# Source code for mchammer.calculators.target_vector_calculator

```
from collections import OrderedDict
from typing import List
import numpy as np
from ase import Atoms
from icet import ClusterSpace
from icet.core.sublattices import Sublattices
from mchammer.calculators.base_calculator import BaseCalculator
[docs]class TargetVectorCalculator(BaseCalculator):
"""
A ``TargetVectorCalculator`` enables evaluation of the similarity
between a structure and a target cluster vector. Such a comparison
can be carried out in many ways, and this implementation follows the
measure proposed by van de Walle *et al.* in Calphad **42**, 13
(2013) [WalTiwJon13]_. Specifically, the objective function
:math:`Q` is calculated as
.. math::
Q = - \\omega L + \\sum_{\\alpha}
\\left| \\Gamma_{\\alpha} - \\Gamma^{\\text{target}}_{\\alpha}
\\right|.
Here, :math:`\\Gamma_{\\alpha}` are components in the cluster vector
and :math:`\\Gamma^\\text{target}_{\\alpha}` the corresponding
target values. The factor :math:`\\omega` is the radius of the
largest pair cluster such that all clusters with the same or smaller
radii have :math:`\\Gamma_{\\alpha} -
\\Gamma^\\text{target}_{\\alpha} = 0`.
Parameters
----------
atoms
structure for which to set up calculator
cluster_space
cluster space from which to build calculator
target_vector
vector to which any vector will be compared
weights
weighting of each component in cluster vector
comparison, by default 1.0 for all components
optimality_weight
factor :math:`L`, a high value of which effectively
favors a complete series of optimal cluster correlations
for the smallest pairs (see above)
optimality_tol
tolerance for determining whether a perfect match
has been achieved (used in conjunction with :math:`L`)
name
human-readable identifier for this calculator
"""
def __init__(self, atoms: Atoms, cluster_space: ClusterSpace,
target_vector: List[float],
weights: List[float] = None,
optimality_weight: float = 1.0,
optimality_tol: float = 1e-5,
name: str = 'Target vector calculator') -> None:
super().__init__(atoms=atoms, name=name)
if len(target_vector) != len(cluster_space):
raise ValueError('Cluster space and target vector '
'must have the same length')
self.cluster_space = cluster_space
self.target_vector = target_vector
if weights is None:
weights = np.array([1.0] * len(cluster_space))
else:
if len(weights) != len(cluster_space):
raise ValueError('Cluster space and weights '
'must have the same length')
self.weights = np.array(weights)
if optimality_weight is not None:
self.optimality_weight = optimality_weight
self.optimality_tol = optimality_tol
self.orbit_data = self.cluster_space.orbit_data
else:
self.optimality_weight = None
self.optimality_tol = None
self.orbit_data = None
self._cluster_space = cluster_space
[docs] def calculate_total(self, occupations: List[int]) -> float:
"""
Calculates and returns the similarity value :math:`Q`
of the current configuration.
Parameters
----------
occupations
the entire occupation vector (i.e. list of atomic species)
"""
self.atoms.set_atomic_numbers(occupations)
cv = self.cluster_space.get_cluster_vector(self.atoms)
return compare_cluster_vectors(cv, self.target_vector,
self.orbit_data,
weights=self.weights,
optimality_weight=self.optimality_weight,
tol=self.optimality_tol)
[docs] def calculate_local_contribution(self, occupations: List[int]) -> float:
"""
Not yet implemented, forwards calculation to
calculate_total.
"""
return self.calulate_total(occupations)
@property
def sublattices(self) -> Sublattices:
"""Sublattices of the calculators structure."""
sl = self.cluster_space.get_sublattices(self.atoms)
return sl
[docs]def compare_cluster_vectors(cv_1: np.ndarray, cv_2: np.ndarray,
orbit_data: OrderedDict,
weights: List[float] = None,
optimality_weight: float = 1.0,
tol: float = 1e-5) -> float:
"""
Calculate a quantity that measures similarity between two cluster
vecors.
Parameters
----------
cv_1
cluster vector 1
cv_2
cluster vector 2
orbit_data
orbit data as obtained by ``ClusterSpace.orbit_data``
weights
Weight assigned to each cluster vector element
optimality_weight
quantity :math:`L` in [WalTiwJon13]_
(see :class:`mchammer.calculators.TargetVectorCalculator`)
tol
numerical tolerance for determining whether two elements are
exactly equal
"""
if weights is None:
weights = np.ones(len(cv_1))
diff = abs(cv_1 - cv_2)
score = np.dot(diff, weights)
if optimality_weight:
longest_optimal_radius = 0
for orbit_index, d in enumerate(diff):
orbit = orbit_data[orbit_index]
if orbit['order'] != 2:
continue
if d < tol:
longest_optimal_radius = orbit['radius']
else:
break
score -= optimality_weight * longest_optimal_radius
return score
```