structuretoolkit
structuretoolkit extends the ase.atoms.Atoms class from the
Atomic Simulation Environment (ASE) with a large collection of additional
functions for building, analysing and visualising atomistic structures in materials science. It does
not introduce a structure class of its own – every function takes an ase.atoms.Atoms object as input and,
where applicable, returns one again, so structuretoolkit combines freely with the rest of the ASE ecosystem
(ase.build, ASE calculators, ASE I/O, ...). structuretoolkit also powers the structure-analysis backend of
pyiron_atomistics, where the same functions are available as
methods directly on the structure object.
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()- find the nearest neighbors of every atom, by count or cutoff radius, periodic-boundary-awarestk.analyse.get_neighborhood()- find the nearest neighbors of an arbitrary point in space, e.g. an interstitial sitestk.analyse.get_equivalent_atoms()- label atoms that map onto each other under the structure's symmetry operationsstk.analyse.get_steinhardt_parameters()- compute rotationally invariant Steinhardt bond-orientational order parametersstk.analyse.get_centro_symmetry_descriptors()- compute the centrosymmetry parameter, large for atoms near a defectstk.analyse.get_diamond_structure_descriptors()- identify cubic/hexagonal diamond local environmentsstk.analyse.get_adaptive_cna_descriptors()- classify local crystal structure (fcc/hcp/bcc/icosahedral/other) via common neighbor analysisstk.analyse.get_voronoi_volumes()- compute the Voronoi cell volume of every atomstk.analyse.find_solids()- count how many atoms are "solid" vs. "liquid"-like, e.g. for melting-point calculationsstk.analyse.get_mean_positions()- average atomic positions across periodic boundary conditionsstk.analyse.get_average_of_unique_labels()- average values that share the same (possibly repeated) integer labelstk.analyse.get_interstitials()- locate interstitial sites of a given coordination number (e.g. tetrahedral, octahedral)stk.analyse.get_layers()- group atoms into layers along the cell directions or arbitrary planesstk.analyse.get_voronoi_vertices()- compute the Voronoi vertices of the (periodic) structurestk.analyse.get_voronoi_neighbors()- find pairs of atoms sharing a Voronoi facetstk.analyse.get_delaunay_neighbors()- find pairs of atoms sharing a Delaunay tetrahedronstk.analyse.get_cluster_positions()- cluster nearby positions together via DBSCANstk.analyse.get_strain()- compute the per-atom Lagrangian strain tensor relative to a reference structure
Build
stk.build.get_grainboundary_info()- list the geometrically possible grain boundaries (by CSL sigma value) for a rotation axisstk.build.grainboundary()- build a bicrystal grain-boundary structure for a chosen sigma value and planestk.build.high_index_surface()- build a stepped/kinked high-index surface slabstk.build.get_high_index_surface_info()- derive the Miller index for a given terrace/step/kink orientationstk.build.sqs_structures()- generate special quasirandom structures (SQS) for disordered alloysstk.build.B2()- build a cubic AB B2 (CsCl-type) intermetallic structurestk.build.C14()- build a hexagonal AB2 C14 Laves phase structurestk.build.C15()- build a cubic AB2 C15 Laves phase structurestk.build.C36()- build a hexagonal AB2 C36 Laves phase structurestk.build.D03()- build a cubic AB3 D03 structure
Visualize
stk.visualize.plot3d()- render anAtomsobject in 3d, via NGLView or plotly
Common
stk.common.ase_to_pymatgen()- convert anase.atoms.Atomsobject to apymatgen.core.Structurestk.common.pymatgen_to_ase()- convert apymatgen.core.Structureback to anase.atoms.Atomsobjectstk.common.pymatgen_read_from_file()- read a structure file directly into anase.atoms.Atomsobject via pymatgenstk.common.ase_to_pyscal()- convert anase.atoms.Atomsobject to apyscal3.core.Systemstk.common.apply_strain()- apply a homogeneous strain to a structure's cell, and its atomsstk.common.center_coordinates_in_unit_cell()- wrap atomic coordinates back into the unit cellstk.common.get_extended_positions()- repeat atoms across the periodic boundary to include neighbor imagesstk.common.get_vertical_length()- get the height of the cell perpendicular to each facestk.common.get_wrapped_coordinates()- wrap arbitrary Cartesian coordinates into the periodic cellstk.common.select_index()- get the indices of atoms of a given chemical element
Documentation
2 maintainers
Metadata
2 maintainers
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