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)
def test_particle_comparators():
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
ico1 = Icosahedron('Cu', 4)
ico1.info['confid'] = 1
ico2 = Icosahedron('Ni', 4)
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()
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)
def looks_like(self, a1, a2):
""" Return if structure a1 or a2 are similar or not. """
elements = self.elements
if elements == []:
elements = sorted(set(a1.get_chemical_symbols()))
a1, a2 = a1.copy(), a2.copy()
del a1[[a.index for a in a1 if a.symbol not in elements]]
del a2[[a.index for a in a2 if a.symbol not in elements]]
nnmat_a1 = get_nnmat(a1)
nnmat_a2 = get_nnmat(a2)
diff = np.linalg.norm(nnmat_a1 - nnmat_a2)
if diff < self.d:
return True
else:
return False
def looks_like(self, a1, a2):
""" Return if structure a1 or a2 are similar or not. """
elements = self.elements
if elements == []:
elements = sorted(set(a1.get_chemical_symbols()))
a1, a2 = a1.copy(), a2.copy()
del a1[[a.index for a in a1 if a.symbol not in elements]]
del a2[[a.index for a in a2 if a.symbol not in elements]]
nnmat_a1 = get_nnmat(a1)
nnmat_a2 = get_nnmat(a2)
diff = np.linalg.norm(nnmat_a1 - nnmat_a2)
if diff < self.d:
return True
else:
return False
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
ico1 = Icosahedron('Cu', 4)
ico1.info['confid'] = 1
ico2 = Icosahedron('Ni', 4)
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()
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)