Input
The input required for the generation of graphs is a dictionary containing the relevant QM data in a specific format. For each molecule there needs to be a dictionary holding all of the following data:
- id: str
The identifier of the molecule.
- stoichiometry: str
The stoichiometric formula of the molecule.
- geometric_data: list[list[float]]
A 2-dimensional list representing the xyz coordinates of the system.
- n_atoms: int
The number of atoms.
- atomic_numbers: list[int]
A list of integers corresponding to the atomic numbers of the atoms.
- charge: float
The overall charge of the system.
- molecular_mass: float
The molecular mass of the system.
- wiberg_bond_order_matrix: list[list[float]]
A 2-dimensional list corresponding to the Wiberg bond order matrix.
- lmo_bond_order_matrix: list[list[float]]
A 2-dimensional list corresponding to the LMO bond order matrix.
- nlmo_bond_order_matrix
A 2-dimensional list corresponding to the NLMO bond order matrix.
- natural_atomic_charges: list[float]
A list of the natural atomic charges.
- natural_electron_configuration: list[list[float]]
A 2-dimensional list containing the natural electron configurations for each atom and orbitals s, p, d, and f.
- natural_electron_population: list[list[float]]
A 2-dimensional list containing the Core, Valence and Rydberg contributions to the natural population of each atom.
- nbo_data: list[list]
A nested list containing all information of the Natural Bond Order (NBO) analysis. For each NBO entry there is a list containing 7 elements. These are:
nbo_id: int
The ID of the NBO entry.
nbo_typ: str
The type of NBO (LP, LV, BD, BD*).
atom_indices: list[int]
A list containing the atom indices of the atoms involved in the NBO.
energy: float
The energy of the NBO.
contributions: list[float]
A list of contributions that indicate how much each of the atoms involve contributes to the NBO. Sums to 1.
occupation: float
The occupation of the NBO.
orbital_occupations: list[float]
A list of length 4 that holds the orbital occupations in terms of the s, p, d and f symmetries.
- sopa_data:
A nested list containing all information of the Second Order Perturbation Analysis (SOPA). For each SOPA entry there is a list containing two elements. These are:
nbo_ids: list[int]
A list of length two that holds the ids of the interacting NBO entries.
energies: list[float]
A list of length three that contains the stabilisation energy, E(NL)-E(L) and F(L,NL).
- polarisability: float
The isotropic polarisability.
- svp_dipole_moment: float
The magnitude of the SVP dipole moment.
- tzvp_dipole_moment: float
The magnitude of the TZVP dipole moment.
- svp_dispersion_energy: float
The SVP dispersion energy.
- tzvp_dispersion_energy: float
The TZVP dispersion energy.
- svp_electronic_energy: float
The SVP electronic energy.
- tzvp_electronic_energy: float
The TZVP electronic energy.
- enthalpy_energy: float
The enthalpy energy.
- gibbs_energy: float
The Gibbs energy.
- entropy: float
The entropy.
- heat_capacity: float
The heat capacity.
- zpe_correction: float
The ZPE correction.
- svp_occupied_orbital_energies
A list of the SVP energies of the occupied orbitals.
- svp_virtual_orbital_energies
A list of the SVP energies of the virtual orbitals.
- tzvp_occupied_orbital_energies: list[float]
A list of the TZVP energies of the occupied orbitals.
- tzvp_virtual_orbital_energies: list[float]
A list of the TZVP energies of the virtual orbitals.
- frequencies: list[float]
A list of the vibrational frequencies.