QuantumWavesComplex

Overview

QuantumWavesComplex inherits from QuantumComplex and specializes in wavefunction-based quantum calculations with extended capabilities.

Methods

• compute_long_range_interactions() → Calculates long-range molecular interactions.
• get_quadrupole_moment() → Returns quadrupole moments.
• get_radius_of_gyration() → Returns radius of gyration.
• get_free_energy() → Returns the computed free energy.
• get_dispersion_energy() → Returns dispersion energy contributions.
• get_forces() → Returns force matrix.
• get_positions() → Returns atomic positions.
• get_distance_matrix() → Returns the distance matrix.
• get_fermi_level() → Returns the Fermi level energy.
• get_eigenvalues() → Returns the eigenvalues of the Kohn-Sham matrix.
• get_homo_lumo_gap() → Returns the HOMO-LUMO gap.
• get_dipole_moment() → Returns dipole moment calculation.
• get_effective_potential() → Returns effective potential.
• get_electrostatic_potentials() → Returns electrostatic potential.
• get_wavefunctions() → Returns calculated wavefunctions.
• get_potential_energy() → Returns the potential energy of the molecule.
• get_zpe_hartree() → Returns zero-point energy in Hartree units.
• get_E0_elec_plus_zpe() → Returns electronic energy plus ZPE.
• get_freqs_cm() → Returns vibrational frequency values.
• get_thermal_corr_internal_energy() → Returns thermal correction to internal energy.

Usage Example

from polyatomic_complexes.src.complexes import PolyatomicGeometrySMILE
from polyatomic_complexes.src.complexes.quantum_theor_complex import QuantumWavesComplex

pg = PolyatomicGeometrySMILE(smile="CC(=O)OC", mode="quantum-waves")
quantum_w_mol = pg.smiles_to_geom_complex()
energy = quantum_w_mol.get_potential_energy()
dispersion = quantum_w_mol.get_dispersion_energy()
interactions = quantum_w_mol.compute_long_range_interactions()
radius = quantum_w_mol.get_radius_of_gyration()
free_energy = quantum_w_mol.get_free_energy()

Methods Explained

compute_long_range_interactions()

This method computes quantum-level properties at a DFT (B3LYP) level of theory including geometry optimization, thermal corrections via a frequency calculation (harmonic approximation).

get_quadrupole_moment()

This method returns the quadrupole moment tensor. Recall $$ Q_{ij} = \sum_k q_k \left( 3r_{ki} r_{kj} - \delta_{ij} r_k^2 \right) $$ where \(q_k\) is the charge at nucleus/electron \(k\), \(r_{ki}\) is the \(i\)-th coordinate charge of \(k\) and \(\delta_{ij}\) is the Kronecker delta.

Essentially we return \([Q_{xx}, Q_{yy}, Q_{zz}, Q_{xy}, Q_{xz}, Q_{yz}]\) as a List.

get_radius_of_gyration()

This method returns the radius of gyration. Recall that \(R_{g}\) is a measure of the spatial distribution of atomic positions around the center of mass (compactness). Moreover, $$ R_g = \sqrt{\frac{\sum_{i} m_i r_i^2}{\sum_{i} m_i}} $$ Note that a small \(R_g\) usually corresponds to a compact structure like a folded protein or dense polymer. Large \(R_g\) usually correspons to extended structures (stretched polymer). We return the mass weighted radius of gyration in Angstroms as a float.

get_free_energy()

This method returns the thermal and dispersion corrected total/free energy. Recall $$ G = E_{\text{elec}} + U_{\text{thermal}} + PV - TS $$ where \(E_{\text{elec}}\) is the electronic energy from HF/DFT, \(U_{\text{thermal}}\) is the thermal correction, \(PV\) is pressure-volume work, and \(TS\) is temperature times entropy from a harmonic analysis (aka via hessian). From here we can compute $$ E_{\text{corrected}} = E_{\text{elec}} + U_{\text{thermal}} + E_{\text{dispersion}} $$ where \(E_{\text{dispersion}}\) accounts for van der Waals interactions. We return \(E_{\text{corrected}}\) as a float in Hartree.

get_dispersion_energy()

This method returns the dispersion correction used above. Recall that dispersion energy accounts for long-range weak interactions that are not captured by standard DFT functionals. This method returns \(E_{\text{dispersion}}\) as a float.