def findAtoms(self, identifiers, initialized=True, coordinates='orth_defect'):
extra_atoms = self.surface().extraAtoms(coordinates='orth_surface')
crystal_atoms = self.surface().crystalAtoms(end_layer=1, coordinates='orth_surface')
unit_cell = self.surface().cell('orth_surface')
atoms = findAtoms(extra_atoms, crystal_atoms, identifiers, unit_cell)
atoms = self.change(atoms, to='orth_defect', fro='orth_surface')
atoms = makeAtomsRelaxed(
atoms,
self.relaxation(),
tolerance=2.0,
)
atoms = self.change(atoms, to=coordinates, fro='orth_defect')
if initialized and not (self.initialState() is None):
initial_identifiers = [s['identifier'] for s in self.initialState()]
initial_identifiers = self.initialStateIdentifiers(initial_identifiers)
for i in range(len(atoms)):
identifier = identifiers[i]
if identifier in initial_identifiers:
index = initial_identifiers.index(identifier)
move = self.__initial_state[index]['move_vector']
atoms[index].position += move
return atoms
def makeAtomsRelaxed(self, atoms, relaxation, tolerance=1):
factor = self.relaxationFactor()
atoms.positions *= factor
atoms.cell[2] *= factor
atoms = makeAtomsRelaxed(atoms, self.relaxation(), tolerance=tolerance)
return atoms
def makeAtomsRelaxed(self, atoms, relaxation):
atoms = atoms.copy()
atoms = self.fullyUnrelaxed().change(atoms, fro='orth_surface', to='orth_crystal')
atoms = self.crystal().makeAtomsRelaxed(atoms, self.crystal().relaxation())
atoms = self.change(atoms, to='orth_surface', fro='orth_crystal')
atoms = makeAtomsRelaxed(atoms, self.relaxation(), tolerance=1.5)
return atoms
def makeAtomsRelaxed(self, atoms, relaxation):
atoms = self.makeSubsystemsRelaxed(atoms)
if relaxation is None:
return atoms.copy()
size = len(self.molecule())
slab_atoms = atoms[:-size]
relaxed_slab_atoms = relaxation[:-size]
atoms.positions[:-size] = makeAtomsRelaxed(slab_atoms, relaxed_slab_atoms, 1.0).positions
atoms.positions[-size:] = relaxation[-size:].positions
return atoms
def makeAtomsRelaxed(self, atoms, relaxation, tolerance=1.0):
if relaxation is None:
return atoms
factor = relaxationFactor(self.__atoms, relaxation)
atoms.positions *= factor
atoms.cell *= factor
atoms = makeAtomsRelaxed(atoms, relaxation, tolerance=tolerance)
for electrode in atoms.electrodes():
electrode.setCell(electrode.cell()*factor)
return atoms
def makeAtomsRelaxed(self, atoms, relaxation, tolerance=1.0):
atoms = self.makeSubsystemsRelaxed(atoms, tolerance=0.1)
atoms = makeAtomsRelaxed(atoms, relaxation, tolerance=tolerance)
return atoms
def makeAtomsRelaxed(self, atoms):
return makeAtomsRelaxed(atoms, self.relaxation())