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core

Core recipes for Lennard-Jones Potential.

NOTE: This set of minimal recipes is mainly for demonstration purposes

freq_job 

freq_job(
    atoms: Atoms,
    energy: float = 0.0,
    temperature: float = 298.15,
    pressure: float = 1.0,
    vib_kwargs: VibKwargs | None = None,
    copy_files: (
        SourceDirectory
        | dict[SourceDirectory, Filenames]
        | None
    ) = None,
    **calc_kwargs
) -> VibThermoSchema

Run a frequency job and calculate thermochemistry.

Parameters:

  • atoms (Atoms) –

    Atoms object

  • energy (float, default: 0.0 ) –

    Potential energy in eV. If 0, then the output is just the correction.

  • temperature (float, default: 298.15 ) –

    Temperature in Kelvins.

  • pressure (float, default: 1.0 ) –

    Pressure in bar.

  • vib_kwargs (VibKwargs | None, default: None ) –

    Dictionary of kwargs for the ase.vibrations.Vibrations class.

  • 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 LJ 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.lj.LennardJones] calculator.

Returns:

Source code in quacc/recipes/lj/core.py 
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@job
def freq_job(
    atoms: Atoms,
    energy: float = 0.0,
    temperature: float = 298.15,
    pressure: float = 1.0,
    vib_kwargs: VibKwargs | None = None,
    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
    **calc_kwargs,
) -> VibThermoSchema:
    """
    Run a frequency job and calculate thermochemistry.

    Parameters
    ----------
    atoms
        Atoms object
    energy
        Potential energy in eV. If 0, then the output is just the correction.
    temperature
        Temperature in Kelvins.
    pressure
        Pressure in bar.
    vib_kwargs
        Dictionary of kwargs for the [ase.vibrations.Vibrations][] class.
    copy_files
        Files to copy (and decompress) from source to the runtime directory.
    **calc_kwargs
        Dictionary of custom kwargs for the LJ 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.lj.LennardJones] calculator.

    Returns
    -------
    VibThermoSchema
        Dictionary of results, specified in [quacc.schemas.ase.summarize_vib_and_thermo][].
        See the type-hint for the data structure.
    """
    vib_kwargs = vib_kwargs or {}

    atoms.calc = LennardJones(**calc_kwargs)
    vibrations = run_vib(atoms, vib_kwargs=vib_kwargs, copy_files=copy_files)
    igt = run_ideal_gas(atoms, vibrations.get_frequencies(), energy=energy)

    return summarize_vib_and_thermo(
        vibrations,
        igt,
        temperature=temperature,
        pressure=pressure,
        additional_fields={"name": "LJ Frequency and Thermo"},
    )

relax_job 

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

Function to carry out a geometry optimization.

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 –

    Custom kwargs for the LJ 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.lj.LennardJones] calculator.

Returns:

Source code in quacc/recipes/lj/core.py 
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@job
def relax_job(
    atoms: Atoms,
    opt_params: OptParams | None = None,
    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
    **calc_kwargs,
) -> OptSchema:
    """
    Function to carry out a geometry optimization.

    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
        Custom kwargs for the LJ 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.lj.LennardJones] calculator.

    Returns
    -------
    OptSchema
        Dictionary of results, specified in [quacc.schemas.ase.summarize_run][].
        See the type-hint for the data structure.
    """
    opt_params = opt_params or {}

    atoms.calc = LennardJones(**calc_kwargs)
    dyn = run_opt(atoms, copy_files=copy_files, **opt_params)

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

static_job 

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

Function to carry out a static 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 –

    Dictionary of custom kwargs for the LJ 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.lj.LennardJones] calculator.

Returns:

Source code in quacc/recipes/lj/core.py 
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@job
def static_job(
    atoms: Atoms,
    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
    **calc_kwargs,
) -> RunSchema:
    """
    Function to carry out a static calculation.

    Parameters
    ----------
    atoms
        Atoms object
    copy_files
        Files to copy (and decompress) from source to the runtime directory.
    **calc_kwargs
        Dictionary of custom kwargs for the LJ 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.lj.LennardJones] calculator.

    Returns
    -------
    RunSchema
        Dictionary of results, specified in [quacc.schemas.ase.summarize_run][].
        See the type-hint for the data structure.
    """
    atoms.calc = LennardJones(**calc_kwargs)
    final_atoms = run_calc(atoms, copy_files=copy_files)

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