pydft_qmmm.interfaces.psi4 package

Submodules

pydft_qmmm.interfaces.psi4.psi4_interface module

The basic Psi4 software interface.

class pydft_qmmm.interfaces.psi4.psi4_interface.Psi4Interface(settings, options, functional, context)

Bases: QMInterface

A software interface wrapping Psi4 functionality.

Parameters:

• settings (QMSettings) – The settings used to build the Psi4 interface.

• options (Psi4Options) – The Psi4 global options derived from the settings.

• functional (str) – The name of the functional to use for exchange-correlation calculations.

• context (Psi4Context) – An object which holds system information to feed into Psi4.

compute_components()

Compute the components of energy using OpenMM.

Returns:

The components of the energy (\(\mathrm{kJ\;mol^{-1}}\)) of the system.

Return type:

dict[str, float]

compute_energy()

Compute the energy of the system using Psi4.

Returns:

The energy (\(\mathrm{kJ\;mol^{-1}}\)) of the system.

Return type:

float

compute_forces()

Compute the forces on the system using Psi4.

Returns:

The forces (\(\mathrm{kJ\;mol^{-1}\;\mathring{A}^{-1}}\)) acting on atoms in the system.

Return type:

ndarray[Any, dtype[float64]]

disable_embedding()

Disable electrostatic embedding.

Return type:

None

update_charges(charges)

Set the atomic partial charges used by Psi4 for embedding.

Parameters:

charges (ndarray[Any, dtype[float64]]) – The partial charges (\(e\)) of the atoms.

Return type:

None

update_memory(memory)

Set the amount of memory used by Psi4.

Parameters:

memory (str) – The amount of memory to utilize.

Return type:

None

update_positions(positions)

Set the atomic positions used by Psi4.

Parameters:

positions (ndarray[Any, dtype[float64]]) – The positions (\(\mathrm{\mathring{A}}\)) of the atoms within the system.

Return type:

None

update_subsystems(subsystems)

Adjust which atoms are embedded by subsystem membership.

Parameters:

subsystems (np.ndarray[Any, np.dtype[np.object_]]) – The subsystems of which the atoms are a part.

Return type:

None

update_threads(threads)

Set the number of threads used by Psi4.

Parameters:

threads (int) – The number of threads to utilize.

Return type:

None

pydft_qmmm.interfaces.psi4.psi4_utils module

Functionality for building the Psi4 interface and some helper classes.

class pydft_qmmm.interfaces.psi4.psi4_utils.Psi4Context(atoms, embedding, elements, positions, charges, charge, spin)

Bases: object

A wrapper class for managing Psi4 Geometry object generation.

Parameters:

• atoms (set[int]) – The indices of atoms that are treated at the QM level of theory.

• embedding (set[int]) – The indices of atoms that are electrostatically embedded.

• elements (list[str]) – The element symbols of the atoms in the system.

• positions (NDArray[np.float64]) – The positions (\(\mathrm{\mathring{A}}\)) of the atoms within the system.

• charges (NDArray[np.float64]) – The partial charges (\(e\)) of the atoms in the system.

• charge (int) – The net charge (\(e\)) of the system represented at the QM level of theory.

• spin (int) – The net spin of the system represented by the QM level of theory.

generate_external_potential()

Create the data structures read by Psi4 to perform embedding.

Returns:

The list of coordinates (\(\mathrm{a.u.}\)) and charges (\(e\)) that will be read by Psi4 during calculations and electrostatically embedded.

Return type:

list[list[int | list[int]]] | None

generate_molecule()

Create the Geometry object for Psi4 calculations.

Returns:

The Psi4 Geometry object, which contains the positions, net charge, and net spin of atoms treated at the QM level of theory.

Return type:

Molecule

update_charges(charges)

Set the atomic partial charges used by Psi4 for embedding.

Parameters:

charges (ndarray[Any, dtype[float64]]) – The partial charges (\(e\)) of the atoms.

Return type:

None

update_embedding(embedding)

Set the atoms are electrostatically embedded.

Parameters:

embedding (set[int]) – The indices of atoms that are electrostatically embedded.

Return type:

None

update_positions(positions)

Set the atomic positions used by Psi4.

Parameters:

positions (ndarray[Any, dtype[float64]]) – The positions (\(\mathrm{\mathring{A}}\)) of the atoms within the system.

Return type:

None

class pydft_qmmm.interfaces.psi4.psi4_utils.Psi4Options(basis, dft_spherical_points, dft_radial_points, scf_type, scf__reference, scf__guess)

Bases: object

An immutable wrapper class for storing Psi4 global options.

Parameters:

• basis (str) – The name of the basis set to be used by Psi4.

• dft_spherical_points (int) – The number of spherical Lebedev points to use in the DFT quadrature.

• dft_radial_points (int) – The number of radial points to use in the DFT quadrature.

• scf_type (str) – The name of the type of SCF to perform, as in the JK build algorithms as in Psi4.

• scf__reference (str) – The name of the reference to use, including restricted Kohn-Sham or unrestricted Kohn-Sham.

• scf__guess (str) – The name of the algorithm used to generate the initial guess at the start of an SCF procedure.

basis: str

dft_radial_points: int

dft_spherical_points: int

scf__guess: str

scf__reference: str

scf_type: str

pydft_qmmm.interfaces.psi4.psi4_utils.psi4_interface_factory(settings)

Build the interface to Psi4 given the settings.

Parameters:

settings (QMSettings) – The settings used to build the Psi4 interface.

Returns:

The Psi4 interface.

Return type:

Psi4Interface

Module contents

A sub-package for interfacing with Psi4.