1. SIG_9.1: Crystallographic Computing: Advanced Computational Tools for Small Molecules and Materials (Monday, 27th August 2001) New features in existing powder diffraction software to help battle ever more complex crystallographic problems. L. 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. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 2 Talk Aims Show that within a year there have been developments in many freely available powder diffraction programs to enable the tacking of more complex / difficult / tedious powder diffraction and crystallographic problems. Demonstrate how some of this functionality can make the difference and possibly help put your intractable problems from the “intractable bin” into the “doable folder”. Show that what might be considered superficial software modifications can make a major impact to assist in solving intractable problems.

3. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 3 Notes Free Zone - they are on the web http://www.ccp14.ac.uk/poster-talks/ecm2001/

4. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 4 A snapshot of programs (can’t do justice to all the updates in freely available software) Chekcell Powder Indexing Tool Rietica Rietveld for mass Le Bail fitting to obtaining cell volumes and follow reactions GSAS Rietveld for restrained refinement of large inorganic polymeric framework structrures Platon’s Addsym for finding higher symmetry in polymeric inorganics - from a) initial hand built models and b) Rietveld refined structures

5. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 5 New features in Chekcell and Rietica Chekcell –http://www.ccp14.ac.uk/tutorial/lmgp/ –New: Incorporates Ton Spek and A. Meetsma’s Le Page *** (the new addition that can really count) sub-cell / super-cell searching –New: GUI Cell transformation –New: Misc bug fixes improving usability and reliability Rietica Rietveld –http://www.rietica.org/ –New: Easy to use mass Le Bail fitting of angular and energy dispersive data –All files are ASCII Files –Handles alpha 1 /alpha 2 (if relevant) –Flexible : can manually edit Le Bail HKL files to add or remove HKLs and change intensities of individual HKLs

6. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 6 New features in Chekcell and Rietica Why Bother? Project headed by Professor Dave Walker of the Lamont-Doherty Earth Observatory of Columbia University, New York, USA Use energy dispersive X-ray diffraction; and high pressure / high temperature phase transitions to help determine the volume of Oxygen at high pressure and temperature (~550°C and 2 to 9 GPa). Then see if the volume this has interesting implications for Oxygen being involved in the Earth’s Outer Core

7. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 7 New Features in Chekcell and Rietica: What do we need from the diffraction data? Accurate Unit Cell volumes to obtain the “equations of state” of the phases of interest (how the volume of the phases change with pressure and temperature) T - RbClO 4  B2-RbCl + 2O 2 4 R-KClO3 = 3 O-KClO4 + B2-KCl O-KClO4 = B2-KCl + 2 O2 O 2 from the differences in the unit cell volumes

8. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 8 Problems that need to be overcome by (Crysfire); Chekcell and Rietica Energy Dispersive Diffraction setup and calibration can be very ad-hoc and problematic Possible Detector instability over short time spans Possible long term non- linearity of the detector (more neurotic of these problems only obvious when doing whole pattern Le Bail fitting)

9. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 9 Problems that need to be overcome by (Crysfire); Chekcell and Rietica Poor resolution data with multiple sources of spurious peaks Phase transitions give unknown cells Got to track how diffraction patterns are changing through the experiments Experimental configuration of the “Walker Cell”

10. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 10 Problems that need to be overcome by (XFIT, Crysfire, Refcel, UNITCELL); Chekcell and Rietica (No Struggle - No Joy!) Overlapping multi-phase powder patterns Large amounts of raw diffraction data! (collecting 3 patterns each 5 to 300 seconds) Intensities are near meaningless –no incident intensity spectrum –particle statistics problems –preferred orientation problems –X-ray absorption

11. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 11 Graphical Interpretation of powder indexing results Full Windows Graphical User Interface (GUI) Automatic Cell searching and spacegroup assignment Sorting lists of trial cells based on several criteria Reads the following raw powder diffraction file formats: – Bruker RAW, Philips RD, RIET7 and CPI Reads the following peak files: –Bruker DIF, Philip DI, XFIT TXT, Winfit DAT, Column format, Crysfire CDT Reads Crysfire Summary SUM files. As well as Crysfire summary files produced for the individual indexing programs: –dicvol, ito, treor, taup, lzon, fjzn, kohl Chekcell - Jean Laugier and Bernard Bochu http://www.ccp14.ac.uk/tutorial/lmgp/

12. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 12 Open a data file (optional if you only have a peak listing) Routine operation of Chekcell (1 of 5)

13. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 13 Routine operation of Chekcell (2 of 5) Open the peak listing (In this case generated by the XFIT program)

14. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 14 Routine operation of Chekcell (3 of 5) Import the Crysfire summary file listing of found trial cells.

15. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 15 Routine operation of Chekcell (4 of 5) Play with the list of trial cells and spacegroups and hopefully obtain a good cell that is also the “true” cell.

16. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 16 Routine operation of Chekcell (4 of 5) Automatic Cell and Spacegroup searching –can trudge through a single selected unitcell; or over 1000s of trial cells looking for the best cell and spacegroup combination based on parsimony of extra reflections criteria.

17. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 17 Chekcell: Major new feature of Chekcell Porting and “integration” of Ton Spek and A. Meetsma’s Le Page Obtaining the Reduced Cell –which many powder indexing programs to not reliably determined –Refer: "'Reduced Cells', M.J. Buerger, (Zeitschift fur Kristallographie, BD 109, S. 42-60 (1957)” Efficient Sub-cell and super-cell searching, then easy reviewing of newly derived cells within the Chekcell interface

18. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 18 Chekcell: GUI Cell transformation Easily transform cells and test them withing Chekcell Knows about common transformations Can manually look at sub-cells and super-cells

19. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 19 Chekcell: result of using Le Page An example: Orthorhombic cell with good FOM (Figure of Merit) Le Page combined with automatic “Best Solution” easily finds a better hexagonal cell based on parsimony of extra reflections criteria

20. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 20 1. Chekcell: indexing unknown cells from unexpected phase transitions in high pressure experiments While quality of Energy Dispersive diffraction data is low: indexing is doable thanks to Crysfire and Chekcell. Due to LePage, can have more confidence in finding a good cell; and checking for other sub-cells and super-cells. In this screen image, a new monoclinic cell has been found

21. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 21 2. Chekcell: re-indexing lost cells (maybe transformed) from big pressure jumps in high pressure experiments due to racing a synchrotron beam-dump. Can also use “expected volumes” as a guide in refinding cells. Re-found a monoclinic cell despite I/I20 = 19 (19 out of the 20 first peaks were indexed)

22. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 22 3. Chekcell: re-index again (big jumps due to trying to beat a synchrotron beam dump) Again, re-found a monoclinic cell despite I/I20 = 16! (only 16 out of the first 20 peaks were indexed) (With 23 starting peaks)

23. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 23 Chekcell / LePage Summary: These programs give you the maximum chance of indexing unknown unit-cells from powder diffraction data, even of low data quality.

24. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 24 Rietica Rietveld for Mass Le Bail fitting to get cell vol. Example of 3 phase setup : KClO3; KClO4, B2-KCl Easy to use and setup via GUI Le Bail is Structureless whole profile fitting - just need cell and spacegroup Easy to add and delete structures All files are ASCII files (Data, HKL and input file) which can edited manually if required or convenient Auto-marquardt damping for initial unstable refinement if required Impurities can be very obvious when Le Bail fitting

25. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 25 Rietica Rietveld for Mass Le Bail fitting : Rietica Database of Structure Can store structures and Le Bail derived unit cells at various pressures for later retrieval Add to the database at the click of a button Select from Database option with the Phase dialog box. When having 100s to 1000s of datasets, ease and speed are very important.

26. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 26 Rietica Rietveld for Mass Le Bail fitting At simplest: 3 step process after initial setup has been done Some beamlines give the option of converting into 2-theta space or refining native in KeV (2-theta can be convenient for using search match and related software) Le Bailing Sequence: 1. Copy over INP and HKL file (using windows explorer) 2. Perform whole profile LB fit 3. Access / plot results - (check need to add or delete phases) 4. Repeat above

27. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 27 Rietica Rietveld for Mass Le Bail fitting 1 of 10 Before the phase transition

28. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 28 Rietica Rietveld for Mass Le Bail fitting 2 of 10 In the phase transition No completely freestanding peak for KCl

29. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 29 Rietica Rietveld for Mass Le Bail fitting 3 of 10 Repeat as required No completely freestanding peak for KCl

30. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 30 Rietica Rietveld for Mass Le Bail fitting 4 of 10 Repeat as required No completely freestanding peak for KCl

31. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 31 Rietica Rietveld for Mass Le Bail fitting 5 of 10 Repeat as required Still no completely freestanding peak for KCl

32. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 32 Rietica Rietveld for Mass Le Bail fitting 6 of 10 Repeat as required

33. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 33 Rietica Rietveld for Mass Le Bail fitting 7 of 10 Repeat as required

34. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 34 Rietica Rietveld for Mass Le Bail fitting 8 of 10 Repeat as required

35. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 35 Rietica Rietveld for Mass Le Bail fitting 9 of 10 Repeat as required

36. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 36 Rietica Rietveld for Mass Le Bail fitting 10 of 10 Done!!!

37. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 37 Rietica Rietveld for Mass Le Bail :Graphing up the results Using Le Bail fittingUsing Traditional Methods

38. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 38 New Rietica Macro Language - RIET BASIC In theory, mass Le Bailing of the easy parts of a temperature / pressure run can be done in a fully automatic mode On present set of EDX data, have found it is best to not refine too quickly and instead continually check individual results and Le Bail fits.

39. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 39 1. Rietica and Le Bailing : Short-term non-linearities of an Energy Dispersive Detector(?) NaCl / Halite at Room Temperature and Pressure (thus is not crystal strain) Very nasty miss-fits on peak positions Possible short term non- linearity in the detector. Possible instability in the detector Combination of both - and more?

40. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 40 2. Rietica and Le Bailing : Short-term non-linearities of an Energy Dispersive Detector(?) Le Bail fitting Non-unit weighting of reflections Isotherm data of different temperatures colliding Inappropriate to use Le Bail fitting on this data Though Le Bail can detect these problems on the beam-line!! Traditional Unitcell refinement Unit weighting of reflections (over a wide KeV range - the data is “on average” linear) Isotherm data no longer overlapping

41. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 41 Chekcell and Rietica: results of the volume of Oxygen and the earth’s other core Energy Dispersive XRD: vol O 2 ~10 cc/mol Established vol O 2 from shockwave experiments: ~15 cc/mol (50% difference) –15 cc/mol means there cannot be Oxygen –10 cc/mol means there can be Oxygen and has implications for possible transport mechanisms between the lower mantle and outer core. Shockwave / Molecular Dynamics / Impulsively Stimulated Scattering Measurements (~15 cc/mol) vs Energy Dispersive Data (~10 cc/mol) beyond the scope of this talk

42. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 42 GSAS for large “restraint” Rietveld refinements of polymeric inorganics by Bob von Dreele and Alan Larsen - ftp://ftp.lanl.gov/public/gsas/ EXPGUI GSAS Graphical user interface by Brian Toby –http://www.ncnr.nist.gov/programs/crystall ography/software/expgui/ 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.

43. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 43 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

44. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 44 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.

45. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 45 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 98% finished Ian Grey or Gus Mumme of CSIRO Australia or Bob Roth of NIST USA would be more appropriate to talk about the crystal chemistry

46. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 46 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) (microdomain twinning problems) Single Crystal Work: Gus Mumme and Ian Grey (CSIRO, Melbourne) (microdomain twinning problems) Powder Indexing / Le Bail fitting : Lachlan Cranswick (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 (Columbia University)

47. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 47 GSAS: Some Relevant Background by Bob von Dreele and Alan Larsen 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

48. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 48 Is GSAS the only effective program for large restrained inorganic Rietveld Refinements(?) Ability to handle 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)

49. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 49 GSAS : YES! - at present the only effective Rietveld system for these types of large problems GSAS (by the Anna Karenina principle - a happy family): Can handle large numbers of atoms and restraints Large variety of restraints Menu based control amenable to scripts and automation Easy enabling and disable of histograms Integrated Fourier map including peak search TOF Neutron / EDX as well Other Rietveld Programs affected by one or more of the following problems Cannot handle large numbers of atoms or restraints Don’t have many types of restraints Manual editing of ASCII files or GUIs that do not easily allow quick changes to large numbers of atoms Problematic enabling and disabling of restrains and histograms No integrated Fourier map generation and viewing Can only handle constant wavelength neutron and angular dispersive X-ray diffraction data.

50. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 50 GSAS - relevant new features Weighting of individual histograms / powder patterns Larger arrays for atom constraints Larger arrays for total chemistry constraints Viewing of larger Fourier electron density contour maps Other misc. changes

51. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 51 GSAS: Individual Histogram Weighting You don’t always have a choice on data collection Thus may need to weight histograms such that they are roughly of equal weighting

52. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 52 GSAS: Individual Histogram Weighting In this example, you need to zoom up a bit. –XRD pattern is ~1500 times more intense than the corresponding neutron pattern –Problematic for combined refinement and setting restraints

53. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 53 GSAS: Individual Histogram Weighting (use Sum(w*d**2) as a guide) Set via EXPEDT (changing weight on Histogram 1 - XRD) –y !backup –p !powder prep –h !histograms –f 1 !weighting on hist 1 –.001 !set the weighting –x x x !exit expedt Run Powpref for new weighting to take effect

54. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 54 GSAS: If you DON’T Use Histogram Weighting X-ray 8.0% R(F**2)Neutron 28.1% R(F**2)

55. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 55 GSAS: If you DO Use Histogram Weighting X-ray 8.3% R(F**2)Neutron 11.7% R(F**2)

56. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 56 GSAS: Rod Hill and Ian Madsen VCT data collection If you do have a choice of data collection strategies for XRD - use variable count time (VCT) Commercial vendors partially to blame for only having obsolescent data collection options in their data logging software. Still may need to play with weighting of histograms for “fine” control of the combined refinement. VCT Fortran Source Code with references is available: http://www.ccp14.ac.uk/ccp/ccp14/ftp-mirror/csirominerals-anon-ftp/pub/xtallography/

57. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 57 Setting up a Restrained Rietveld refinement of > 300 atom polymeric inorganic structures in GSAS Initial problem is setting everything up and the control of the refinement. But need the flexibility to change as you may only find new information while refining the structure. (change of spacegroup being the most obvious) –Eric Dowty’s Cryscon can be very quick and effective for transforming structures from one cell and spacegroup to another. http://www.shapesoftware.com/#anchor_cryscon One solution is to use a spreadsheet program that allows for flexibility and extendability (MS-EXCEL for Windows)

58. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 58 Restrained refinement in GSAS: setting up an EXCEL spreadsheet CCP14 based tutorial and example files at : http://www.ccp14.ac.uk/solution/gsas/restrained_inorganic.html Create GSAS script commands in EXCEL and save into txt MACRO files for importing into GSAS. –(if applicable - model in arbitrary co-ordinates) –Structure co-ordinates (if applicable - generated from previous model) –Crystals (Watkin, Cooper, et al) structure co-ordinates for generating bond restraint lists for conversion by Scott Belmonte’s “coue” software into GSAS macro format. Crystals:http://www.xtl.ox.ac.uk/ Coue: http://www.ccp14.ac.uk/ccp/web-mirrors/scott-belmonte-software/ –Atom constraints –Total cell contents and/or charge balance constraints –If applicable, other scripts for controlling GSAS

59. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 59 GSAS: setting up an EXCEL spreadsheet: Example Atom Co-ordinates Calculate or import an atom list. Inputting the atom list via EXPEDT –k l a

60. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 60 GSAS: setting up an EXCEL spreadsheet: Input for Crystals to generate GSAS bond restraints lists Just use EXCEL “=“ commands to copy over values from GSAS atom list Got to keep the atom numbers the same as GSAS atoms controls are based on the atom numbers Inputting bond length restraints in EXPEDT: –k l s d Again more details given at: http://www.ccp14.ac.uk/solution/gsas/restrained _inorganic.html

61. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 61 GSAS: setting up an EXCEL spreadsheet: Dual Occupancy Atom Constraints (in expedt: k l a k) Just copy and paste to extend the atom constraints to the desired number of atom sites. In this example for 108 atoms which would be painful to set up manually in GSAS.

62. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 62 GSAS: setting up an EXCEL spreadsheet: Total Cell Content Restraints (in expedt: k l s c) Extend as required depending on the number of atoms you wish to link into the constraint. The total number of atoms on the defined sites in this example is restrainted to 81

63. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 63 GSAS: setting up an EXCEL spreadsheet: Charge Balance Restraints (in expedt: k l s c) Just use the Total Cell Contents Restraint which does not care what the value physically represent. To enforce charge balance just put the ionization value of each atom site - which should sum to zero. Simple example in the screen dump. The Total Chemistry Restraint will performs the sum calculation for you and tell you what the present sum is in the restraints menu. Even if you don’t use the restraint, inputting this can be a useful, quick check that you have charge balance.

64. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 64 GSAS: importing all these macro files into GSAS Copy the Excel cells to a TXT file. Use an Editor such as PFE to replace all TABS with a space: –http://www.ccp14.ac.uk/ccp/web-mirrors/pfe/people/cpaap/pfe/ Use the @r - import macro file command while in the relevant menu Done!

65. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 65 GSAS: turning off /on histograms, restraints, atoms Easily done in GSAS’s EXPEDT –k l s –u - The use command e.g., turn off X-ray data (histogram 1), turn on bond restraints (histogram 2) and neutron data (histogram 3) k l s! Go into EXPEDT restraints menu u 1 ! Use histogram 1 - X-ray Data n! No u 2! Use histogram 2 - Bond Restraints y! Yes u 3! Use histogram 3 - Neutron Data y! Yes x x x! Exit EXPEDIT menus and quit

66. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 66 GSAS: using restraints as diagnostics Restraints don’t have to be enabled to exist inside GSAS Restraints can also be used diagnostically even if they are not enabled E.g., Charge Balance : Following screen dumps shows that the occupancies of the various metals are such that the total cell is out of charge balance. –In EXPEDT: k l s c l ! last l is for list

67. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 67 GSAS: spiraling in on the minimum and final structure May have to refine in quite a spiral manner Initially - have found circular refinement to be more controllable than combined refinement to be more controllable –heavy atoms using X-ray data –Oxygens using neutron data Restraints - problem with cemented structure vs having the structure fall apart –If restraints cement the structure, turning off restraints; doing small numbers of cycles and manually resetting errant atoms can get things rolling quite nicely. –Relaxing restraints sometimes can improve the regular co-ordination. !? If structure goes haywire, it can be easier to start again from the initial model Wall paper bubble effect - tighten one errant atom causes 1 to 4 more to go out Interested in other people’s experiences here for large polymeric structures

68. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 68 GSAS: lessening the tedium: batch file control of the refinement : ( fully ordered model) –Combatting impatience - tedious refinement strategy –Can leave a strategy to run overnight (though you may suffer for this) can be better to look after set periods of time and reset wandering atoms - which can wander even if constrained!? –Following examples for DOS / Windows (Linux / Unix is more flexible) –The @m command can be used to log a command sequence to a file to server as the starting point for editing a custom macro file.

69. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 69 GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: script to increase the refined angular range) In this case setting up histogram 1 (powder XRD) File titled 70_2t_x.txt The BAT control file would then enabled (“use”) all relevant histograms and run powpref after this file before going through a genles run. p ! powder setup h ! histogram setup e 1 ! edit histogram 1 (X-ray) t ! set end of two theta 70 ! set 70 degrees / ! confirm this then exit x

70. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 70 GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: changing the bond restraint weighting) File titled bondr10.txt k ! don't make a backup of the file l ! least squares s ! soft constraints d ! bond length restraints f 10 ! set bond restr. weighting to 10 x ! exit expedt x

71. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 71 GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: only refining on neutron data) File titled neuonly.txt k l ! least squares s ! soft restraints menu u 1 ! use histogram 1 - X-rays n ! set to no u 3 ! use histogram 3 - neutron y ! set to yes x

72. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 72 GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: refine heavy metal framework atoms) File titled ref_fmh.txt k ! don't make a backup of the file l ! least squares a ! atom options v 1:324 -x ! get rid of any X parameters refining q ! quit atom list v 1:324 -u ! get rid of any UISO parameters refining q ! quit atom list v 1:324 -f ! get rid of any FRAC parameters refining q ! quit atom list v 29:108 x ! set framework M sites refine on coords q ! quit atom list x

73. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 73 GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: refine light metal framework atoms) File titled ref_fml.txt k ! don't make a backup of the file l ! least squares a ! atom options v 1:324 -x ! get rid of any X parameters refining q ! quit atom list v 1:324 -u ! get rid of any UISO parameters refining q ! quit atom list v 1:324 -f ! get rid of any FRAC parameters refining q ! quit atom list v 1:28 x ! set framework M sites refine on coords q ! quit atom list x

74. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 74 GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: refine interstitial metal atoms - less vacancies) File titled ref_int.txt k ! don't make a backup of the file l ! least squares a ! atom options v 1:324 -x ! get rid of any X parameters refining q ! quit atom list v 1:324 -u ! get rid of any UISO parameters refining q ! quit atom list v 1:324 -f ! get rid of any FRAC parameters refining q ! quit atom list v 133:144 x ! set interstitial Met to refine v 147:154 x ! set interstitial Met to refine v 157:162 x ! set interstitial Met to refine x

75. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 75 GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: refine oxygens) File titled refoxy.txt k ! don't make a backup of the file l ! least squares a ! atom options v 1:324 -x ! get rid of any X parameters refining q ! quit atom list v 1:324 -u ! get rid of any UISO parameters refining q ! quit atom list v 1:324 -f ! get rid of any FRAC parameters refining q ! quit atom list v 163:324 x ! set oxygens to refine q ! quit atom list x

76. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 76 GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: refine UISO) File titled refoxy.txt k ! don't make a backup of the file l ! least squares a ! atom options v 1:324 -x ! get rid of any X parameters refining q ! quit atom list v 1:324 -u ! get rid of any UISO parameters refining q ! quit atom list v 1:324 -f ! get rid of any FRAC parameters refining q ! quit atom list v 1:324 u ! set UISO of all atoms to refine q ! quit atom list x

77. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 77 GSAS: lessen the tedium: batch file control of the refinement : (Create a Batch File to follow your desired command sequence) File titled: refine.bat In early stage of refinement, a “cycle” of refinement involves: –Set bond restraint weight –Enable only X-ray data –refine framework metal atoms –refine interstitial atoms –Enable only Neutron data –refine light oxygen atoms –refine constrained UISO Batch files can be made more complicated with respect to logging what is happening expedt model < batchjob\bondr1.txt echo step 1 bond weight > autolog.txt expedt model < batchjob\xrayonly.txt echo step 2 XRAYS ONLY >> autolog.txt expedt model < batchjob\ref_fhm.txt genles model echo step 3 completed >> autolog.txt expedt model < batchjob\ref_flm.txt genles model echo step 4 completed >> autolog.txt expedt model < batchjob\neuonly.txt echo step 5 NEUTRON ONLY >> autolog.txt expedt model < batchjob\refoxy.txt genles model echo step 6 completed >> autolog.txt expedt model < batchjob\refuiso.txt genles model echo step 7 completed >> autolog.txt

78. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 78 GSAS : If the refinement is not happy The tools are there for difficult refinements, but: –May not be easy! –May only find problems when in the middle of the refinement Impurities in many and varied forms XRD and Neutron data are different enough –different impurities showing up –different systematic effects –different volumes of sample having their effect Wrong spacegroup Non-optimum atom ordering Non-optimum tilt model

79. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 79 GSAS : “wall paper bubble effect trying to keep all bonds physically reasonable One problem trying to keep everything physically reasonable: trying to fix gives a “wall paper bubble effect” - fixed one bond causes 1 to 5 other bonds to become physically unreasonable. Suggestions on this appreciated (though this could be implying data purity problems).

80. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 80 GSAS : Combined refinement on both XRD and Neutron (bond length problems - “bubbles” - to stomp on) May be problems with overlapping impurities (possible impurity problems only found during the refinement). X-ray 7.6% R(F**2) (~3.8% R Bragg) Neutron 4.2% R(F**2) (~2.1% R Bragg)

81. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 81 Ton Spek’s Platon Addsym - finding extra symmetry and exploring symmetry in simple to complex polymeric inorganics WWW: http://www.cryst.chem.uu.nl/platon/ One of the best programs for finding missing symmetry from crystal structure information. Now has enhanced subcell finding Now has enhanced defaults for inorganics

82. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 82 Ton Spek’s Platon Addsym - spectacular example Triclinic Cell - P1 –(96 independent Carbon atoms)

83. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 83 Ton Spek’s Platon Addsym - spectacular example Run Platon’s Addsym in default mode Addsym finds the true cell - which is a 1/8th subcell –(3 independent Carbon atoms) –Monoclinic P 21/c –(compared to 96 atom starting structure)

84. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 84 Platon’s Addsym - (1 of 2) finding extra symmetry in inorganics and minerals - P1 triclinic starting structure. Unpublished Mineral Example –Default Addsym gives C2/C Tighten the addsym values: –calc ADDSYM SHELX 1 0.2 0.4 0.2 –addsym gives P 2/c and exact fit on Pc Loosening defaults: –calc addsym shelx exact 1.2.4.4 –P-31m

85. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 85 Platon’s Addsym - (2 of 2) finding extra symmetry in inorganics and minerals - P1 triclinic starting structure. Update new refinement in triclinic: –Lower R factor in Shelx –Addsym now finds P21/c in default mode Thus need to be careful!

86. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 86 Platon’s Addsym - finding extra symmetry in hand- build inorganic models In the GSAS refined ceramic - original starting “model” is in R3 Platon’s Addsym (default values) gives R-3c –plus option of a new Shelx RES file with the structure in the new spacegroup –and the directions to find the extra symmetry elements from the old R3 model

87. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 87 Platon’s Addsym - finding extra symmetry in powder refined structure in triclinic Starting Model of C 1 Platon’s Addsym can get back to R3 except one interstitial metal site seems to be breaking the symmetry and keeping the triclinic symmetry. A refinement with a new sample without problematic impurities may change this.

88. ECM 2001: "New features in existing powder diffraction software" Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk Slide 88 Summary A year can make a big difference in the enhanced use of software to tackle more complicated powder diffraction problems. Many programs are also mirrored at the CCP14 project website: http://www.ccp14.ac.uk Thanks: –Bob von Dreele and Alan Larsen - GSAS Rietveld –Jean Laugier and Bernard Bochu - Chekcell –Brett Hunter - Rietica Rietveld –Ton Spek - Platon / Addsym –Dave Walker, et al - Earth Sciences example –Ian Grey, Gus Mumme, Bob Roth, et al - High-tech ceramic example Apologies: no time to mention a few dozen other programs that have been significantly enhanced in the last 12 months