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import numpy as np
from ase.cluster import Icosahedron
from ase.ga.particle_comparator import NNMatComparator
from ase.ga.utilities import get_nnmat
from ase.ga.particle_mutations import RandomPermutation
def make_ico(sym):
atoms = Icosahedron(sym, 4)
atoms.center(vacuum=4.0)
return atoms
def test_particle_comparators(seed):
# set up the random number generator
rng = np.random.RandomState(seed)
ico1 = make_ico('Cu')
ico1.info['confid'] = 1
ico2 = make_ico('Ni')
ico1.numbers[:55] = [28] * 55
ico2.numbers[:92] = [29] * 92
ico1.info['data'] = {}
ico1.info['data']['nnmat'] = get_nnmat(ico1)
ico2.info['data'] = {}
ico2.info['data']['nnmat'] = get_nnmat(ico2)
comp = NNMatComparator()
assert not comp.looks_like(ico1, ico2)
op = RandomPermutation(rng=rng)
a3, desc = op.get_new_individual([ico1])
assert a3.get_chemical_formula() == ico1.get_chemical_formula()
hard_comp = NNMatComparator(d=100)
assert hard_comp.looks_like(ico1, a3)
soft_comp = NNMatComparator(d=.0001)
assert not soft_comp.looks_like(ico1, a3)
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