Jobschnet

The Jobschnet class is the base class defining a SchnetPack calculation.

class mybigdft.jobschnet.Jobschnet(name='', posinp=None)[source]

Bases: object

This class defines a SchnetPack calculation similarly to the Job class for BigDFT.

Parameters

  • name (str) – Name of the job. Will be used to name the created files.

  • posinp (Posinp) – Base atomic positions for the job

property name
Returns

Base name of the calculation used to set the names of files and directories.

Return type

str

property posinp
Returns

Initial positions of the calculation

Return type

Posinp

property number_of_structures
Returns

Number of different structures when the job is declared

Return type

int

property logfile
Returns

Object empty or containing the results of the calculation.

Return type

Logfileschnet

property outfile_name
Returns

Name of the output file

Return type

str

run(model_dir=None, forces=False, device='cpu', write_to_disk=False, batch_size=128, overwrite=False)[source]
Parameters

  • model_dir (str) – Absolute path to the SchnetPack model to use in calculation

  • forces (int or bool) – Order of the force calculations (0, 1 or 2) If 0 (or False), forces are not evaluated. If 1, forces are evaluated on first-order (6N calculations) If 2 (or True), forces are evaluated on second-order (12N calculations)

  • device (str) – Either ‘cpu’ or ‘cuda’ to run on cpu or gpu

  • write_to_disk (bool) – If True, an outfile will be written after the calculation.

  • batch_size (int) – Size of the mini-batches used in predictions

  • overwrite (bool) – If True, all .db files are removed from the directory before the calculation is done.

class mybigdft.jobschnet.Logfileschnet(posinp)[source]

Bases: object

Container class to emulate the Logfile object used in BigDFT calculations

property posinp
Returns

List containing the base Posinp objects for the predictions.

Return type

list of Posinps

property n_at
Returns

List containing the number of atoms of each structure.

Return type

list of ints

property atom_types
Returns

List containing sets of the elements present in each structure.

Return type

list of sets

property boundary_conditions
Returns

List containing the boundary conditions, either free, surface or periodic, of each structure.

Return type

list of strings

property cell
Returns

List containing cell dimensions of each structure, None for free boundary conditions.

Return type

list of lists of floats

property energy
Returns

List containing the energy value for each structure. If None, the energies have not been calculated yet.

Return type

list of floats or None

property forces
Returns

List containing the forces values for each structure. If None, the forces have not been calculated yet.

Return type

list of arrays of floats or None

property dipole
Returns

List containing the dipole values for each structure. If None, the dipoles have not been calculated yet.

Return type

list of arrays of floats or None