schrodinger.application.matsci.anharmonic module¶
Utilities for the anharmonic corrections workflow.
Copyright Schrodinger, LLC. All rights reserved.
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class
schrodinger.application.matsci.anharmonic.
SeqData
(start, step, n_points)¶ Bases:
tuple
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__contains__
¶ Return key in self.
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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__len__
¶ Return len(self).
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count
(value) → integer -- return number of occurrences of value¶
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index
(value[, start[, stop]]) → integer -- return first index of value.¶ Raises ValueError if the value is not present.
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n_points
¶ Alias for field number 2
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start
¶ Alias for field number 0
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step
¶ Alias for field number 1
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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: Returns: the sequence data
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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
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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
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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
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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
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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
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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
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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: Returns: the structure
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exception
schrodinger.application.matsci.anharmonic.
AnharmonicException
¶ Bases:
Exception
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__init__
¶ Initialize self. See help(type(self)) for accurate signature.
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args
¶
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with_traceback
()¶ Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.
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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
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__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
- st (
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runFrequencyJob
()¶ Run a Jaguar frequency job on the input structure.
Raises: AnharmonicException – if there is an issue
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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
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getExtendedFactors
()¶ Return the extended factors.
Return type: tuple Returns: the extended factors
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getRealNormalModes
()¶ Generator for normal modes with real frequencies.
Ytype: tuple Yield: the normal mode index, 1-based, and schrodinger.application.jaguar.results.NormalMode
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runSinglePointJobs
()¶ Run the Jaguar single point jobs from which to calculate the anharmonic potentials.
Raises: AnharmonicException – if there is an issue
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collectEnergies
()¶ Update self.potentials with the Jaguar single point energies.
Raises: AnharmonicException – if there is an issue
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collectFits
()¶ Update self.potentials with the anharmonic fit data.
Raises: AnharmonicException – if there is an issue
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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
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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
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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
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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
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collectAnharmonicFrequencies
()¶ Update self.potentials with the anharmonic frequencies in wavenumbers (cm^-1).
Raises: AnharmonicException – if there is an issue
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plotPotentials
()¶ Plot the potentials.
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logCoefficientsTable
()¶ Log coefficients table.
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logFrequencyTable
()¶ Log frequency table.
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run
()¶ Calculate the anharmonic potentials.
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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
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static
getBeta
(temperature)¶ Return beta.
Parameters: temperature (float) – the temperature in K Return type: float Returns: beta in 1/J
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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.
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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)
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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.
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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
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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
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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
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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
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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
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logLnQTable
(temperature, lnz_a_vibs, lnz_h_vibs)¶ Log lnQ table.
Parameters: temperature (float) – the temperature in K
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setJaguarThermo
()¶ Set the Jaguar thermo objects that will be anharmonically corrected.
Raises: AnharmonicException – if there is an issue
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run
()¶ Calculate the anharmonic partition function.
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__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
- st (
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collectAnharmonicFrequencies
()¶ Update self.potentials with the anharmonic frequencies in wavenumbers (cm^-1).
Raises: AnharmonicException – if there is an issue
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collectEnergies
()¶ Update self.potentials with the Jaguar single point energies.
Raises: AnharmonicException – if there is an issue
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collectFits
()¶ Update self.potentials with the anharmonic fit data.
Raises: AnharmonicException – if there is an issue
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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
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getExtendedFactors
()¶ Return the extended factors.
Return type: tuple Returns: the extended factors
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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
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getRealNormalModes
()¶ Generator for normal modes with real frequencies.
Ytype: tuple Yield: the normal mode index, 1-based, and schrodinger.application.jaguar.results.NormalMode
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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
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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
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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
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logCoefficientsTable
()¶ Log coefficients table.
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logFrequencyTable
()¶ Log frequency table.
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plotPotentials
()¶ Plot the potentials.
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runFrequencyJob
()¶ Run a Jaguar frequency job on the input structure.
Raises: AnharmonicException – if there is an issue
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runSinglePointJobs
()¶ Run the Jaguar single point jobs from which to calculate the anharmonic potentials.
Raises: AnharmonicException – if there is an issue
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static
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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
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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
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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
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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)
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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)
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getEnthalpy
(thermo)¶ Return the enthalpy.
Parameters: thermo (schrodinger.application.jaguar.results.ThermoCollection) – the thermo object Return type: float Returns: the enthalpy in kcal/mol
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__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
- st (
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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
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collectAnharmonicFrequencies
()¶ Update self.potentials with the anharmonic frequencies in wavenumbers (cm^-1).
Raises: AnharmonicException – if there is an issue
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collectEnergies
()¶ Update self.potentials with the Jaguar single point energies.
Raises: AnharmonicException – if there is an issue
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collectFits
()¶ Update self.potentials with the anharmonic fit data.
Raises: AnharmonicException – if there is an issue
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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
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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
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static
getBeta
(temperature)¶ Return beta.
Parameters: temperature (float) – the temperature in K Return type: float Returns: beta in 1/J
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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.
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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)
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getExtendedFactors
()¶ Return the extended factors.
Return type: tuple Returns: the extended factors
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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
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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
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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
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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.
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getRealNormalModes
()¶ Generator for normal modes with real frequencies.
Ytype: tuple Yield: the normal mode index, 1-based, and schrodinger.application.jaguar.results.NormalMode
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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
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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
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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
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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
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logCoefficientsTable
()¶ Log coefficients table.
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logFrequencyTable
()¶ Log frequency table.
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logLnQTable
(temperature, lnz_a_vibs, lnz_h_vibs)¶ Log lnQ table.
Parameters: temperature (float) – the temperature in K
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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
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plotPotentials
()¶ Plot the potentials.
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runFrequencyJob
()¶ Run a Jaguar frequency job on the input structure.
Raises: AnharmonicException – if there is an issue
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runSinglePointJobs
()¶ Run the Jaguar single point jobs from which to calculate the anharmonic potentials.
Raises: AnharmonicException – if there is an issue
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setJaguarThermo
()¶ Set the Jaguar thermo objects that will be anharmonically corrected.
Raises: AnharmonicException – if there is an issue
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logPropertyTable
(thermo)¶ Log property table.
Parameters: thermo (schrodinger.application.jaguar.results.ThermoCollection) – the thermo object
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run
()¶ Calculate the anharmonic thermochemical properties.
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