crystal_torture.Graph

class crystal_torture.Graph(clusters, structure=None)

Bases: object

Graph class: group of disconnected clusters making up full graph

minimal_clusters

output_clusters(fmt, periodic=None)

Outputs the unique unit cell clusters from the graph

Args: fmt (str): output format for pymatgen structures set up from clusters periodic (Boolean): Whether to output only periodic clusters

Outputs: CLUS_*.”fmt”: A cluster structure file for each cluster in the graph

return_frac_percolating()

Calculates the fraction of nodes in the graph that are in a periodic cluster

Args:

• None

Returns:

• frac(real): nodes in graph in periodic clusers / total number of nodes

return_periodic_structure(fmt)

Gathers all periodic clusters in the graph as a single pymatgen Structure

Args: fmt (str): output format for pymatgen structure set up from cluster

Returns: #CLUS_PER.”fmt”: A structure file containing periodic sites in the graph. cluster_structure (pymatgen Structure): Structure object containing all periodic clusters

set_minimal_clusters()

Access to the information on unique unit cell clusters. Cycles through the halo clusters, gets a set unique cluster sites and sets up minimal_Cluster object to store and access the data

Args:

• None

Output:

• self.unit_clusters (set(minimal_Cluster)): a set of minimal_Cluster objects for unit cell in graph

set_site_tortuosity()

Sets a dict containing the site by site tortuosity for sites in the graph unit cell

torture()

Torture the graph and set node tortuosity for UC nodes in cluster. This only tortures UC nodes in each cluster, but the graph contains a halo of clusters.

Args:

• none

torture_py()

Torture the graph and set node tortuosity for UC nodes in cluster. This only tortures UC nodes in each cluster, but the graph contains a halo of clusters.

Args:

• none