Symmetrization of crystal structures
Currently supports translational and inversion symmetries only.
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
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])
evgraf is written by Peter M. Larsen. The software is provided under the MIT license.