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__
(key, /)¶ Return key in self.
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__len__
()¶ Return len(self).
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count
(value, /)¶ Return number of occurrences of value.
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index
(value, start=0, stop=9223372036854775807, /)¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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, x_values=None)[source]¶ 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
x_values (list or None) – if not None then contains x values for points to show in the plot
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schrodinger.application.matsci.anharmonic.
get_normal_modes
(jagout, max_i_freq=- inf)[source]¶ Return the normal modes from the given JaguarOutput.
- Parameters
jagout (schrodinger.application.jaguar.output.JaguarOutput) – the Jaguar output object
max_i_freq (float) – tolerate small imaginary frequencies less than this value in wavenumbers (cm^-1)
- Return type
list
- Returns
contains pair tuples, (normal mode index (1-based), schrodinger.application.jaguar.results.NormalMode)
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schrodinger.application.matsci.anharmonic.
check_imaginary_frequencies
(jag_out, jag_in, max_i_freq=0)[source]¶ 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)[source]¶ 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
[source]¶ Bases:
Exception
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__init__
(*args, **kwargs)¶ 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)[source]¶ 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)[source]¶ 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 directlyjagout_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
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runFrequencyJob
()[source]¶ Run a Jaguar frequency job on the input structure.
- Raises
AnharmonicException – if there is an issue
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static
getFactors
(factor_data)[source]¶ 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
()[source]¶ Return the extended factors.
- Return type
tuple
- Returns
the extended factors
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runSinglePointJobs
()[source]¶ Run the Jaguar single point jobs from which to calculate the anharmonic potentials.
- Raises
AnharmonicException – if there is an issue
-
collectEnergies
()[source]¶ Update self.potentials with the Jaguar single point energies.
- Raises
AnharmonicException – if there is an issue
-
getEnergies
(idx)[source]¶ Return the energies (Hartree) used to build the potential for the given normal mode.
- Parameters
idx (int) – the normal mode index, 1-based
- Raises
AnharmonicException – if there is an issue
- Return type
list
- Returns
the energies
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collectFits
()[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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
()[source]¶ Update self.potentials with the anharmonic frequencies in wavenumbers (cm^-1).
- Raises
AnharmonicException – if there is an issue
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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)[source]¶ Bases:
schrodinger.application.matsci.anharmonic.AnharmonicPotentials
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static
getBeta
(temperature)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ Log lnQ table.
- Parameters
temperature (float) – the temperature in K
-
__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 directlyjagout_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
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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
-
getEnergies
(idx)¶ Return the energies (Hartree) used to build the potential for the given normal mode.
- Parameters
idx (int) – the normal mode index, 1-based
- Raises
AnharmonicException – if there is an issue
- Return type
list
- Returns
the energies
-
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
-
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
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logCoefficientsTable
()¶ Log coefficients table.
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logFrequencyTable
()¶ Log frequency table.
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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
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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)[source]¶ Bases:
schrodinger.application.matsci.anharmonic.AnharmonicPartitionFunction
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getVibrationalTemperature
(idx)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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)[source]¶ 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 directlyjagout_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)
-
getEnergies
(idx)¶ Return the energies (Hartree) used to build the potential for the given normal mode.
- Parameters
idx (int) – the normal mode index, 1-based
- Raises
AnharmonicException – if there is an issue
- Return type
list
- Returns
the energies
-
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)[source]¶ 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.
-
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
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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
-
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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setDivergencies
()¶ Set divergencies.
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logPropertyTable
(thermo)[source]¶ Log property table.
- Parameters
thermo (schrodinger.application.jaguar.results.ThermoCollection) – the thermo object
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