Source code for hiphive.core.orbit

Contains the Orbit class which hold onformation about equivalent clusters.

import numpy as np
import tarfile

from .orientation_family import OrientationFamily
from import (add_items_to_tarfile_hdf5,

[docs]class Orbit: """ This class serves as a container for storing data pertaining to an orbit. Attributes ---------- orientation_families : list of OrientationFamily objs The orientation families of the orbit eigensymmetries : list of tuples Each eigensymmetry correspond to a pair where the first index is the symmetry and the second is the permutation eigentensors : list of NumPy arrays The decomposition of the force constant into symmetry elements """ # TODO: Make properties of the parameters def __init__(self): self.orientation_families = [] self.eigensymmetries = [] self.eigentensors = [] @property def prototype_index(self): """int : index of cluster that serves as prototype for this orbit In the code the first symmetry is always the identity so the first orientation family should always correspond to the prototype""" return self.orientation_families[0].cluster_indices[0]
[docs] def write(self, f): """Write a Orbit instance to a file. Parameters ---------- f : str or file object name of input file (str) or stream to write to (file object) """ tar_file ='w', fileobj=f) # add eigentensors as NumPy array items_hdf5 = dict(eigentensors=np.array(self.eigentensors), ) add_items_to_tarfile_hdf5(tar_file, items_hdf5, 'eigentensors') # add eigensymmetries as list items_pickle = dict(eigensymmetries=self.eigensymmetries, order=self.order, radius=self.radius, maximum_distance=self.maximum_distance) add_items_to_tarfile_pickle(tar_file, items_pickle, 'attributes') # add orientation families add_list_to_tarfile_custom(tar_file, self.orientation_families, 'orientation_families') tar_file.close()
[docs] def read(f): """Load a ClusterSpace from file Parameters ---------- f : string or file object name of input file (string) or stream to load from (file object) """ orb = Orbit() tar_file ='r', fileobj=f) # read eigentensors hdf5 items_hdf5 = read_items_hdf5(tar_file, 'eigentensors') orb.eigentensors = [et for et in items_hdf5['eigentensors']] # read attributes pickle attributes = read_items_pickle(tar_file, 'attributes') for name, value in attributes.items(): orb.__setattr__(name, value) # read orientation families ofs = read_list_custom(tar_file, 'orientation_families', orb.orientation_families = ofs return orb
[docs]def get_geometrical_radius(positions): """Compute the geometrical size of a 3-dimensional point cloud. The geometrical size is defined as the average distance to the geometric center. Parameters ---------- positions : list of 3-dimensional vectors positions of points in cloud Returns ------- float geometric size of point cloud """ geometric_center = np.mean(positions, axis=0) return np.mean(np.sqrt(np.sum((positions - geometric_center)**2, axis=1)))
[docs]def get_maximum_distance(positions): """Compute the maximum distance between any two points in a 3-dimensional point cloud. This is equivalent to the "size" criterion used when imposing a certain (pair) cutoff criterion during construction of a set of clusters. Parameters ---------- positions : list of 3-dimensional vectors positions of points in cloud Returns ------- float maximum distance betwee any two points """ if len(positions) == 0: return 0.0 max_distance = 0.0 for pt1 in positions[:-1]: for pt2 in positions[1:]: max_distance = max(max_distance, np.linalg.norm(pt1 - pt2)) return max_distance