Table of Contents
Perform Rietveld or Pawley refinement of lattice parameters on a diffraction spectrum using GSAS-II scriptable API
Name | Direction | Type | Default | Description |
---|---|---|---|---|
RefinementMethod | Input | string | Pawley refinement | Refinement method (Rietvield or Pawley). Allowed values: [‘Pawley refinement’, ‘Rietveld refinement’] |
InputWorkspace | Input | Workspace | Mandatory | Workspace with spectra to fit peaks |
WorkspaceIndex | Input | number | 0 | Index of the spectrum in InputWorkspace to fit. By default, the first spectrum (ie the only one for a focused workspace) is used |
InstrumentFile | Input | string | Mandatory | Location of the phase file. Allowed extensions: [‘.prm’] |
PhaseInfoFiles | Input | list of str lists | Mandatory | Paths to each required phase file. Allowed extensions: [‘.cif’] |
PathToGSASII | Input | string | Mandatory | Path to the directory containing GSASII executable on the user’s machine |
XMin | Input | number | 0 | Minimum x value to use for refinement, in the same units as the input workspace. Leave blank to refine from the start of the data to XMax. Note, if PawleyDMin corresponds to a greater TOF value than this, then PawleyDMin is used |
XMax | Input | number | 0 | Maximum x value to use for refinement, in the same units as the input workspace. Leave blank to refine in the range XMin to the end of the data |
RefineSigma | Input | boolean | False | Whether to refine the sigma-1 profile coefficient |
RefineGamma | Input | boolean | False | Whether to refine the gamma-1 (called ‘X’ in GSAS-II) profile coefficient |
OutputWorkspace | Output | Workspace | Mandatory | Workspace with fitted peaks |
LatticeParameters | Output | TableWorkspace | LatticeParameters | Table to output the lattice parameters (refined) |
Rwp | Output | number | Weighted profile R factor (as a percentage) | |
Sigma | Output | number | Sigma-1 profile coefficient | |
Gamma | Output | number | Gamma-1 profile coefficient (called X in GSAS-II) | |
SaveGSASIIProjectFile | Input | string | Mandatory | GSASII Project to work on. Allowed extensions: [‘.gpx’] |
PawleyDMin | Input | number | 1 | For Pawley refiment: as defined in GSAS-II, the minimum d-spacing to be used in a Pawley refinement. Please refer to the GSAS-II documentation for full details. Note, if this corresponds to a TOF value less than XMin or the lowest TOF value in the data, the greatest of the 3 values is used as XMin |
PawleyNegativeWeight | Input | number | 0 | For Pawley refinement: as defined in GSAS-II, the weight for a penalty function applied during a Pawley refinement on resulting negative intensities. Please refer to the GSAS-II documentation for full details. |
MuteGSASII | Input | boolean | False | Set to True to prevent GSAS run info from being printed (not recommended, but can be useful for debugging) |
Warning
This algorithm requires GSAS-II to be installed on your computer. A version of GSAS-II containing the module GSASIIscriptable (added in April 2017) is required. See Installing_GSASII for how to get the correct version of GSAS-II.
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 two refinement methods: Pawley refinement and Rietveld refinement. 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.
The refinement methods of this algorithm are equivalent to the function “Calculate / Refine” from the main menu of the GSAS-II GUI.
The main inputs required are histogram data, an instrument definition parameter (in GSAS format, readable by GSAS-II), phase information and various parameters for the fitting/refinement process.
The phase information must be provided in CIF format
(Crystallographic Information File).
When phase information is available 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.
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 simultaneously 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).
On Windows, run either scripts\GSAS-II\install_gsas_latest.bat or scripts\GSAS-II\install_gsas_vetted.bat. Use the former for the latest version of GSAS-II and the latter for the most recent version to have been manually verified to work with GSASIIRefineFitPeaks. This will install GSAS-II to your current working drive (usually C) in a directory called g2conda.
On Linux, from scripts\GSAS-II run python install_gsas_proxy.py. Optionally, you can supply a desired revision number (defaults to the latest) with the -v flag and a directory (defaults to /) to install GSAS-II to with the -d flag.
References:
[LeBail2005] | Le Bail, A (2005). “Whole Powder Pattern Decomposition Methods and Applications: A Retrospection”. Powder Diffraction 20(4): 316-326. |
[TobyVonDreele2013] | Toby, B. H., & Von Dreele, R. B. (2013). “GSAS-II: the genesis of a modern open-source all purpose crystallography software package”. Journal of Applied Crystallography, 46(2), 544-549. |
[Toby2008] | Toby, B. H. (2008). “R factors in Rietveld analysis: How good is good enough?”. Powder Diffraction, 21(1), 67-70. |
Warning
Take these usage examples with a pinch of salt, as they are not tested for correctness on our servers, due to the requirement to have GSAS-II installed. Please contact the Mantid developers if something is awry.
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:
#
# ws_to_focus = 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')
peaks, lattice_params, rwp, sigma, gamma = \
GSASIIRefineFitPeaks(InputWorkspace=wks,
RefinementMethod="Pawley refinement",
InstrumentFile='template_ENGINX_241391_236516_North_bank.prm',
PhaseInfoFiles='Fe-alpha.cif,Fe-gamma.cif',
PathToGSASII='/home/user/g2conda/GSASII',
RefineSigma=True,
RefineGamma=True,
SaveGSASIIProjectFile='example_gsas2_project.gpx',
OutputWorkspace="FittedPeaks")
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_params.row(0)))
print("Sigma={}, Gamma={}".format(sigma, gamma))
Output:
Weighted profile R-factor (Rwp): 77.75515
Lattice parameters, a: 2.8665, b: 2.8665, c: 2.8665, alpha: 90.0, beta: 90.0, gamma: 90.0, Volume: 23.554
Sigma=81.0939, Gamma=0.1855
Example - Rietveld refinement of lattice parameters from a diffraction spectrum
wks=Load('focused_bank1_ENGINX00256663.nxs')
peaks, lattice_params, rwp, sigma, gamma = \
GSASIIRefineFitPeaks(InputWorkspace=wks,
RefinementMethod='Rietveld refinement',
InstrumentFile='template_ENGINX_241391_236516_North_bank.prm',
PhaseInfoFiles='Fe-alpha.cif,Fe-gamma.cif',
PathToGSASII='/home/user/g2conda/GSASII',
SaveGSASIIProjectFile='example_gsas2_project.gpx',
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_params.row(0)))
print("Sigma={}, Gamma={}".format(sigma, gamma))
Output:
Weighted profile R-factor (Rwp): 77.75499
Lattice parameters, a: 2.8665, b: 2.8665, c: 2.8665, alpha: 90.0, beta: 90.0, gamma: 90.0, Volume: 23.554
Sigma=81.0939, Gamma=0.1855
Categories: Algorithm Index | Diffraction\Engineering | Diffraction\Fitting
Python: GSASIIRefineFitPeaks.py (last modified: 2018-10-05)