Source code for hiphive.core.eigentensors

import numpy as np
import itertools
import sympy
from .tensors import rotate_tensor
from import logger
from .utilities import SparseMatrix

logger = logger.getChild('eigensymmetries')

[docs]def create_eigentensors(cs): for orbit in cs.orbits: prototype_cluster = cs._cluster_list[orbit.prototype_index] # The first round of eigentensors are created from the atom label # permutation condition ets = init_ets_from_label_symmetry(prototype_cluster) # Loop over the symmetries and apply them iteratively to reduce the # number of eigentensors for rotation_index, permutation_index in orbit.eigensymmetries: # Rotation amtrix in scaled coordinates R = cs.rotation_matrices[rotation_index] p = cs._permutations[permutation_index] # permutation vector # Skip if the symmetry is the trivial identity operation if np.allclose(R, np.eye(3)) and p == tuple(range(orbit.order)): continue p_inv = np.argsort(p) # Create the intermediate constraint matrix and populate it M = SparseMatrix.zeros(3**orbit.order, len(ets)) populate_constraint_matrix(M, ets, R, p_inv) nullspace = M.nullspace() new_ets = [] for solution in nullspace: # Normalize the solution vector so it is inly integers # Done by multiplying with the greatest common multiple of the # denominators present solution = renormalize_to_integer(solution) # From the solution vector and the old eigentensors a new et is # created new_ets.append(assemble_new_eigentensor(ets, solution)) ets = new_ets # If the force constant is forbidden by symmetry, break early if len(ets) == 0: break orbit.eigentensors = ets
[docs]def populate_constraint_matrix(M, ets, R, p_inv): for et_index, et in enumerate(ets): tmp = rotate_tensor(et.transpose(p_inv), R) tmp = tmp - et for element_index, v in enumerate(tmp.flat): if v != 0: M[element_index, et_index] = v
[docs]def init_ets_from_label_symmetry(cluster): """ This function creates eigentensor which fulfill the atom label symmetry. The only information needed is the corresponding cluster """ order = len(cluster) assert sorted(cluster) == list(cluster) multiplicities = np.unique(cluster, return_counts=True)[1] ets = {} # Loop over all elements, represented by multi indices for multi_index in itertools.product([0, 1, 2], repeat=order): # Sort the multi index based on the multiplicities # e.g. cluster [1 1 2] # -> [z y x] == [y z x] sorted_multi_index = [] j = 0 for m in multiplicities: sorted_multi_index.extend(sorted(multi_index[j:j + m])) j += m sorted_multi_index = tuple(sorted_multi_index) if sorted_multi_index not in ets: ets[sorted_multi_index] = np.zeros([3]*order, dtype=np.int64) ets[sorted_multi_index][multi_index] = 1 return list(ets.values())
[docs]def assemble_new_eigentensor(eigentensors, solution): new_eigentensor = np.zeros(eigentensors[0].shape, dtype=np.int64) for parameter, eigentensor in zip(solution, eigentensors): new_eigentensor += np.int64(parameter) * eigentensor return new_eigentensor
[docs]def renormalize_to_integer(vector): gcm = 1 # greates common multiple for v in vector: if v.is_Integer: continue den = v.q # Denomonator gcd = sympy.gcd(gcm, den) # greates common divisor tmp = den / gcd gcm = gcm * tmp # Now all elements should be smallest possible integers vector = vector * gcm return vector