https://github.com/nomad-coe/matid

https://github.com/nomad-coe/matid

Last synced: about 2 months ago
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• Host: GitHub
• URL: https://github.com/nomad-coe/matid
• Owner: nomad-coe
• License: apache-2.0
• Created: 2023-06-05T19:56:20.000Z (over 1 year ago)
• Default Branch: main
• Last Pushed: 2024-10-21T19:10:39.000Z (2 months ago)
• Last Synced: 2024-10-22T11:41:09.143Z (2 months ago)
• Language: Python
• Size: 38.7 MB
• Stars: 2
• Watchers: 1
• Forks: 2
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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MatID is a Python package for identifying and analyzing atomistic systems based

on their structure.

# Documentation

For more details and tutorials, visit the documentation at:

[https://nomad-coe.github.io/matid/](https://nomad-coe.github.io/matid/)

You can find even more details in the following articles:

- [Materials structure genealogy and high-throughput topological classification of surfaces and 2D materials]()

## Example: Surface detection and analysis

```python

import ase.io

from ase.visualize import view

from matid.clustering import SBC

from matid.symmetry import SymmetryAnalyzer

# Load structure from a file

system = ase.io.read('data/system.xyz')

# Find interesting substructures using Symmetry-based Clustering (SBC)

sbc = SBC()

clusters = sbc.get_clusters(system)

# Analyze each found cluster printing out the indices of the atoms belonging to

# this cluster and visualizing the conventional cell from which the cluster was

# built from.

for cluster in clusters:

    # Get the indices of the atoms belonging to this cluster

    indices = cluster.indices

    print(indices)

    # Get the dimensionality of the cluster

    dimensionality = cluster.get_dimensionality()

    print(dimensionality)

    # Get the cell from which the cluster is constructed from. The periodicity

    # of this cell indicates in which directions the unit cell has been found to

    # be repeated in (at least once, possibly infinitely).

    cell = cluster.get_cell()

    n_repeated_directions = sum(cell.get_pbc())

    print(n_repeated_directions)

    # Analyze some symmetry properties of the underlying cell to better identify

    # the material from which the cluster has been constructed from.

    analyzer = SymmetryAnalyzer(cell, symmetry_tol=0.5)

    conv_sys = analyzer.get_conventional_system()

    view(conv_sys)

```

# Installation

## pip

```sh

pip install matid

```

## From source

```sh

git clone https://github.com/nomad-coe/matid.git

cd matid

pip install .

```