QMolecule
QMolecule(filename=None)
Molecule data class containing driver result.
When one of the chemistry drivers is run and instance of this class is returned. This contains various properties that are made available in a consistent manner across the various drivers.
Note that values here, for the same input molecule to each driver, may be vary across the drivers underlying code implementation. Also some drivers may not provide certain fields such as dipole integrals in the case of PyQuanteDriver.
This class provides methods to save it and load it again from an HDF5 file
Attributes
BOHR
= 0.52917721092
DEBYE
= 0.393430307
QMOLECULE_VERSION
= 2
core_orbitals
List[int]
Returns: A list of core orbital indices.
Return type
List[int]
filename
returns temp file path
one_body_integrals
Returns one body electron integrals.
symbols
= ['_', 'H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co', 'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te', 'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir', 'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn', 'Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No', 'Lr', 'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt', 'Ds', 'Rg', 'Cn', 'Nh', 'Fl', 'Mc', 'Lv', 'Ts', 'Og']
two_body_integrals
Returns two body electron integrals.
x_dipole_integrals
returns x_dipole_integrals
y_dipole_integrals
returns y_dipole_integrals
z_dipole_integrals
returns z_dipole_integrals
Methods
Z
QMolecule.Z(natom)
has_dipole_integrals
QMolecule.has_dipole_integrals()
Check if dipole integrals are present.
load
QMolecule.load()
loads info saved.
log
QMolecule.log()
log properties
onee_to_spin
static QMolecule.onee_to_spin(mohij, mohij_b=None, threshold=1e-12)
Convert one-body MO integrals to spin orbital basis
Takes one body integrals in molecular orbital basis and returns integrals in spin orbitals ready for use as coefficients to one body terms 2nd quantized Hamiltonian.
Parameters
- mohij (numpy.ndarray) – One body orbitals in molecular basis (Alpha)
- mohij_b (numpy.ndarray) – One body orbitals in molecular basis (Beta)
- threshold (float) – Threshold value for assignments
Returns
One body integrals in spin orbitals
Return type
numpy.ndarray
oneeints2mo
static QMolecule.oneeints2mo(ints, moc)
Converts one-body integrals from AO to MO basis
Returns one electron integrals in AO basis converted to given MO basis
Parameters
- ints (numpy.ndarray) – N^2 one electron integrals in AO basis
- moc (numpy.ndarray) – Molecular orbital coefficients
Returns
integrals in MO basis
Return type
numpy.ndarray
remove_file
QMolecule.remove_file(file_name=None)
remove file
save
QMolecule.save(file_name=None)
Saves the info from the driver.
twoe_to_spin
static QMolecule.twoe_to_spin(mohijkl, mohijkl_bb=None, mohijkl_ba=None, threshold=1e-12)
Convert two-body MO integrals to spin orbital basis
Takes two body integrals in molecular orbital basis and returns integrals in spin orbitals ready for use as coefficients to two body terms in 2nd quantized Hamiltonian.
Parameters
- mohijkl (numpy.ndarray) – Two body orbitals in molecular basis (AlphaAlpha)
- mohijkl_bb (numpy.ndarray) – Two body orbitals in molecular basis (BetaBeta)
- mohijkl_ba (numpy.ndarray) – Two body orbitals in molecular basis (BetaAlpha)
- threshold (float) – Threshold value for assignments
Returns
Two body integrals in spin orbitals
Return type
numpy.ndarray
twoeints2mo
static QMolecule.twoeints2mo(ints, moc)
Converts two-body integrals from AO to MO basis
Returns two electron integrals in AO basis converted to given MO basis
Parameters
- ints (numpy.ndarray) – N^2 two electron integrals in AO basis
- moc (numpy.ndarray) – Molecular orbital coefficients
Returns
integrals in MO basis
Return type
numpy.ndarray
twoeints2mo_general
static QMolecule.twoeints2mo_general(ints, moc1, moc2, moc3, moc4)