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
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)