Copying SecondQuantizedMolecule

[alexfleury-sb]

Feature Request: Deepcopy of SecondQuantizedMolecule

At this time, the SecondQuantizedMolecule can't be deepcopied:

from copy import deepcopy
from tangelo import SecondQuantizedMolecule

xyz_H2 = """
    H 0. 0. 0.00
    H 0. 0. 0.75
"""
mol = SecondQuantizedMolecule(xyz_H2)
deepcopy(mol)

outputs

Traceback (most recent call last):
  File "/home/alex/Scratch/mo_coeff_bug.py", line 14, in <module>
    deepcopy(mol)
  File "/home/alex/.pyenv/versions/3.10.13/lib/python3.10/copy.py", line 172, in deepcopy
    y = _reconstruct(x, memo, *rv)
  File "/home/alex/.pyenv/versions/3.10.13/lib/python3.10/copy.py", line 271, in _reconstruct
    state = deepcopy(state, memo)
  File "/home/alex/.pyenv/versions/3.10.13/lib/python3.10/copy.py", line 146, in deepcopy
    y = copier(x, memo)
  File "/home/alex/.pyenv/versions/3.10.13/lib/python3.10/copy.py", line 231, in _deepcopy_dict
    y[deepcopy(key, memo)] = deepcopy(value, memo)
  File "/home/alex/.pyenv/versions/3.10.13/lib/python3.10/copy.py", line 172, in deepcopy
    y = _reconstruct(x, memo, *rv)
  File "/home/alex/.pyenv/versions/3.10.13/lib/python3.10/copy.py", line 271, in _reconstruct
    state = deepcopy(state, memo)
  File "/home/alex/.pyenv/versions/3.10.13/lib/python3.10/copy.py", line 146, in deepcopy
    y = copier(x, memo)
  File "/home/alex/.pyenv/versions/3.10.13/lib/python3.10/copy.py", line 231, in _deepcopy_dict
    y[deepcopy(key, memo)] = deepcopy(value, memo)
  File "/home/alex/.pyenv/versions/3.10.13/lib/python3.10/copy.py", line 161, in deepcopy
    rv = reductor(4)
TypeError: cannot pickle 'module' object

This is not a critical bug at this moment, but it would be useful to be able to create a copy and update its attributes. For e.g.,

from copy import copy
from openfermion.linalg import eigenspectrum

def doing_something_with_molecule(sqmol):
    sqmol_copy = copy(sqmol)
    # Doing awesome stuff with mo_coeff and creating new_mo_coeff.
    sqmol_copy.mo_coeff = new_coeff
    return sqmol_copy

eigenvalues_original = eigenspectrum(mol.fermionic_hamiltonian)
updated_mol = doing_something_with_molecule(mol)
eigenvalues_verif = eigenspectrum(mol.fermionic_hamiltonian) # Should be the same as eigenvalues_original, but it is not.

# Doing other stuff with updated_mol...

The function doing_something_with_molecule is changing the MO coefficients of the sqmol_copy, but as the copy is shallow, it is also changing the MO coefficients of the mol object. This can introduce unexpected behaviour, as I experienced when working with FNO -> the MO coefficients were bound to the active space selection, so the fermionic Hamiltonian computed after the doing_something_with_molecule call wasn't trowing an error, but was physically wrong.