lsdalton
Initialize LSDalton interface module.
- class daltonproject.lsdalton.OutputParser(filename: str)
Parse LSDalton output files.
- property dipole: ndarray
Not implemented.
- property dipole_gradients: ndarray
Extract Cartesian dipole gradients from OpenRSP tensor file.
- property electronic_energy: float
Extract the electronic energy from LSDalton output file.
- property energy: float
Extract the final energy from LSDalton output file.
- property excitation_energies: ndarray
Extract one-photon excitation energies from LSDalton output file.
- property filename: str
Name of the LSDalton output files without the extension.
- property final_geometry: ndarray
Extract final geometry from LSDalton output file.
- property first_hyperpolarizability: ndarray
Not implemented.
- property gradients: ndarray
Extract molecular gradient from LSDalton output file.
- property hessian: ndarray
Extract molecular hessian from OpenRSP tensor file.
- property homo_energy: OrbitalEnergy
Not implemented.
- property hyperfine_couplings: HyperfineCouplings
Not implemented.
- property lumo_energy: OrbitalEnergy
Not implemented.
- property mo_energies: OrbitalEnergies
Not implemented.
- property natural_occupations: Dict[int, List[float]]
Not implemented.
- property nmr_shieldings: ndarray
Not implemented.
- property nuclear_repulsion_energy: float
Extract the nuclear repulsion energy from LSDalton output file.
- property num_basis_functions: Union[NumBasisFunctions, int]
Not implemented.
- property num_electrons: int
Not implemented.
- property num_orbitals: Union[NumOrbitals, int]
Not implemented.
- property orbital_coefficients: Union[ndarray, Dict[int, ndarray]]
Not implemented.
- property oscillator_strengths: ndarray
Extract one-photon oscillator strengths from LSDalton output file.
- property polarizability: ndarray
Not implemented.
- property polarizability_gradients: PolarizabilityGradients
Extract Cartesian polarizability gradients from OpenRSP tensor file.
- property two_photon_cross_sections: ndarray
Not implemented.
- property two_photon_strengths: ndarray
Not implemented.
- property two_photon_tensors: ndarray
Not implemented.
- daltonproject.lsdalton.compute(molecule: Molecule, basis: Basis, qc_method: QCMethod, properties: Property, environment: Optional[Environment] = None, compute_settings: Optional[ComputeSettings] = None, filename: Optional[str] = None, force_recompute: Optional[bool] = False) OutputParser
Run a calculation using the LSDalton program.
- Parameters
molecule – Molecule on which a calculations is performed. This can also be an atom, a fragment, or any collection of atoms.
basis – Basis set to use in the calculation.
qc_method – Quantum chemistry method, e.g., HF, DFT, or CC, and associated settings.
properties – Properties of molecule to be calculated, geometry optimization, excitation energies, etc.
environment – TODO Environment…
compute_settings – Settings for the calculation, e.g., number of MPI processes and OpenMP threads, work and scratch directory, etc.
filename – Optional user-specified filename that will be used for input and output files. If not specified a name will be generated as a hash of the input.
force_recompute – Recompute even if the output files already exist.
- Returns
OutputParser instance that contains the filename of the output produced in the calculation and can be used to extract results from the output.
- daltonproject.lsdalton.compute_farm(molecules: List[Molecule], basis: Basis, qc_method: QCMethod, properties: Property, compute_settings: Optional[ComputeSettings] = None, filenames: Optional[List[str]] = None, force_recompute: bool = False) List[OutputParser]
Run a series of calculations using the LSDalton program.
- Parameters
molecules – List of molecules on which calculations are performed.
basis – Basis set to use in the calculations.
qc_method – Quantum chemistry method, e.g., HF, DFT, or CC, and associated settings used for all calculations.
properties – Properties of molecule to be calculated, geometry optimization, excitation energies, etc., computed for all molecules.
compute_settings – Settings for the calculations, e.g., number of MPI processes and OpenMP threads, work and scratch directory, and more.
filenames – Optional list of user-specified filenames that will be used for input and output files. If not specified names will be generated as a hash of the individual inputs.
force_recompute – Recompute even if the output files already exist.
- Returns
List of OutputParser instances each of which contains the filename of the output produced in the calculation and can be used to extract results from the output.
- daltonproject.lsdalton.coulomb_matrix(density_matrix: ndarray, molecule: Molecule, basis: Basis, qc_method: QCMethod, geometric_derivative_order: int = 0, magnetic_derivative_order: int = 0) ndarray
Calculate the Coulomb matrix.
- Parameters
density_matrix – Density matrix
molecule – Molecule object.
basis – Basis object.
qc_method – QCMethod object.
geometric_derivative_order – Order of the derivative with respect to nuclear displacements.
magnetic_derivative_order – Order of the derivative with respect to magnetic field.
- Returns
Coulomb matrix
- daltonproject.lsdalton.diagonal_density(hamiltonian: ndarray, metric: ndarray, molecule: Molecule, basis: Basis, qc_method: QCMethod) ndarray
Form an AO density matrix from occupied MOs through diagonalization.
- Parameters
hamiltonian – Hamiltonian matrix.
metric – Metric matrix (i.e. overlap matrix)
molecule – Molecule object.
basis – Basis object.
qc_method – QCMethod object.
- Returns
Density matrix
- daltonproject.lsdalton.electronic_electrostatic_potential(density_matrix: ndarray, points: ndarray, molecule: Molecule, basis: Basis, qc_method: QCMethod, ep_derivative_order: Tuple[int, int] = (0, 0), geometric_derivative_order: int = 0, magnetic_derivative_order: int = 0) ndarray
Calculate the electronic electrostatic potential at a set of points.
Derivatives of the electrostatic potential can be calculated using the ep_derivative_order argument, e.g., ep_derivative_order = (0, 1) will calculate both the zeroth- and first-order derivatives while ep_derivative_order = (1, 1) will calculate first-order derivatives only.
- Parameters
density_matrix – Density matrix.
points – Set of points where the electrostatic potential will be evaluated.
molecule – Molecule object.
basis – Basis object.
qc_method – QCMethod object.
ep_derivative_order – Range of orders of the derivative of the electrostatic potential.
geometric_derivative_order – Order of the derivative with respect to nuclear displacements.
magnetic_derivative_order – Order of the derivative with respect to magnetic field.
- Returns
Electronic electrostatic potential
- daltonproject.lsdalton.electrostatic_potential(density_matrix: ndarray, points: ndarray, molecule: Molecule, basis: Basis, qc_method: QCMethod, ep_derivative_order: Tuple[int, int] = (0, 0), geometric_derivative_order: int = 0, magnetic_derivative_order: int = 0) ndarray
Calculate the molecular electrostatic potential at a set of points.
Derivatives of the electrostatic potential can be calculated using the ep_derivative_order argument, e.g., ep_derivative_order = (0, 1) will calculate both the zeroth- and first-order derivatives while ep_derivative_order = (1, 1) will calculate first-order derivatives only.
- Parameters
density_matrix – Density matrix.
points – Set of points where the electrostatic potential will be evaluated.
molecule – Molecule object.
basis – Basis object.
qc_method – QCMethod object.
ep_derivative_order – Range of orders of the derivative of the electrostatic potential.
geometric_derivative_order – Order of the derivative with respect to nuclear displacements.
magnetic_derivative_order – Order of the derivative with respect to magnetic field.
- Returns
Point-wise electronic multipol-moment potential
- daltonproject.lsdalton.electrostatic_potential_integrals(points: ndarray, molecule: Molecule, basis: Basis, qc_method: QCMethod, ep_derivative_order: Tuple[int, int] = (0, 0), geometric_derivative_order: int = 0, magnetic_derivative_order: int = 0) ndarray
Calculate electrostatic-potential integrals.
Derivatives of the electrostatic potential can be calculated using the ep_derivative_order argument, e.g., ep_derivative_order = (0, 1) will calculate both the zeroth- and first-order derivatives while ep_derivative_order = (1, 1) will calculate first-order derivatives only.
Let a and b be AO basis functions, C a point, and \(\xi\) and \(\zeta\) Cartesian components, then order 0: \((ab|C) = \int a(r) b(r) V(r,C) dr\), with the potential: \(V(r,C) = 1/|r-C|\) order 1: \(\int a(r) b(r) V_\xi(r,C) dr\), with first-order potential derivative: \(V_\xi(r,C) = \partial{V(r,C)}{\partial{C_\xi}}= C_\xi/|r-C|^3\) order 2: \(\int a(r) b(r) V_{\xi,\zeta}(r,C) dr\), with second-order potential derivative: \(V_{\xi,\zeta}(r,C) = \partial^2{V(r,C)}{\partial{C_\xi}\partial{C_\zeta}}\)
- Parameters
points – Set of points where the electrostatic-potential integrals will be evaluated.
molecule – Molecule object.
basis – Basis object.
qc_method – QCMethod object.
ep_derivative_order – Range of orders of the derivative of the electrostatic potential.
geometric_derivative_order – Order of the derivative with respect to nuclear displacements.
magnetic_derivative_order – Order of the derivative with respect to magnetic field.
- Returns
Electrostatic-potential integrals
- daltonproject.lsdalton.eri(specs: str, molecule: Molecule, basis: Basis, qc_method: QCMethod, geometric_derivative_order: int = 0, magnetic_derivative_order: int = 0) ndarray
Calculate electron-repulsion integrals for different operator choices.
\[g_{ijkl} = \int\mathrm{d}\mathbf{r}\int\mathrm{d}\mathbf{r}^{\prime} \chi_{i}(\mathbf{r})\chi_{j}(\mathbf{r}^\prime) g(\mathbf{r},\mathbf{r}^\prime) \chi_{k}(\mathbf{r})\chi_{l}(\mathbf{r}^\prime)\]The first character of the specs string specifies the operator \(g(\mathbf{r}, \mathbf{r}^\prime)\). Valid values are:
C for Coulomb (\(g(\mathbf{r}, \mathbf{r}^\prime) = \frac{1}{|\mathbf{r} - \mathbf{r}^\prime|}\))
G for Gaussian geminal (\(g\))
F geminal divided by the Coulomb operator (\(\frac{g}{|\mathbf{r} - \mathbf{r}^\prime|}\))
D double commutator (\([[T,g],g]\))
2 Gaussian geminal operator squared (\(g^2\))
The last four characters of the specs string specify the AO basis to use for the four basis functions \(\chi_{i}\), \(\chi_{j}\), \(\chi_{k}\), and \(\chi_{l}\). Valid values are:
R for regular AO basis
D for auxiliary (RI) AO basis
E for empty AO basis (i.e. for 2- and 3-center ERIs)
N for nuclei
- Parameters
specs – A 5-character-long string with the specification for AO basis and operator to use (see description above).
molecule – Molecule object.
basis – Basis object.
qc_method – QCMethod object.
geometric_derivative_order – Order of the derivative with respect to nuclear displacements.
magnetic_derivative_order – Order of the derivative with respect to magnetic field.
- Returns
Electron-repulsion integral tensor.
- daltonproject.lsdalton.eri4(molecule: Molecule, basis: Basis, qc_method: QCMethod, geometric_derivative_order: int = 0, magnetic_derivative_order: int = 0) ndarray
Calculate four-center electron-repulsion integrals.
\[(ab|cd) = g_{acbd}\]with
\[g(\mathbf{r},\mathbf{r}^\prime) = \frac{1}{|\mathbf{r}-\mathbf{r}^\prime|}\]- Parameters
molecule – Molecule object.
basis – Basis object.
qc_method – QCMethod object.
geometric_derivative_order – Order of the derivative with respect to nuclear displacements.
magnetic_derivative_order – Order of the derivative with respect to magnetic field.
- Returns
Four-center electron-repulsion integral tensor.
- daltonproject.lsdalton.exchange_correlation(density_matrix: ndarray, molecule: Molecule, basis: Basis, qc_method: QCMethod, geometric_derivative_order: int = 0, magnetic_derivative_order: int = 0) Tuple[float, ndarray]
Calculate the exchange-correlation energy and matrix.
- Parameters
density_matrix – Density matrix.
molecule – Molecule object.
basis – Basis object.
qc_method – QCMethod object.
geometric_derivative_order – Order of the derivative with respect to nuclear displacements.
magnetic_derivative_order – Order of the derivative with respect to magnetic field.
- Returns
Exchange-correlation energy and matrix
- daltonproject.lsdalton.exchange_matrix(density_matrix: ndarray, molecule: Molecule, basis: Basis, qc_method: QCMethod, geometric_derivative_order: int = 0, magnetic_derivative_order: int = 0) ndarray
Calculate the exchange matrix.
- Parameters
density_matrix – Density matrix.
molecule – Molecule object.
basis – Basis object.
qc_method – QCMethod object.
geometric_derivative_order – Order of the derivative with respect to nuclear displacements.
magnetic_derivative_order – Order of the derivative with respect to magnetic field.
- Returns
Exchange matrix
- daltonproject.lsdalton.fock_matrix(density_matrix: ndarray, molecule: Molecule, basis: Basis, qc_method: QCMethod, geometric_derivative_order: int = 0, magnetic_derivative_order: int = 0) ndarray
Calculate the Fock/KS matrix.
- Parameters
density_matrix – Density matrix
molecule – Molecule object.
basis – Basis object.
qc_method – QCMethod object.
geometric_derivative_order – Order of the derivative with respect to nuclear displacements.
magnetic_derivative_order – Order of the derivative with respect to magnetic field.
- Returns
Fock/KS matrix
- daltonproject.lsdalton.kinetic_energy_matrix(molecule: Molecule, basis: Basis, qc_method: QCMethod, geometric_derivative_order: int = 0, magnetic_derivative_order: int = 0) ndarray
Calculate the kinetic energy matrix.
- Parameters
molecule – Molecule object.
basis – Basis object.
qc_method – QCMethod object.
geometric_derivative_order – Order of the derivative with respect to nuclear displacements.
magnetic_derivative_order – Order of the derivative with respect to magnetic field.
- Returns
Kinetic energy matrix
- daltonproject.lsdalton.multipole_interaction_matrix(moments: ndarray, points: ndarray, molecule: Molecule, basis: Basis, qc_method: QCMethod, multipole_orders: Tuple[int, int] = (0, 0), geometric_derivative_order: int = 0, magnetic_derivative_order: int = 0) ndarray
Calculate the electron-multipole electrostatic interaction matrix in atomic-orbital (AO) basis.
Minimum and maximum orders of the multipole moments are provided by the multipole_orders argument, e.g., multipole_orders = (0, 1) includes charges (order 0) and dipoles (order 1) while multipole_orders = (1, 1) includes only dipoles.
- Parameters
moments – Multipole moments.
points – Positions of the multipole moments.
molecule – Molecule object.
basis – Basis object.
qc_method – QCMethod object.
multipole_orders – Minimum and maximum orders of the multipole moments, where 0 = charge, 1 = dipole, etc.
geometric_derivative_order – Order of the derivative with respect to nuclear displacements.
magnetic_derivative_order – Order of the derivative with respect to magnetic field.
- Returns
Electron-multipole electrostatic interaction matrix
- daltonproject.lsdalton.nuclear_electron_attraction_matrix(molecule: Molecule, basis: Basis, qc_method: QCMethod, geometric_derivative_order: int = 0, magnetic_derivative_order: int = 0) ndarray
Calculate the nuclear-electron attraction matrix.
- Parameters
molecule – Molecule object.
basis – Basis object.
qc_method – QCMethod object.
geometric_derivative_order – Order of the derivative with respect to nuclear displacements.
magnetic_derivative_order – Order of the derivative with respect to magnetic field.
- Returns
Nuclear-electron attraction matrix
- daltonproject.lsdalton.nuclear_electrostatic_potential(points: ndarray, molecule: Molecule, ep_derivative_order: Tuple[int, int] = (0, 0), geometric_derivative_order: int = 0, magnetic_derivative_order: int = 0) ndarray
Calculate the nuclear electrostatic potential at a set of points.
Derivatives of the electrostatic potential can be calculated using the ep_derivative_order argument, e.g., ep_derivative_order = (0, 1) will calculate both the zeroth- and first-order derivatives while ep_derivative_order = (1, 1) will calculate first-order derivatives only.
- Parameters
points – Set of points where the electrostatic potential will be evaluated.
molecule – Molecule object.
ep_derivative_order – Range of orders of the derivative of the electrostatic potential.
geometric_derivative_order – Order of the derivative with respect to nuclear displacements.
magnetic_derivative_order – Order of the derivative with respect to magnetic field.
- Returns
Nuclear electrostatic potential
- daltonproject.lsdalton.nuclear_energy(molecule: Molecule) float
Calculate the nuclear-repulsion energy.
- Parameters
molecule – Molecule object.
- Returns
Nuclear-repulsion energy
- daltonproject.lsdalton.num_atoms(molecule: Molecule, basis: Basis, qc_method: QCMethod) int
Return the number of atoms.
- Parameters
molecule – Molecule object.
basis – Basis object.
qc_method – QCMethod object.
- Returns
Number of atoms
- daltonproject.lsdalton.num_basis_functions(molecule: Molecule, basis: Basis, qc_method: QCMethod) int
Return the number of basis functions.
- Parameters
molecule – Molecule object.
basis – Basis object.
qc_method – QCMethod object.
- Returns
Number of basis functions
- daltonproject.lsdalton.num_electrons(molecule: Molecule, basis: Basis, qc_method: QCMethod) int
Return the number of electrons.
- Parameters
molecule – Molecule object.
basis – Basis object.
qc_method – QCMethod object.
- Returns
Number of electrons
- daltonproject.lsdalton.num_ri_basis_functions(molecule: Molecule, basis: Basis, qc_method: QCMethod) int
Return the number of auxiliary (RI) basis functions.
- Parameters
molecule – Molecule object.
basis – Basis object.
qc_method – QCMethod object.
- Returns
Number of auxiliary (RI) basis functions
- daltonproject.lsdalton.overlap_matrix(molecule: Molecule, basis: Basis, qc_method: QCMethod, geometric_derivative_order: int = 0, magnetic_derivative_order: int = 0) ndarray
Calculate the overlap matrix.
- Parameters
molecule – Molecule object.
basis – Basis object.
qc_method – QCMethod object.
geometric_derivative_order – Order of the derivative with respect to nuclear displacements.
magnetic_derivative_order – Order of the derivative with respect to magnetic field.
- Returns
Overlap matrix
- daltonproject.lsdalton.ri2(molecule: Molecule, basis: Basis, qc_method: QCMethod) ndarray
Calculate two-center electron-repulsion integrals.
\[(I|J) = g_{I00J}\]with
\[g(\mathbf{r},\mathbf{r}^\prime) = \frac{1}{|\mathbf{r}-\mathbf{r}^\prime|}\]- Parameters
molecule – Molecule object.
basis – Basis object.
qc_method – QCMethod object.
- Returns
Two-center RI integrals
- daltonproject.lsdalton.ri3(molecule: Molecule, basis: Basis, qc_method: QCMethod) ndarray
Calculate three-center electron-repulsion integrals.
\[(ab|I) = g_{a0bI}\]with
\[g(\mathbf{r},\mathbf{r}^\prime) = \frac{1}{|\mathbf{r}-\mathbf{r}^\prime|}\]- Parameters
molecule – Molecule object.
basis – Basis object.
qc_method – QCMethod object.
- Returns
Three-center RI integrals