pyiron_workflow_atomistics

Overview

This repository contains a pyiron module for atomistic simulation workflows, providing tools and utilities for working with atomic structures, grain boundaries, and various atomistic calculations.

Features

• Grain Boundary Analysis: Tools for analyzing and manipulating grain boundaries, including:

  • GB plane detection and analysis
  • Cleavage plane identification
  • Structure manipulation for GB studies

• Structure Manipulation: Utilities for working with atomic structures:

  • Bulk structure handling
  • Structure featurization
  • Calculator integration

• Workflow Integration: Seamless integration with pyiron workflow system for:

  • Automated structure calculations
  • Data processing and analysis
  • Results visualization

Installation

The package can be installed via pip:

pip install pyiron_workflow_atomistics

Or via conda:

conda install -c conda-forge pyiron_workflow_atomistics

Dependencies

The package requires:

• Python >= 3.9, < 3.13
• numpy < 2.0.0
• pandas >= 1.3.0
• matplotlib >= 3.4.0
• ase >= 3.22.0
• scipy >= 1.7.0
• pyiron_workflow
• pymatgen >= 2024.8.8
• pyiron_snippets
• scikit-learn >= 1.0.0

Usage

Grain Boundary Analysis

from pyiron_workflow_atomistics.gb.analysis import find_GB_plane
from pyiron_workflow_atomistics.gb.cleavage import cleave_gb_structure

# Find GB plane in a structure
gb_info = find_GB_plane(atoms, featuriser, axis="c")

# Cleave structure at GB
cleaved_structures, cleavage_planes = cleave_gb_structure(
    base_structure=atoms,
    axis_to_cleave="c",
    target_coord=target_coord
)

Structure Calculations

from pyiron_workflow_atomistics.calculator import calculate_structure_node

# Run structure calculations
results = calculate_structure_node(
    structure=atoms,
    calc=calculator,
    output_dir="calculations"
)

Documentation

For detailed documentation, visit our ReadTheDocs page.

Contributing

We welcome contributions! Please see our Contributing Guide for details.

License

This project is licensed under the BSD License - see the LICENSE file for details.

Citation

If you use this package in your research, please cite:

@software{pyiron_workflow_atomistics,
  author = {pyiron team},
  title = {pyiron_workflow_atomistics},
  year = {2024},
  url = {https://github.com/pyiron/pyiron_workflow_atomistics}
}