ccu.thermo.gibbs

Functions for calculating Gibbs free energies from vibrational data.

ccu.thermo.gibbs._alert_imaginary_frequencies(approximation: Literal['IDEAL_GAS', 'HARMONIC'] = 'HARMONIC', lower_frequency_threshold: float = 12.0) → None[source]

Issue an appropriate warning when there are imaginary frequencies.

ccu.thermo.gibbs._normalize_frequencies(frequencies: list[complex], approximation: Literal['IDEAL_GAS', 'HARMONIC'] = 'HARMONIC', transition_state: bool = False, frequency_threshold: float = 12) → list[float][source]

Add real frequencies and normalize sub-threshold frequencies.

ccu.thermo.gibbs.calculate_free_energy(*, freq: list[float] | None = None, log_file: TextIO | None = None, vib_file: TextIO | None = None, approximation: Literal['IDEAL_GAS', 'HARMONIC'] = 'HARMONIC', symmetry: int = 1, geometry: Literal['linear', 'nonlinear'] = 'nonlinear', transition_state: bool = False, frequency_threshold: float = 12.0, temperature: float = 273.15, pressure: float = 1.0, spin: int = 0, atoms_file: str = 'in.traj') → tuple[float, float, list[float]][source]

Calculate the thermodynamic corrections in the specified approximation.

Parameters:

  • freq – A list of frequencies to use for free energy calculations.

  • log_file – A file in which to log the results.

  • vib_file – A file from which to read the frequencies.

  • approximation – Which approximation to use. One of "IDEAL_GAS" or "HARMONIC". Defaults to "HARMONIC".

  • symmetry – The symmetry number of the system. Defaults to 1.

  • geometry – The geometry of the system. One of "linear" or "nonlinear" Defaults to "nonlinear".

  • transition_state – Whether to treat the system as a transition state. Defaults to False.

  • frequency_threshold – All frequencies below this value with be normalized to this value. Defaults to 12.

  • temperature – The temperature for the system (in Kelvin). Note that this is only relevant if approximation="IDEAL_GAS". Defaults to 273.15.

  • pressure – The pressure for the system (in bar). Note that this is only relevant if approximation="IDEAL_GAS". Defaults to 1.0.

  • spin – The spin for the system. Note that this is only relevant if approximation="IDEAL_GAS". Defaults to 0.

  • atoms_file – A string pointing to the structure to which the vibrational calculations correspond. This is only required if approximation="IDEAL_GAS". Defaults to "in.traj".

Returns:

A 3-tuple (ts, zpe, freq) where ts is the entropic correction (\(-TS\)), zpe is the vibrational zero-point energy (\(ZPE\)), and freq is a list of floats representing the frequencies used to calculate the zero-point energy.

Note

The free energy of the system can be calculated using (1)

ccu.thermo.gibbs.select_frequencies(vib_file: TextIO | None = None, geometry: Literal['linear', 'nonlinear'] = 'nonlinear', approximation: Literal['IDEAL_GAS', 'HARMONIC'] = 'HARMONIC', transition_state: bool = False, frequency_threshold: float = 12) → list[float][source]

Discard frequencies according to the geometry and approximations.

Parameters:

  • vib_file – An opened text file in which to save the vibrational data.

  • geometry – A string indicating the geometry. One of "linear" or "nonlinear". Defaults to "nonlinear".

  • approximation – A string indicating the approximation used in the treatment of the free energy. Defaults to "HARMONIC".

  • transition_state – Whether the frequencies correspond to a transition state. Defaults to False.

  • frequency_threshold – All frequencies below this value will be normalized to this value. Defaults to 12 cm-1.

Returns:

The appropriate frequencies for the system.