Molecule¶
Qibochem provides the Molecule
class to save various properties related to the molecular system,
and to drive the classical quantum chemistry calculation to obtain the necessary quantities for any subsequent quantum compute calculations.
- class qibochem.driver.molecule.Molecule(geometry=None, charge=0, multiplicity=1, basis=None, xyz_file=None, active=None)¶
Class representing a single molecule
- Parameters:
geometry (list) – Molecular coordinates in OpenFermion format, e.g.
[('H', (0.0, 0.0, 0.0)), ('H', (0.0, 0.0, 0.7))]
charge (int) – Net electronic charge of molecule
multiplicity (int) – Spin multiplicity of molecule, given as 2S + 1, where S is half the number of unpaired electrons
basis (str) – Atomic orbital basis set, used for the PySCF/PSI4 calculations. Default: “STO-3G” (minimal basis)
xyz_file (str) – .xyz file containing the molecular coordinates. The comment line can be used to define the electronic charge and spin multiplity if it is given in this format: “{charge} {multiplicity}”
active – Iterable representing the set of MOs to be included in the quantum simulation e.g.
list(range(3,6))
for an active space with orbitals 3, 4 and 5.
- nelec¶
Total number of electrons for the molecule
- norb¶
Number of molecular orbitals considered for the molecule
- nso¶
Number of molecular spin-orbitals considered for the molecule
- e_hf¶
Hartree-Fock energy
- oei¶
One-electron integrals
- tei¶
Two-electron integrals, order follows the second quantization notation
- active¶
Iterable of molecular orbitals included in the active space
- frozen¶
Iterable representing the occupied molecular orbitals removed from the simulation
- n_active_e¶
Number of electrons included in the active space if HF embedding is used
- n_active_orbs¶
Number of spin-orbitals in the active space if HF embedding is used
- run_pyscf(max_scf_cycles=50)¶
- Run a Hartree-Fock calculation with PySCF to obtain molecule quantities and
molecular integrals
- Parameters:
max_scf_cycles – Maximum number of SCF cycles in PySCF
- hf_embedding(active=None, frozen=None)¶
- Turns on HF embedding for a given active/frozen space, and fills in the class attributes:
inactive_energy
,embed_oei
, andembed_tei
.
- Parameters:
active – Iterable representing the active-space for quantum simulation
frozen – Iterable representing the occupied orbitals to be removed from the simulation
- hamiltonian(ham_type=None, oei=None, tei=None, constant=None, ferm_qubit_map=None)¶
Builds a molecular Hamiltonian using the one-/two- electron integrals. If HF embedding has been applied, (i.e. the
embed_oei
,embed_tei
, andinactive_energy
attributes are all notNone
), the corresponding values for the molecular integrals will be used instead.- Parameters:
ham_type – Format of molecular Hamiltonian returned. The available options are:
("f", "ferm")
: OpenFermionFermionOperator
,("q", "qubit")
: OpenFermionQubitOperator
, or("s", "sym")
: QiboSymbolicHamiltonian
(default)oei – 1-electron integrals (in the MO basis). The default value is the
oei
class attribute , unless theembed_oei
attribute exists and is notNone
, thenembed_oei
is used.tei – 2-electron integrals in the second-quantization notation (and MO basis). The default value is the
tei
class attribute , unless theembed_tei
attribute exists and is notNone
, thenembed_tei
is used.constant – Constant value to be added to the electronic energy. Mainly used for adding the inactive Fock energy if HF embedding was applied. Default: 0.0, unless the
inactive_energy
class attribute exists and is notNone
, theninactive_energy
is used.ferm_qubit_map – Which fermion to qubit transformation to use. Must be either
jw
(default) orbk
- Returns:
Molecular Hamiltonian in the format of choice
- static eigenvalues(hamiltonian)¶
- Finds the lowest 6 exact eigenvalues of the molecular Hamiltonian
Note: Uses the
eigenvalues()
class method for a QiboSymbolicHamiltonian
object
- Parameters:
hamiltonian – Molecular Hamiltonian, given as a
FermionOperator
,QubitOperator
, orSymbolicHamiltonian
(not recommended)