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SelectCellOfType v1

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Summary

Select a conventional cell with a specific lattice type and centering, 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

CellType

Input

string

Cubic

The conventional cell type to use. Allowed values: [‘Cubic’, ‘Hexagonal’, ‘Rhombohedral’, ‘Tetragonal’, ‘Orthorhombic’, ‘Monoclinic’, ‘Triclinic’]

Centering

Input

string

P

The centering for the conventional cell. Allowed values: [‘F’, ‘I’, ‘C’, ‘P’, ‘R’]

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 with a specified cell type and centering. 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 SelectCellOfType:")
lattice = ws.sample().getOrientedLattice()
print(" ".join("{:.9f}".format(x) for x in [lattice.a(), lattice.b(), lattice.c(),
                                             lattice.alpha(), lattice.beta(), lattice.gamma()]))
SelectCellOfType(PeaksWorkspace=ws, CellType='Monoclinic', Centering='C', Apply=True)
print("\nLattice after SelectCellOfType:")
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 SelectCellOfType:
8.605818643 11.935925461 11.941812766 107.429088323 98.752912466 98.951193475

Lattice after SelectCellOfType:
14.131051152 19.247332564 8.605818643 89.881170675 105.071333770 89.970386662

Categories: AlgorithmIndex | Crystal\Cell

Source

C++ header: SelectCellOfType.h

C++ source: SelectCellOfType.cpp