build, analyse and visualise atomistic structures for materials science
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structuretoolkit
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.pyxtal()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()
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