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-aware
• stk.analyse.get_neighborhood() - find the nearest neighbors of an arbitrary point in space, e.g. an interstitial site
• stk.analyse.get_equivalent_atoms() - label atoms that map onto each other under the structure's symmetry operations
• stk.analyse.get_steinhardt_parameters() - compute rotationally invariant Steinhardt bond-orientational order parameters
• stk.analyse.get_centro_symmetry_descriptors() - compute the centrosymmetry parameter, large for atoms near a defect
• stk.analyse.get_diamond_structure_descriptors() - identify cubic/hexagonal diamond local environments
• stk.analyse.get_adaptive_cna_descriptors() - classify local crystal structure (fcc/hcp/bcc/icosahedral/other) via common neighbor analysis
• stk.analyse.get_voronoi_volumes() - compute the Voronoi cell volume of every atom
• stk.analyse.find_solids() - count how many atoms are "solid" vs. "liquid"-like, e.g. for melting-point calculations
• stk.analyse.get_mean_positions() - average atomic positions across periodic boundary conditions
• stk.analyse.get_average_of_unique_labels() - average values that share the same (possibly repeated) integer label
• stk.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 planes
• stk.analyse.get_voronoi_vertices() - compute the Voronoi vertices of the (periodic) structure
• stk.analyse.get_voronoi_neighbors() - find pairs of atoms sharing a Voronoi facet
• stk.analyse.get_delaunay_neighbors() - find pairs of atoms sharing a Delaunay tetrahedron
• stk.analyse.get_cluster_positions() - cluster nearby positions together via DBSCAN
• stk.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 axis
• stk.build.grainboundary() - build a bicrystal grain-boundary structure for a chosen sigma value and plane
• stk.build.high_index_surface() - build a stepped/kinked high-index surface slab
• stk.build.get_high_index_surface_info() - derive the Miller index for a given terrace/step/kink orientation
• stk.build.sqs_structures() - generate special quasirandom structures (SQS) for disordered alloys
• stk.build.B2() - build a cubic AB B2 (CsCl-type) intermetallic structure
• stk.build.C14() - build a hexagonal AB2 C14 Laves phase structure
• stk.build.C15() - build a cubic AB2 C15 Laves phase structure
• stk.build.C36() - build a hexagonal AB2 C36 Laves phase structure
• stk.build.D03() - build a cubic AB3 D03 structure

Visualize

• stk.visualize.plot3d() - render an Atoms object in 3d, via NGLView or plotly

Common

• stk.common.ase_to_pymatgen() - convert an ase.atoms.Atoms object to a pymatgen.core.Structure
• stk.common.pymatgen_to_ase() - convert a pymatgen.core.Structure back to an ase.atoms.Atoms object
• stk.common.pymatgen_read_from_file() - read a structure file directly into an ase.atoms.Atoms object via pymatgen
• stk.common.ase_to_pyscal() - convert an ase.atoms.Atoms object to a pyscal3.core.System
• stk.common.apply_strain() - apply a homogeneous strain to a structure's cell, and its atoms
• stk.common.center_coordinates_in_unit_cell() - wrap atomic coordinates back into the unit cell
• stk.common.get_extended_positions() - repeat atoms across the periodic boundary to include neighbor images
• stk.common.get_vertical_length() - get the height of the cell perpendicular to each face
• stk.common.get_wrapped_coordinates() - wrap arbitrary Cartesian coordinates into the periodic cell
• stk.common.select_index() - get the indices of atoms of a given chemical element

Documentation

• structuretoolkit
  • Example
  • Features
• Introduction
  • How the package is organised
  • Helpers and converters
  • Analysing existing structures
  • Constructing new structures
  • Looking at structures
  • Where to go from here
• Interface