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SimulatedDensityOfStates v1

Summary

Calculates phonon densities of states, Raman and IR spectrum.

Properties

Name	Direction	Type	Default	Description
CASTEPFile	Input	string		Filename of the CASTEP file. Allowed values: [‘castep’]
PHONONFile	Input	string		Filename of the PHONON file. Allowed values: [‘phonon’]
ForceConstantsFile	Input	string		Allowed extensions: [‘.castep_bin’, ‘.json’, ‘.yaml’]
ForceConstantsSampling	Input	number	20	Real-space cutoff in Angstrom for Brillouin zone sampling.
Function	Input	string	Gaussian	Type of function to fit to peaks. Allowed values: [‘Gaussian’, ‘Lorentzian’]
PeakWidth	Input	string	10.0	Set Gaussian/Lorentzian FWHM for broadening. Default is 10
SpectrumType	Input	string	DOS	Type of intensities to extract and model (fundamentals-only) from .phonon. Allowed values: [‘IonTable’, ‘DOS’, ‘IR_Active’, ‘Raman_Active’, ‘BondTable’]
CalculateIonIndices	Input	boolean	False	Calculates the individual index of all Ions in the simulated data.
StickHeight	Input	number	0.01	Intensity of peaks in stick diagram.
Scale	Input	number	1	Scale the intesity by the given factor. Default is no scaling.
BinWidth	Input	number	1	Set histogram resolution for binning (eV or cm**-1). Default is 1
Temperature	Input	number	300	Temperature to use (in raman spectrum modelling). Default is 300
ZeroThreshold	Input	number	3	Ignore frequencies below the this threshold. Default is 3.0
Ions	Input	str list		List of Ions to use to calculate partial density of states.If left blank, total density of states will be calculated
SumContributions	Input	boolean	False	Sum the partial density of states into a single workspace.
ScaleByCrossSection	Input	string	None	Sum the partial density of states by the scattering cross section. Allowed values: [‘None’, ‘Total’, ‘Incoherent’, ‘Coherent’]
OutputWorkspace	Output	Workspace	Mandatory	Name to give the output workspace.

Description

Calculates phonon densities of states, Raman and IR spectrum from the output of CASTEP code obtained in the form of .phonon and .castep files.

The PeakWidth property may be passed a function containing the variable “energy” (e.g. 0.1*energy) to set the FWHM of the peak as a function of the energy (centre point of the peak). This can be useful for comparison with experimental data by allowing the peak width to change according to the resolution of the instrument.

If the IonTable spectrum type is used then the output workspace will be a table workspace containing each ion that is present in a .phonon file.

If the BondTable spectrum type is used then the output workspace will be a table workspace containing details of the bonds defined in the .castep file.

Workflow

Usage

Note

To run these usage examples please first download the usage data, and add these to your path. In Mantid this is done using Manage User Directories.

Example - loading data from phonon & castep files:

# Loading the same data from a castep and phonon file
phonon_ws = SimulatedDensityOfStates(PHONONFile='squaricn.phonon')
castep_ws = SimulatedDensityOfStates(CASTEPFile='squaricn.castep')
result = CompareWorkspaces(phonon_ws, castep_ws)

print(result[0])

Output:

True

Example - loading partial contributions of ions:

squaricn = SimulatedDensityOfStates(PHONONFile='squaricn.phonon',
                                    Ions=['H', 'C', 'O'])

for name in squaricn.getNames():
  print(name)

Output:

squaricn_H
squaricn_C
squaricn_O

Example - loading summed partial contributions of ions:

sum_ws = SimulatedDensityOfStates(PHONONFile='squaricn.phonon',
                                  Ions=['H', 'C', 'O'],
                                  SumContributions=True)
total_ws = SimulatedDensityOfStates(PHONONFile='squaricn.phonon')

print(CompareWorkspaces(total_ws, sum_ws, Tolerance=1e-12)[0])

Output:

True

Example - Getting the list of ions in a phonon file:

ion_ws = SimulatedDensityOfStates(PHONONFile='squaricn.phonon',
                                  SpectrumType='IonTable')
print(', '.join(ion_ws.column('Species')))

Output:

H, H, H, H, C, C, C, C, C, C, C, C, O, O, O, O, O, O, O, O

Categories: AlgorithmIndex | Simulation

Source

Python: SimulatedDensityOfStates.py