Metadata-Version: 2.4
Name: atomix
Version: 0.2.0
Summary: Read-only VASP workflow inspection and experimental atomistic modeling tools
Author: atomix developers
Project-URL: Homepage, https://github.com/vpasumarthi/atomix
Project-URL: Documentation, https://github.com/vpasumarthi/atomix#readme
Project-URL: Repository, https://github.com/vpasumarthi/atomix
Keywords: computational chemistry,DFT,VASP,materials science,atomistic simulation,machine learning potentials
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Topic :: Scientific/Engineering :: Chemistry
Classifier: Topic :: Scientific/Engineering :: Physics
Requires-Python: >=3.10
Description-Content-Type: text/markdown
Requires-Dist: click>=8.0.0
Provides-Extra: science
Requires-Dist: ase>=3.22.0; extra == "science"
Requires-Dist: numpy>=1.21.0; extra == "science"
Requires-Dist: scipy>=1.7.0; extra == "science"
Requires-Dist: pymatgen>=2023.0.0; extra == "science"
Requires-Dist: pyyaml>=6.0; extra == "science"
Requires-Dist: requests>=2.28.0; extra == "science"
Provides-Extra: mlip
Requires-Dist: mace-torch>=0.3.0; extra == "mlip"
Requires-Dist: torch>=2.0.0; extra == "mlip"
Provides-Extra: llm
Requires-Dist: openai>=1.0.0; extra == "llm"
Requires-Dist: anthropic>=0.18.0; extra == "llm"
Provides-Extra: dev
Requires-Dist: build>=1.2.0; extra == "dev"
Requires-Dist: pytest>=7.0.0; extra == "dev"
Requires-Dist: pytest-cov>=4.0.0; extra == "dev"
Requires-Dist: ruff>=0.1.0; extra == "dev"
Requires-Dist: mypy>=1.0.0; extra == "dev"
Provides-Extra: all
Requires-Dist: atomix[dev,llm,mlip,science]; extra == "all"

# atomix

[![CI](https://github.com/vpasumarthi/atomix/actions/workflows/ci.yml/badge.svg)](https://github.com/vpasumarthi/atomix/actions/workflows/ci.yml)

Atomistic Modeling Interface for eXploration — a natural language driven toolkit for ab initio / DFT / atomistic modeling workflows.

## Installation

Atomix is currently installed from a source checkout. The segmented VASP
reader requires the scientific dependencies:

```bash
conda activate atomix
pip install -e ".[science]"
```

## Status

Early development. The supported surface is deliberately narrow: read-only
inspection of VASP calculations stored as `seg01`, `seg02`, ... directories.
Other commands and modules remain experimental scaffolding.

### Command line

```bash
atomix inspect-vasp path/to/calculation
atomix inspect-vasp path/to/calculation --json
atomix inspect-vasp path/to/calculation --diagnostics
```

The command exits nonzero when the reader finds an error-level ambiguity, such
as both `seg1` and `seg01` representing the same segment number.

### Python

```python
from atomix.calculators import VASPSegmentReader

result = VASPSegmentReader("path/to/calculation").read()

for frame in result.frames:
    print(frame.segment_number, frame.time_fs, frame.source_file)

for warning in result.warnings:
    print(warning.level, warning.code, warning.path)
```

The reader sorts segments numerically, prefers `XDATCAR` trajectories with an
`OUTCAR` fallback, removes repeated boundary frames, and retains raw `OUTCAR`
and `REPORT` records with source metadata. It never modifies calculation files.

## Development

```bash
pip install -e ".[science,dev]"
pytest tests/
ruff check .
```
