catlearn.api¶
catlearn.api.ase_atoms_api¶
Functions that interface ase with CatLearn.
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catlearn.api.ase_atoms_api.
database_to_list
(fname, selection=None)¶ Return a list of atoms objects imported from an ase database.
Parameters: - fname (str) – path/filename of ase database.
- selection (list) – search filters to limit the import.
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catlearn.api.ase_atoms_api.
extend_atoms_class
(atoms)¶ A wrapper to add extra functionality to ase atoms objects.
Parameters: atoms (class) – An ase atoms object.
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catlearn.api.ase_atoms_api.
get_features
(self)¶ Function to read feature vector from ase atoms object.
This function provides a uniform way in which to return a feature vector from an atoms object.
Parameters: self (class) – An ase atoms object to attach feature vector to. Returns: fp – The feature vector attached to the atoms object. Return type: array
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catlearn.api.ase_atoms_api.
get_graph
(self)¶ Function to read networkx graph from ase atoms object.
This function provides a uniform way in which to return a graph object from an atoms object.
Parameters: self (class) – An ase atoms object to attach feature vector to. Returns: graph – The networkx graph object attached to the atoms object. Return type: object
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catlearn.api.ase_atoms_api.
get_neighborlist
(self)¶ Function to read neighborlist from ase atoms object.
This function provides a uniform way in which to return a neighborlist from an atoms object.
Parameters: self (class) – An ase atoms object to attach feature vector to. Returns: neighborlist – The neighbor list attached to the atoms object. Return type: dict
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catlearn.api.ase_atoms_api.
images_connectivity
(images, check_cn_max=False)¶ Return a list of atoms objects imported from an ase database.
Parameters: - fname (str) – path/filename of ase database.
- selection (list) – search filters to limit the import.
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catlearn.api.ase_atoms_api.
images_pair_distances
(images, mic=True)¶ Return a list of atoms objects imported from an ase database.
Parameters: - fname (str) – path/filename of ase database.
- selection (list) – search filters to limit the import.
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catlearn.api.ase_atoms_api.
set_features
(self, fp)¶ Function to write feature vector to ase atoms object.
This function provides a uniform way in which to attach a feature vector to an atoms object. Can be used in conjunction with the get_features function.
Parameters: - self (class) – An ase atoms object to attach feature vector to.
- fp (array) – The feature vector to attach.
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catlearn.api.ase_atoms_api.
set_graph
(self, graph)¶ Function to write networkx graph to ase atoms object.
This function provides a uniform way in which to attach a graph object to an atoms object. Can be used in conjunction with the ase_to_networkx function.
Parameters: - self (class) – An ase atoms object to attach feature vector to.
- graph (object) – The networkx graph object to attach.
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catlearn.api.ase_atoms_api.
set_neighborlist
(self, neighborlist)¶ Function to write neighborlist to ase atoms object.
This function provides a uniform way in which to attach a neighbor list to an atoms object. Can be used in conjunction with the get_neighborlist function.
Parameters: - self (class) – An ase atoms object to attach feature vector to.
- neighborlist (dict) – The neighbor list dict to attach.
catlearn.api.ase_data_setup¶
Data generation functions to interact with ASE atoms objects.
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catlearn.api.ase_data_setup.
get_train
(atoms, key, size=None, taken=None)¶ Return a training dataset.
Parameters: - atoms (list) – A list of ASE atoms objects.
- size (int) – Size of training dataset.
- taken (list) – List of candidates that have been used in unique dataset.
- key (string) – Property on which to base the predictions stored in the atoms object as atoms.info[‘key_value_pairs’][key].
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catlearn.api.ase_data_setup.
get_unique
(atoms, size, key)¶ Return a unique test dataset.
Parameters: - atoms (list) – A list of ASE atoms objects.
- size (int) – Size of unique dataset to be returned.
- key (string) – Property on which to base the predictions stored in the atoms object as atoms.info[‘key_value_pairs’][key].
catlearn.api.networkx_graph_api¶
API to convert from ASE and NetworkX.
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catlearn.api.networkx_graph_api.
ase_to_networkx
(atoms, cutoffs=None)¶ Make the NetworkX graph form ASE atoms object.
The graph is dependent on the generation of the neighborlist. Currently this is handled by the version implemented in ASE.
Parameters: - atoms (object) – An ASE atoms object.
- cutoffs (list) – A list of distance paramteres for each atom.
Returns: atoms_graph – A networkx graph object.
Return type: object
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catlearn.api.networkx_graph_api.
matrix_to_nl
(matrix)¶ Returns a neighborlist as a dictionary. :param matrix: symmetric connection matrix. :type matrix: numpy array
Returns: nl – neighborlist. Return type: dict
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catlearn.api.networkx_graph_api.
networkx_to_adjacency
(graph)¶ Simple wrapper for graph to adjacency matrix.
Parameters: graph (object) – The networkx graph object. Returns: matrix – The numpy adjacency matrix. Return type: array