RefineSingleCrystalGoniometer v1

Summary

Refines the UB-matrix and goniometer offsets simultaneously.This improves the indexing of the peaks for those cases when there is sample misorientation.

Properties

Name	Direction	Type	Default	Description
Peaks	Input	PeaksWorkspace	Mandatory	The PeaksWorkspace to be refined.
Tolerance	Input	number	0.12	The tolerance used in IndexPeaks.
Cell	Input	string	Triclinic	The cell type to optimize. Must be one of: {Fixed, Cubic, Rhombohedral, Tetragonal,Hexagonal, Orthorhombic, Monoclinic, Triclinic}. Allowed values: [‘Fixed’, ‘Cubic’, ‘Rhombohedral’, ‘Tetragonal’, ‘Hexagonal’, ‘Orthorhombic’, ‘Monoclinic’, ‘Triclinic’]
NumIterations	Input	number	1	The number of IndexPeaks iterations.
LargeOffset	Input	boolean	False	If True, index each run independently with FindUBUsingFFT (robust to large/unreliable goniometer offsets) instead of a single IndexPeaks pass across all runs using the existing UB. Runs whose independently-indexed lattice constants are inconsistent with the other runs are logged and excluded before refinement.
MinD	Input	number	1	Minimum d-spacing passed to FindUBUsingFFT. Only used when LargeOffset=True.
MaxD	Input	number	15	Maximum d-spacing passed to FindUBUsingFFT. Only used when LargeOffset=True.
LatticeOutlierTolerance	Input	number	5	Number of median-absolute-deviations a run’s independently-indexed lattice constants (a, b, c, alpha, beta, gamma) may differ from the across-run median before that run is excluded. Only used when LargeOffset=True.

Description

The purpose of this algorithm is to improve the indexing of peaks in special cases where FindUBUsingIndexedPeaks does not index all peaks due to sample misorientation.

The example below demonstrates a case where FindUBUsingIndexedPeaks is insufficient:

from mantid.simpleapi import *
import matplotlib.pyplot as plt
import numpy as np

from scipy.spatial.transform import Rotation
import scipy.optimize

filename = '/SNS/TOPAZ/IPTS-33878/shared/RFMBA2PbI4/RFMBA2PbI4_mantid_295K_find_peaks/RFMBA2PbI4_Monoclinic_P_5sig.integrate'
LoadIsawPeaks(Filename=filename, OutputWorkspace='peaks')

FindUBUsingIndexedPeaks(PeaksWorkspace='peaks', Tolerance=0.12)
IndexPeaks(PeaksWorkspace='peaks', Tolerance=0.12)

This code will only index about half of the peaks.

The solution is to use this algorithm that refines the UB-matrix and goniometer offsets simultaneously.

from mantid.simpleapi import mtd, RefineSingleCrystalGoniometer, LoadIsawPeaks, FindUBUsingIndexedPeaks, IndexPeaks

filename = "/SNS/TOPAZ/IPTS-33878/shared/RFMBA2PbI4/RFMBA2PbI4_mantid_295K_find_peaks/RFMBA2PbI4_Monoclinic_P_5sig.integrate"

LoadIsawPeaks(Filename=filename, OutputWorkspace="peaks")
FindUBUsingIndexedPeaks(PeaksWorkspace="peaks")
IndexPeaks(PeaksWorkspace="peaks", CommonUBForAll=True)

RefineSingleCrystalGoniometer("peaks", tol=0.25, cell="Monoclinic", n_iter=5)
IndexPeaks(PeaksWorkspace="peaks", CommonUBForAll=True)

This will result in a better indexing of the peaks.

Large or unreliable goniometer offsets

When the goniometer offset is large enough (or the motor readback is unreliable enough) that no single UB can index more than a handful of peaks across all runs, set LargeOffset=True. Each run is then indexed independently with FindUBUsingFFT (which does not depend on the existing orientation) before the UB and goniometer offsets are refined jointly as above. Runs whose independently-indexed lattice constants (a, b, c, alpha, beta, gamma) are inconsistent with the other runs are logged and excluded, since an inconsistent cell usually indicates a bad per-run indexing rather than a real difference in the sample.

from mantid.simpleapi import RefineSingleCrystalGoniometer, LoadIsawPeaks, IndexPeaks

filename = "/SNS/TOPAZ/IPTS-33878/shared/unreliable_motors/peaks.nxs"

LoadIsawPeaks(Filename=filename, OutputWorkspace="peaks")

RefineSingleCrystalGoniometer(
    Peaks="peaks",
    Tolerance=0.12,
    Cell="Triclinic",
    NumIterations=8,
    LargeOffset=True,
    MinD=5,
    MaxD=15,
)
IndexPeaks(PeaksWorkspace="peaks", CommonUBForAll=True)

Categories: AlgorithmIndex | Crystal\Fitting

Source

Python: RefineSingleCrystalGoniometer.py