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
