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BeH2_sto-3g
H2O_sto-3g
H2_line_sto-3g
H4_line_sto-3g
H4_ring_sto-3g
H6_line_sto-3g
H6_ring_sto-3g
LiH_sto-3g
BeH2.pdf
H2O.pdf
H2_line.pdf
H4_line.pdf
H4_ring.pdf
H6_line.pdf
H6_ring.pdf
LiH.pdf
README.md

README.md

Small_Molecules_1 dataset

This dataset contains electronic Hamiltonians of several small molecules with various configurations.

This dataset is used in the following competitions:

Details of dataset

Molecules

This dataset contains electronic Hamiltonians of the following molecules:

  • H2
  • H4 (line)
  • H6 (line)
  • H4 (ring)
  • H6 (ring)
  • LiH
  • BeH2
  • H2O

Here, Hn (line) denotes the molecule where n hydrogen atoms are aligned in line and have the same distance between each adjacent atom. For Hn (ring), n hydrogen atoms are placed on the circle with the same adjacent bond length. The bond lengths of Be-H in BeH2 are taken as the same and all atoms are aligned in line. The angle of two O-H bond in H2O is taken as 104.5 degree and each bond length is taken as the same.

Therefore, the configurations of each molecule are specified by a single scaler (bond_length). We choose bond_length from 0.5 to 2.0 with spacing of 0.01 (unit is Angstrom). Also, we add a datum at the optimal bond_length, where the exact molecular energy calculated by the full configuration interactions is minimized, for each molecule.

Dataformat

All data contained in Small_Molecules_1 dataset are openfermion.hamiltonian.MolecularData class of OpenFermion in .hdf5 format, which contain information on self-consistent field (SCF) molecular orbitals and their overlaps. The data are constructed through run_pyscf function provided by OpenFermion-PySCF.

The conditions for SCF calculations are

  • basis set: sto-3g minimal basis set
  • spin: singlet ($S^2=0$)
  • charge: neutral (0)

Filename convention

Data for each molecule are contained in {MoleculeName} directories, named as {MoleculeName}_sto-3g_singlet_{bond_length}.hdf5. MolecularName denotes the name of molecule, and bond_length denotes a distance between atoms in the unit of Angstrom (see "Molecules" section above for definition).

  • For hydrogenic molecules, we set MolecularName = H{n}_{line,ring} where n is the number of H atoms and {line,ring} denotes the type of arrangement.
  • For H2O molecule, we set bond_length = {length1}_{angle}_{length2} where length1, length2 are two individual bond lengths of H-O and angle is an angle between two H-O bonds.

Additional attributes in data

  • MolecularData.description: MolecularName
  • MolecularData.general_calculations - a python dictionary having
    • key bond_length: value=bond_length
    • key 1st_excited_energy: value = (1st excited state energy in the singlet sector ($S^2=0$) in Hartree calculated by the full configuration interactions)

Usage

An example code to use the file in the dataset are following:

from openfermion.hamiltonians import MolecularData
from openfermion.transforms import get_fermion_operator, jordan_wigner

molecular_data = MolecularData(filename="path/to/hdf5 file") # load hdf5 file
molecular_hamiltonian = get_fermion_operator(molecule_data.get_molecular_hamiltonian()) # get an instance of second quantized hamiltonian
jw_hamiltonian = jordan_wigner(molecular_hamiltonian) # get a Pauli operator representation of the hamiltonian
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