def __copy_kwargs__(self):
kw = InternalCoordinate.__copy_kwargs__(self)
# Give precidence to FunctionCoordinate over InternalCoordinate
kw.update(FunctionCoordinate.__copy_kwargs__(self))
kw.update(
b_vector_same_function = self.b_vector_same_function,
b_vector_function = self.b_vector_function,
b_vector_takes_coords = self.b_vector_takes_coords,
b_tensor_same_function = self.b_tensor_same_function,
b_tensor_function = self.b_tensor_function,
b_tensor_takes_coords = self.b_tensor_takes_coords,
value_takes_coords = self.value_takes_coords
)
return kw
def copy_with_atoms(self, atoms, **kwargs):
copykw = InternalCoordinate.__copy_kwargs__(self)
# Give precidence to FunctionCoordinate over InternalCoordinate
copykw.update(FunctionCoordinate.__copy_kwargs__(self))
copykw.update(self.__copy_kwargs__())
copykw['base_analog'] = self
# allow manual override of any of the above
copykw.update(kwargs)
new_sc = []
for isc, sc in enumerate(self.subcoordinates):
atmap = self._idxmap[isc]
catoms = [atoms[a] for _, a in sorted(atmap.items())]
new_sc.append(sc.copy_with_atoms(catoms))
copykw.update(subcoordinates=new_sc)
return self.__class__(**copykw)
