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core

Core recipes for the NewtonNet code.

freq_job 

freq_job(
    atoms: Atoms,
    temperature: float = 298.15,
    pressure: float = 1.0,
    copy_files: (
        SourceDirectory
        | dict[SourceDirectory, Filenames]
        | None
    ) = None,
    **calc_kwargs
) -> VibThermoSchema

Perform a frequency calculation using the given atoms object.

Parameters:

  • atoms (Atoms) –

    The atoms object representing the system.

  • temperature (float, default: 298.15 ) –

    The temperature for the thermodynamic analysis.

  • pressure (float, default: 1.0 ) –

    The pressure for the thermodynamic analysis.

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

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

  • **calc_kwargs –

    Custom kwargs for the NewtonNet calculator. Set a value to quacc.Remove to remove a pre-existing key entirely. For a list of available keys, refer to the newtonnet.utils.ase_interface.MLAseCalculator calculator.

Returns:

  • VibThermoSchema –

    Dictionary of results. See the type-hint for the data structure.

Source code in quacc/recipes/newtonnet/core.py 
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@job
@requires(NewtonNet, "NewtonNet must be installed. Refer to the quacc documentation.")
def freq_job(
    atoms: Atoms,
    temperature: float = 298.15,
    pressure: float = 1.0,
    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
    **calc_kwargs,
) -> VibThermoSchema:
    """
    Perform a frequency calculation using the given atoms object.

    Parameters
    ----------
    atoms
        The atoms object representing the system.
    temperature
        The temperature for the thermodynamic analysis.
    pressure
        The pressure for the thermodynamic analysis.
    copy_files
        Files to copy (and decompress) from source to the runtime directory.
    **calc_kwargs
        Custom kwargs for the NewtonNet calculator. Set a value to
        `quacc.Remove` to remove a pre-existing key entirely. For a list of available
        keys, refer to the `newtonnet.utils.ase_interface.MLAseCalculator` calculator.

    Returns
    -------
    VibThermoSchema
        Dictionary of results. See the type-hint for the data structure.
    """
    calc_defaults = {
        "model_path": SETTINGS.NEWTONNET_MODEL_PATH,
        "settings_path": SETTINGS.NEWTONNET_CONFIG_PATH,
        "hess_method": "autograd",
    }
    calc_flags = recursive_dict_merge(calc_defaults, calc_kwargs)

    ml_calculator = NewtonNet(**calc_flags)
    atoms.calc = ml_calculator
    final_atoms = run_calc(atoms, copy_files=copy_files)

    summary = summarize_run(
        final_atoms, atoms, additional_fields={"name": "NewtonNet Hessian"}
    )
    energy = summary["results"]["energy"]
    hessian = summary["results"]["hessian"]

    vib = VibrationsData(final_atoms, hessian)

    igt = run_ideal_gas(final_atoms, vib.get_frequencies(), energy=energy)

    return summarize_vib_and_thermo(
        vib,
        igt,
        temperature=temperature,
        pressure=pressure,
        additional_fields={"name": "ASE Vibrations and Thermo Analysis"},
    )

relax_job 

relax_job(
    atoms: Atoms,
    opt_params: OptParams | None = None,
    copy_files: (
        SourceDirectory
        | dict[SourceDirectory, Filenames]
        | None
    ) = None,
    **calc_kwargs
) -> OptSchema

Relax a structure.

Parameters:

  • atoms (Atoms) –

    Atoms object

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

    Dictionary of custom kwargs for the optimization process. For a list of available keys, refer to quacc.runners.ase.run_opt.

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

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

  • **calc_kwargs –

    Dictionary of custom kwargs for the NewtonNet calculator. Set a value to quacc.Remove to remove a pre-existing key entirely. For a list of available keys, refer to the newtonnet.utils.ase_interface.MLAseCalculator calculator.

Returns:

Source code in quacc/recipes/newtonnet/core.py 
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@job
@requires(NewtonNet, "NewtonNet must be installed. Refer to the quacc documentation.")
def relax_job(
    atoms: Atoms,
    opt_params: OptParams | None = None,
    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
    **calc_kwargs,
) -> OptSchema:
    """
    Relax a structure.

    Parameters
    ----------
    atoms
        Atoms object
    opt_params
        Dictionary of custom kwargs for the optimization process. For a list
        of available keys, refer to [quacc.runners.ase.run_opt][].
    copy_files
        Files to copy (and decompress) from source to the runtime directory.
    **calc_kwargs
        Dictionary of custom kwargs for the NewtonNet calculator. Set a value to
        `quacc.Remove` to remove a pre-existing key entirely. For a list of available
        keys, refer to the `newtonnet.utils.ase_interface.MLAseCalculator` calculator.

    Returns
    -------
    OptSchema
        Dictionary of results, specified in [quacc.schemas.ase.summarize_opt_run][].
        See the type-hint for the data structure.
    """
    calc_defaults = {
        "model_path": SETTINGS.NEWTONNET_MODEL_PATH,
        "settings_path": SETTINGS.NEWTONNET_CONFIG_PATH,
    }
    opt_defaults = {"optimizer": Sella} if Sella else {}

    calc_flags = recursive_dict_merge(calc_defaults, calc_kwargs)
    opt_flags = recursive_dict_merge(opt_defaults, opt_params)

    atoms.calc = NewtonNet(**calc_flags)
    dyn = run_opt(atoms, copy_files=copy_files, **opt_flags)

    return _add_stdev_and_hess(
        summarize_opt_run(dyn, additional_fields={"name": "NewtonNet Relax"})
    )

static_job 

static_job(
    atoms: Atoms,
    copy_files: (
        SourceDirectory
        | dict[SourceDirectory, Filenames]
        | None
    ) = None,
    **calc_kwargs
) -> RunSchema

Carry out a single-point calculation.

Parameters:

  • atoms (Atoms) –

    Atoms object

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

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

  • **calc_kwargs –

    Custom kwargs for the NewtonNet calculator. Set a value to quacc.Remove to remove a pre-existing key entirely. For a list of available keys, refer to the newtonnet.utils.ase_interface.MLAseCalculator calculator.

Returns:

Source code in quacc/recipes/newtonnet/core.py 
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@job
@requires(NewtonNet, "NewtonNet must be installed. Refer to the quacc documentation.")
def static_job(
    atoms: Atoms,
    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
    **calc_kwargs,
) -> RunSchema:
    """
    Carry out a single-point calculation.

    Parameters
    ----------
    atoms
        Atoms object
    copy_files
        Files to copy (and decompress) from source to the runtime directory.
    **calc_kwargs
        Custom kwargs for the NewtonNet calculator. Set a value to
        `quacc.Remove` to remove a pre-existing key entirely. For a list of available
        keys, refer to the `newtonnet.utils.ase_interface.MLAseCalculator` calculator.

    Returns
    -------
    RunSchema
        Dictionary of results, specified in [quacc.schemas.ase.summarize_run][].
        See the type-hint for the data structure.
    """
    calc_defaults = {
        "model_path": SETTINGS.NEWTONNET_MODEL_PATH,
        "settings_path": SETTINGS.NEWTONNET_CONFIG_PATH,
    }
    calc_flags = recursive_dict_merge(calc_defaults, calc_kwargs)

    atoms.calc = NewtonNet(**calc_flags)
    final_atoms = run_calc(atoms, copy_files=copy_files)

    return summarize_run(
        final_atoms, atoms, additional_fields={"name": "NewtonNet Static"}
    )