pymatgen.analysis.interfaces.substrate_analyzer module

This module provides classes to identify optimal substrates for film growth

class SubstrateAnalyzer(film_max_miller=1, substrate_max_miller=1, **kwargs)[source]

Bases: pymatgen.analysis.interfaces.zsl.ZSLGenerator

This class applies a set of search criteria to identify suitable substrates for film growth. It first uses a topoplogical search by Zur and McGill to identify matching super-lattices on various faces of the two materials. Additional criteria can then be used to identify the most suitable substrate. Currently, the only additional criteria is the elastic strain energy of the super-lattices

Initializes the substrate analyzer :param zslgen: Defaults to a ZSLGenerator with standard

tolerances, but can be fed one with custom tolerances

  • film_max_miller (int) – maximum miller index to generate for film surfaces

  • substrate_max_miller (int) – maximum miller index to generate for substrate surfaces

calculate(film, substrate, elasticity_tensor=None, film_millers=None, substrate_millers=None, ground_state_energy=0, lowest=False)[source]

Finds all topological matches for the substrate and calculates elastic strain energy and total energy for the film if elasticity tensor and ground state energy are provided:

  • film (Structure) – conventional standard structure for the film

  • substrate (Structure) – conventional standard structure for the substrate

  • elasticity_tensor (ElasticTensor) – elasticity tensor for the film in the IEEE orientation

  • film_millers (array) – film facets to consider in search as defined by miller indicies

  • substrate_millers (array) – substrate facets to consider in search as defined by miller indicies

  • ground_state_energy (float) – ground state energy for the film

  • lowest (bool) – only consider lowest matching area for each surface

generate_surface_vectors(film_millers, substrate_millers)[source]

Generates the film/substrate slab combinations for a set of given miller indicies

  • film_millers (array) – all miller indices to generate slabs for film

  • substrate_millers (array) – all miller indicies to generate slabs for substrate

class SubstrateMatch(film_sl_vectors: numpy.ndarray, substrate_sl_vectors: numpy.ndarray, film_vectors: numpy.ndarray, substrate_vectors: numpy.ndarray, film_transformation: numpy.ndarray, substrate_transformation: numpy.ndarray, film_miller: Tuple[int, int, int], substrate_miller: Tuple[int, int, int], strain: pymatgen.analysis.elasticity.strain.Strain, von_mises_strain: float, ground_state_energy: float, elastic_energy: float)[source]

Bases: pymatgen.analysis.interfaces.zsl.ZSLMatch

A substrate match building on the Zur and McGill algorithm. This match class inlcudes the miller planes of the film and substrate the full strain tensor, the Von Mises strain, the ground state energy if provided, and the elastic energy

elastic_energy: float[source]
film_miller: Miller3D[source]
classmethod from_zsl(match: pymatgen.analysis.interfaces.zsl.ZSLMatch, film: pymatgen.core.structure.Structure, film_miller, substrate_miller, elasticity_tensor=None, ground_state_energy=0)[source]

Generate a substrate match from a ZSL match plus metadata

ground_state_energy: float[source]
strain: Strain[source]
substrate_miller: Miller3D[source]
property total_energy[source]

Total energy of this match

von_mises_strain: float[source]