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SimulatedDensityOfStates v1

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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

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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