Force constant models¶
ForceConstantPotential¶

class
hiphive.
ForceConstantPotential
(cs, parameters)[source]¶ A finalized force constant model. Can produce force constants for any structure compatible with the structure for which the model was set up.
Parameters:  cs (ClusterSpace) – The cluster space the model is based upon
 parameters (numpy.ndarray) – The fitted paramteres

get_force_constants
(atoms)[source]¶ Return the force constants of a compatible structure.
Parameters: atoms (ase.Atoms) – input structure Returns: force constants Return type: ForceConstants

orbit_data
¶ list of dictionaries containing detailed information for each orbit, e.g. cluster radius and force constant
Type: list

parameters
¶

static
read
(f)[source]¶ Reads a force constant potential from file.
Parameters: f (str or file object) – name of input file (str) or stream to load from (file object) Returns: the original object as stored in the file Return type: ForceConstantPotential

symprec
¶
ForceConstantCalculator¶

class
hiphive.calculators.
ForceConstantCalculator
(fcs)[source]¶ This class provides an ASE calculator that can be used in conjunction with integrators and optimizers with the atomic simulation environment (ASE). To initialize an object of this class one must provide the ideal atomic configuration along with a compatible force constant model.
Parameters: fcs (ForceConstants) – the force constants instance must include the atomic configuration 
calculate
(atoms=None, properties=['energy'], system_changes=['positions', 'numbers', 'cell', 'pbc', 'initial_charges', 'initial_magmoms'])[source]¶ Do the calculation.
 properties: list of str
 List of what needs to be calculated. Can be any combination of ‘energy’, ‘forces’, ‘stress’, ‘dipole’, ‘charges’, ‘magmom’ and ‘magmoms’.
 system_changes: list of str
 List of what has changed since last calculation. Can be any combination of these six: ‘positions’, ‘numbers’, ‘cell’, ‘pbc’, ‘initial_charges’ and ‘initial_magmoms’.
Subclasses need to implement this, but can ignore properties and system_changes if they want. Calculated properties should be inserted into results dictionary like shown in this dummy example:
self.results = {'energy': 0.0, 'forces': np.zeros((len(atoms), 3)), 'stress': np.zeros(6), 'dipole': np.zeros(3), 'charges': np.zeros(len(atoms)), 'magmom': 0.0, 'magmoms': np.zeros(len(atoms))}
The subclass implementation should first call this implementation to set the atoms attribute.

compute_energy_and_forces
()[source]¶ Compute energy and forces.
Returns: energy and forces Return type: float, list(list(float))

implemented_properties
= ['energy', 'forces']¶

ForceConstants¶
This module provides functionality for storing and handling of force constants.

class
hiphive.force_constants.
ForceConstants
(supercell)[source]¶ Base class for force constants

assert_acoustic_sum_rules
(order=None, tol=1e06)[source]¶ Asserts that acoustic sum rules are enforced for force constants.
Parameters:  order (int) – specifies which order to check, if None all are checked
 tol (float) – numeric tolerance for checking sum rules
Raises: AssertionError
– if acoustic sum rules are not enforced

clusters
¶ sorted list of clusters
Type: list

compute_gamma_frequencies
()[source]¶ Computes gamma frequencies using the secondorder force constants.
Returns: gamma_frequencies – Gamma frequencies in THz Return type: numpy.ndarray

classmethod
from_arrays
(supercell, fc2_array=None, fc3_array=None)[source]¶ Constructs FCs from numpy arrays.
One or both of fc2_array and fc3_array must not be None
Parameters:  supercell (ase.Atoms) – supercell structure
 fc2_array (np.ndarray) – secondorder force constant in phonopy format
 fc3_array (np.ndarray) – thirdorder force constant in phonopy format

classmethod
from_dense_dict
(fc_dict, supercell)[source]¶ All permutations of clusters that are not zero must be listed, if label symmetries are fullfilled will return a SortedForceConstants
Parameters:  fc_dict (dict) – keys corresponding to clusters and values to the force constants
 supercell (ase.Atoms) –

classmethod
from_sparse_dict
(fc_dict, supercell)[source]¶ Assumes label symmetries, meaning only one cluster for each permuation should be included
Parameters:  fc_dict (dict) – keys corresponding to clusters and values to the force constants
 supercell (ase.Atoms) –

get_fc_array
(order, format='phonopy')[source]¶ Returns force constants in array format for specified order.
Parameters:  order (int) – force constants for this order will be returned
 format (str) – specify which format (shape) the NumPy array should have, possible values are phonopy and ase
Returns: NumPy array with shape (N,)*order + (3,)*order where N is the number of atoms
Return type:

get_fc_dict
(order=None)[source]¶ Returns force constant dictionary for one specific order.
The returned dict may be sparse or may be dense depending on the underlying force constants.
Parameters: order (int) – force constants returned for this order Returns: dictionary with keys corresponding to clusters and values to respective force constant Return type: dict

n_atoms
¶ number of atoms
Type: int

print_force_constant
(cluster)[source]¶ Prints force constants for a cluster in a nice format.
Parameters: cluster (tuple(int)) – sites belonging to the cluster

classmethod
read_phono3py
(supercell, fname)[source]¶ Reads force constants from a phono3py calculation.
Parameters:  supercell (ase.Atoms) – supercell structure (SPOSCAR)
 fname (str) – name of thirdorder force constant file

classmethod
read_phonopy
(supercell, fname, format=None)[source]¶ Reads force constants from a phonopy calculation.
Parameters:  supercell (ase.Atoms) – supercell structure (SPOSCAR)
 fname (str) – name of secondorder force constant file
 format (str) – format for secondorder force constants

classmethod
read_shengBTE
(supercell, fname, prim)[source]¶ Reads third order force constants from a shengBTE calculation.
shengBTE force constants will be mapped onto a supercell.
Parameters:  supercell (str) – supercell structure
 fname (str) – name of thirdorder force constant file
 prim (ase.Atoms) – primitive configuration (must be equivalent to structure used in the shengBTE calculation)

write_to_phono3py
(fname)[source]¶ Writes force constants in phono3py format.
Parameters: fname (str) – name of file to which to write thirdorder force constant


class
hiphive.force_constants.
RawForceConstants
(fc_dict, supercell)[source]¶ Force constants without label symmetries.
Parameters:  fc_dict (dict) – keys corresponding to clusters and values to the force constants, should contain all clusters with nonzero force constants
 supercell (ase.Atoms) –

orders
¶ orders for which force constants exist
Type: list

class
hiphive.force_constants.
SortedForceConstants
(fc_dict, supercell)[source]¶ Force constants with label symmetries.
Parameters:  fc_dict (dict) – keys corresponding to clusters and values to the force constants, should only contain sorted clusters
 supercell (ase.Atoms) –

orders
¶ orders for which force constants exist
Type: list

hiphive.force_constants.
array_to_dense_dict
(fc_array, fc_tol=1e10)[source]¶ Constructs a dense dict from an fc array in phonopy format.
Force constants with norm smaller than fc_tol will be considered zero and therefore not included in the fc_dict.
Parameters:  fc_array (np.ndarray) – force constant array in phonopy format
 fc_tol (float) – tolerance for considering force constants zero or not

hiphive.force_constants.
check_label_symmetries
(fc_dict)[source]¶ Checks label symmetries for dense fc dict.
Todo
tol, which one to use etc
Parameters: fc_dict (dict) – keys corresponding to clusters and values to the force constants

hiphive.force_constants.
dense_dict_to_sparse_dict
(fc_dict)[source]¶ Converts dense dict to sparse dict.
This does not check if label symmetry is True, but rather will just keep the sorted clusters and their force constants.
Parameters: fc_dict (dict) – keys corresponding to clusters and values to the force constants

hiphive.force_constants.
symbolize_force_constant
(fc, tol=1e10)[source]¶ Carries out a symbolic symmetrization of a force constant tensor.
Parameters:  fc (numpy.ndarray) – force constant tensor
 tol (float) – tolerance used to decide whether two elements are identical
Returns: symbolic representation of force constant matrix
Return type:
Constraints¶

hiphive.
enforce_rotational_sum_rules
(cs, parameters, sum_rules, **kwargs)[source] Enforces rotational sum rules by projecting parameters.
Note
The interface to this function might change in future releases.
Parameters:  cs (ClusterSpace) – the underlying cluster space
 parameters (numpy.ndarray) – parameters to be constrained
 sum_rules (list(str)) – type of sum rules to enforce; possible values: ‘Huang’, ‘BornHuang’
 ridge_alpha (float) – hyperparameter to the ridge regression algorithm; keyword argument passed to the optimizer; larger values specify stronger regularization, i.e. less correction but higher stability [default: 1e6]
 iterations (int) – number of iterations to run the projection since each step projects the solution down to each nullspace in serial; keyword argument passed to the optimizer [default: 10]
Returns: constrained parameters
Return type: Examples
The rotational sum rules can be enforced to the parameters before constructing a force constant potential as illustrated by the following snippet:
cs = ClusterSpace(reference_structure, cutoffs) sc = StructureContainer(cs) # add structures to structure container opt = Optimizer(sc.get_fit_data()) opt.train() new_params = enforce_rotational_sum_rules(cs, opt.parameters, sum_rules=['Huang', 'BornHuang']) fcp = ForceConstantPotential(cs, new_params)