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ts

Transition state recipes for Q-Chem.

has_sella module-attribute 

has_sella = True

irc_job 

irc_job(
    atoms: Atoms,
    charge: int = 0,
    spin_multiplicity: int = 1,
    direction: Literal["forward", "reverse"] = "forward",
    method: str = "wb97mv",
    basis: str = "def2-svpd",
    opt_params: OptParams | None = None,
    copy_files: (
        SourceDirectory
        | dict[SourceDirectory, Filenames]
        | None
    ) = None,
    **calc_kwargs
) -> OptSchema

IRC optimize a molecular structure.

Parameters:

  • atoms (Atoms) –

    Atoms object

  • charge (int, default: 0 ) –

    Charge of the system.

  • spin_multiplicity (int, default: 1 ) –

    Multiplicity of the system.

  • direction (Literal['forward', 'reverse'], default: 'forward' ) –

    Direction of the IRC. Should be "forward" or "reverse".

  • method (str, default: 'wb97mv' ) –

    DFT exchange-correlation functional or other electronic structure method.

  • basis (str, default: 'def2-svpd' ) –

    Basis set.

  • 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 calculator. Set a value to quacc.Remove to remove a pre-existing key entirely. See quacc.calculators.qchem.qchem.QChem for more details.

Returns:

Source code in quacc/recipes/qchem/ts.py 
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@job
@requires(has_sella, "Sella must be installed. Refer to the quacc documentation.")
def irc_job(
    atoms: Atoms,
    charge: int = 0,
    spin_multiplicity: int = 1,
    direction: Literal["forward", "reverse"] = "forward",
    method: str = "wb97mv",
    basis: str = "def2-svpd",
    opt_params: OptParams | None = None,
    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
    **calc_kwargs,
) -> OptSchema:
    """
    IRC optimize a molecular structure.

    Parameters
    ----------
    atoms
        Atoms object
    charge
        Charge of the system.
    spin_multiplicity
        Multiplicity of the system.
    direction
        Direction of the IRC. Should be "forward" or "reverse".
    method
        DFT exchange-correlation functional or other electronic structure
        method.
    basis
        Basis set.
    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 calculator. Set a value to `quacc.Remove` to remove
        a pre-existing key entirely. See [quacc.calculators.qchem.qchem.QChem][] for more
        details.

    Returns
    -------
    OptSchema
        Dictionary of results from [quacc.schemas.ase.summarize_opt_run][]
    """
    calc_defaults = recursive_dict_merge(
        _BASE_SET, {"rem": {"job_type": "force", "method": method, "basis": basis}}
    )
    opt_defaults = {
        "optimizer": IRC,
        "optimizer_kwargs": {"keep_going": True},
        "run_kwargs": {"direction": direction},
    }
    if opt_params and opt_params.get("optimizer", IRC) is not IRC:
        raise ValueError("Only Sella's IRC should be used for IRC optimization.")

    return run_and_summarize_opt(
        atoms,
        charge,
        spin_multiplicity,
        calc_defaults=calc_defaults,
        calc_swaps=calc_kwargs,
        opt_defaults=opt_defaults,
        opt_params=opt_params,
        additional_fields={"name": "Q-Chem IRC"},
        copy_files=copy_files,
    )

quasi_irc_job 

quasi_irc_job(
    atoms: Atoms,
    charge: int = 0,
    spin_multiplicity: int = 1,
    direction: Literal["forward", "reverse"] = "forward",
    method: str = "wb97mv",
    basis: str = "def2-svpd",
    irc_job_kwargs: dict[str, Any] | None = None,
    relax_job_kwargs: dict[str, Any] | None = None,
    copy_files: (
        SourceDirectory
        | dict[SourceDirectory, Filenames]
        | None
    ) = None,
) -> OptSchema

Quasi-IRC optimize a molecular structure. Runs irc_job for 10 steps (default) followed by relax_job.

Parameters:

  • atoms (Atoms) –

    Atoms object.

  • charge (int, default: 0 ) –

    Charge of the system.

  • spin_multiplicity (int, default: 1 ) –

    Multiplicity of the system.

  • direction (Literal['forward', 'reverse'], default: 'forward' ) –

    Direction of the IRC. Should be "forward" or "reverse".

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

    Dictionary of kwargs for the irc_job.

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

    Dictionary of kwargs for the relax_job.

  • 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/qchem/ts.py 
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@job
@requires(has_sella, "Sella must be installed. Refer to the quacc documentation.")
def quasi_irc_job(
    atoms: Atoms,
    charge: int = 0,
    spin_multiplicity: int = 1,
    direction: Literal["forward", "reverse"] = "forward",
    method: str = "wb97mv",
    basis: str = "def2-svpd",
    irc_job_kwargs: dict[str, Any] | None = None,
    relax_job_kwargs: dict[str, Any] | None = None,
    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
) -> OptSchema:
    """
    Quasi-IRC optimize a molecular structure. Runs `irc_job` for 10 steps (default)
    followed by `relax_job`.

    Parameters
    ----------
    atoms
        Atoms object.
    charge
        Charge of the system.
    spin_multiplicity
        Multiplicity of the system.
    direction
        Direction of the IRC. Should be "forward" or "reverse".
    irc_job_kwargs
        Dictionary of kwargs for the `irc_job`.
    relax_job_kwargs
        Dictionary of kwargs for the `relax_job`.
    copy_files
        Files to copy (and decompress) from source to the runtime directory.

    Returns
    -------
    OptSchema
        Dictionary of results from [quacc.schemas.ase.summarize_opt_run][]
    """
    irc_job_defaults = {
        "charge": charge,
        "spin_multiplicity": spin_multiplicity,
        "direction": direction,
        "method": method,
        "basis": basis,
        "opt_params": {"max_steps": 10},
        "copy_files": copy_files,
    }
    relax_job_defaults = {
        "charge": charge,
        "spin_multiplicity": spin_multiplicity,
        "method": method,
        "basis": basis,
    }
    irc_job_kwargs = recursive_dict_merge(irc_job_defaults, irc_job_kwargs)
    relax_job_kwargs = recursive_dict_merge(relax_job_defaults, relax_job_kwargs)

    with change_settings({"CHECK_CONVERGENCE": False}):
        irc_summary = strip_decorator(irc_job)(atoms, **irc_job_kwargs)

    relax_summary = strip_decorator(relax_job)(irc_summary["atoms"], **relax_job_kwargs)
    relax_summary["initial_irc"] = irc_summary

    return relax_summary

quasi_irc_perturb_job 

quasi_irc_perturb_job(
    atoms: Atoms,
    mode: list[list[float]] | NDArray,
    perturb_magnitude: float = 0.6,
    direction: Literal["forward", "reverse"] = "forward",
    charge: int = 0,
    spin_multiplicity: int = 1,
    method: str = "wb97mv",
    basis: str = "def2-svpd",
    opt_params: OptParams | None = None,
    copy_files: (
        SourceDirectory
        | dict[SourceDirectory, Filenames]
        | None
    ) = None,
    **calc_kwargs
) -> OptSchema

Quasi-IRC to optimize a reaction endpoint from a transition-state with known vibrational frequency modes. Perturbs the structure of atoms by a finite amount (0.6 * the normalized mode magnitude) along the specified vibrational frequency mode (assumed to be the transition mode), and then performs a relax_job on the perturbed structure.

Parameters:

  • atoms (Atoms) –

    Atoms object.

  • mode (list[list[float]] | NDArray) –

    Transition mode. This should be an Nx3 matrix, where N is the number of atoms in atoms.

  • perturb_magnitude (float, default: 0.6 ) –

    Factor to multiply the transition mode. Default is 0.6. In some cases, it may be advisable to increase this factor, perhaps to 1.0 or 1.1. Lowering it is not generally found to be helpful.

  • direction (Literal['forward', 'reverse'], default: 'forward' ) –

    Direction of the (Quasi)IRC. Should be "forward" or "reverse".

  • charge (int, default: 0 ) –

    Charge of the system.

  • spin_multiplicity (int, default: 1 ) –

    Multiplicity of the system.

  • method (str, default: 'wb97mv' ) –

    DFT exchange-correlation functional or other electronic structure method.

  • basis (str, default: 'def2-svpd' ) –

    Basis set.

  • 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 calculator. Set a value to quacc.Remove to remove a pre-existing key entirely. See quacc.calculators.qchem.qchem.QChem for more details.

Returns:

Source code in quacc/recipes/qchem/ts.py 
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@job
@requires(has_sella, "Sella must be installed. Refer to the quacc documentation.")
def quasi_irc_perturb_job(
    atoms: Atoms,
    mode: list[list[float]] | NDArray,
    perturb_magnitude: float = 0.6,
    direction: Literal["forward", "reverse"] = "forward",
    charge: int = 0,
    spin_multiplicity: int = 1,
    method: str = "wb97mv",
    basis: str = "def2-svpd",
    opt_params: OptParams | None = None,
    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
    **calc_kwargs,
) -> OptSchema:
    """
    Quasi-IRC to optimize a reaction endpoint from a transition-state with known vibrational frequency modes.
    Perturbs the structure of `atoms` by a finite amount (0.6 * the normalized mode magnitude) along the specified
    vibrational frequency mode (assumed to be the transition mode), and then performs a `relax_job` on the perturbed
    structure.

    Parameters
    ----------
    atoms
        Atoms object.
    mode
        Transition mode. This should be an Nx3 matrix, where N is the number of atoms in `atoms`.
    perturb_magnitude
        Factor to multiply the transition mode. Default is 0.6. In some cases, it may be advisable to increase this
        factor, perhaps to 1.0 or 1.1. Lowering it is not generally found to be helpful.
    direction
        Direction of the (Quasi)IRC. Should be "forward" or "reverse".
    charge
        Charge of the system.
    spin_multiplicity
        Multiplicity of the system.
    method
        DFT exchange-correlation functional or other electronic structure
        method.
    basis
        Basis set.
    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 calculator. Set a value to `quacc.Remove` to remove
        a pre-existing key entirely. See [quacc.calculators.qchem.qchem.QChem][] for more
        details.


    Returns
    -------
    OptSchema
        Dictionary of results from [quacc.schemas.ase.summarize_opt_run][]
    """

    calc_defaults = recursive_dict_merge(
        _BASE_SET, {"rem": {"job_type": "force", "method": method, "basis": basis}}
    )
    opt_defaults = {"optimizer": Sella} if has_sella else {}

    scale = perturb_magnitude if direction == "forward" else perturb_magnitude * -1

    return run_and_summarize_opt(
        perturb(atoms, mode, scale),
        charge=charge,
        spin_multiplicity=spin_multiplicity,
        calc_defaults=calc_defaults,
        calc_swaps=calc_kwargs,
        opt_defaults=opt_defaults,
        opt_params=opt_params,
        additional_fields={"name": "Q-Chem Quasi-IRC perturbed optimization"},
        copy_files=copy_files,
    )

ts_job 

ts_job(
    atoms: Atoms,
    charge: int = 0,
    spin_multiplicity: int = 1,
    method: str = "wb97mv",
    basis: str = "def2-svpd",
    opt_params: OptParams | None = None,
    copy_files: (
        SourceDirectory
        | dict[SourceDirectory, Filenames]
        | None
    ) = None,
    **calc_kwargs
) -> OptSchema

TS optimize a molecular structure.

Parameters:

  • atoms (Atoms) –

    Atoms object

  • charge (int, default: 0 ) –

    Charge of the system.

  • spin_multiplicity (int, default: 1 ) –

    Multiplicity of the system.

  • method (str, default: 'wb97mv' ) –

    DFT exchange-correlation functional or other electronic structure method.

  • basis (str, default: 'def2-svpd' ) –

    Basis set.

  • 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 calculator. Set a value to quacc.Remove to remove a pre-existing key entirely. See quacc.calculators.qchem.qchem.QChem for more details.

Returns:

Source code in quacc/recipes/qchem/ts.py 
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@job
@requires(has_sella, "Sella must be installed. Refer to the quacc documentation.")
def ts_job(
    atoms: Atoms,
    charge: int = 0,
    spin_multiplicity: int = 1,
    method: str = "wb97mv",
    basis: str = "def2-svpd",
    opt_params: OptParams | None = None,
    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
    **calc_kwargs,
) -> OptSchema:
    """
    TS optimize a molecular structure.

    Parameters
    ----------
    atoms
        Atoms object
    charge
        Charge of the system.
    spin_multiplicity
        Multiplicity of the system.
    method
        DFT exchange-correlation functional or other electronic structure
        method.
    basis
        Basis set.
    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 calculator. Set a value to `quacc.Remove` to remove
        a pre-existing key entirely. See [quacc.calculators.qchem.qchem.QChem][] for more
        details.

    Returns
    -------
    OptSchema
        Dictionary of results from [quacc.schemas.ase.summarize_opt_run][].
        See the type-hint for the data structure.
    """
    calc_defaults = recursive_dict_merge(
        _BASE_SET, {"rem": {"job_type": "force", "method": method, "basis": basis}}
    )
    opt_defaults = {"optimizer": Sella, "optimizer_kwargs": {"order": 1}}

    if opt_params and opt_params.get("optimizer", Sella) is not Sella:
        raise ValueError("Only Sella should be used for TS optimization.")

    return run_and_summarize_opt(
        atoms,
        charge,
        spin_multiplicity,
        calc_defaults=calc_defaults,
        calc_swaps=calc_kwargs,
        opt_defaults=opt_defaults,
        opt_params=opt_params,
        additional_fields={"name": "Q-Chem TS"},
        copy_files=copy_files,
    )