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LoadSassena v1

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Summary

load a Sassena output file into a group workspace.

Properties

Name	Direction	Type	Default	Description
Filename	Input	string	Mandatory	A Sassena file. Allowed extensions: [‘.h5’, ‘.hd5’]
OutputWorkspace	Output	Workspace	Mandatory	The name of the group workspace to be created.
TimeUnit	Input	number	1	The Time unit in between data points, in picoseconds. Default is 1.0 picosec.
SortByQVectors	Input	boolean	True	Sort structure factors by increasing momentum transfer?

Description

The Sassena application 1 generates intermediate scattering factors from molecular dynamics trajectories. This algorithm reads Sassena output and stores all data in workspaces of type Workspace2D, grouped under a single WorkspaceGroup.

Sassena output files are in HDF5 format 2, and can be made up of the following datasets: qvectors, fq, fq0, fq2, and fqt

Time units: Current Sassena version does not specify the time unit, thus the user is required to enter the time in between consecutive data points. Enter the number of picoseconds separating consecutive datapoints.

The workspace for qvectors:

• X-values for the origin of the vector, default: (0,0,0)

• Y-values for the tip of the vector

• one spectra with three bins for each q-vector, one bin per vector component. If orientational average was performed by Sassena, then only the first component is non-zero.

The workspaces for fq, fq0, and fq2 contains two spectra:

• First spectrum is the real part, second spectrum is the imaginary part

• X-values contain the moduli of the q vector

• Y-values contain the structure factors

Dataset fqt is split into two workspaces, one for the real part and the other for the imaginary part. The structure of these two workspaces is the same:

• X-values contain the time variable

• Y-values contain the structure factors

• one spectra for each q-vector

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.

ws = LoadSassena("loadSassenaExample.h5", TimeUnit=1.0)
print('workspaces instantiated:  {}'.format(', '.join(ws.getNames())))
fqtReal = ws[1] # Real part of F(Q,t)
# Let's fit it to a Gaussian. We start with an initial guess
intensity = 0.5
center = 0.0
sigma = 200.0
startX = -900.0
endX = 900.0
myFunc = 'name=Gaussian,Height={0},PeakCentre={1},Sigma={2}'.format(intensity,center,sigma)

# Call the Fit algorithm and perform the fit
fit_output = Fit(Function=myFunc, InputWorkspace=fqtReal, WorkspaceIndex=0, StartX = startX, EndX=endX, Output='fit')
paramTable = fit_output.OutputParameters  # table containing the optimal fit parameters
fitWorkspace = fit_output.OutputWorkspace

print("The fit was: {}".format(fit_output.OutputStatus))
print("Fitted Height value is: {:.2f}".format(paramTable.column(1)[0]))
print("Fitted centre value is: {:.2f}".format(abs(paramTable.column(1)[1])))
print("Fitted sigma value is: {:.1f}".format(paramTable.column(1)[2]))
# fitWorkspace contains the data, the calculated and the difference patterns
print("Number of spectra in fitWorkspace is: {}".format(fitWorkspace.getNumberHistograms()))
print("The 989th y-value of the fitted curve: {:.3f}".format(fitWorkspace.readY(1)[989]))

Output:

workspaces instantiated:  ws_qvectors, ws_fqt.Re, ws_fqt.Im
The fit was: success
Fitted Height value is: 1.00
Fitted centre value is: 0.00
Fitted sigma value is: 100.0
Number of spectra in fitWorkspace is: 3
The 989th y-value of the fitted curve: 0.673

Categories: AlgorithmIndex | DataHandling\Sassena

Source

C++ header: LoadSassena.h

C++ source: LoadSassena.cpp