Cluster space¶
ClusterSpace¶
- class hiphive.ClusterSpace(prototype_structure, cutoffs, config=None, cluster_filter=None, **kwargs)[source]¶
Primitive object for handling clusters and force constants of a structure.
- Parameters
prototype_structure (ase.Atoms) – prototype structure; spglib will be used to find a suitable cell based on this structure unless the cell is already a primitive cell.
cutoffs (list or Cutoffs) – cutoff radii for different orders starting with second order
cluster_filter (ClusterFilter) – accepts a subclass of hiphive.filters.BaseClusterFilter to further control which orbits to include.
config (Config object) – a configuration object that holds information on how the cluster space should be built, e.g., values for tolerances and specifications regarding the handling of acoustic sum rules; if
config
is not given then the keyword arguments that follow below can be used for configuration.acoustic_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 aClusterSpace
object for a body-centered-cubic (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 >>> from hiphive import ClusterSpace >>> prim = bulk('W') >>> cs = ClusterSpace(prim, [5.0, 4.0])
- property acoustic_sum_rules¶
True if acoustic sum rules are enforced
- Type
bool
- property atom_list¶
atoms inside the cutoff relative to the of the center cell
- Type
BiMap
- property cluster_list¶
clusters possible within the cutoff
- Type
BiMap
- get_n_dofs_by_order(order)[source]¶
Returns number of degrees of freedom for the given order.
- Parameters
order (int) – order for which to return the number of dofs
- Returns
number of degrees of freedom
- Return type
int
- get_parameter_indices(order)[source]¶
Returns a list of the parameter indices associated with the requested order.
- Parameters
order (int) – order for which to return the parameter indices
- Returns
list of parameter indices associated with the requested order
- Return type
list(int)
- Raises
ValueError – if the order is not included in the cluster space
- property length_scale¶
normalization constant of the force constants
- Type
float
- property n_dofs¶
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.
- Type
int
- property orbit_data¶
detailed information for each orbit, e.g., cluster radius and atom types.
- Type
list(dict)
- property orbits¶
orbits associated with the lattice structure.
- Type
list(Orbit)
- property permutations¶
lookup for permutation references
- Type
list(numpy.ndarray)
- print_tables()[source]¶
Prints information concerning the underlying cluster space to stdout,including, e.g., the number of cluster, orbits, and parameters by order and number of bodies.
- read()[source]¶
Reads a cluster space from file.
- Parameters
f (str or file object) – name of input file (str) or stream to load from (file object)
- property rotation_matrices¶
symmetry elements (3x3 matrices) representing rotations
- Type
list(numpy.ndarray)
- property spacegroup¶
space group of the lattice structure obtained from spglib
- Type
str
- property symprec¶
symprec value used when constructing the cluster space
- Type
float
- property translation_vectors¶
symmetry elements representing translations
- Type
list(numpy.ndarray)
- write(fileobj)[source]¶
Writes cluster space to file.
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.
- property wyckoff_sites¶
wyckoff sites in the primitive cell
- Type
list
Cutoffs¶
- class hiphive.cutoffs.BaseClusterFilter[source]¶
Base cluster filter class.
This filter simply accepts all proposed clusters. A proper subclass must implement the same methods.
- class hiphive.cutoffs.CutoffMaximumBody(cutoff_list, max_nbody)[source]¶
Specify cutoff-list plus maximum body
Usefull when creating e.g. 6th order expansions but with only 3-body interactions.
- Parameters
cutoff_list (list) – list of cutoffs for order 2, 3, etc. Must be in decresing order
max_nbody (int) – No clusters containing more than max_nbody atoms will be generated
- class hiphive.cutoffs.Cutoffs(cutoff_matrix)[source]¶
This class maintains information about the cutoff configuration, i.e. which clusters will be included (=”inside cutoff”). It also encapsulates functionality that is used e.g., during cluster space construction.
Here, n-body refers to number of atoms in a cluster. For example the cluster (0011) is a two-body cluster of fourth order and the cluster (123) is a three-body cluster of third order.
- Parameters
cutoff_matrix (numpy.ndarray) – the matrix element ij provides to the cutoff for order j+2 and nbody i+2; elements with i>j will be ignored
- property cutoff_matrix¶
copy of cutoff matrix
- Type
- get_cutoff(order, nbody)[source]¶
Returns cutoff for a given body and order.
- Parameters
order (int) –
nbody (int) –
- Raises
ValueError – if order is not in orders
ValueError – if nbody is not in nbodies
ValueError – if nbody is larger than order
- Return type
float
- property max_cutoff¶
maximum cutoff
- Type
float
- property max_nbody¶
maximum body
- Type
int
- property max_order¶
maximum order
- Type
int
- property nbodies¶
allowed bodies
- Type
list(int)
- property orders¶
allowed orders
- Type
list(int)
- read()[source]¶
Reads an instance from file.
- Parameters
fileobj (file-like object) – input file to read from
- hiphive.cutoffs.estimate_maximum_cutoff(atoms, max_iter=11)[source]¶
Estimates the maximum possible cutoff given the atoms object
- Parameters
atoms (ase.Atoms) – structure used for checking compatibility with cutoff
max_iter (int) – number of iterations in binary search
- hiphive.cutoffs.is_cutoff_allowed(atoms, cutoff)[source]¶
Checks if atoms is compatible with cutoff
- Parameters
atoms (ase.Atoms) – structure used for checking compatibility with cutoff
cutoff (float) – cutoff to be tested
- Returns
True if cutoff compatible with atoms object, else False
- Return type
bool