WARNING: This package has been renamed to MatID: https://singroup.github.io/matid/
pip install systax==0.1.3
Systax is a python package for the structural analysis and classification of atomistic systems.
The package is compatible with Python 2.7, 3.4-3.6, and the dependencies are given in the file 'requirements.txt. These dependencies will be automatically installed during the setup of the package.
The latest stable release is available through pip, and can be installed with the command:
pip install systax
To install the most recent development version, you can clone this repository and perform the install with pip directly from the source code:
git clone https://gitlab.com/laurih/systax.git
cd systax
pip install .
import ase.io
from ase.visualize import view
from systax import Classifier
from systax.classifications import Surface
# Read a geometry from file with ASE. Ensure that the cell and periodicity are
# correctly given for the structure.
system = ase.io.read("geometry.xyz")
view(system)
# Run the classification
classifier = Classifier(pos_tol=0.5, max_cell_size=6)
classification = classifier.classify(system)
if type(classification) == Surface:
# View the conventional cell corresponding to this surface
conventional_cell = classification.conventional_cell
view(conventional_cell)
# View the outlier atoms
outliers = classification.outliers
view(system[outliers])
# Inspect more symmetry details about the cell
analyzer = classification.cell_analyzer
space_group = analyzer.get_space_group_number()
print(space_group)
primitive_cell = analyzer.get_primitive_system()
view(primitive_cell)