program

Classes and functions related to interfaces to executable programs.

Defines methods that are required for interfaces to external programs that will run as executables and produce output that will be parsed.

class daltonproject.program.ComputeSettings(work_dir: Optional[str] = None, scratch_dir: Optional[str] = None, node_list: Optional[List[str]] = None, jobs_per_node: Optional[int] = None, mpi_command: Optional[str] = None, mpi_num_procs: Optional[int] = None, omp_num_threads: Optional[int] = None, memory: Optional[int] = None, comm_port: Optional[int] = None, launcher: Optional[str] = None)

Compute settings to be used by Program.compute() implementations.

The settings can be given as arguments during initialization. Defaults are used for any missing argument(s).

property comm_port: Return communication port.

property jobs_per_node: int: Return the number of jobs per node.

property launcher: Optional[str]: Return launcher command.

property memory: int: Return the total amount of memory in MB per node.

property mpi_command: str: Return MPI command.

property mpi_num_procs: int: Return the number of MPI processes.

property node_list: List[str]: Return the list of nodes.

property num_nodes: Return the number of nodes.

property omp_num_threads: int: Return the number of OpenMP threads (per MPI process).

property scratch_dir: str: Return scratch directory.

property work_dir: str: Return work directory.

class daltonproject.program.ExcitationEnergies(excitation_energies: ndarray, excitation_energies_per_sym: Dict[str, ndarray])

Data structure for excitation energies.

excitation_energies: ndarray: Alias for field number 0

excitation_energies_per_sym: Dict[str, ndarray]: Alias for field number 1

class daltonproject.program.HyperfineCouplings(polarization: ndarray, direct: ndarray, total: ndarray)

Data structure for hyperfine couplings.

direct: ndarray: Alias for field number 1

polarization: ndarray: Alias for field number 0

total: ndarray: Alias for field number 2

class daltonproject.program.NumBasisFunctions(tot_num_basis_functions: int, num_basis_functions_per_sym: List[int])

Data structure for the number of basis functions.

num_basis_functions_per_sym: List[int]: Alias for field number 1

tot_num_basis_functions: int: Alias for field number 0

class daltonproject.program.NumOrbitals(tot_num_orbitals: int, num_orbitals_per_sym: List[int])

Data structure for the number of orbitals.

num_orbitals_per_sym: List[int]: Alias for field number 1

tot_num_orbitals: int: Alias for field number 0

class daltonproject.program.OrbitalCoefficients(orbital_coefficients: ndarray, orbital_coefficients_per_sym: Dict[str, ndarray])

Data structure for molecular orbital coefficients.

orbital_coefficients: ndarray: Alias for field number 0

orbital_coefficients_per_sym: Dict[str, ndarray]: Alias for field number 1

class daltonproject.program.OrbitalEnergies(orbital_energies: ndarray, orbital_energies_per_sym: Dict[str, ndarray])

Data structure for molecular orbital energies.

orbital_energies: ndarray: Alias for field number 0

orbital_energies_per_sym: Dict[str, ndarray]: Alias for field number 1

class daltonproject.program.OrbitalEnergy(orbital_energy: float, symmetry: str)

Data structure for a single molecular orbital energy.

orbital_energy: float: Alias for field number 0

symmetry: str: Alias for field number 1

class daltonproject.program.OscillatorStrengths(oscillator_strengths: ndarray, oscillator_strengths_per_sym: Dict[str, ndarray])

Data structure for oscillator strengths.

oscillator_strengths: ndarray: Alias for field number 0

oscillator_strengths_per_sym: Dict[str, ndarray]: Alias for field number 1

class daltonproject.program.OutputParser

Abstract OutputParser class.

The implementation of this class defines methods for parsing output files produced by a program.

abstract property dipole: ndarray: Retrieve dipole.

abstract property dipole_gradients: ndarray: Retrieve gradients of dipole moment with respect to nuclear displacements in Cartesian coordinates.

abstract property electronic_energy: float: Retrieve electronic energy.

abstract property energy: float: Retrieve energy.

abstract property excitation_energies: ndarray: Retrieve excitation energies.

abstract property filename: str: Retrieve filename.

abstract property final_geometry: ndarray: Retrieve final geometry.

abstract property first_hyperpolarizability: ndarray: Retrieve the first hyperpolarizability.

abstract property gradients: ndarray: Retrieve gradients with respect to nuclear displacements in Cartesian coordinates.

abstract property hessian: ndarray: Retrieve second derivatives with respect to nuclear displacements in Cartesian coordinates.

abstract property homo_energy: OrbitalEnergy: Retrieve the highest occupied molecular orbital energy.

abstract property hyperfine_couplings: HyperfineCouplings: Retrieve hyperfine couplings.

abstract property lumo_energy: OrbitalEnergy: Retrieve the lowest unoccupied molecular orbital energy.

abstract property mo_energies: OrbitalEnergies: Retrieve molecular orbital energies.

abstract property natural_occupations: Union[ndarray, Dict[int, ndarray]]: Retrieve natural orbital occupations.

abstract property nmr_shieldings: ndarray: Retrieve NMR shieldings.

abstract property nuclear_repulsion_energy: float: Retrieve nuclear-repulsion energy.

abstract property num_basis_functions: Union[int, NumBasisFunctions]: Retrieve the number of basis functions.

abstract property num_electrons: int: Retrieve the number of electrons.

abstract property num_orbitals: Union[int, NumOrbitals]: Retrieve the number of orbitals.

abstract property orbital_coefficients: Union[ndarray, Dict[int, ndarray]]: Retrieve molecular orbital coefficients.

abstract property oscillator_strengths: ndarray: Retrieve oscillator strengths.

abstract property polarizability: ndarray: Retrieve polarizability.

abstract property polarizability_gradients: PolarizabilityGradients: Retrieve gradients of the polarizability with respect to nuclear displacements in Cartesian coordinates.

abstract property two_photon_cross_sections: ndarray: Retrieve two-photon cross-sections.

abstract property two_photon_strengths: ndarray: Retrieve two-photon strengths.

abstract property two_photon_tensors: ndarray: Retrieve two-photon tensors.

class daltonproject.program.PolarizabilityGradients(frequencies: ndarray, values: ndarray)

Data structure for polarizability gradients.

frequencies: ndarray: Alias for field number 0

values: ndarray: Alias for field number 1

class daltonproject.program.Program

Program base class to enforce program interface.

The interface must implement a compute() method that prepares and executes a calculation, and returns an instance of the OutputParser class.

abstract classmethod 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: bool = False) → OutputParser

Run a calculation.

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….
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 with a reference to the filename used in the calculation.