def mutate(self, cluster: Cluster, *args, **kwargs) -> Cluster:
"""Applies small random rotations to a all initial_molecules in the cluster"""
successful = False
while not successful:
for particle in range(len(cluster.molecules)):
theta = self.random(self.step_size)
cluster.molecules[particle].rotate(axis=random_axis(),
theta=theta)
successful = self.check_cluster(cluster)
return cluster
def mutate(self, old_cluster: Cluster, *args, **kwargs) -> Cluster:
"""Generates a new cluster and returns it.
Args:
old_cluster: Cluster object, required, The template for the cluster
*args: unused
**kwargs: unused
Returns:
A new cluster with new molecular positions and orientations
"""
max_step = self.box_length or len(old_cluster.molecules)**(5. / 4)
# new_cluster = copy.deepcopy(old_cluster)
#
# base_molecules = copy.deepcopy(old_cluster.molecules)
#
# new_cluster.molecules = []
#
# for m in base_molecules:
# m.center()
# vec = np.random.uniform(low=0.1, high=max_step, size=3)
# m.translate(vec)
#
# m.rotate(random_axis(), np.random.uniform(0, 2 * np.pi))
#
# new_cluster.molecules.append(m)
#
# return new_cluster
new_molecules = [
Molecule(coordinates=copy.deepcopy(m.coordinates),
particle_names=m.particle_names)
for m in old_cluster.molecules
]
for m in new_molecules:
m.center()
vec = np.random.uniform(low=0.1, high=max_step, size=3)
m.translate(vec)
m.rotate(random_axis(), np.random.uniform(0, 2 * np.pi))
new_cluster = Cluster(molecules=new_molecules)
return new_cluster
def mutate(self, cluster: Cluster, *args, **kwargs) -> Cluster:
"""Applies a rotation to a single member of a cluster
Args:
cluster (Cluster): required, the cluster to be mutated
"""
successful = False
while not successful:
selection = np.random.randint(len(cluster.molecules))
# Step length is distributed according to the distribution selected at __init__
theta = self.random(self.step_size)
cluster.molecules[selection].rotate(axis=random_axis(),
theta=theta)
successful = self.check_cluster(cluster)
return cluster
def mutate(self, cluster: Cluster, *args, **kwargs) -> Cluster:
"""Applies rotations to several members of a cluster
Args:
cluster (Cluster): required, the cluster to be mutated
"""
successful = False
while not successful:
selection = np.random.randint(len(cluster.molecules),
size=np.random.randint(
len(cluster.molecules)))
for particle in selection:
theta = self.random(self.step_size)
cluster.molecules[particle].rotate(axis=random_axis(),
theta=theta)
successful = self.check_cluster(cluster)
return cluster
def prepare_parents(self, parents: List[Cluster]) -> List[Cluster]:
"""Shuffles, centers and rotates the parent clusters
Args:
parents: List[Clusters], required, parents for mating.
Returns:
List[Clusters] shuffled, centered and rotated clusters, Note: order is not preserved.
"""
# Shuffle the order of the parents
np.random.shuffle(parents)
prepared_parents = []
# Center and then apply uniformly random rotations to each parent
for parent in parents:
axis = random_axis()
parent.center()
parent.rotate(axis, np.random.uniform(2.0 * np.pi))
prepared_parents.append(copy.deepcopy(parent))
return prepared_parents