]
+readme = "README.md"
+license = { text = "MIT" }
+
+requires-python = ">=3.9"
+
+dependencies = [
+    "numpy",
+    "pandas",
+    "matplotlib",
+    "seaborn",
+    "scipy",
+    "tqdm",
+    "rich",
+    "freud-analysis",
+    "ovito",
+    "tabulate",
+    "ase",
+    "imageio",
+    "mp_api",
+    "PyYAML",
+    "rapidfuzz",
+]
+
+[project.scripts]
+reaxkit = "reaxkit.cli:main"
+
+[tool.setuptools]
+package-dir = {"" = "src"}
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.setuptools.package-data]
+reaxkit = ["**/*.yaml"]
+

reaxkit-1.0.0/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+