6.2. Psi4 Input/Output interfaces

class pharmaforge.interfaces.psi4io.Psi4Interface(default=False, **options)[source]

Bases: AbstractIO

This class is used to interface with Psi4 for quantum chemistry calculations, and will be used to calculate the energies and forces of the system.

self.psi4_options = {
    "method": "B3LYP",
    "basis": "6-31G",
    "num_threads": 1,
}

Parameters:

basis_set (str) – The basis set to use for the calculations. Default is “6-31G”.
functional (str) – The functional to use for the calculations. Default is “B3LYP”.
num_threads (int) – The number of threads to use for an individual calculation. Default is 1.

calculator

The Psi4 calculator object.

Type:: object

allow_parallel

Whether to allow parallelization. Default is True.

Type:: bool

level_of_theory

The level of theory used for the calculations. Default is “Psi4”.

Type:: str

options_dict

A dictionary of options for the Psi4 calculator, that can include things not sent to the calculator.

Type:: dict

psi4_options

A dictionary of options for the Psi4 calculator that are passed to the calculator.

Type:: dict

See also

pharmaforge.interfaces.abstractio.AbstractIO: The abstract interface class for the Psi4Interface.
ase.calculators.psi4.Psi4: The Psi4 calculator object.

Example

>>> from pharmaforge.interfaces.psi4io import Psi4Interface
>>> from ase import Atoms
>>> import numpy as np
>>> h2 = Atoms('HH', positions=[(0, 0, 0), (0, 0, 1)])
>>> psi4 = Psi4Interface(default=True)
>>> calc = psi4._calculate(h2)
>>> e, f = psi4._report_data(calc)
>>> print(np.round(e,4))
-31.2467

Methods

`ObtainDeepData`(filename)	Obtain the system data from the DeepIO interface and converts each configuration to an ASE atoms object.
`ObtainQueryData`(queryresults)	Obtain the system data from a query
`calculate`([limit, verbose, num_workers])	Calculate the energies and forces of the system using the interface.
`find_clusters`(structure[, cutoff])	Identify clusters of atoms in a structure based on a distance cutoff.

process_structure

Initialize the Psi4Interface class.

Methods

`ObtainDeepData`(filename)	Obtain the system data from the DeepIO interface and converts each configuration to an ASE atoms object.
`ObtainQueryData`(queryresults)	Obtain the system data from a query
`calculate`([limit, verbose, num_workers])	Calculate the energies and forces of the system using the interface.
`find_clusters`(structure[, cutoff])	Identify clusters of atoms in a structure based on a distance cutoff.

process_structure