psiresp.job.Job

pydantic model psiresp.job.Job[source]

Class to manage RESP jobs. It is expected that all RESP calculations will be run through this class.

Fields
field charge_constraints: psiresp.charge.ChargeConstraintOptions = ChargeConstraintOptions(charge_sum_constraints=[], charge_equivalence_constraints=[], symmetric_methyls=True, symmetric_methylenes=True)

Charge constraints

field defer_errors: bool = False

Whether to raise an error immediately, or gather all errors during ESP computation and raise at the end

field grid_options: psiresp.grid.GridOptions = GridOptions(grid_rmin=0, grid_rmax=-1, use_radii='msk', vdw_radii={}, vdw_scale_factors=[1.4, 1.6, 1.8, 2.0], vdw_point_density=1.0)

Options for generating grid for ESP computation

field molecules: List[psiresp.molecule.Molecule] [Required]

Molecules to use for the RESP job

field n_processes: Optional[int] = None

Number of processes to use in multiprocessing during ESP computation. n_processes=None uses the number of CPUs.

field qm_esp_options: psiresp.qm.QMEnergyOptions = QMEnergyOptions(method='hf', basis='6-31g*', pcm_options=None, driver='energy', query_interval=20, protocols={'wavefunction': 'orbitals_and_eigenvalues'}, jobname='single_point')

QM options for ESP computation

field qm_optimization_options: psiresp.qm.QMGeometryOptimizationOptions = QMGeometryOptimizationOptions(method='hf', basis='6-31g*', pcm_options=None, driver='gradient', query_interval=20, protocols={'wavefunction': 'orbitals_and_eigenvalues'}, g_convergence='gau_tight', max_iter=200, full_hess_every=10, jobname='optimization')

QM options for geometry optimization

field resp_options: psiresp.resp.RespOptions = RespOptions(restraint_slope=0.1, restrained_fit=True, exclude_hydrogens=True, convergence_tolerance=1e-06, max_iter=500, restraint_height_stage_1=0.0005, restraint_height_stage_2=0.001, stage_2=True)

Options for fitting ESP for charges

field stage_1_charges: Optional[psiresp.resp.RespCharges] = None

Stage 1 charges. These need to be computed by calling run() or compute_charges() directly.

field stage_2_charges: Optional[psiresp.resp.RespCharges] = None

Stage 2 charges. These need to be computed by calling run() or compute_charges() directly.

field temperature: float = 298.15

Temperature (in Kelvin) to use when Boltzmann-weighting conformers.

field working_directory: pathlib.Path = PosixPath('psiresp_working_directory')

Working directory for saving intermediate files

compute_charges(update_molecules=True)[source]

Compute the charges for each molecule. Each Orientation must have had the ESP computed, and there must be at least one orientation present.

Return type

numpy.ndarray

compute_esps()[source]

Compute ESP on a grid for each orientation in a multiprocessing pool

compute_esps_and_charges(client=None, update_molecules=True)[source]
Parameters

update_molecules (bool) –

Return type

numpy.ndarray

compute_orientation_energies(client=None, **kwargs)[source]

Compute wavefunction for each orientation

construct_surface_constraint_matrix()[source]

Construct the constraint matrix for each atom, as generated by the ESP at each grid point

Return type

psiresp.constraint.ESPSurfaceConstraintMatrix

generate_conformers()[source]

Generate conformers for every molecule

generate_molecule_charge_constraints()[source]

Gather the charge constraints pertaining to the molecules in this RESP job

Return type

psiresp.charge.MoleculeChargeConstraints

generate_orientations()[source]

Generate orientations for every conformer of every molecule

get_hash()
iter_conformers()[source]
iter_orientations()[source]
optimize_geometries(client=None, **kwargs)[source]

Compute optimized geometries

run(client=None, update_molecules=True)[source]

Run the whole job

Parameters

update_molecules (bool) –

Return type

numpy.ndarray

update_molecule_charges()[source]

Update the molecules in the job with the calculated charges

property charges
property n_conformers
property n_orientations