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LinkedUBs v1

../_images/LinkedUBs-v1_dlg.png

LinkedUBs dialog.

Summary

Links the indexing of a given run to the UB of a reference run. PredictedPeaks should be calculated via goniometer rotation of the reference UB. Use of this algorithm will result in a seperate (linked) UB for each goniometer setting considered.

Properties

Name Direction Type Default Description
QTolerance Input number 0.5 Radius of isotropic q envelope to search within.
QDecrement Input number 0.95 Multiplicative factor by which to decrement q envelope on each iteration.
DTolerance Input number 0.01 Observed peak is linked if abs(dSpacing) < dPredicted + dTolerance.
NumPeaks Input number 15 Number of peaks, ordered from highest to lowest dSpacing to consider.
PeakIncrement Input number 10 Number of peaks to add to numPeaks on each iteration.
Iterations Input number 10 Number of cycles of refinement.
a Input number 1 Lattice parameter a.
b Input number 1 Lattice parameter b.
c Input number 1 Lattice parameter c.
alpha Input number 90 Lattice parameter alpha.
beta Input number 90 Lattice parameter beta.
gamma Input number 90 Lattice parameter gamma.
MinWavelength Input number 0.8 Minimum wavelength for LinkedPredictedPeaks.
MaxWavelength Input number 9.3 Maximum wavelength for LinkedPredictedPeaks.
MinDSpacing Input number 0.6 Minimum dSpacing for LinkedPredictedPeaks.
MaxDSpacing Input number 20 Maximum dSpacing for LinkedPredictedPeaks.
ReflectionCondition Input string Primitive Reflection condition for LinkedPredictedPeaks. Allowed values: [‘Primitive’, ‘C-face centred’, ‘A-face centred’, ‘B-face centred’, ‘Body centred’, ‘All-face centred’, ‘Rhombohedrally centred, obverse’, ‘Rhombohedrally centred, reverse’, ‘Hexagonally centred, reverse’]
Workspace Input Workspace Mandatory Instrument workspace on which observed peaks are defined.
ObservedPeaks Input TableWorkspace Mandatory FindPeaks table to which PredictedPeaks are compared.
PredictedPeaks Input TableWorkspace Mandatory PredictedPeaks table to which ObservedPeaks are compared.
LinkedPeaks Output TableWorkspace Mandatory Linked peaks: UB matrix consistent with that of PredictedPeaks.
LinkedPredictedPeaks Output TableWorkspace Mandatory LinkedPredictedPeaks: UB matrix consistent with PredictedPeaks.
DeleteWorkspace Input boolean False Delete workspace after execution for memory management.

Description

Given an initial UB at some goniometer configuration, this algorithm facilitates the ‘linking’ of the UBs across orientations - in other words, ensuring the continuity of the indexing of reflections throughout reciprocal space allowing for grouping of reflections and refinement.

On chopper instruments, when the sample is lowered into the blockhouse there is often no possibility to adjust its position. When rotating the crystal via the goniometer, since the crystal is likely not centred exactly, the predicted peaks from the initial UB often do not capture the data. As well as consistently indexing the peaks, the algorithm also effectively carries out a U matrix correction that accounts for sample miscentering. Use of this algorithm will result in a seperate UB matrix for each orientation which can then be used for integration.

The algorithm requires a set of predicted peaks that have been generated from the initial UB via goniometer rotation, a set of observed (found) peaks, and the lattice parameters in order to calculate the B matrix. A search within a Q-envelope is carried out in which all peaks within the envelope are screened as potential ‘matches’ to the observed peaks by comparing dspacing values.

This approach works well in simple cases, but for large unit cells and modulated structures where lots of peaks with small and similar dspacings appear, it is useful to make use of the NumPeaks parameter. This sorts the predicted peaks from largest to smallest dspacing and defines which peaks are used for the first cycle. As the refinement of the UB is carried out, more peaks at shorter d are added, encoded by the PeakIncrement parameter. This adds a defined number of peaks after each cycle.

The main limitation of this approach is that the lattice parameters of the sample should be known accurately. It is recommended that at least 10 iterations are carried out, but in cases where the crystal is well centred and the goniometer angles are known accurately fewer iterations are necessary.

Useage

Example:

# WISH single crystal
# demonstration of linkedUBs algorithm on D10 Ruby (cyle 18/1)

from mantid.simpleapi import *

# lattice parameters
a = 4.764407
b = 4.76440
c = 13.037904
alpha = 90
beta = 90
gamma = 120

# parameters for PredictPeaks
MinDSpacing = 0.5
MaxDSpacing = 20
MinWavelength = 0.8
MaxWavelength = 9.3
ReflectionCondition='Primitive'

# parameters for LinkedUBs
QTolerance = 0.5
QDecrement = 0.95
DTolerance = 0.02
NumPeaks = 25
PeakIncrement = 10
Iterations = 10
DeleteWorkspace = False

# phi axis at omega = 270
u_phi_x, u_phi_y, u_phi_z = 0.58779, 0.80902, 0.0

# load and process 41598
LoadRaw(Filename='WISH00041598.raw', OutputWorkspace='WISH00041598')
CropWorkspace(InputWorkspace='WISH00041598', OutputWorkspace='WISH00041598', XMin=6000, XMax=99000)
ConvertUnits(InputWorkspace='WISH00041598', OutputWorkspace='WISH00041598', Target='dSpacing', ConvertFromPointData=False)

# load and process 41599
LoadRaw(Filename='WISH00041599.raw', OutputWorkspace='WISH00041599')
CropWorkspace(InputWorkspace='WISH00041599', OutputWorkspace='WISH00041599', XMin=6000, XMax=99000)
ConvertUnits(InputWorkspace='WISH00041599', OutputWorkspace='WISH00041599', Target='dSpacing', ConvertFromPointData=False)

# find peaks on 41598 and 41599
FindSXPeaks(InputWorkspace='WISH00041598', PeakFindingStrategy='AllPeaks', ResolutionStrategy='AbsoluteResolution', XResolution=0.2, PhiResolution=2, TwoThetaResolution=2, OutputWorkspace='WISH00041598_find_peaks')

FindSXPeaks(InputWorkspace='WISH00041599', PeakFindingStrategy='AllPeaks', ResolutionStrategy='AbsoluteResolution', XResolution=0.2, PhiResolution=2, TwoThetaResolution=2, OutputWorkspace='WISH00041599_find_peaks')

# find and optimise UB on 41598 using lattice parameters
FindUBUsingLatticeParameters(PeaksWorkspace='WISH00041598_find_peaks', a=a, b=b, c=c, alpha=alpha, beta=beta, gamma=gamma, NumInitial=10, Tolerance=0.1, Iterations=10)

PredictPeaks(InputWorkspace='WISH00041598_find_peaks', WavelengthMin=MinWavelength, WavelengthMax=MaxWavelength, MinDSpacing=MinDSpacing, ReflectionCondition=ReflectionCondition, OutputWorkspace='WISH00041598_predict_peaks')

OptimizeLatticeForCellType(PeaksWorkspace='WISH00041598_predict_peaks', CellType='Hexagonal', Apply=True)

CopySample(InputWorkspace='WISH00041598_predict_peaks', OutputWorkspace='WISH00041598', CopyName=False, CopyMaterial=False, CopyEnvironment=False, CopyShape=False)

# set gonio on 41598 and predict the peaks of 41599
SetGoniometer(Workspace='WISH00041598', Axis0='0,0,1,0,1', Axis1='25,{},{},{},-1'.format(u_phi_x, u_phi_y, u_phi_z))
PredictPeaks(InputWorkspace='WISH00041598', WavelengthMin=MinWavelength, WavelengthMax=MaxWavelength, MinDSpacing=MinDSpacing, ReflectionCondition=ReflectionCondition, OutputWorkspace='WISH00041599_predict_peaks')

# linkedUBs
LinkedUBs(QTolerance=QTolerance,
          QDecrement=QDecrement,
          DTolerance=DTolerance,
          NumPeaks=NumPeaks,
          PeakIncrement=PeakIncrement,
          Iterations=Iterations,
          a=a,
          b=b,
          c=c,
          alpha=alpha,
          beta=beta,
          gamma=gamma,
          MinWavelength=MinWavelength,
          MaxWavelength=MaxWavelength,
          MinDSpacing=MinDSpacing,
          MaxDSpacing=MaxDSpacing,
          ReflectionCondition=ReflectionCondition,
          Workspace='WISH00041599',
          ObservedPeaks='WISH00041599_find_peaks',
          PredictedPeaks='WISH00041599_predict_peaks',
          LinkedPeaks='WISH00041599_linked_peaks',
          LinkedPredictedPeaks='WISH00041599_linked_peaks_predicted',
          DeleteWorkspace=DeleteWorkspace)

Categories: AlgorithmIndex | Diffraction\Reduction

Source

Python: LinkedUBs.py (last modified: 2020-08-26)