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OptimizeCrystalPlacement v1¶

../_images/ImageNotFound.png — Enable screenshots using DOCS_SCREENSHOTS in CMake¶

Summary ¶

This algorithm optimizes goniometer settings and sample orientation to better index the peaks.

Properties ¶

Name	Direction	Type	Default	Description
PeaksWorkspace	Input	PeaksWorkspace	Mandatory	Workspace of Peaks with UB loaded
KeepGoniometerFixedfor	Input	int list		List of run Numbers for which the goniometer settings will NOT be changed
ModifiedPeaksWorkspace	Output	PeaksWorkspace	Mandatory	Output Workspace of Peaks with optimized sample Orientations
FitInfoTable	Output	TableWorkspace	FitInfoTable	Workspace of Results
AdjustSampleOffsets	Input	boolean	False	If true sample offsets will be adjusted to give better fits, otherwise they will be fixed as zero(def=true)
OptimizeGoniometerTilt	Input	boolean	False	Set true if main error is due to a tilted Goniometer(def=false)
Chi2overDoF	Output	number		chi squared over dof
nPeaks	Output	number		Number of Peaks Used
nParams	Output	number		Number of Parameters fit
nIndexed	Output	number		Number of new Peaks that WOULD be indexed at ‘MaxIndexingError’
MaxAngularChange	Input	number	5	Max offset in degrees from current settings(def=5)
MaxIndexingError	Input	number	0.15	Use only peaks whose fractional hkl values are below this tolerance(def=0.15)
MaxHKLPeaks2Use	Input	number	-1	If less than 0 all peaks are used, otherwise only peaks whose h,k, and l values are below the level are used(def=-1)
MaxSamplePositionChangeMeters	Input	number	0.0005	Maximum Change in Sample position in meters(def=.0005)
OutputNormalisedCovarianceMatrixOptX	Output	TableWorkspace	CovarianceInfo	The name of the TableWorkspace in which to store the final covariance matrix

This algorithm basically optimizes h,k, and l offsets from an integer by varying the parameters sample positions, sample orientations ( chi,phi, and omega), and/or the tilt of the goniometer for an experiment.

If the crystal orientation matrix, UB, was created from one run, that run may not need to have its goniometer settings optimized. There is a property to list the run numbers to NOT have their goniometer settings changed. This entry is IGNORED if the tilt or sample positions are included in the optimization. In this case NONE of the goniometer angles, relative to any tilt, will be changed.

The goniometer angles displayed are relative to the tilt,i,e, phi is the rotation around the axis perpendicular to the tilted plane. The resultant PeaksWorkspace has the goniometer angles relative to the Y and Z axes at that time.

The crystal orientation matrix, UB matrix, from the PeaksWorkspace should index all the runs “very well”. Otherwise iterations that slowly build a UB matrix with corrected sample orientations may be needed.

The parameters for the tilt are GRotx, GRoty, and GRotz in degrees. The usage for this information is as follows:

\(rotate(x,GRotx)*rotate(y,GRoty)*rotate(z,GRotz)* SampleOrientation\) \(( i.e. omegaRot*chiRot*phiRot)).\)

Note: To optimize by the tilt in the goniometer and then by the angles or by the sample position, it is possible to run with one optimization, then using the resultant PeaksWorkspace for input, run another optimization.

Rerunning the same optimization with the result is also a good idea. If the first guess is very close, the optimize algorithm does try cases far away and may not get back to the best value. Check the chisquared values. If they increase, that optimization should probably not be used.

Usage ¶

Example:

ws=LoadIsawPeaks("TOPAZ_3007.peaks")
LoadIsawUB(ws,"TOPAZ_3007.mat")
wsd = OptimizeCrystalPlacement(ws)
(wsPeakOut,fitInfoTable,chi2overDoF,nPeaks,nParams,nIndexed,covrianceInfoTable) = OptimizeCrystalPlacement(ws,AdjustSampleOffsets=True)
print("Chi2: {:.4f}".format(chi2overDoF))