Force constant models¶
ForceConstantPotential¶

class
hiphive.
ForceConstantPotential
(cs, parameters, metadata=None)[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
metadata (dict) – metadata dictionary, will be pickled when object is written to file

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

property
metadata
¶ metadata associated with force constant potential
 Type
dict

property
orbit_data
¶ list of dictionaries containing detailed information for each orbit, e.g. cluster radius and force constant
 Type
List[dict]

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

property
symprec
¶
ForceConstantCalculator¶

class
hiphive.calculators.
ForceConstantCalculator
(fcs, max_disp=3.0)[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
max_disp (float) – maximum allowed displacement before calculator raises ValueError

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.
 Return type
None

compute_energy_and_forces
()[source]¶ Computes 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 force constants obey acoustic sum rules.
 Parameters
order (
Optional
[int
]) – specifies which order to check, if None all are checkedtol (
float
) – numeric tolerance for checking sum rules
 Raises
AssertionError – if acoustic sum rules are violated

property
clusters
¶ sorted list of clusters
 Return type
list

compute_gamma_frequencies
()[source]¶ Returns the Gamma frequencies in THz using the secondorder force constants.
 Return type

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

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 constantssupercell (
Atoms
) – atomic configuration

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 constantssupercell (
Atoms
) – atomic configuration

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 returnedformat (
str
) – specify which format (shape) the NumPy array should have, possible values are phonopy and ase
 Return type
 Returns
NumPy array with shape (N,)*order + (3,)*order where N is
the number of atoms

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 (
Optional
[int
]) – force constants returned for this order Return type
dict
 Returns
dictionary with keys corresponding to clusters and values to
respective force constant

property
n_atoms
¶ number of atoms
 Return 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 Return type
None

classmethod
read
(fname)[source]¶ Reads ForceConstants from file.
 Parameters
fname (
str
) – name of file from which to read

classmethod
read_phono3py
(supercell, fname)[source]¶ Reads force constants from a phono3py calculation.
 Parameters
supercell (
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 (
Atoms
) – supercell structure (SPOSCAR)fname (
str
) – name of secondorder force constant fileformat (
Optional
[str
]) – format for secondorder force constants; possible values: “text”, “hdf5”

classmethod
read_shengBTE
(supercell, fname, prim, symprec=1e05)[source]¶ Reads third order force constants from a shengBTE calculation.
shengBTE force constants will be mapped onto a supercell.
 Parameters
supercell (
Atoms
) – supercell structurefname (
str
) – name of thirdorder force constant fileprim (
Atoms
) – primitive configuration (must be equivalent to structure used in the shengBTE calculation)symprec – structural symmetry tolerance

property
supercell
¶ supercell associated with force constants
 Return type
Atoms

write
(fname)[source]¶ Writes entire ForceConstants object to file.
 Parameters
fname (
str
) – name of file to which to write Return type
None

write_to_phono3py
(fname)[source]¶ Writes force constants in phono3py format.
 Parameters
fname (
str
) – name of file to which to write thirdorder force constant Return type
None

write_to_phonopy
(fname, format=None)[source]¶ Writes force constants in phonopy format.
 Parameters
fname (
str
) – name of file to which to write secondorder force constantformat (
Optional
[str
]) – format for secondorder force constants;
possible values: “text”, “hdf5”
 Return type
None

write_to_shengBTE
(fname, prim, **kwargs)[source]¶ Writes third order force constants in shengBTE format.
 Parameters
fname (
str
) – name of file to which to write thirdorder force constantprim (
Atoms
) – primitive configuration (must be equivalent to structure used in the shengBTE calculation)
 Return type
None


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) –

property
orders
¶ orders for which force constants exist
 Return type
List
[int
]

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) –

property
orders
¶ orders for which force constants exist
 Return type
List
[int
]

write_to_GPUMD
(fname_fc, fname_clusters, order, tol=1e10)[source]¶ Writes force constants of the specified order in GPUMD format.
 Parameters
fname_fc (str) – name of file which contains the lookup force constants
fname_clusters (str) – name of file which contains the clusters and the fc lookup index
order (int) – force constants for this order will be written to file
tol (float) – if the norm of a force constant is less than tol then it is not written. if two forceconstants are within tol; they are considered equal.

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 (
ndarray
) – force constant array in phonopy formatfc_tol (
float
) – tolerance for considering force constants zero or not
 Return type
dict

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 Return type
bool

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 Return type
dict

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

hiphive.
enforce_rotational_sum_rules
(cs, parameters, sum_rules=None, alpha=1e06, **ridge_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’
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]
ridge_kwargs (dict) – kwargs to be passed to sklearn Ridge
 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)