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 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 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