QM_engines.dftb_wrapper module

Description

This module defines the ParaMol.QM_engines.dftb_wrapper.DFTBWrapper class, which is a ParaMol implementation of a DFTB+ wrapper.

class ParaMol.QM_engines.dftb_wrapper.DFTBWrapper(system_name, interface, n_atoms, atom_list, n_calculations, slater_koster_files_prefix, work_dir_prefix='DFTBWorkDir_', calc_file='dftb_in.hsd', geometry_file='geometry.gen', calc_dir_prefix='dftb_', detailed_file_output='detailed.out', calc_file_output='dftb_output.out', max_ang_mom={'C': 'p', 'F': 'p', 'H': 's', 'N': 'p', 'O': 'p', 'S': 'p'})

Bases: object

ParaMol implementation of a DFTB+ wrapper.

Parameters

  • system_name (str) – Name of the system to which this wrapper is associated.

  • interface (ParaMol.Utils.interface.ParaMolInterface) – ParaMol interface object instance.

  • n_atoms (int) – number of atoms

  • atom_list (list of str) – List with the atom symbols

  • n_calculations (int) – Number of parallel calculations.

  • slater_koster_files_prefix (str) – Path to the Slater-Koster files.

  • work_dir (str, default="DFTBWorkDir") – Path to the working directory.

  • calc_file (str, default="dftb_output.out") – Name given to the DFTB+ calculation file.

  • calc_file – Name given to the DFTB+ stdout file.

  • detailed_file_output (str, default="detailed.out") – Name of the detailed output file written by DFTB+. By default DFTB+ writes this to ‘detailed.out’. Don’t change this unless you know what you’re doing.

  • geometry_file (str, default="geometry.gen") – Name given to the DFTB+ .gen geometry file.

  • calc_dir_prefix (str, default="dftb_") – Prefix given to the directories where the calculations will be performed.

  • max_ang_mom (dict, default={"H": "s", "C": "p", "N": "p", "O": "p", "F": "p", "S": "p"}) – Dictionary that defines the maximum angular momentum for each chemical element.

_prepare_work_dir()

Method that prepares the working directory.

Returns

None

_write_geometry_gen_format(coords)

Method that writes the geometry in gen format.

Parameters

coords (list or np.array) – (n_atoms,3) coordinates array

Returns

True if file was closed successfully. False otherwise.

_write_input_file(dispersion_correction=False)

Method that writes the input file necessary to run single-point with forces calculation.

Notes

It only needs to be run upon creation of the QM wrapper.

Parameters

dispersion_correction (bool) – Whether or not to include D3 dispersion correction section.

Returns

True if file was closed successfully. False otherwise.

run_calculation(coords, label)

Method that perform a single-point calculation with forces.

Parameters

  • coords (np.ndarray, shape=(n_atoms, 3), dtype=float) – Coordinates array.

  • label (str) – Seed for the calculation.

Returns

  • energy (float) – Energy in kJ/mol.

  • forces (np.ndarray, shape=np.array(n_atoms,3)) – Forces in kJ/mol/nm