6.5. DFTB+ Input/Output interfaces

Warning

DFTB+ must be installed separately from the pharmaforge package. The DFTB+ package is not included in the pharmaforge package and must be installed separately. You can find the installation instructions for DFTB+ on their official website: DFTB+, but the installation is relatively straightforward (mamba install dftbplus). You will also need to download the Slater-Koster files that describe the dftb3 parameters.

class pharmaforge.interfaces.dftbio.DFTBInterface(skf_loc='./', default=False, **options)[source]

Bases: AbstractIO

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

self.dftb_options = {
        "Hamiltonian_SCC": "Yes",
        "Hamiltonian_SccTolerance": 1e-8,
        "Hamiltonian_MaxAngularMomentum_": "",
        "Hamiltonian_MaxAngularMomentum_H": "s",
        "Hamiltonian_MaxAngularMomentum_O": "p",
        "Hamiltonian_MaxAngularMomentum_C": "p",
        "Hamiltonian_MaxAngularMomentum_N": "p",
    }

Warning

Currently, this interface does not support parallelization because it runs by creating an input file, which is not thread safe.

Parameters:

skf_loc (str) – The location of the DFTB+ skf files. Default is “./”.
default (bool) – If True, use the default options for the DFTB+ calculator. Default is False.
options (dict) – A dictionary of options to pass to the DFTB+ calculator. Default is an empty dictionary.

calculator

The DFTB+ calculator object.

Type:: object

allow_parallel

Whether to allow parallelization. Default is False.

Type:: bool

level_of_theory

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

Type:: str

options_dict

A dictionary of options for the DFTB+ calculator.

Type:: dict

See also

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

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.
`set_environment`()	Set the environment for the DFTB+ calculator.

process_structure

set_environment()[source]: Set the environment for the DFTB+ calculator.