GOFEE¶

Below an overview of the inputs to GOFEE is shown. Many of the inputs can be safely kept at default settings. However calc, defining the calculator, as well as either startgenerator or structures, defining the system, must always be set. In addition it is recomended to also set the candidate_generatior.

StartGenerator¶

The StartGenerator is used to generate initial structures for the search. In addition it can be used to generate new candidates during the search, if it is included as an operation in the CandidateGenerator.

class gofee.candidates.StartGenerator(slab, stoichiometry, box_to_place_in, cluster=False, description='StartGenerator', *args, **kwargs)¶

Class used to generate random initial candidates.

Generates new candidates by iteratively adding one atom at a time within a user-defined box.

Parameters:

slab: Atoms object: The atoms object describing the super cell to optimize within. Can be an empty cell or a cell containing the atoms of a slab.
stoichiometry: list: A list of atomic numbers for the atoms that are placed on top of the slab (if one is present).
box_to_place_in: list: The box within which atoms are placed. The box should be on the form [p0, vspan] where ‘p0’ is the position of the box corner and ‘vspan’ is a matrix containing the three spanning vectors.
blmin: float: The minimum allowed distance between atoms in units of the covalent distance between atoms, where d_cov=r_cov_i+r_cov_j.
blmax: float: The maximum allowed distance, in units of the covalent distance, from a single isolated atom to the closest atom. If blmax=None, no constraint is enforced on isolated atoms.
cluster: bool: If True atoms are required to be placed within blmin*d_cov of one of the other atoms to be placed. If False the atoms in the slab are also included.

CandidateGenerator¶

The CandidateGenerator is used in each iteration in the GOFEE search to generate new candidates based on a list on operations to use. Possible operation can be found below under the “Mutations” section.

class gofee.candidates.CandidateGenerator(probabilities, operations)¶

Class to produce new candidates by applying one of the candidate generation operations which is supplied in the ‘operations’-list. The operations are drawn randomly according to the ‘probabilities’-list.

operationslist or list of lists: Defines the operations to generate new candidates in GOFEE. of mutations/crossovers. Either a list of mutations, e.g. the RattleMutation, or alternatively a list of lists of such mutations, in which case consecutive operations, one drawn from each list, are performed.
probabilitieslist or list of lists: probability for each of the mutations/crossovers in operations. Must have the same dimensions as operations.

get_new_candidate(parents)¶: Generate new candidate by applying a randomly drawn operation on the structures. This is done successively for each list of operations, if multiple are present.

Mutations¶

The mutations to chose from are listed below.

RattleMutation¶

class gofee.candidates.RattleMutation(n_top, Nrattle=3, rattle_range=3, description='RattleMutation', *args, **kwargs)¶

Class to perform rattle mutations on structures.

Rattles a number of randomly selected atoms within a sphere of radius ‘rattle_range’ of their original positions. - Moves one involved atom at a time.

Parameters:

n_top: int: The number of atoms to optimize. Specifically the atoms with indices [-n_top:] are optimized.
Nrattle: float: The average number of atoms to rattle.
rattle_range: float: The maximum distance within witch to rattle the atoms. Atoms are rattled uniformly within a sphere of this radius.
blmin: float: The minimum allowed distance between atoms in units of the covalent distance between atoms, where d_cov=r_cov_i+r_cov_j.
blmax: float: The maximum allowed distance, in units of the covalent distance, from a single isolated atom to the closest atom. If blmax=None, no constraint is enforced on isolated atoms.
description: str: Name of the operation, which will be saved in info-dict of structures, on which the operation is applied.

RattleMutation2¶

class gofee.candidates.RattleMutation2(n_top, Nrattle=3, description='RattleMutation', cluster=False, *args, **kwargs)¶

Class to perform rattle mutations on structures.

Rattles a number of randomly selected atom to the visinity of other randomly selected atoms. - Moves one involved atom at a time.

Parameters:

n_top: int: The number of atoms to optimize. Specifically the atoms with indices [-n_top:] are optimized.
Nrattle: float: The average number of atoms to rattle.
description: str: Name of the operation, which will be saved in info-dict of structures, on which the operation is applied.

PermutationMutation¶

class gofee.candidates.PermutationMutation(n_top, Npermute=3, description='PermutationMutation', *args, **kwargs)¶

Class to perform permutation mutations on structures.

Swaps the positions of a number of pairs of unlike atoms.

Parameters:

n_top: int: The number of atoms to optimize. Specifically the atoms with indices [-n_top:] are optimized.
Npermute: float: The average number of permutations to perform.
blmin: float: The minimum allowed distance between atoms in units of the covalent distance between atoms, where d_cov=r_cov_i+r_cov_j.
blmax: float: The maximum allowed distance, in units of the covalent distance, from a single isolated atom to the closest atom. If blmax=None, no constraint is enforced on isolated atoms.
description: str: Name of the operation, which will be saved in info-dict of structures, on which the operation is applied.