MatID is a Python package for identifying and analyzing atomistic systems based on their structure.

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Project description

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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/

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

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

pip install matid

From source

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

Project details

These details have not been verified by PyPI

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Release history Release notifications | RSS feed

2.1.4

Oct 21, 2024

2.1.3

Oct 10, 2024

2.1.2

Aug 28, 2024

2.1.1

Aug 22, 2024

This version

2.1.0

Jul 30, 2024

2.0.1

May 15, 2024

2.0.0

May 14, 2024

2.0.0.dev2 pre-release

Jan 17, 2024

2.0.0.dev1 pre-release

Jan 16, 2024

2.0.0.dev0 pre-release

Jan 16, 2024

0.6.3

Jun 10, 2022

0.6.2

Nov 26, 2020

0.6.1

Jul 17, 2020

0.6.0

Apr 30, 2020

0.5.9

Apr 3, 2020

0.5.8

Apr 1, 2020

0.5.7

Mar 31, 2020

0.5.6

Mar 4, 2020

0.5.5

Dec 17, 2019

0.5.4

Dec 17, 2019

0.5.3

Feb 28, 2019

0.5.1

Nov 14, 2018

0.5.0

Jun 25, 2018

0.4.0

Jun 5, 2018

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