schrodinger.application.matsci.anharmonic module¶

Utilities for the anharmonic corrections workflow.

class schrodinger.application.matsci.anharmonic.SeqData(start, step, n_points)¶

Bases: tuple

__contains__¶: Return key in self.

__init__¶: Initialize self. See help(type(self)) for accurate signature.

__len__¶: Return len(self).

count(value) → integer -- return number of occurrences of value¶

index(value[, start[, stop]]) → integer -- return first index of value.¶: Raises ValueError if the value is not present.

n_points¶: Alias for field number 2

start¶: Alias for field number 0

step¶: Alias for field number 1

schrodinger.application.matsci.anharmonic.get_seq_data(options, flag)¶

Return a sequence data for the given flag.

Parameters:	options (argparse.Namespace) – the options flag (str) – the flag
Return type:	SeqData
Returns:	the sequence data

schrodinger.application.matsci.anharmonic.evaluate_f(x, deriv_idx, coeffs)¶

Evaluate the nth derivative of a polynomial described by the given coefficients.

Parameters:	x (float) – the point at which to evaluate deriv_idx (int) – indicates what derivative of the polynomial to evaluate, 0 is the polynomial itself, 1 is the first derivative, etc. coeffs (tuple) – the coefficents of the polynomial, for a mth order polynomial must be of lenth m + 1
Return type:	float
Returns:	the evaluated value

schrodinger.application.matsci.anharmonic.angular_freq_to_freq(angular_freq)¶

Convert the given angular frequency to frequency.

Parameters:	angular_freq (float) – the angular frequency in s**-1
Return type:	float
Returns:	the frequency in cm**-1

schrodinger.application.matsci.anharmonic.freq_to_angular_freq(freq)¶

Convert the given frequency to angular frequency.

Parameters:	freq (float) – the frequency in cm**-1
Return type:	float
Returns:	the angular frequency in s**-1

schrodinger.application.matsci.anharmonic.plotter(x_min, x_max, x_e_min, x_e_max, x_step, y_func, file_name, title, y_label)¶

Plot the given function.

Parameters:

x_min (float) – the minimum value on the x-axis
x_max (float) – the maximum value on the x-axis
x_e_min (float) – the minimum value on the extended x-axis
x_e_max (float) – the maximum value on the extended x-axis
x_step (float) – the step size to use on the x-axis
y_func (function) – the function to use to obtain y-axis values
file_name (str) – the file name used to write the plot image
title (str) – the title for the plot image
y_label (str) – the y-axis label for the plot image

schrodinger.application.matsci.anharmonic.get_normal_modes(jagout)¶

Return the normal modes from the given JaguarOutput.

Parameters:	jagout (schrodinger.application.jaguar.output.JaguarOutput) – the Jaguar output object
Return type:	list
Returns:	contains schrodinger.application.jaguar.results.NormalMode

schrodinger.application.matsci.anharmonic.check_imaginary_frequencies(jag_out, jag_in, max_i_freq=0)¶

Check imaginary frequencies.

Parameters:	jag_out (JaguarOutput) – the Jaguar output object jag_in (JaguarInput) – the Jaguar input object max_i_freq (float) – tolerate small imaginary frequencies less than this value in wavenumbers (cm^-1)
Raises:	AnharmonicException – if there is an issue

schrodinger.application.matsci.anharmonic.get_st_jaguar_output(jagout_file_name, allow_new_dummies=False)¶

Return a structure from the given Jaguar output file.

Parameters:	jagout_file_name (str) – the name of a Jaguar output file allow_new_dummies (bool) – whether to allow mmjag’s lewis structure build to possibly add new dummy atoms
Return type:	schrodinger.structure.Structure
Returns:	the structure

exception schrodinger.application.matsci.anharmonic.AnharmonicException¶

Bases: Exception

__init__¶: Initialize self. See help(type(self)) for accurate signature.

args¶

with_traceback()¶: Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

class schrodinger.application.matsci.anharmonic.AnharmonicPotentials(st=None, jagout_file_name=None, jagrin_file_name=None, max_freq=300, factor_data=None, jaguar_kwargs={'basis': 'LACVP**', 'dftname': 'B3LYP', 'igeopt': 1, 'molchg': 0, 'multip': 1}, temperature_data=None, pressure_data=None, max_i_freq=0, plot=False, process_no_anharmonicities=False, tpp=1, logger=None)¶

Bases: object

__init__(st=None, jagout_file_name=None, jagrin_file_name=None, max_freq=300, factor_data=None, jaguar_kwargs={'basis': 'LACVP**', 'dftname': 'B3LYP', 'igeopt': 1, 'molchg': 0, 'multip': 1}, temperature_data=None, pressure_data=None, max_i_freq=0, plot=False, process_no_anharmonicities=False, tpp=1, logger=None)¶

Create an instance.

Parameters:

st (schrodinger.structure.Structure or None) – a structure for which to calculate anharmonic potentials or None if using Jaguar frequency files directly
jagout_file_name (str or None) – the name of a Jaguar frequency output file for which to calculate anharmonic potentials or None if using an input structure
jagrin_file_name (str or None) – the name of a Jaguar freqency restart input file for which to calculate anharmonic potentials or None if using an input structure
max_freq (float) – anharmonic potentials are created for normal modes with harmonic frequencies less than this value in wavenumbers (cm^-1)
factor_data (SeqData or None) – unitless factor data for factors that multiply a normal mode displacement, if None then the defaults are used, the number of points is in the positive direction only, excluding zero and the negative direction, for example using a value of 4 in turn means 2 * 4 + 1 = 9 points total
jaguar_kwargs (dict) – Jaguar &gen section keyword arguments, used only if the anharmonic potentials are being calculated from an input structure rather than directly from Jaguar frequency files
temperature_data (SeqData or None) – temperature data in K, if None then the defaults are used
pressure_data (SeqData or None) – pressure data in atm, if None then the defaults are used
max_i_freq (float) – tolerate small imaginary frequencies less than this value in wavenumbers (cm^-1)
plot (bool) – if True then return plots of the potentials and particle densities
process_no_anharmonicities (bool) – if True then do not exit with an error if the given max_freq results in zero normal modes to be treated anharmonically
tpp (int) – the threads-per-process to use for running Jaguar calculations
logger (logging.Logger or None) – output logger or None if there isn’t one

runFrequencyJob()¶

Run a Jaguar frequency job on the input structure.

Raises:	AnharmonicException – if there is an issue

static getFactors(factor_data)¶

Return the factors.

Parameters:	factor_data (SeqData) – unitless factor data for factors that multiply a normal mode displacement, the number of points is in the positive direction only, excluding zero and the negative direction, for example using a value of 4 in turn means 2 * 4 + 1 = 9 points total
Return type:	tuple
Returns:	the factors

getExtendedFactors()¶

Return the extended factors.

Return type:	tuple
Returns:	the extended factors

getRealNormalModes()¶

Generator for normal modes with real frequencies.

Ytype:	tuple
Yield:	the normal mode index, 1-based, and schrodinger.application.jaguar.results.NormalMode

runSinglePointJobs()¶

Run the Jaguar single point jobs from which to calculate the anharmonic potentials.

Raises:	AnharmonicException – if there is an issue

collectEnergies()¶

Update self.potentials with the Jaguar single point energies.

Raises:	AnharmonicException – if there is an issue

collectFits()¶

Update self.potentials with the anharmonic fit data.

Raises:	AnharmonicException – if there is an issue

evaluate_f(idx, factor, deriv_idx, convert_to_si=False)¶

Evaluate the nth derivative of the anharmonic potential for the given normal mode index.

Parameters:	idx (int) – the normal mode index, 1-based factor (float) – the point at which to evaluate deriv_idx (int) – indicates what derivative of the polynomial to evaluate, 0 is the polynomial itself, 1 is the first derivative, etc. convert_to_si (bool) – if True convert the returned value from units of H/Ang.deriv_idx to J/mderiv_idx
Raises:	AnharmonicException – if there is an issue
Return type:	float
Returns:	the evaluated value in units of H/Ang.deriv_idx or if convert_to_si is True in units of J/mderiv_idx

getReducedMass1(idx)¶

Return the reduced mass of the given normal mode using the Jaguar definition.

Parameters:	idx (int) – the normal mode index, 1-based
Return type:	float
Returns:	the reduced mass in kg

getReducedMass2(idx)¶

Return the reduced mass of the given normal mode using the definition in the publications followed in this module.

Parameters:	idx (int) – the normal mode index, 1-based
Return type:	float
Returns:	the reduced mass in kg

getReducedMass(idx)¶

Return the reduced mass of the given normal mode.

Parameters:	idx (int) – the normal mode index, 1-based
Return type:	float
Returns:	the reduced mass in kg

collectAnharmonicFrequencies()¶

Update self.potentials with the anharmonic frequencies in wavenumbers (cm^-1).

Raises:	AnharmonicException – if there is an issue

plotPotentials()¶: Plot the potentials.

logCoefficientsTable()¶: Log coefficients table.

logFrequencyTable()¶: Log frequency table.

run()¶: Calculate the anharmonic potentials.

class schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction(st=None, jagout_file_name=None, jagrin_file_name=None, max_freq=300, factor_data=None, jaguar_kwargs={'basis': 'LACVP**', 'dftname': 'B3LYP', 'igeopt': 1, 'molchg': 0, 'multip': 1}, temperature_data=None, pressure_data=None, max_i_freq=0, plot=False, process_no_anharmonicities=False, tpp=1, logger=None)¶

Bases: schrodinger.application.matsci.anharmonic.AnharmonicPotentials

static getBeta(temperature)¶

Return beta.

Parameters:	temperature (float) – the temperature in K
Return type:	float
Returns:	beta in 1/J

getClassicalParticleDensity(idx, temperature, factor)¶

For the given normal mode return the classical particle density evaluated at the given factor.

Parameters:	idx (int) – the normal mode index, 1-based temperature (float) – the temperature in K factor (float) – the point at which to evaluate
Return type:	float
Returns:	the classical particle density in 1/Ang.

getCorrectionParticleDensity(idx, temperature, factor)¶

For the given normal mode return the particle density multiplicative correction evaluated at the given factor.

Parameters:	idx (int) – the normal mode index, 1-based temperature (float) – the temperature in K factor (float) – the point at which to evaluate
Return type:	float
Returns:	the particle density multiplicative correction (unitless)

getParticleDensity(idx, temperature, factor)¶

For the given normal mode return the particle density evaluated at the given factor.

Parameters:	idx (int) – the normal mode index, 1-based temperature (float) – the temperature in K factor (float) – the point at which to evaluate
Return type:	float
Returns:	the particle density in 1/Ang.

plotParticleDensity(idx, temperature)¶

For the given normal mode plot the particle density.

Parameters:	idx (int) – the normal mode index, 1-based temperature (float) – the temperature in K

checkCorrectionParticleDensity(idx, temperature)¶

For the given normal mode check the particle density multiplicative correction.

Parameters:	idx (int) – the normal mode index, 1-based temperature (float) – the temperature in K
Raises:	AnharmonicException – if there is an issue

getAnharmonicVibPartitionFunctions(temperature)¶

Return the ln of the anharmonic vibrational partition functions.

Parameters:	temperature (float) – the temperature in K
Return type:	dict
Returns:	keys are normal mode indices, 1-based, values are ln of the anharmonic vibrational partition functions

getHarmonicVibPartitionFunctions(temperature)¶

Return the ln of the harmonic vibrational partition functions.

Parameters:	temperature (float) – the temperature in K
Return type:	dict
Returns:	keys are normal mode indices, 1-based, values are ln of the harmonic vibrational partition functions

static getVibPartitionFunction(lnz_a_vibs, lnz_h_vibs)¶

Return the ln of the vibrational partition function.

Return type:	float
Returns:	the ln of the vibrational partition function

logLnQTable(temperature, lnz_a_vibs, lnz_h_vibs)¶

Log lnQ table.

Parameters:	temperature (float) – the temperature in K

setJaguarThermo()¶

Set the Jaguar thermo objects that will be anharmonically corrected.

Raises:	AnharmonicException – if there is an issue

run()¶: Calculate the anharmonic partition function.

__init__(st=None, jagout_file_name=None, jagrin_file_name=None, max_freq=300, factor_data=None, jaguar_kwargs={'basis': 'LACVP**', 'dftname': 'B3LYP', 'igeopt': 1, 'molchg': 0, 'multip': 1}, temperature_data=None, pressure_data=None, max_i_freq=0, plot=False, process_no_anharmonicities=False, tpp=1, logger=None)¶

Create an instance.

Parameters:

st (schrodinger.structure.Structure or None) – a structure for which to calculate anharmonic potentials or None if using Jaguar frequency files directly
jagout_file_name (str or None) – the name of a Jaguar frequency output file for which to calculate anharmonic potentials or None if using an input structure
jagrin_file_name (str or None) – the name of a Jaguar freqency restart input file for which to calculate anharmonic potentials or None if using an input structure
max_freq (float) – anharmonic potentials are created for normal modes with harmonic frequencies less than this value in wavenumbers (cm^-1)
factor_data (SeqData or None) – unitless factor data for factors that multiply a normal mode displacement, if None then the defaults are used, the number of points is in the positive direction only, excluding zero and the negative direction, for example using a value of 4 in turn means 2 * 4 + 1 = 9 points total
jaguar_kwargs (dict) – Jaguar &gen section keyword arguments, used only if the anharmonic potentials are being calculated from an input structure rather than directly from Jaguar frequency files
temperature_data (SeqData or None) – temperature data in K, if None then the defaults are used
pressure_data (SeqData or None) – pressure data in atm, if None then the defaults are used
max_i_freq (float) – tolerate small imaginary frequencies less than this value in wavenumbers (cm^-1)
plot (bool) – if True then return plots of the potentials and particle densities
process_no_anharmonicities (bool) – if True then do not exit with an error if the given max_freq results in zero normal modes to be treated anharmonically
tpp (int) – the threads-per-process to use for running Jaguar calculations
logger (logging.Logger or None) – output logger or None if there isn’t one

collectAnharmonicFrequencies()¶

Update self.potentials with the anharmonic frequencies in wavenumbers (cm^-1).

Raises:	AnharmonicException – if there is an issue

collectEnergies()¶

Update self.potentials with the Jaguar single point energies.

Raises:	AnharmonicException – if there is an issue

collectFits()¶

Update self.potentials with the anharmonic fit data.

Raises:	AnharmonicException – if there is an issue

evaluate_f(idx, factor, deriv_idx, convert_to_si=False)¶

Evaluate the nth derivative of the anharmonic potential for the given normal mode index.

Parameters:	idx (int) – the normal mode index, 1-based factor (float) – the point at which to evaluate deriv_idx (int) – indicates what derivative of the polynomial to evaluate, 0 is the polynomial itself, 1 is the first derivative, etc. convert_to_si (bool) – if True convert the returned value from units of H/Ang.deriv_idx to J/mderiv_idx
Raises:	AnharmonicException – if there is an issue
Return type:	float
Returns:	the evaluated value in units of H/Ang.deriv_idx or if convert_to_si is True in units of J/mderiv_idx

getExtendedFactors()¶

Return the extended factors.

Return type:	tuple
Returns:	the extended factors

static getFactors(factor_data)¶

Return the factors.

Parameters:	factor_data (SeqData) – unitless factor data for factors that multiply a normal mode displacement, the number of points is in the positive direction only, excluding zero and the negative direction, for example using a value of 4 in turn means 2 * 4 + 1 = 9 points total
Return type:	tuple
Returns:	the factors

getRealNormalModes()¶

Generator for normal modes with real frequencies.

Ytype:	tuple
Yield:	the normal mode index, 1-based, and schrodinger.application.jaguar.results.NormalMode

getReducedMass(idx)¶

Return the reduced mass of the given normal mode.

Parameters:	idx (int) – the normal mode index, 1-based
Return type:	float
Returns:	the reduced mass in kg

getReducedMass1(idx)¶

Return the reduced mass of the given normal mode using the Jaguar definition.

Parameters:	idx (int) – the normal mode index, 1-based
Return type:	float
Returns:	the reduced mass in kg

getReducedMass2(idx)¶

Return the reduced mass of the given normal mode using the definition in the publications followed in this module.

Parameters:	idx (int) – the normal mode index, 1-based
Return type:	float
Returns:	the reduced mass in kg

logCoefficientsTable()¶: Log coefficients table.

logFrequencyTable()¶: Log frequency table.

plotPotentials()¶: Plot the potentials.

runFrequencyJob()¶

Run a Jaguar frequency job on the input structure.

Raises:	AnharmonicException – if there is an issue

runSinglePointJobs()¶

Run the Jaguar single point jobs from which to calculate the anharmonic potentials.

Raises:	AnharmonicException – if there is an issue

class schrodinger.application.matsci.anharmonic.AnharmonicThermochemicalProperties(st=None, jagout_file_name=None, jagrin_file_name=None, max_freq=300, factor_data=None, jaguar_kwargs={'basis': 'LACVP**', 'dftname': 'B3LYP', 'igeopt': 1, 'molchg': 0, 'multip': 1}, temperature_data=None, pressure_data=None, max_i_freq=0, plot=False, process_no_anharmonicities=False, tpp=1, logger=None)¶

Bases: schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction

getVibrationalTemperature(idx)¶

Return the vibrational temperature of the given normal mode.

Parameters:	idx (int) – the normal mode index, 1-based
Return type:	float
Returns:	the vibrational temperature in K

getInternalEnergy(thermo)¶

Return the internal energy.

Parameters:	thermo (schrodinger.application.jaguar.results.ThermoCollection) – the thermo object
Return type:	float
Returns:	the internal energy in kcal/mol

getHeatCapacity(thermo)¶

Return the heat capacity.

Parameters:	thermo (schrodinger.application.jaguar.results.ThermoCollection) – the thermo object
Return type:	float
Returns:	the heat capacity in cal/(mol * K)

getEntropy(thermo)¶

Return the entropy.

Parameters:	thermo (schrodinger.application.jaguar.results.ThermoCollection) – the thermo object
Return type:	float
Returns:	the entropy in cal/(mol * K)

getEnthalpy(thermo)¶

Return the enthalpy.

Parameters:	thermo (schrodinger.application.jaguar.results.ThermoCollection) – the thermo object
Return type:	float
Returns:	the enthalpy in kcal/mol

__init__(st=None, jagout_file_name=None, jagrin_file_name=None, max_freq=300, factor_data=None, jaguar_kwargs={'basis': 'LACVP**', 'dftname': 'B3LYP', 'igeopt': 1, 'molchg': 0, 'multip': 1}, temperature_data=None, pressure_data=None, max_i_freq=0, plot=False, process_no_anharmonicities=False, tpp=1, logger=None)¶

Create an instance.

Parameters:

st (schrodinger.structure.Structure or None) – a structure for which to calculate anharmonic potentials or None if using Jaguar frequency files directly
jagout_file_name (str or None) – the name of a Jaguar frequency output file for which to calculate anharmonic potentials or None if using an input structure
jagrin_file_name (str or None) – the name of a Jaguar freqency restart input file for which to calculate anharmonic potentials or None if using an input structure
max_freq (float) – anharmonic potentials are created for normal modes with harmonic frequencies less than this value in wavenumbers (cm^-1)
factor_data (SeqData or None) – unitless factor data for factors that multiply a normal mode displacement, if None then the defaults are used, the number of points is in the positive direction only, excluding zero and the negative direction, for example using a value of 4 in turn means 2 * 4 + 1 = 9 points total
jaguar_kwargs (dict) – Jaguar &gen section keyword arguments, used only if the anharmonic potentials are being calculated from an input structure rather than directly from Jaguar frequency files
temperature_data (SeqData or None) – temperature data in K, if None then the defaults are used
pressure_data (SeqData or None) – pressure data in atm, if None then the defaults are used
max_i_freq (float) – tolerate small imaginary frequencies less than this value in wavenumbers (cm^-1)
plot (bool) – if True then return plots of the potentials and particle densities
process_no_anharmonicities (bool) – if True then do not exit with an error if the given max_freq results in zero normal modes to be treated anharmonically
tpp (int) – the threads-per-process to use for running Jaguar calculations
logger (logging.Logger or None) – output logger or None if there isn’t one

checkCorrectionParticleDensity(idx, temperature)¶

For the given normal mode check the particle density multiplicative correction.

Parameters:	idx (int) – the normal mode index, 1-based temperature (float) – the temperature in K
Raises:	AnharmonicException – if there is an issue

collectAnharmonicFrequencies()¶

Update self.potentials with the anharmonic frequencies in wavenumbers (cm^-1).

Raises:	AnharmonicException – if there is an issue

collectEnergies()¶

Update self.potentials with the Jaguar single point energies.

Raises:	AnharmonicException – if there is an issue

collectFits()¶

Update self.potentials with the anharmonic fit data.

Raises:	AnharmonicException – if there is an issue

evaluate_f(idx, factor, deriv_idx, convert_to_si=False)¶

Evaluate the nth derivative of the anharmonic potential for the given normal mode index.

Parameters:	idx (int) – the normal mode index, 1-based factor (float) – the point at which to evaluate deriv_idx (int) – indicates what derivative of the polynomial to evaluate, 0 is the polynomial itself, 1 is the first derivative, etc. convert_to_si (bool) – if True convert the returned value from units of H/Ang.deriv_idx to J/mderiv_idx
Raises:	AnharmonicException – if there is an issue
Return type:	float
Returns:	the evaluated value in units of H/Ang.deriv_idx or if convert_to_si is True in units of J/mderiv_idx

getAnharmonicVibPartitionFunctions(temperature)¶

Return the ln of the anharmonic vibrational partition functions.

Parameters:	temperature (float) – the temperature in K
Return type:	dict
Returns:	keys are normal mode indices, 1-based, values are ln of the anharmonic vibrational partition functions

static getBeta(temperature)¶

Return beta.

Parameters:	temperature (float) – the temperature in K
Return type:	float
Returns:	beta in 1/J

getClassicalParticleDensity(idx, temperature, factor)¶

For the given normal mode return the classical particle density evaluated at the given factor.

Parameters:	idx (int) – the normal mode index, 1-based temperature (float) – the temperature in K factor (float) – the point at which to evaluate
Return type:	float
Returns:	the classical particle density in 1/Ang.

getCorrectionParticleDensity(idx, temperature, factor)¶

For the given normal mode return the particle density multiplicative correction evaluated at the given factor.

Parameters:	idx (int) – the normal mode index, 1-based temperature (float) – the temperature in K factor (float) – the point at which to evaluate
Return type:	float
Returns:	the particle density multiplicative correction (unitless)

getExtendedFactors()¶

Return the extended factors.

Return type:	tuple
Returns:	the extended factors

static getFactors(factor_data)¶

Return the factors.

Parameters:	factor_data (SeqData) – unitless factor data for factors that multiply a normal mode displacement, the number of points is in the positive direction only, excluding zero and the negative direction, for example using a value of 4 in turn means 2 * 4 + 1 = 9 points total
Return type:	tuple
Returns:	the factors

getGibbsFreeEnergy(thermo)¶

Return the Gibbs free energy.

Parameters:	thermo (schrodinger.application.jaguar.results.ThermoCollection) – the thermo object
Return type:	float
Returns:	the Gibbs free energy in kcal/mol

getHarmonicVibPartitionFunctions(temperature)¶

Return the ln of the harmonic vibrational partition functions.

Parameters:	temperature (float) – the temperature in K
Return type:	dict
Returns:	keys are normal mode indices, 1-based, values are ln of the harmonic vibrational partition functions

getParticleDensity(idx, temperature, factor)¶

For the given normal mode return the particle density evaluated at the given factor.

Parameters:	idx (int) – the normal mode index, 1-based temperature (float) – the temperature in K factor (float) – the point at which to evaluate
Return type:	float
Returns:	the particle density in 1/Ang.

getRealNormalModes()¶

Generator for normal modes with real frequencies.

Ytype:	tuple
Yield:	the normal mode index, 1-based, and schrodinger.application.jaguar.results.NormalMode

getReducedMass(idx)¶

Return the reduced mass of the given normal mode.

Parameters:	idx (int) – the normal mode index, 1-based
Return type:	float
Returns:	the reduced mass in kg

getReducedMass1(idx)¶

Return the reduced mass of the given normal mode using the Jaguar definition.

Parameters:	idx (int) – the normal mode index, 1-based
Return type:	float
Returns:	the reduced mass in kg

getReducedMass2(idx)¶

Return the reduced mass of the given normal mode using the definition in the publications followed in this module.

Parameters:	idx (int) – the normal mode index, 1-based
Return type:	float
Returns:	the reduced mass in kg

static getVibPartitionFunction(lnz_a_vibs, lnz_h_vibs)¶

Return the ln of the vibrational partition function.

Return type:	float
Returns:	the ln of the vibrational partition function

logCoefficientsTable()¶: Log coefficients table.

logFrequencyTable()¶: Log frequency table.

logLnQTable(temperature, lnz_a_vibs, lnz_h_vibs)¶

Log lnQ table.

Parameters:	temperature (float) – the temperature in K

plotParticleDensity(idx, temperature)¶

For the given normal mode plot the particle density.

Parameters:	idx (int) – the normal mode index, 1-based temperature (float) – the temperature in K

plotPotentials()¶: Plot the potentials.

runFrequencyJob()¶

Run a Jaguar frequency job on the input structure.

Raises:	AnharmonicException – if there is an issue

runSinglePointJobs()¶

Run the Jaguar single point jobs from which to calculate the anharmonic potentials.

Raises:	AnharmonicException – if there is an issue

setJaguarThermo()¶

Set the Jaguar thermo objects that will be anharmonically corrected.

Raises:	AnharmonicException – if there is an issue

logPropertyTable(thermo)¶

Log property table.

Parameters:	thermo (schrodinger.application.jaguar.results.ThermoCollection) – the thermo object

run()¶: Calculate the anharmonic thermochemical properties.

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