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_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 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 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 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 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 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 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