def get_offspring(self, cluster_a, cluster_b):
'''Generate an offspring structure from two parent structures.'''
#Prepare clusters
for cluster in [cluster_a, cluster_b]:
cluster.centre()
cluster.rotate_random()
cluster.sort_z()
#Choose cutting plane
cut = np.random.randint(1, cluster_a.natoms)
#Make new cluster
coords = np.empty(shape=(cluster_a.natoms, 3))
atom_types = []
for i in range(0, cut):
coords[i] = cluster_a.get_coords(i)
atom_types.append(cluster_a.atom_types[i])
for i in range(cut, cluster_a.natoms):
coords[i] = cluster_b.get_coords(i)
atom_types.append(cluster_b.atom_types[i])
composition = get_composition(cluster_a.atom_types)
atom_types = fix_composition(composition, atom_types)
offspring = Cluster(cluster_a.natoms,
coords,
cluster_a.minimiser,
atom_types=atom_types,
labels=cluster_a.labels)
offspring.quenched = False
offspring.sort_type()
cluster_a.sort_type()
cluster_b.sort_type()
return offspring
def get_mutant(self, cluster):
coords = (np.random.rand(cluster.natoms, 3) - 0.5) * 1.4 * float(
cluster.natoms)**(1. / 3.)
mutant = Cluster(cluster.natoms,
coords,
cluster.minimiser,
atom_types=list(cluster.atom_types),
labels=cluster.labels)
return mutant
def read_db(self, minimum):
'''Read structure from Pele minimum'''
cluster = Cluster(self.natoms,
np.reshape(minimum.coords, (-1, 3)),
self.minimiser,
atom_types=get_atom_types(self.composition),
labels=self.labels)
cluster.energy = minimum.energy
cluster.quenched = True
return cluster
def setUp(self):
self.natoms = 3
minimiser = PeleMinimiser(BLJCut(3, 1))
coords = np.array(((0., 0., 0.1), (1., 1., 0.3), (0., 2., 0.2)))
types = [0, 1, 0]
labels = ["X", "Y"]
self.cluster = Cluster(self.natoms,
coords,
minimiser,
atom_types=types,
labels=labels)
def get_random_cluster(self):
'''Return a cluster with random coordinates'''
coords = (np.random.rand(self.natoms, 3) - 0.5) * 1.4 * float(
self.natoms)**(1. / 3.)
cluster = Cluster(self.natoms,
coords,
self.minimiser,
atom_types=get_atom_types(self.composition),
labels=self.labels)
cluster.quenched = False
return cluster
def get_mutant(self, cluster):
cluster.sort_type()
atom_types = list(cluster.atom_types)
swap0 = np.random.randint(0, get_composition(atom_types)[0])
swap1 = np.random.randint(
get_composition(atom_types)[0], cluster.natoms)
atom_types[swap0] = 1
atom_types[swap1] = 0
mutant = Cluster(cluster.natoms,
np.array(cluster._coords),
cluster.minimiser,
atom_types=atom_types,
labels=cluster.labels)
mutant.sort_type()
return mutant
def read_xyz(self, xyz_file):
'''Read structure from xyz file.'''
natoms = int(xyz_file.readline())
coords = np.empty(shape=(natoms, 3))
energy = float(xyz_file.readline().split()[1])
for i in range(0, natoms):
coords[i] = xyz_file.readline().split()[1:4]
cluster = Cluster(natoms,
coords,
self.minimiser,
atom_types=get_atom_types(self.composition),
labels=self.labels)
cluster.energy = energy
cluster.quenched = True
return cluster
def setUp(self):
self.natoms = 3
minimiser = PeleMinimiser(lj.LJ())
coords = np.array(((0., 0., 0.1), (0.1, 0.1, 0.1), (0., 0.2, 0.2)))
self.cluster = Cluster(self.natoms, coords, minimiser)
def setUp(self):
natoms = 3
self.minimiser = PeleMinimiser(lj.LJ())
coords = np.array(((0., 0., 0.1), (1., 1., 0.3), (0., 2., 0.2)))
self.cluster = Cluster(natoms, coords, self.minimiser)
