Cluster space

ClusterSpace

class hiphive.ClusterSpace(prototype_structure, cutoffs, sum_rules=True, symprec=1e-05, length_scale=0.1)[source]

Primitive object handling cluster and force constants for a structure.

Parameters:
  • prototype_struture (ASE Atoms object) – prototype structure; spglib will be used to find a suitable cell based on this structure.
  • cutoffs (list or Cutoffs obj) – cutoff radii for different orders starting with second order
  • sum_rules (bool) – If True the aucostic sum rules will be enforced by constraining the parameters.
  • symprec (float) – numerical precision that will be used for analyzing the symmetry (this parameter will be forwarded to spglib)
  • length_scale (float) – This will be used as a normalization constant for the eigentensors

Examples

To instantiate a ClusterSpace object one has to specify a prototype structure and cutoff radii for each cluster order that should be included. For example the following snippet will set up a ClusterSpace object for a BCC structure including second order terms up to a distance of 5 A and third order terms up to a distance of 4 A.

>>> from ase.build import bulk
>>> prim = bulk('W')
>>> cs = ClusterSpace(prim, [5.0, 4.0])
atom_list

BiMap object – atoms inside the cutoff relative to the of the center cell

cluster_list

BiMap object – clusters possible within the cutoff

copy()[source]
cutoffs

Cutoffs object – cutoffs used for constructing the cluster space

length_scale

float – normalization constant of the force constants

number_of_dofs

int – number of free parameters in the model

If the sum rules are not enforced the number of DOFs is the same as the total number of eigentensors in all orbits.

orbit_data

list – list of dictionaries containing detailed information for each orbit, e.g., cluster radius and atom types.

orbits

list of Orbit objects – orbits associated with the lattice structure.

permutations

list of vectors – lookup for permutation references

primitive_structure

ASE Atoms object – structure of the lattice

print_orbits()[source]

Prints a list of all orbits.

read(f)[source]

Reads a ClusterSpace instance from file.

Parameters:f (string or file object) – name of input file (string) or stream to load from (file object)
rotation_matrices

list of 3x3 matrices – symmetry elements representing rotations

spacegroup

str – space group of the lattice structure obtained from spglib

sum_rules

bool – True if sum rules are enforced

symprec

float – symprec value used when constructing the cluster space

translation_vectors

list of 3-vectors – symmetry elements representin translations

write(fileobj)[source]

Saves to file or to a file-like object.

The instance is saved into a custom format based on tar-files. The resulting file will be a valid tar file and can be browsed by by a tar reader. The included objects are themself either pickles, npz or other tars.

Parameters:fileobj (str or file-like object) – If the input is a string a tar archive will be created in the current directory. Otherwise the input must be a valid file like object.
wyckoff_sites

list – wyckoff sites in the primitive cell

Cutoffs

class hiphive.cluster_filter.Cutoffs(cutoff_matrix)[source]

Contains information about cutoff config

Contains conventient functionality to be used in the algorithms

Parameters:cutoff_matrix – cutoff_matrix[i][j] corresponds to the cutoff for order i+2 and nbody j+2. Elements where j>i will be ignored.
get_cutoff(order=None, nbody=None)[source]
max_cutoff
max_nbody
max_nbody_cutoff(nbody)[source]
max_nbody_order(nbody)[source]
max_order
orders
read(fileobj)[source]
write(fileobj)[source]