perostruc.utility

Functions

BFS_cluster_analysis(cluster_flag)
calculate_cluster_surface_size(cluster_flag)	Calculate the surface size of a cluster Parameters: cluster_flag: np.ndarray[int] with shape (l1, l2, l3). 1 for in the cluster, 0 for out of the cluster. the flag of the cluster Returns: surface_size: int the surface size of the cluster.
find_clusters(atoms, lattice_map, element[, ...])	Find the clusters of the given element in the trajectory. :param traj: list[ase.Atoms] The trajectory of the atoms. :param lattice_map: np.ndarray[int] The lattice map of the atoms. The integer value is the index of the site atom. :param element: str The element to find the clusters. :param tolerance: int The tolerance for a site to be considered as part of the cluster. The number of neighboring elements that are not the given element.
find_neighbor_values(lattice_values, i, j, k)
get_neighbor(atoms, idx[, cutoff])
get_neighbor_indices(i, j, k, l1, l2, l3)
printenergy(a)	Function to print the potential, kinetic and total energy
update_element(atoms, element_list)