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SelectCellWithForm v1

Summary

Select a conventional cell with a specific form number, corresponding to the UB stored with the sample for this peaks works space.

See Also

FindUBUsingFFT, FindUBUsingIndexedPeaks, FindUBUsingLatticeParameters

Properties

Name	Direction	Type	Default	Description
PeaksWorkspace	InOut	IPeaksWorkspace	Mandatory	Input Peaks Workspace
FormNumber	Input	number	Mandatory	Form number for the desired cell
Apply	Input	boolean	False	Update UB and re-index the peaks
Tolerance	Input	number	0.12	Indexing Tolerance
NumIndexed	Output	number		The number of indexed peaks if apply==true.
AverageError	Output	number		The average HKL indexing error if apply==true.
AllowPermutations	Input	boolean	True	Allow permutations of conventional cells
TransformationMatrix	Output	dbl list		The transformation matrix

Description

Given a PeaksWorkspace with a UB matrix corresponding to a Niggli reduced cell, this algorithm will allow the user to select a conventional cell corresponding to a specific form number from the Mighell paper. If the apply flag is not set, the information about the selected cell will just be displayed. If the apply flag is set, the UB matrix associated with the sample in the PeaksWorkspace will be updated to a UB matrix corresponding to the selected cell AND the peaks will be re-indexed using the new UB matrix. The output transformation matrix \(M\) will change \(UB\) to \(UBM^{-1}\) and map each \((HKL)\) vector to \(M(HKL)\). It can be further used by the TransformHKL algorithm. NOTE: The possible conventional cells, together with the corresponding errors in the cell scalars can be seen by running the ShowPossibleCells algorithm, provided the stored UB matrix corresponds to a Niggli reduced cell.

This algorithm is based on the paper: Alan D. Mighell, Lattice Symmetry and Identification—The Fundamental Role of Reduced Cells in Materials Characterization. Journal of research of the National Institute of Standards and Technology 106.6 (2001): 983, available from: nvlpubs.

Usage

Example:

ws=LoadIsawPeaks("TOPAZ_3007.peaks")
FindUBUsingFFT(ws,MinD=8.0,MaxD=13.0)
print("Lattice before SelectCellWithForm:")
lattice = ws.sample().getOrientedLattice()
print(" ".join("{:.9f}".format(x) for x in [lattice.a(), lattice.b(), lattice.c(),
                                             lattice.alpha(), lattice.beta(), lattice.gamma()]))
SelectCellWithForm(PeaksWorkspace='ws', FormNumber=25, Apply=True)
print("\nLattice after SelectCellWithForm:")
lattice = ws.sample().getOrientedLattice()
print(" ".join("{:.9f}".format(x) for x in [lattice.a(), lattice.b(), lattice.c(),
                                             lattice.alpha(), lattice.beta(), lattice.gamma()]))

Output:

Lattice before SelectCellWithForm:
8.605818643 11.935925461 11.941812766 107.429088323 98.752912466 98.951193475

Lattice after SelectCellWithForm:
14.131051152 19.247332564 8.605818643 89.881170675 105.071333770 89.970386662

Categories: AlgorithmIndex | Crystal\Cell

Source

C++ header: SelectCellWithForm.h

C++ source: SelectCellWithForm.cpp