GSASIIRefineFitPeaks v1¶

Summary¶

Uses GSAS-II (powder diffraction and structure modules) to perform whole pattern refinement of lattice parameters (or fit peaks) on an diffraction spectrum

Properties¶

Description¶

Uses GSAS-II [TobyVonDreele2013] as external software to fit peaks to a powder / engineering diffraction pattern. Here the process of peak fitting is in the context of Rietveld / Pawley / Le Bail analysis [LeBail2005]

The algorithm supports three refinement or fitting methods: Pawley refinement, Rietveld refinement, and single peak fitting (or “Peaks List” of GSAS-II). The first two methods of this algorithm implement whole diffraction pattern fitting whereas the third method fits peaks individually. The use of this algorithm is very close to the examples described in these two GSAS-II tutorials: Rietveld fitting / CW Neutron Powder fit for Yttrium-Iron Garnet, and Getting started / Fitting individual peaks & autoindexing, The functionality of this algorithm is based on the powder calculation module and the structure routines of GSAS-II.

To run this algorithm GSAS-II must be installed and it must be available for importing from the Mantid Python interpreter. This algorithm requires a modified version of GSAS-II. Please contact the developers for details.

The methods “Pawley refinement” and “Rietveld refinement” of this algorithm are equivalent to the function “Calculate / Refine” from the main menu of the GSAS-II GUI. The method “Peak fitting” is equivalent to the “Peak Fitting / Peak fit” action of the “Peaks List” window menu of the GSAS-II GUI.

The main inputs required are histogram data, an instrument definition parameter (in GSAS format, readable by GSAS-II), and various parameters for the fitting/refinement process. Phase information is also required to use the Pawley and Rietveld refinement.

The phase information must be provided in CIF format (Crystallographic Information File). When phase information is available and the Rietveld/Pawley method is used the algorithm will output the lattice parameters in a table workspace. The values are given for the the full set of lattice parameters (three lattice constants, three angles, and volume in this sequence: a, b, c, alpha, beta, gamma, volume). The a,b, and c values are given in Angstroms (). The angles are given in degrees, and the volume in .

The algorithm provides goodness-of-fit estimates in the outputs GoF and Rwp or weighted profile R-factor [Toby2008]. The Rwp is given as a percentage value.

Note that the option to save the GSAS-II project file (SaveGSASIIProjectFile) is mandatory. This is a requirement of GSAS-II. These project files can be opened in the GSAS-II GUI for further processing and analysis of the data.

When Pawley refinement is selected as refinement method the flag for histogram scale factor refinement is disabled, as recommended in the GSAS-II documentation, as this cannot be refined simultaenously with the Pawley reflection intensities.

The GSAS-II Rietveld/Pawley refinement process writes lattice parameters and extensive additional information in an output file with the same name as the output GSAS-II project file but with extension ”.lst”. This is noted in a log message that specifies where the file has been written (next to the output project file).

When fitting individual peaks using the peak fitting method (not using Rietveld/Pawley refinement), the algorithm only supports peaks with shape of type back-to-back exponential convoluted with pseudo-voigt (BackToBackExponentialPV). It is possible to enable the refinement of the different function parameters via several properties (RefineAlpha, RefineSigma, etc.). The fitted peak parameters are given in an output table with as many rows as peaks have been found. The columns of the table give the parameters fitted, similarly to the information found in the “Peaks List” window of the GSAS-II GUI. These results are printed in the log messages as well.

For fitting single peaks, one at a time, see also EnggFitPeaks. For other algorithms that implement different variants of whole diffraction pattern refinement and fitting see also PawleyFit and LeBailFit.

References:

Usage¶

Example - Pawley refinement of lattice parameters from a diffraction spectrum

# You would normally generate the focused file using the Engg GUI or,
# alternatively, with commands like these:
#
# wks = Load('ENGINX00256663-256675')
# wks_ceria = Load('ENGINX00255924')
# wks_vana = Load('ENGINX00254854')
# # Using default expected peaks for Ceria
# difa, difc, tzero, peaks_tbl = EnggCalibrate(InputWorkspace=wks_ceria, VanadiumWorkspace=wks_vana, Bank='North')
# wks_focused = EnggFocus(InputWorkspace=wks, VanadiumWorkspace=wks_vana, Bank='North')
# SaveNexus(InputWorkspace=wks_focused, Filename='focused_bank1_ENGINX00256663.nxs')
#
wks=Load('focused_bank1_ENGINX00256663.nxs')
GoF, Rwp, lattice_tbl = GSASIIRefineFitPeaks(InputWorkspace=wks,
                                             InstrumentFile='ENGINX_255924_254854_North_bank.par',
                                             PhaseInfoFile='FE_ALPHA.cif',
                                             PathToGSASII='/home/user/gsas',
                                             SaveGSASIIProjectFile='example_gsas2_project',
                                             LatticeParameters='lattice_tbl')
print "Goodness of fit coefficient: {0:.5f}".format(GoF)
print "Weighted profile R-factor (Rwp): {0:.5f}".format(Rwp)
print ("Lattice parameters, a: {a}, b: {b}, c: {c}, alpha: {alpha}, beta: {beta}, gamma: {gamma}, "
       "Volume: {volume:.3f}".format(**lattice_tbl.row(0)))

Output:

Goodness of fit coefficient: 3.63591
Weighted profile R-factor (Rwp): 77.27831
Lattice parameters, a: 2.8665, b: 2.8665, c: 2.8665, alpha: 90.0, beta: 90.0, gamma: 90.0, Volume: 23.554

Example - Rietveld refinement of lattice parameters from a diffraction spectrum

wks=Load('focused_bank1_ENGINX00256663.nxs')
GoF, Rwp, lattice_tbl = GSASIIRefineFitPeaks(InputWorkspace=wks,
                                             Method='Rietveld refinement',
                                             InstrumentFile='ENGINX_255924_254854_North_bank.par',
                                             PhaseInfoFile='FE_ALPHA.cif',
                                             PathToGSASII='/home/user/gsas',
                                             SaveGSASIIProjectFile='example_gsas2_project',
                                             LatticeParameters='lattice_tbl')
print "Goodness of fit coefficient: {0:.5f}".format(GoF)
print "Weighted profile R-factor (Rwp): {0:.5f}".format(Rwp)
print ("Lattice parameters, a: {a}, b: {b}, c: {c}, alpha: {alpha}, beta: {beta}, gamma: {gamma}, "
       "Volume: {volume:.3f}".format(**lattice_tbl.row(0)))

Output:

Goodness of fit coefficient: 3.62483
Weighted profile R-factor (Rwp): 77.03530
Lattice parameters, a: 2.8665, b: 2.8665, c: 2.8665, alpha: 90.0, beta: 90.0, gamma: 90.0, Volume: 23.554

Example - Fit several peaks from a diffraction spectrum

wks=Load('focused_bank1_ENGINX00256663.nxs')
params_tbl_name = 'tbl_fitted_params'
GoF, Rwp, lattice_tbl = GSASIIRefineFitPeaks(InputWorkspace=wks,
                                             Method='Peak fitting',
                                             FittedPeakParameters=params_tbl_name,
                                             InstrumentFile='ENGINX_255924_254854_North_bank.par',
                                             PhaseInfoFile='FE_ALPHA.cif',
                                             PathToGSASII='/home/user/mantid-repos/gsas',
                                             SaveGSASIIProjectFile='test_gsas2_project',
                                             FittedPeakParameters=params_tbl_name)
tbl_fitted_params = mtd[params_tbl_name]
print "Fitted {0} peaks.".format(tbl_fitted_params.rowCount())
print ("Parameters of the first peak. Center: {Center:.6g}, intensity: {Intensity:.5f}, "
       "alpha: {Alpha:.5f}, beta: {Beta:.5f}, sigma: {Sigma:.5f}, gamma: {Gamma:.5f}".
       format(**tbl_fitted_params.row(0)))

Output:

Fitted 18 peaks.
Parameters of the first peak. Center: 38563.8, intensity: 26.22137, alpha: 0.13125, beta: 0.01990, sigma: 125475.11036, gamma: -6681.38965

Categories: Algorithms | Diffraction\Engineering | Diffraction\Fitting

Source¶

Python: GSASIIRefineFitPeaks.py