Originally developed as part of the pyiron_atomistics module the structuretoolkit was release as standalone library for analysing, building and visualising atomistic structures. Internally it uses the ase.atoms.Atoms class to represent atomistic structures in python. The structuretoolkit is integrated inside pyiron_atomistics.

Disclaimer

The structuretoolkit is currently under development.

Example

import structuretoolkit as stk
from ase.build import bulk

structure = bulk("Al", cubic=True)
stk.analyse.get_adaptive_cna_descriptors(structure)
stk.plot3d(structure)

Features

Analysis

• stk.analyse.get_neighbors()
• stk.analyse.get_neighborhood()
• stk.analyse.get_equivalent_atoms()
• stk.analyse.get_steinhardt_parameters()
• stk.analyse.get_centro_symmetry_descriptors()
• stk.analyse.get_diamond_structure_descriptors()
• stk.analyse.get_adaptive_cna_descriptors()
• stk.analyse.get_voronoi_volumes()
• stk.analyse.find_solids()
• stk.analyse.get_mean_positions()
• stk.analyse.get_average_of_unique_labels()
• stk.analyse.get_interstitials()
• stk.analyse.get_layers()
• stk.analyse.get_voronoi_vertices()
• stk.analyse.get_voronoi_neighbors()
• stk.analyse.get_delaunay_neighbors()
• stk.analyse.get_cluster_positions()
• stk.analyse.get_strain()

Build

• stk.build.get_grainboundary_info()
• stk.build.grainboundary()
• stk.build.high_index_surface()
• stk.build.get_high_index_surface_info()
• stk.build.sqs_structures()
• stk.build.B2()
• stk.build.C14()
• stk.build.C15()
• stk.build.C36()
• stk.build.D03()

Visualize

• stk.visualize.plot3d()

Common

• stk.common.ase_to_pymatgen()
• stk.common.pymatgen_to_ase()
• stk.common.pymatgen_read_from_file()
• stk.common.ase_to_pyscal()
• stk.common.apply_strain()
• stk.common.center_coordinates_in_unit_cell()
• stk.common.get_extended_positions()
• stk.common.get_vertical_length()
• stk.common.get_wrapped_coordinates()
• stk.common.select_index()