schrodinger.application.matsci.anharmonic module¶

Utilities for the anharmonic corrections workflow.

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

Bases: tuple

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, x_values=None)¶

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

schrodinger.application.matsci.anharmonic.get_normal_modes(jagout, max_i_freq=- inf)¶

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)

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

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, robust=False)¶

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, robust=False)¶

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
robust (bool) – If True, use the robust Jaguar driver to run Jaguar jobs. If False, use Jaguar directly.

getJaguarJob(base_name, input_name)¶

Get the job to run Jaguar with the given job base name and input name. The job will run either Jaguar directly or the robust Jaguar driver based on the current robust setting.

Parameters

base_name (str) – The base name of this job
input_name (str) – The name of the input file

Return type

jobutils.RobustSubmissionJob

Returns

The job (suitable for JobDJ that will run Jaguar

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

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

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

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, robust=False)¶

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

setDivergencies()¶: Set divergencies.

run()¶: Calculate the anharmonic partition function.

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, robust=False)¶

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

getZeroPointEnergy()¶

Return the zero point energy.

Return type: float
Returns: the zero point 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

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

logZeroPointEnergy()¶: Log zero point energy.

logPropertyTable(thermo)¶

Log property table.

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

run()¶: Calculate the anharmonic thermochemical properties.