Metadata-Version: 2.4
Name: a2c_ase
Version: 0.0.5
Summary: ASE friendly implementation of the a2c workflow with MLIPs
Author-email: Abhijeet Gangan <abhijeetgangan@g.ucla.edu>
License: MIT License
        
        Copyright (c) 2025 Abhijeet Gangan
        
        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.
        
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: ase
Requires-Dist: numpy
Requires-Dist: pymatgen
Requires-Dist: tqdm
Provides-Extra: dev
Requires-Dist: pre-commit; extra == "dev"
Requires-Dist: ruff; extra == "dev"
Requires-Dist: ty>=0.0.1a20; extra == "dev"
Provides-Extra: test
Requires-Dist: pytest; extra == "test"
Requires-Dist: pytest-cov; extra == "test"
Provides-Extra: docs
Requires-Dist: mkdocs-material>=9.0; extra == "docs"
Requires-Dist: mkdocstrings[python]>=0.24; extra == "docs"
Requires-Dist: mkdocs-jupyter>=0.24; extra == "docs"
Requires-Dist: jupytext>=1.16; extra == "docs"
Requires-Dist: ipykernel>=6.0; extra == "docs"
Dynamic: license-file

# a2c_ase

[![PyPI](https://img.shields.io/pypi/v/a2c-ase.svg)](https://pypi.org/project/a2c-ase/)
[![CI](https://github.com/abhijeetgangan/a2c_ase/actions/workflows/ci.yml/badge.svg)](https://github.com/abhijeetgangan/a2c_ase/actions/workflows/ci.yml)
[![codecov](https://codecov.io/gh/abhijeetgangan/a2c_ase/branch/main/graph/badge.svg)](https://codecov.io/gh/abhijeetgangan/a2c_ase)
[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
[![Python 3.10+](https://img.shields.io/badge/python-3.10+-blue.svg)](https://www.python.org/downloads/)
[![DOI](https://zenodo.org/badge/940895212.svg)](https://doi.org/10.5281/zenodo.17355689)


An ASE-friendly implementation of the amorphous-to-crystalline (a2c) workflow.

## Installation

### From PyPI

**With uv (recommended):**
```bash
uv pip install a2c-ase
```


Or with pip

```bash
pip install a2c-ase
```


### From Source

**With uv:**
```bash
git clone https://github.com/abhijeetgangan/a2c_ase.git
cd a2c_ase
uv pip install .
```


Or with pip

```bash
git clone https://github.com/abhijeetgangan/a2c_ase.git
cd a2c_ase
pip install .
```


## Usage
See [example/Si64.py](https://github.com/abhijeetgangan/a2c_ase/blob/main/example/Si64.py) for basic usage.

To use a specific calculator you need to install the corresponding package.

In the example above, MACE is used as the calculator, so you need to install the corresponding package.

```bash
pip install mace-torch
```

## Workflow Overview

1. **Initial Structure**: Generate a random atomic configuration with specified composition and volume.
2. **Melt-Quench**: Run MD simulation to create an amorphous structure.
3. **Subcell Extraction**: Identify potential crystalline motifs within the amorphous structure.
4. **Structure Optimization**: Relax subcells to find stable crystalline phases.
5. **Analysis**: Characterize discovered structures using symmetry analysis.

## Development

Install dev dependencies:
```bash
# with pip
pip install -e ".[dev,test]"
```

Set up pre-commit hooks:
```bash
pre-commit install
```

Run checks:
```bash
ruff check         # lint
ruff format        # format
ty check           # type check
pytest             # test
```

## Citation

If you use this software in your research, please cite it: [DOI:https://doi.org/10.5281/zenodo.17355689](https://doi.org/10.5281/zenodo.17355689)

## References

1. Aykol, M., Merchant, A., Batzner, S. et al. Predicting emergence of crystals from amorphous precursors with deep learning potentials. Nat Comput Sci 5, 105–111 (2025). [DOI: 10.1038/s43588-024-00752-y](https://doi.org/10.1038/s43588-024-00752-y)
2. Reference implementation: [a2c-workflow](https://github.com/jax-md/jax-md/blob/main/jax_md/a2c/a2c_workflow.py)
