def average_structure(self, force_update=False):
""" Calculates the atom positions of the average structure of the aligned clusters in the group. """
if not force_update and self._average is not None:
return self._average
nsuccessful = sum(self.successful)
avg_coords = [[0.0, 0.0, 0.0] for i in range(self.natoms)]
for cluster in self.clusters:
if not cluster.successful: continue
# The order of atoms in aligned_targets is the same for every target so we don't need to reorder by result.ind. That has been done during the alignment.
for i,atom in enumerate(cluster.aligned_target):
if i == len(cluster.aligned_target): break # This is a weird bug...
avg_coords[i][0] += atom.coord[0]/nsuccessful
avg_coords[i][1] += atom.coord[1]/nsuccessful
avg_coords[i][2] += atom.coord[2]/nsuccessful
m = Cluster(center_included=False, comment='averaged structure', xsize=100.,ysize=100.,zsize=100., atoms=[Atom(i, 'Si', *coord) for i,coord in enumerate(avg_coords)])
m.add(Atom(m.natoms, 'Si', *[0., 0., 0.])) # Add a center atom at (0,0,0)
m.center = m.atoms[-1]
m.center.neighs = m.atoms[:-1]
#m.rescale_bond_distances(3.5)
VT.calculate_atom(m, atom=m.center, cutoff=max(m.dist(m.atoms[-1],atom) for atom in m.atoms[:-1])+0.1) #VP calculation
#print(" Center atom's VP index is {0}".format(m.center.vp))
self._average = m
return m
def voronoi(self, atom=None, atoms=None, cutoff=None, atol=0.03, tol=0.03, tltol=0.03):
if atoms is not None and isinstance(atoms, list):
for atom in atoms:
if atom.neighs is None:
raise Exception("Atom {0} does not have neighbors.".format(atom))
voronoi_3d.calculate_atom(self, atom, cutoff, atol=0.03, tol=0.03, tltol=0.03)
elif atom is not None:
if atom.neighs is None:
raise Exception("Atom {0} does not have neighbors.".format(atom))
voronoi_3d.calculate_atom(self, atom, cutoff, atol=0.03, tol=0.03, tltol=0.03)
else:
self.voronoi(atoms=self.atoms, atol=atol, tol=tol, tltol=tltol)
return None