BUG: Tolerances from ClusterSpace not passed down the chain in structure_alignment
Example from @hybelius with structure prim_moire.xyz
From discussion today it seems like tolerance from ClusterSpace is not used in all comparisons in structure_alignment which likely causes the example to fail.
from hiphive import ClusterSpace, StructureContainer
from ase.io import read
import numpy as np
# setup
cutoffs = [3.0]
symprec = 1e-3
prim = read('prim_moire.xyz')
cs = ClusterSpace(prim, cutoffs, symprec=symprec)
sc = StructureContainer(cs)
# make supercell
supercell = prim.repeat((1, 1, 2))
supercell.arrays['displacements'] = np.zeros((len(supercell), 3))
supercell.arrays['forces'] = np.zeros((len(supercell), 3))
sc.add_structure(supercell)