schrodinger.application.matsci.anharmonic module

Utilities for the anharmonic corrections workflow.

Copyright Schrodinger, LLC. All rights reserved.

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/m**deriv_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/m**deriv_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/m**deriv_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/m**deriv_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/m**deriv_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/m**deriv_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.