atomID

Welcome to the atomID package! This README will guide you through the initial steps required to start using the AnnotateCrystal class for annotating crystal structures and defects. Follow the steps outlined below to get started.

Overview

"AtomID" is an open-source Python package designed to annotate crystal structure data, enhancing data standardisation and interoperability in the field of computational materials science.

Key Features

• Multi-format Data Input: Supports data import from multiple commonly used formats, such as CIF, POSCAR, and LAMMPS, ensuring compatibility across various modelling tools and workflows.
• Crystal Structure Identification: Utilises Common Neighbour Analysis to accurately identify crystal structures within different lattices.
• Defect Detection and Characterisation: Applies Wigner-Seitz analysis to detect and categorise various types of lattice defects.
• Defect Concentration Calculation: Computes the concentration of different point defects.
• Knowledge Graph Creation: Generates a knowledge graph for crystal structures using the Computational Material Sample Ontology (CMSO), which can be exported and stored in Turtle (TTL) format, enabling sharing and complex querying on the data.

Installation

To begin, you need to install the atomID package. This can be done using pip:

pip install atomid

Usage

This section provides a step-by-step guide on how to utilise the AnnotateCrystal class within the atomID package.

1. Import the Required Class

Start by importing the AnnotateCrystal class from the atomid.annotate module:

from atomid.annotate import AnnotateCrystal

2. Create an Instance of AnnotateCrystal

Next, create an instance of the AnnotateCrystal class:

crystal = AnnotateCrystal()

3. Read the Crystal Structure File

Read the crystal structure file by using the read_crystal_structure_file method. Make sure to replace crystal_data_file_path with the actual path to your crystal structure file:

crystal.read_crystal_structure_file(crystal_data_file_path, "vasp")

4. Annotate the Crystal Structure

You can now annotate the crystal structure with the annotate_crystal_structure method:

crystal.annotate_crystal_structure()

5. Annotate Defects

To annotate defects, provide a reference file path. Replace ref_file_path with the actual path to your reference file:

crystal.annotate_defects(ref_file_path, "vasp")

6. Write to File

Finally, write the annotated data to a file using the write_to_file method. Specify the output file name and format:

crystal.write_to_file(output_file_path, "ttl")

Example

Here is a complete example that combines all the steps:

from atomid.annotate import AnnotateCrystal

# Create an instance of AnnotateCrystal
crystal = AnnotateCrystal()

# Read the crystal structure file
crystal.read_crystal_structure_file("path/to/your/interstitial_file.poscar", "vasp")

# Annotate the crystal structure
crystal.annotate_crystal_structure()

# Annotate defects using a reference file
crystal.annotate_defects("path/to/your/reference_file.poscar", "vasp")

# Write the annotated data to a file
crystal.write_to_file("Al_inter.ttl", "ttl")

Documentation

Detailed documentation for the atomID package can be found in the docs folder.

Contributing

Please refer to the CONTRIBUTING GUIDE on contributing to the atomID package.

Contact

For any queries or feedback, kindly create an issue on the GitHub repository.