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_base

Base jobs for Onetep.

prep_calculator 

prep_calculator(
    calc_defaults: dict[str, Any] | None = None,
    calc_swaps: dict[str, Any] | None = None,
) -> Onetep

Prepare the Onetep calculator.

Parameters:

  • calc_defaults (dict[str, Any] | None, default: None ) –

    The default calculator parameters.

  • calc_swaps (dict[str, Any] | None, default: None ) –

    Custom kwargs for the ONETEP calculator. Set a value to quacc.Remove to remove a pre-existing key entirely. For a list of available keys, refer to the ase.calculators.onetep.Onetep calculator.

Returns:

  • Onetep –

    The Onetep calculator.

Source code in quacc/recipes/onetep/_base.py 
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def prep_calculator(
    calc_defaults: dict[str, Any] | None = None,
    calc_swaps: dict[str, Any] | None = None,
) -> Onetep:
    """
    Prepare the Onetep calculator.

    Parameters
    ----------
    calc_defaults
        The default calculator parameters.
    calc_swaps
        Custom kwargs for the ONETEP calculator. Set a value to
        `quacc.Remove` to remove a pre-existing key entirely. For a list of available
        keys, refer to the [ase.calculators.onetep.Onetep][] calculator.

    Returns
    -------
    Onetep
        The Onetep calculator.
    """
    calc_flags = recursive_dict_merge(calc_defaults, calc_swaps)

    return Onetep(
        pseudo_path=str(SETTINGS.ONETEP_PP_PATH) if SETTINGS.ONETEP_PP_PATH else ".",
        parallel_info=SETTINGS.ONETEP_PARALLEL_CMD,
        profile=OnetepProfile(SETTINGS.ONETEP_CMD),
        **calc_flags,
    )

run_and_summarize 

run_and_summarize(
    atoms: Atoms,
    calc_defaults: dict[str, Any] | None = None,
    calc_swaps: dict[str, Any] | None = None,
    additional_fields: dict[str, Any] | None = None,
    copy_files: (
        SourceDirectory
        | dict[SourceDirectory, Filenames]
        | None
    ) = None,
) -> RunSchema

Base function to carry out Onetep recipes.

Parameters:

  • atoms (Atoms) –

    Atoms object

  • calc_defaults (dict[str, Any] | None, default: None ) –

    The default calculator parameters.

  • calc_swaps (dict[str, Any] | None, default: None ) –

    Custom kwargs for the ONETEP calculator. Set a value to quacc.Remove to remove a pre-existing key entirely. For a list of available keys, refer to the ase.calculators.onetep.Onetep calculator.

  • additional_fields (dict[str, Any] | None, default: None ) –

    Any additional fields to supply to the summarizer.

  • copy_files (SourceDirectory | dict[SourceDirectory, Filenames] | None, default: None ) –

    Files to copy (and decompress) from source to the runtime directory.

Returns:

Source code in quacc/recipes/onetep/_base.py 
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def run_and_summarize(
    atoms: Atoms,
    calc_defaults: dict[str, Any] | None = None,
    calc_swaps: dict[str, Any] | None = None,
    additional_fields: dict[str, Any] | None = None,
    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
) -> RunSchema:
    """
    Base function to carry out Onetep recipes.

    Parameters
    ----------
    atoms
        Atoms object
    calc_defaults
        The default calculator parameters.
    calc_swaps
        Custom kwargs for the ONETEP calculator. Set a value to
        `quacc.Remove` to remove a pre-existing key entirely. For a list of available
        keys, refer to the [ase.calculators.onetep.Onetep][] calculator.
    additional_fields
        Any additional fields to supply to the summarizer.
    copy_files
        Files to copy (and decompress) from source to the runtime directory.

    Returns
    -------
    RunSchema
        Dictionary of results from [quacc.schemas.ase.summarize_run][]
    """
    atoms.calc = prep_calculator(calc_defaults=calc_defaults, calc_swaps=calc_swaps)
    final_atoms = run_calc(atoms, copy_files=copy_files)

    return summarize_run(final_atoms, atoms, additional_fields=additional_fields)

run_and_summarize_opt 

run_and_summarize_opt(
    atoms: Atoms,
    calc_defaults: dict[str, Any] | None = None,
    calc_swaps: dict[str, Any] | None = None,
    opt_defaults: dict[str, Any] | None = None,
    opt_params: OptParams | None = None,
    additional_fields: dict[str, Any] | None = None,
    copy_files: (
        SourceDirectory
        | dict[SourceDirectory, Filenames]
        | None
    ) = None,
) -> RunSchema

Base function to carry out Onetep recipes with ASE optimizers.

Parameters:

  • atoms (Atoms) –

    Atoms object

  • calc_defaults (dict[str, Any] | None, default: None ) –

    The default calculator parameters.

  • calc_swaps (dict[str, Any] | None, default: None ) –

    Custom kwargs for the ONETEP calculator. Set a value to quacc.Remove to remove a pre-existing key entirely. For a list of available keys, refer to the ase.calculators.onetep.Onetep calculator.

  • opt_defaults (dict[str, Any] | None, default: None ) –

    The default optimization parameters.

  • opt_params (OptParams | None, default: None ) –

    Dictionary of parameters to pass to the optimizer. pass "optimizer" to change the optimizer being used. "fmax" and "max_steps" are commonly used keywords. See the ASE documentation for more information.

  • additional_fields (dict[str, Any] | None, default: None ) –

    Any additional fields to supply to the summarizer.

  • copy_files (SourceDirectory | dict[SourceDirectory, Filenames] | None, default: None ) –

    Files to copy (and decompress) from source to the runtime directory.

Returns:

Source code in quacc/recipes/onetep/_base.py 
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def run_and_summarize_opt(
    atoms: Atoms,
    calc_defaults: dict[str, Any] | None = None,
    calc_swaps: dict[str, Any] | None = None,
    opt_defaults: dict[str, Any] | None = None,
    opt_params: OptParams | None = None,
    additional_fields: dict[str, Any] | None = None,
    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
) -> RunSchema:
    """
    Base function to carry out Onetep recipes with ASE optimizers.

    Parameters
    ----------
    atoms
        Atoms object
    calc_defaults
        The default calculator parameters.
    calc_swaps
        Custom kwargs for the ONETEP calculator. Set a value to
        `quacc.Remove` to remove a pre-existing key entirely. For a list of available
        keys, refer to the [ase.calculators.onetep.Onetep][] calculator.
    opt_defaults
        The default optimization parameters.
    opt_params
        Dictionary of parameters to pass to the optimizer. pass "optimizer"
        to change the optimizer being used. "fmax" and "max_steps" are commonly
        used keywords. See the ASE documentation for more information.
    additional_fields
        Any additional fields to supply to the summarizer.
    copy_files
        Files to copy (and decompress) from source to the runtime directory.

    Returns
    -------
    RunSchema
        Dictionary of results from [quacc.schemas.ase.summarize_run][]
    """
    opt_flags = recursive_dict_merge(opt_defaults, opt_params)

    atoms.calc = prep_calculator(calc_defaults=calc_defaults, calc_swaps=calc_swaps)

    dyn = run_opt(atoms, copy_files=copy_files, **opt_flags)

    return summarize_opt_run(dyn, additional_fields=additional_fields)