Cutoffs and cluster filters¶
In this tutorial the usage of cutoffs and cluster filters will be discussed.
A cluster of lattice sites (i,j,k,…) is defined to be inside a cutoff if all pairwise interatomic distances in the cluster are less than the cutoff.
Cutoffs can be set for each expansion order as well as for each n-body interaction. This can be seen as a matrix of cutoffs, i.e.
The order of a cluster (i.j,k,…) is given by the number of lattice sites in the cluster, whereas the body (n-body interaction) is given by the number of unique lattice sites in the cluster.
Hiphive allows users to use custom cluster filters. These can be used
to reduce the number of clusters that full within the given
cutoffs. The cluster filter has one main function, which given a
cluster (i,j,k,…) is to return True or False depending on whether
the cluster should be kept or not. The
looks like this:
class BaseClusterFilter: def __init__(self): pass def setup(self, atoms): """ The filter is passed the environment of the primitive cell. """ self._atoms = atoms def __call__(self, cluster): """ Returns True or False when a cluster is proposed. """ return True
Where the setup function can be used to pre-define or pre-calculate quantities that are needed for the subsequent filter. Filtering can be based on both geometrical aspects, e.g., include a cluster if it involves atoms close to a defect. It can also be based on the atomic species, for example the following filter will only consider higher order clusters if they contain at least one oxygen atom.:
class MyOxygenFilter(BaseClusterFilter): def __call__(self, cluster): """ Returns True or False when a cluster is proposed. """ order = len(cluster) if order == 2: return True else: if any(self._atoms[i].symbol == 'O' for i in cluster): return True else: return False cf = MyOxygenFilter() cs = ClusterSpace(prim, [6.0, 6.0, 6.0], cluster_filter=cf)
examples/advanced_topics/cluster_filters an example is provided that
demonstrates how to generate a higher-order model for atoms on the
surface while “bulk” atoms are treated harmonically.
Please note that the cutoffs from the
Cutoffs object are always
enforced first, after which the cluster filter is applied.
Usage of max triplet distance filter
import numpy as np from ase.build import fcc100 from ase.calculators.emt import EMT from ase.optimize import BFGS from hiphive.cutoffs import BaseClusterFilter from hiphive import ClusterSpace, StructureContainer from hiphive.fitting import CrossValidationEstimator from hiphive.structure_generation import generate_rattled_structures from hiphive.utilities import prepare_structures class SurfaceFilter(BaseClusterFilter): def setup(self, atoms): self.atoms = atoms dist_tol = 1e-5 z_pos = atoms.positions[:, 2] z_max = np.max(z_pos) z_min = np.min(z_pos) top_layer = np.where(z_pos + dist_tol > z_max).tolist() bot_layer = np.where(z_pos - dist_tol < z_min).tolist() self.surface_indices = top_layer + bot_layer def __call__(self, cluster): order = len(cluster) if order <= 2: return True else: return any(c in self.surface_indices for c in cluster) def evaluate_cs(cs, structures): sc = StructureContainer(cs) for x in structures: sc.add_structure(x) cve = CrossValidationEstimator(sc.get_fit_data(), n_splits=10) cve.validate() print(cve) return cve.summary # setup atoms and filter atoms = fcc100('Ni', (6, 6, 6), a=4.05, vacuum=20, orthogonal=True) atoms.pbc = True calc = EMT() # relax structure atoms.set_calculator(calc) dyn = BFGS(atoms) converged = dyn.run(fmax=0.0001, steps=1000) # setup cluster filter sf = SurfaceFilter() # build clusterspace cutoffs1 = [6.0] cutoffs2 = [6.0, 3.0, 3.0] cs1 = ClusterSpace(atoms, cutoffs1, cluster_filter=None) cs2 = ClusterSpace(atoms, cutoffs2, cluster_filter=None) cs2_sf = ClusterSpace(atoms, cutoffs2, cluster_filter=sf) print('Degrees of freedom second order :', cs1.n_dofs) print('Degrees of freedom fourth order :', cs2.n_dofs) print('Degrees of freedom fourth order with filter :', cs2_sf.n_dofs) # testing structures = generate_rattled_structures(atoms, n_structures=25, rattle_std=0.03) structures = prepare_structures(structures, atoms, calc) # second order only cve1 = evaluate_cs(cs1, structures) cve2 = evaluate_cs(cs2, structures) cve2_sf = evaluate_cs(cs2_sf, structures)