schrodinger.application.jaguar.thermochemical_properties module¶

Computes thermochemical properties from a previously run Jaguar calculation. When treating low-lying frequencies, they are first discarded by freqcut, then raised to quasi_harmonic_thresh, and then weighted by smooth_vib_cutoff_width if still applicable.

class schrodinger.application.jaguar.thermochemical_properties.ThermoProps(q, zpe, energy, enthalpy, entropy, heat_capacity, gibbs)¶

Bases: tuple

energy: float¶: Alias for field number 2

enthalpy: float¶: Alias for field number 3

entropy: float¶: Alias for field number 4

gibbs: float¶: Alias for field number 6

heat_capacity: float¶: Alias for field number 5

q: float¶: Alias for field number 0

zpe: float¶: Alias for field number 1

class schrodinger.application.jaguar.thermochemical_properties.InputParams(natoms: int, energy: float, mass: float, rotational_constants: list[float], symmetry_number: int, frequencies: list[float], solv_entropy_params: schrodinger.application.jaguar.garza.SolvEntropyParams)¶

Bases: object

natoms: int¶

energy: float¶

mass: float¶

rotational_constants: list[float]¶

symmetry_number: int¶

frequencies: list[float]¶

solv_entropy_params: schrodinger.application.jaguar.garza.SolvEntropyParams¶

get_translational_args() → tuple[float, float, float]¶: Helper function to make calls to translational_properties() take less space

get_rotational_args() → tuple[float, list[float], float, float, float, float, float]¶: Helper function to make calls to rotational_properties() take less space

__init__(natoms: int, energy: float, mass: float, rotational_constants: list[float], symmetry_number: int, frequencies: list[float], solv_entropy_params: schrodinger.application.jaguar.garza.SolvEntropyParams) → None¶

class schrodinger.application.jaguar.thermochemical_properties.LowModeParams(freq_off, quasi_max)¶

Bases: tuple

freq_off: float¶: Alias for field number 0

quasi_max: float¶: Alias for field number 1

schrodinger.application.jaguar.thermochemical_properties.parse_args(args)¶

schrodinger.application.jaguar.thermochemical_properties.translational_properties(temp: float, press: float, solvation_entropy: bool, mass: float, n_c: float, v_c: float) → tuple[schrodinger.application.jaguar.thermochemical_properties.ThermoProps, float | None]¶

Translational contributions to thermodynamic properties

Parameters

temp – temperature in Kelvin
press – pressure in atomic units (apu)
mass – mass of molecule in atomic units (electron mass’)
solvation_entropy – whether to calculate solvation entropy or not
n_c – Number of hopping sites for solute in solvent, unitless
v_c – Solute cavity volume, ang^3

Returns

translational thermodynamic properties, both for ideal gas and solvation entropy

schrodinger.application.jaguar.thermochemical_properties.rotational_properties(temp: float, solvation_entropy: bool, symmetry_number: int, rotational_constants: list[float], mass: float, solute_rad_gyr: float, v_free: float | None, r_c: float | None, n_c: float | None) → tuple[schrodinger.application.jaguar.thermochemical_properties.ThermoProps, float | None]¶

Rotational contributions to thermodynamic properties

Parameters

temp – temperature in Kelvin
solvation_entropy – whether to calculate solvation entropy or not
symmetry_number – number of ways molecule can be rotated into itself
rotational_constants – list of rotational constants in au
mass – mass of solute in atomic units (electron mass’)
solute_rad_gyr – Solute radius of gyration, ang
v_free – Free volume per solvent molecule, ang^3
r_c – Solute cavity radius, ang
n_c – Number of hopping sites for solute in solvent, unitless

Returns

rotational thermodynamic properties, both for ideal gas and solvation entropy

schrodinger.application.jaguar.thermochemical_properties.vibrational_properties(temp: float, frequencies: list[float], low_mode_params: schrodinger.application.jaguar.thermochemical_properties.LowModeParams, solvation_entropy: bool) → tuple[schrodinger.application.jaguar.thermochemical_properties.ThermoProps, float | None]¶

Vibrational contributions to thermodynamic properties

Parameters

temp – temperature in Kelvin
frequencies – list of frequencies in au
low_mode_params – parameters for treatment of low vibrational modes
solvation_entropy – whether to calc solvation entropy or not

Returns

vibrational thermodynamic properties, both for ideal gas and solvation entropy

schrodinger.application.jaguar.thermochemical_properties.parse_solvation_entropy_parameters(jout: schrodinger.application.jaguar.output.JaguarOutput, verbose: bool = True) → schrodinger.application.jaguar.garza.SolvEntropyParams¶

Assemble SolvEntropyParams object for use in solvation entropy calculations.

Parameters

jout – JaguarOutput instance of the inputted Jaguar .out file
verbose – Whether to print information or not

Returns

Parsed solvation entropy parameters

schrodinger.application.jaguar.thermochemical_properties.parse_output(outfile: str, verbose: bool = True) → schrodinger.application.jaguar.thermochemical_properties.InputParams¶

Parse data from jaguar output file

Parameters

outfile – name of jaguar output file
verbose – Whether to print information or not

Returns

Input parameters for this script

Compute thermochemical properties

Parameters

temp – temperature in Kelvin
pressure – pressure in au
input_params – parameters parsed from jaguar output file
low_mode_params – parameters for treatment of low vibrational modes
solvation_entropy – Whether to compute solvation entropy or not

Returns trans, rot, vib, total, solv_entropy_props

ideal gas and solvation entropy thermochemical quantities

schrodinger.application.jaguar.thermochemical_properties.set_up_low_mode(freq_off: float = 0.0, qharmonic: float = 100.0, verbose: bool = True) → schrodinger.application.jaguar.thermochemical_properties.LowModeParams¶

Set up the low frequency mode handling parameters

Parameters

freq_off – frequency cutoff in cm^-1, frequencies below this cutoff are neglected
qharmonic – The quasi harmonic theshold. Frequencies are adjusted to max(frequency, this value).
verbose – Whether to print information or not

Returns

The parameters based on the input arguments

Raises

JaguarUserFacingException – If qharmonic is not positive

schrodinger.application.jaguar.thermochemical_properties.finalize_solvation_entropy_params(args, params: schrodinger.application.jaguar.garza.SolventParams, verbose: bool = True)¶

Solvation entropy parameters can be defined by either the Jaguar outfile or the cmdline, with the cmdline taking precedence. This function is run after the outfile has been parsed, so we’re accounting for the cmdline precdence in here.

Parameters

args – Namespace.args
params – Solvent parameters harvested from the outfile
verbose – Set True to print the changes we are making

schrodinger.application.jaguar.thermochemical_properties.main(args)¶: Parse frequencies and compute thermochemical properties