1 / 88

L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for

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,

ilori
Download Presentation

L. M. D. Cranswick, CCP14 (Collaborative Computation Project No 14 for

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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. 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. 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

  3. Notes Free Zone - they are on the webhttp://www.ccp14.ac.uk/poster-talks/ecm2001/ 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

  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 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

  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 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

  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 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

  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 - RbClO4= B2-RbCl + 2O2 4 R-KClO3 = 3 O-KClO4 + B2-KCl O-KClO4 = B2-KCl + 2 O2 O2 from the differences in the unit cell volumes 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

  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) 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

  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” 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

  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 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

  11. Chekcell - Jean Laugier and Bernard Bochuhttp://www.ccp14.ac.uk/tutorial/lmgp/ • 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 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

  12. Routine operation of Chekcell (1 of 5) Open a data file (optional if you only have a peak listing) 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

  13. Routine operation of Chekcell (2 of 5) Open the peak listing (In this case generated by the XFIT program) 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

  14. Routine operation of Chekcell (3 of 5) Import the Crysfire summary file listing of found trial cells. 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

  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. 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

  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. 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

  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 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

  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 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

  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 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

  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 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

  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) 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

  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) 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

  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. 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

  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 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

  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. 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

  26. Rietica Rietveld for Mass Le Bail fittingAt 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 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

  27. Rietica Rietveld for Mass Le Bail fitting 1 of 10 • Before the phase transition 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

  28. Rietica Rietveld for Mass Le Bail fitting2 of 10 • In the phase transition • No completely freestanding peak for KCl 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

  29. Rietica Rietveld for Mass Le Bail fitting3 of 10 • Repeat as required • No completely freestanding peak for KCl 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

  30. Rietica Rietveld for Mass Le Bail fitting4 of 10 • Repeat as required • No completely freestanding peak for KCl 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

  31. Rietica Rietveld for Mass Le Bail fitting5 of 10 • Repeat as required • Still no completely freestanding peak for KCl 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

  32. Rietica Rietveld for Mass Le Bail fitting6 of 10 • Repeat as required 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

  33. Rietica Rietveld for Mass Le Bail fitting7 of 10 • Repeat as required 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

  34. Rietica Rietveld for Mass Le Bail fitting8 of 10 • Repeat as required 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

  35. Rietica Rietveld for Mass Le Bail fitting9 of 10 • Repeat as required 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

  36. Rietica Rietveld for Mass Le Bail fitting10 of 10 • Done!!! 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

  37. Rietica Rietveld for Mass Le Bail :Graphing up the results Using Traditional Methods Using Le Bail fitting 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

  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. 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

  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? 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

  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 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

  41. Chekcell and Rietica: results of the volume of Oxygen and the earth’s other core • Energy Dispersive XRD: vol O2 ~10 cc/mol • Established vol O2 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 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

  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/crystallography/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. 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

  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 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

  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. 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

  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 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

  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) 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

  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 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

  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) 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

  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. 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

  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 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

More Related