pymatgen.analysis.substrate_analyzer module¶

class
SubstrateAnalyzer
(zslgen=<pymatgen.analysis.substrate_analyzer.ZSLGenerator object>)[source]¶ Bases:
object
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 superlattices 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 superlattices
Initializes the substrate analyzer :param zslgen: Defaults to a ZSLGenerator with standard
tolerances, but can be fed one with custom tolerances
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:
Parameters:  film (Structure) – conventional standard structure for the film
 substrate (Structure) – conventional standard structure for the substrate
 elasticity_tensor (ElasticTensor) – elasticity tensor for the film
 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

calculate_3D_elastic_energy
(film, match, elasticity_tensor=None, include_strain=False)[source]¶ Calculates the multiplane elastic energy. Returns 999 if no elastic tensor was given on init
Parameters:  film (Structure) – conventional standard structure for the film
 match (dictionary) – match dictionary from substrate analyzer
 elasticity_tensor (ElasticTensor) – elasticity tensor for the film
 include_strain (bool) – include strain in the output or not; changes return from just the energy to a tuple with the energy and strain in voigt notation


class
ZSLGenerator
(max_area_ratio_tol=0.09, max_area=400, film_max_miller=1, substrate_max_miller=1, max_length_tol=0.03, max_angle_tol=0.01)[source]¶ Bases:
object
This class generate interface super lattices based on the methodology of lattice vector matching for heterostructural interfaces proposed by Zur and McGill: Journal of Applied Physics 55 (1984), 378 ; doi: 10.1063/1.333084
The process of generating all possible interaces is as such:
 1.) Generate all slabs for the film and substrate for different orientations
 given by maximum miller limitations
 2.) For each film/substrate orientation pair:
1.) Reduce lattice vectors and calculate area 2.) Generate all super lattice transformations within a maximum area
limit that give nearly equal area superlattices for the two surfaces 3.) For each superlattice set:
1.) Reduce super lattice vectors 2.) Check length and angle between film and substrate super lattice
vectors to determine if the super lattices are the nearly same and therefore coincident
 Intialize a Zur Super Lattice Generator for a specific film and
 substrate
Parameters:  max_area_ratio_tol (float) – Max tolerance on ratio of superlattices to consider equal
 max_area (float) – max super lattice area to generate in search
 film_max_miller (int) – maximum miller index to generate for film surfaces
 substrate_max_miller (int) – maximum miller index to generate for substrate surfaces
 max_length_tol – maximum length tolerance in checking if two vectors are of nearly the same length
 max_angle_tol – maximum angle tolerance in checking of two sets of vectors have nearly the same angle between them

check_transformations
(transformation_sets, film_vectors, substrate_vectors)[source]¶ Applies the transformation_sets to the film and substrate vectors to generate superlattices and checks if they matches. Returns all matching vectors sets.
Parameters:  transformation_sets (array) – an array of transformation sets: each transformation set is an array with the (i,j) indicating the area multipes of the film and subtrate it corresponds to, an array with all possible transformations for the film area multiple i and another array for the substrate area multiple j.
 film_vectors (array) – film vectors to generate super lattices
 substrate_vectors (array) – substrate vectors to generate super lattices

generate
(film, substrate, film_millers=None, substrate_millers=None, lowest=False)[source]¶ Generates the film/substrate combinations for either set miller indicies or all possible miller indices up to a max miller index
Parameters:  film (Structure) – Conventional standard pymatgen structure for the film
 substrate (Struture) – Conventional standard pymatgen Structure for the substrate
 film_millers (array) – array of film miller indicies to consider in the matching algorithm
 substrate_millers (array) – array of substrate miller indicies to consider in the matching algorithm

generate_sl_transformation
(area_multiple)[source]¶ Generates the transformation matricies that convert a set of 2D vectors into a super lattice of integer area multiple as proven in Cassels:
Cassels, John William Scott. An introduction to the geometry of numbers. Springer Science & Business Media, 2012.
Parameters:  area_multiple (int) – integer multiple of unit cell area for super
 area (lattice) –
Returns: transformation matricies to covert unit vectors to super lattice vectors
Return type: matrix_list

generate_sl_transformations
(film_area, substrate_area)[source]¶ Generates transformation sets for film/substrate pair given the area of the unit cell area for the film and substrate. The transformation sets map the film and substrate unit cells to super lattices with a maximum area
Parameters:  film_area (int) – the unit cell area for the film
 substrate_area (int) – the unit cell area for the substrate
Returns:  a set of transformation_sets defined as:
1.) the (i,j) pair corresponding to the integer multiple of the film area (i) and substrate area (j) that makes the two equal within tolerance 2.) the transformation matricies for the film to create a super lattice of area i*film area 3.) the tranformation matricies for the substrate to create a super lattice of area j*film area
Return type: transformation_sets

generate_slabs
(film_millers, substrate_millers)[source]¶ Generates the film/substrate slab combinations for a set of given miller indicies
Parameters:  film_millers (array) – all miller indices to generate slabs for film
 substrate_millers (array) – all miller indicies to generate slabs for substrate

is_same_vectors
(vec_set1, vec_set2)[source]¶ Determine if two sets of vectors are the same within length and angle tolerances
Parameters:  vec_set1 (array[array]) – an array of two vectors
 vec_set2 (array[array]) – second array of two vectors

match_as_dict
(film_miller, substrate_miller, film_sl_vectors, substrate_sl_vectors, film_vectors, substrate_vectors, match_area)[source]¶ Returns dict which contains ZSL match
Parameters:  film_miller (array) –
 substrate_miller (array) –