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Lachlan M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for Single Crystal and Powder Diffraction) Depa

Tricks and hints for using Alan Larson and Bob von Dreele's GSAS, and Brian Toby's EXPGUI, for combined X-ray / Neutron refinement and restrained Rietveld refinement of large polymeric inorganics and minerals. Lachlan M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for

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Lachlan M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for Single Crystal and Powder Diffraction) Depa

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  1. Tricks and hints for using Alan Larson and Bob von Dreele's GSAS, and Brian Toby's EXPGUI, for combined X-ray / Neutron refinement and restrained Rietveld refinement of large polymeric inorganics and minerals. Lachlan M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for Single Crystal and Powder Diffraction) Department of Crystallography; Birkbeck College, University of London, Malet Street, Bloomsbury, London, WC1E 7HX, UK. E-mail:l.m.d.cranswick@dl.ac.uk WWW:http://www.ccp14.ac.uk

  2. Hand Written Notes Free Zonethey are on the webhttp://www.ccp14.ac.uk/poster-talks/korea2002b/ AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  3. Talk Aims • Provide hints on performing restrained Rietveld refinement of large inorganics using GSAS including: • Data conversion • Histogram weighting • Charge Balance Restraints • Total cell composition restraints • Bond length restraints • Bond angle restraints • Using Platon and WinGX to help validate the structure AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  4. Topics Discussed • Converting Madsen and Hill VCT data and x,y,weight column data into GSAS format • Using Brian Toby’s EXPGUI as a primary interface into GSAS • Hints on using GSAS for combined X-ray / Neutron refinement • Hints on GSAS Rietveld for restrained refinement of large inorganic polymeric framework structrures • Using macros in GSAS AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  5. An initial point - computer skills • When doing complicated (and not so complicated crystallography and powder diffraction), it is assumed the user has good general computer skills. • General program installation and configuration • Good text editing skills • Having multiple programs open and interacting between them • Cut and paste using both mouse and keyboard speed keys. AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  6. GSAS • by Bob von Dreele and Alan Larson - ftp://ftp.lanl.gov/public/gsas/ • CCP14 based resources: • http://www.ccp14.ac.uk/solution/gsas/ • What may look like minor changes can result in ability to handle what were intractable problems. AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  7. GSAS: Some Relevant Background • by Bob von Dreele and Alan Larson • Menu based control • Available for Windows / DOS / Linux / SGI • Separate GUI by Brian Toby (EXPGUI) • Combined X-ray / Neutron / Single Crystal / Powder Diffraction • Integrated Fourier map generation and viewing • Restraints • Bond angle • Bond length • Planar • Total Chemistry / charge balance • Chiral volume • Phi/psi group • Torsion angle • Manual Marquadt damping • Atom shift limits • Lots of other features AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  8. Brian Toby’s EXPGUI Interface for GSAS User friendlier to start using GSAS via EXPGUI (A new combined installer makes it very easy to start using GSAS.) http://www.ncnr.nist.gov/programs/crystallography/software/expgui/expgui_intro.html AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  9. Brian Toby’s EXPGUI:Easy to start a new refinement(1 of 13) • Run EXPGUI and go to the required directory and enter a new filename (in this case pbso4) and press “read”. When prompted, then press the “Create” icon AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  10. Brian Toby’s EXPGUI:Easy to start a new refinement(2 of 13) • When prompted, enter an experimental title then press the “Set” icon. AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  11. Brian Toby’s EXPGUI:Easy to start a new refinement(3 of 13) • Click on the “Phase” tab and then the “Add Phase” Icon. Input the cell and spacegroup information • (or import structure from Powder Cell *.cel, CIF, GSAS, MSI *.xtl, Platon *.spf) AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  12. Brian Toby’s EXPGUI:Easy to start a new refinement(4 of 13) • Click “Add” then “Continue” to the cell and spacegroup information to be incorporated into GSAS. AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  13. Brian Toby’s EXPGUI:Easy to start a new refinement(5 of 13) • Click “Add New Atoms” and add in the starting model either by hand or importing a PowderCell format file. AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  14. Brian Toby’s EXPGUI:Easy to start a new refinement(6 of 13) • Click “Add Atoms” to get the starting model into GSAS AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  15. Brian Toby’s EXPGUI:Easy to start a new refinement(7 of 13) • Set appropriate damping factors (I tend to like somewhere between 7 and 9) • (Lessen damping factors if parameter shifts are too small) AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  16. Bob von Dreele’s comments on Damping “Damping - I never use damping in any of my refinements unless I actually need it. There is an option in the LS print menu for listing the "summary table of shift/esd" that is helpful for identifying ocsillating parameters. One should first try no damping and then use it only where necessary. Invoking it early can cause trouble. Another option for atom positions is to "limit the shift" to 0.5A or whatever to keep an early refinement from going off base.” AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  17. Brian Toby’s EXPGUI:Easy to start a new refinement(8 of 13) • Add the first XRD diffraction file:Select “Histogram” tab then “Add New Histogram” icon. AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  18. Brian Toby’s EXPGUI:Easy to start a new refinement(9 of 13) • Via the GUI, select the data file and the instrument parameter file. (in this case an XRD data file) AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  19. Brian Toby’s EXPGUI:Easy to start a new refinement(10 of 13) • Click “Add” to add the XRD file into GSAS. Change the damping factors and fix up any incorrect diffractometer constants (I.e., the parameter file may have incorrect information in it) AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  20. Note from Bob von Dreele on POLA Typically iparm files will have "incorrect" POLA values. You might suggest "good" values for graphite monochromators. • Thus while calculated values can be determined, experimentally determined values may be recommended. Not only for laboratory systems, but also synchrotron data where ideal values might be assumed. • In this case using cubic annealed Y2O3 (10.6Å - IA3) AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  21. POLA for your Diffractometer and graphite monochromator • POLA correlates with thermals so be careful checking how robust the resulting value is. (following is determined using annealed Y2O3) AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  22. Another way: POLA, IPOLA and diffracted beam graphite monochromator • Set IPOLA to 1 (POLA should now be cos2 2 of the monochromator.) • In the case of Graphite 002 reflection: 2 = 26.603 (d=3.3480Å). cos2 2=0.80 • Mainly due to problems such as mosaic spread - POLA refines on this diffractometer (again using annealed Y2O3) to 0.911 AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  23. Brian Toby’s EXPGUI:Easy to start a new refinement(11 of 13) • It is easy to add another data file. Select the “Add New Histogram” icon. (select the Bank number if this is relevant) AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  24. Brian Toby’s EXPGUI:Easy to start a new refinement(12 of 13) • Click “Add” to add the second XRD file into GSAS.Again, change the damping factors and fix up any incorrect diffractometer constants (I.e., the parameter file may have incorrect information in it) AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  25. Brian Toby’s EXPGUI:Easy to start a new refinement(13 of 13) • Now you are ready to run Powpref and Genles and start refining the various “relevant” parameters • Under Profile, Powder XRD data might be happier being fitted with a type 3 profile function: • pseudo-Voight with Finger Cox Jephcoat peak asymmetry correction • One extra hint for Bragg-Brentano XRD users - sample displacement parameter is “shft” in the profile options (is preferable to use this instead of “zero offset”) AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  26. Note from Bob von Dreele on shft “Choice of "shft" vs "ZERO" is most important. Diffractometers are aligned to make ZERO=0.000 and the sample is "never" in the right place to make shft=0.0. So always refine shft for Bragg-Brentano data. Synchrotron data is different as the zero can be off and other systematic effects will look like "shft" or "trns". If sample is transparent on B-B diffractometers (especially pharmaceuticals!) then trns should be refined.” AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  27. Brian Toby’s EXPGUI:Profile Screen in EXPGUI with shft AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  28. Estimated Standard Deviations (ESD) vs Standard Deviations • An ESD is the estimated uncertainty derived from a “single measurement”. • A Standard Deviation is an uncertainty obtained from collecting “multiple measurements”. • Rietveld programs ESDs are fine as ESDs go, but they can under estimate “probable error”. • If you want to know what the “Standard Deviation” is, multiple sample preparation, packing and collection of the data a statistically valid number of times is a way to proceed. • It helps if you refine the appropriate parameters. AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  29. Unit-cell “a-axis” parameter of monoclinic zirconia collected repetitively and refining zero offset • Each sample was packed separately and run for a structure refinement quality dataset; Cu Tube, 15 to 154 at 0.025 step size on a Philips 3050/X’pert Bragg Bretano powder diffractometer. AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  30. Rietveld ESD on Unit cell parameter vs the standard deviation from multiple packings and measurements • Rietveld ESD on the “a” unit-cell parameter: 0.00007 • Standard Deviation on the “a” unit-cell parameter:0.00023 • Standard deviation from multiple measurements is over 3 times the estimated standard deviation (ESD) from a single measurement • The IUCr (International Union of Crystallography) has defined various units including “standard uncertainties” but common nomenclature is being used here. AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  31. Unit-cell “a-axis” parameter of monoclinic zirconia collected repetitively and refining sample displacement • Each sample was packed separately and run for a structure refinement quality dataset; Cu Tube, 15 to 154 at 0.025 step size on a Philips 3050/X’pert Bragg Bretano powder diffractometer. AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  32. Rietveld ESD on Unit cell parameter vs the standard deviation from multiple packings and measurements • Rietveld ESD on the “a” unit-cell parameter: 0.00008 • Standard Deviation on the “a” unit-cell parameter:0.00008 • Standard deviation from multiple measurements is not significantly different from the estimated standard deviation (ESD) of a single measurement • However, you can still get problems with accuracy due to misalignment in different powder diffractometers. • Two theta offset should be a constant of the diffractometer • Sample displacement should vary with each inserted sample • Never refine both two-theta and sample displacement AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  33. Brian Toby’s EXPGUI:Writing your own importing options • EXPGUI: customization notes on the web at • http://www.ncnr.nist.gov/programs/crystallography/software/expgui/expgui_cfg.html • Copy over an existing import script and edit it to work with your new data format in tcl/tk. AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  34. New(ish) Features in Brian Toby’s EXPGUI • Graphically define the background • Graphically exclude regions • Can export structures to Cif/Shelx/Platon format (Addsym, etc) / MSI *.xtl formats AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  35. Brian Toby’s EXPGUI:Graphically Defining the Background(1 of 3) • After powpref, select “powder, bkgedit” and use point and click with the mouse to select background points AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  36. Brian Toby’s EXPGUI:Graphically Defining the Background(2 of 3) • Use the Fit icon to fit a Chebyshev function through the data points - increase number of terms as required AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  37. Brian Toby’s EXPGUI:Graphically Defining the Background(3 of 3) • Save into EXP file. Background is now fixed but can be refined at the click of a button. Done. AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  38. Brian Toby’s EXPGUI:Graphically Excluding Regions(1 of 3) • After powpref “and” genles (0 cycles just to perform a “calculation”), select “powder, excledt” AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  39. Brian Toby’s EXPGUI:Graphically Excluding Regions(2 of 3) • Point and click to select excluded regions AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  40. Brian Toby’s EXPGUI:Graphically Excluding Regions(3 of 3) • Run powpref and genles for this to take effect AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  41. Brian Toby’s EXPGUI: If things go beserk: Backtracking through previous runs to when before things went beserk. • Select “File, Open” and the “Include Archived Files” AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  42. Brian Toby’s EXPGUI: Le Bail fitting to get the whole profile fit the data before structure refinement • Various tricks may be required. • Fix the “Scale Factor”. It is meaningless to refine the scale factor when doing a Le Bail fit. • Brian Toby trick: Run zero cycles until the intensities roughly match before releasing any other parameters (peak profile, unit cell, zero offset) • Fit the background manually with Chebyshev coefficients within bkgedt instead of refining the background. This can save you a lot of pain • Running Powpref resets the Le Bail intensities and you have to turn off all parameters and rematch the intensities with the pattern : so you would normally avoid doing this unless you make a change to the “spacegroup” or other relevant parameters such as the “peak cutoff” AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  43. Brian Toby’s EXPGUI: Why Isn’t this Synchrotron data fitting? - 1 • Important to know the instrumental and synchrotron beamline constants AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  44. Brian Toby’s EXPGUI: Why Isn’t this Synchrotron data fitting? - 2 • Polarization is incorrect - is zero instead of ~1 (0.9 to 1) • Reset all synchrotron data sets / histograms to the correct value • The beamline should determine this parameter for users AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  45. Brian Toby’s EXPGUI: Why Isn’t this Synchrotron data fitting? - 3 • With roughly correct polarization value (set at 1), things are looking better (need to get the accurate value) AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  46. GSAS and example ceramic / polymeric inorganic problem In this example, a perovskite based ceramic relevant to the wireless communications and the mobile phone industry (High Q ferroelectric) • >120 atoms in R3 • >320 atoms in C1 • 54 possible “split occupancy” framework metal sites • 54 possible atom / vacancy interstitial sites • 162 oxygen sites • >1600 bond restraints • >200 atom constraints • >150 atoms linked within a single constraint AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  47. GSAS and example ceramic / polymeric inorganic problem: chronic peak overlap • Structure is Pseudo Cubic • a=b=c= 23.9 Å • Chronic peak overlap • No non-overlapping reflections • Screen image from EXPGUI shows some HKLs matching to some “LOW ANGLE” peaks. • Shift Left mouse button in Expgui’s Liveplot AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  48. Will be concentrating on HOW to using GSAS for this type of problem • Often hear that a program can handle a problem. • But often is not obvious or obscure how to go about using a program. • This will be concentrating on the “HOW”. • Structure is presently unpublished and only 99.9% finished • Ian Grey of CSIRO Australia or Bob Roth of NIST USA would be more appropriate to talk about the crystal chemistry and the structure itself. AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  49. Nuances and People Involved in this structure • Lead by Ian Grey (CSIRO, Melbourne Australia) and Bob Roth (NIST, Gaithersburg, USA) • Synthesis: Bob Roth and Julia Chan (NIST, Gaithersburg) (is ~3 months of work and furnace time to synthesize a decent size batch of sample) • TEM: Igor Levin (NIST, Gaithersburg) (looks like microdomain twinning problems) • Single Crystal Work: Gus Mumme and Ian Grey (CSIRO, Melbourne) (looks like microdomain twinning problems) • Powder Indexing / Le Bail fitting for looking at cell and spacegroup: Lachlan Cranswick (done at Columbia University) (Crysfire/Chekcell/Rietica) • Structure Solution: Ian Grey and Gus Mumme (CSIRO, Melbourne) • Atom Ordering: Gus Mumme and Ian Grey (CSIRO, Melbourne) • Tilt Model: Ian Grey and Gus Mumme (CSIRO, Melbourne) • Basic structure from chemical crystallographic arguments • Starting atom ordering model from Shelxl and CSRIET structure refinement • (Complex tilt model obtained from refining the perovskite subcell and looking at the Fourier difference map for peaks giving an indication of tilt directions and magnitudes) • GSAS Structure Refinement: Lachlan Cranswick (done at Columbia University) • New single crystal work based on GSAS Refined structure: Ian Grey and Pierre Bordet AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

  50. Is GSAS the only effective program for large restrained inorganic Rietveld Refinements(?) • Ability to handle very large arrays not the only issue • Controllable - via a menu / scripting system amenable to scripting and automation • Large variety of restraints • Restraints can be disabled but still used for diagnostic purposes • Can easily disable/enable restraints and histograms (cyclic refinement instead of combined X-ray / Neutron refinement) AGU 2002: “hints and tricks for using GSAS Rietveld” Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

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