evgraf

Symmetrization of crystal structures

Currently supports translational and inversion symmetries only.

Installation:

To install the module with pip (recommended):

pip install --user evgraf

To install directly from the git repository:

pip install --user git+https://github.com/pmla/evgraf

To do a manual build and installation:

python3 setup.py build
python3 setup.py install --user

Usage:

We can quantify the breaking of inversion symmetry in BaTiO3. First we create the crystal structure:

>>> from ase import Atoms
>>> atoms = Atoms(symbols='BaTiO3', pbc=True, cell=[4.002, 4.002, 4.216],
...               positions=[[0.000, 0.000, 0.085],
...                          [2.001, 2.001, 2.272],
...                          [2.001, 2.001, 4.092],
...                          [0.000, 2.001, 2.074],
...                          [2.001, 0.000, 2.074]])

We call the inversion symmetry analysis function:

>>> from evgraf import find_inversion_symmetry
>>> result = find_inversion_symmetry(atoms)

We can view the inversion-symmetrized structure:

>>> from ase.visualize import view
>>> view(result.atoms)

The degree of symmetry breaking is given by the root-mean-square distance between the input structure and the symmetrized structure:

>>> result.rmsd
0.10115255804971046

We also obtain the inversion axis:

>>> result.axis
array([2.001 , 2.001 , 2.1194])

Information

evgraf is written by Peter M. Larsen. The software is provided under the MIT license.