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SaveHKL v1

Summary

Save a PeaksWorkspace to a ASCII .hkl file.

See Also

LoadHKL, SaveHKLCW

Properties

Name	Direction	Type	Default	Description
InputWorkspace	Input	PeaksWorkspace	Mandatory	An input PeaksWorkspace.
ScalePeaks	Input	number	1	Multiply FSQ and sig(FSQ) by scaleFactor
MinDSpacing	Input	number	0	Minimum d-spacing (Angstroms)
MinWavelength	Input	number	0	Minimum wavelength (Angstroms)
MaxWavelength	Input	number	100	Maximum wavelength (Angstroms)
AppendFile	Input	boolean	False	Append to file if true. Use same corrections as file. If false, new file (default).
ApplyAnvredCorrections	Input	boolean	False	Apply anvred corrections to peaks if true. If false, no corrections during save (default).
LinearScatteringCoef	Input	number	Optional	Linear scattering coefficient in 1/cm if not set with SetSampleMaterial
LinearAbsorptionCoef	Input	number	Optional	Linear absorption coefficient at 1.8 Angstroms in 1/cm if not set with SetSampleMaterial
Radius	Input	number	Optional	Radius of the sample in centimeters
PowerLambda	Input	number	4	Power of lambda
SpectraFile	Input	string		Spectrum data read from a spectrum file. Allowed extensions: [‘.dat’]
Filename	Input	string	Mandatory	Path to an hkl file to save. Allowed extensions: [‘.hkl’]
SortBy	Input	string		Sort the histograms by bank, run number or both (default). Allowed values: [‘Bank’, ‘RunNumber’, ‘’]
MinIsigI	Input	number	Optional	The minimum I/sig(I) ratio
WidthBorder	Input	number	Optional	Width of border of detectors
MinIntensity	Input	number	Optional	The minimum Intensity
OutputWorkspace	Output	PeaksWorkspace	SaveHKLOutput	Output PeaksWorkspace
HKLDecimalPlaces	Input	number	Optional	Number of decimal places for fractional HKL. Default is integer HKL.
DirectionCosines	Input	boolean	False	Extra columns (22 total) in file if true for direction cosines. If false, original 14 columns (default).
UBFilename	Input	string		Path to an ISAW-style UB matrix text file only needed for DirectionCosines if workspace does not have lattice. Allowed extensions: [‘.mat’, ‘.ub’, ‘.txt’]

Description

SaveHKL outputs the peaks with corrections applied in a format that works successfully in GSAS and SHELX. Peaks that have not been integrated and also peaks that were not indexed are removed.

hklFile.write(‘%4d%4d%4d%8.2f%8.2f%4d%8.4f%7.4f%7d%7d%7.4f%4d%9.5f%9.4f\n’% (H, K, L, FSQ, SIGFSQ, hstnum, WL, TBAR, CURHST, SEQNUM, TRANSMISSION, DN, TWOTH, DSP))

HKL is flipped by -1 due to different q convention in ISAW vs Mantid.

FSQ = integrated intensity of peak (scaled)

SIGFSQ = sigma from integrating peak

hstnum = number of sample orientation (starting at 1)

WL = wavelength of peak

TBAR = output of absorption correction (-log(transmission)/mu)

CURHST = run number of sample

SEQNUM = peak number (unique number for each peak in file)

TRANSMISSION = output of absorption correction (exp(-mu*tbar))

DN = detector bank number

TWOTH = two-theta scattering angle

DSP = d-Spacing of peak (Angstroms)/TR

Last line must have all 0’s

Direction cosines are required for certain absorption and extinction corrections. They are calculated according to [1] and are the dot products of the scattered and reverse incident beam directions with the direction of the reciprocal lattice vectors. The components are interleaved starting with the reverse incident part.

Usage

Example - a simple example of running SaveHKL.

import os

path = os.path.join(os.path.expanduser("~"), "MyPeaks.hkl")

#load a peaks workspace from file
peaks = LoadIsawPeaks(Filename=r'Peaks5637.integrate')
SaveHKL(peaks, path)

print(os.path.isfile(path))

Output:

True

Example - an example of running SaveHKL with sorting and filtering options.

import os

#load a peaks workspace from file
peaks = LoadIsawPeaks(Filename=r'Peaks5637.integrate')
print("Number of peaks in table {}".format(peaks.rowCount()))

path = os.path.join(os.path.expanduser("~"), "MyPeaks.hkl")
SaveHKL(peaks, path, MinWavelength=0.5, MaxWavelength=2, MinDSpacing=0.2, SortBy='Bank')

peaks = LoadHKL(path)
print("Number of peaks in table {}".format(peaks.rowCount()))

Output:

Number of peaks in table 434
Number of peaks in table 234

Example - SaveHKL with shape from SetSample

import os
path = os.path.join(os.path.expanduser("~"), "MyPeaks.hkl")

# load a peaks workspace from file
peaks = LoadIsawPeaks(Filename=r'SXD23767.peaks')
SetSample(peaks,
          Geometry={'Shape': 'Cylinder', 'Height': 4.0,
                    'Radius': 0.8,
                    'Center': [0.,0.,0.]},
          Material={'ChemicalFormula': 'V', 'SampleNumberDensity': 0.1})
SaveHKL(peaks, path)
print(os.path.isfile(path))

Output:

True

References

[1]

1. Katrusiak, Absorption Correction for Crystal-Environment Attachments from Direction Cosines, Zeitschrift für Kristallographie - Crystalline Materials, 216 (2001) 646–647. doi: 10.1524/zkri.216.12.646.22488

Categories: AlgorithmIndex | Crystal\DataHandling | DataHandling\Text

Source

C++ header: SaveHKL.h

C++ source: SaveHKL.cpp