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 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 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
