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)