Using the latest powder diffraction methods and software to solve the problems of the world - can the Earth’s outer core contain Oxygen? 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. WWW:

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 2 Talk Aims Mention the advantages of using Energy Dispersive diffraction Though emphasize that without good and appropriate software analysis tools - you might end up with a pile of Energy Dispersive diffraction data that is too problematic to analyze effectively. Show that what might be considered superficial software modifications can make a major impact to assist in solving intractable problems (such as this example). Minor rant about Synchrotron Hardware Fixation Syndrome (SHFS)

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 3 Notes Free Zone - they are on the web

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 4 Is there Oxygen in the Earth’s outer core 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

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 5 What do we need from the 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 Thus use powder diffraction

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 6 What do we need from the diffraction experiment Ability to penetrate high a “large volume” high pressure cell - high temperature cell (in this case a multi-anvil Walker Cell) Ability to get the X-ray beam in and out of tight spaces Thus Energy Dispersive Diffraction can be advantageous for these types of problems.

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 7 Energy Dispersive Diffraction E(keV) = / (d_space * sin(theta_angle of Energy Dispersive detector)) Angular Dispersive Diffraction (simplification) –Roughly single X-ray wavelength (e.g., Cu k-alpha = Å) –detector collects in 2-theta - measuring intensities of single wavelength (single energy) “diffracted” X-rays as a function of angle (2-theta) Bragg-Bretano / Debye Scherrer, etc laboratory systems (and neutron synchrotron) Energy Dispersive Diffraction –want intense, high-energy / multi-energy (multi-wavelength) “white” X-ray beam –Energy sensitive detector at a “fixed angle” detects multi-energy (multi- wavelength) “diffracted” X-rays as a function of energy (in KeV) –analogous to Time of Flight neutron diffraction (TOF)

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 8 Energy Dispersive Diffraction Schematic Diagram

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 9 Energy Dispersive Diffraction : Advantages Can see “inside” unconventional sample environments –Within limits: can have steel or other materials shielding the sample at pressure and/or temperature thus samples can also be immersed in gas or liquid (hydrothermal synthesis) in-situ studies - reactions / explosions / properties under stress. Particle flows within gases and fluids. Reactions in gas/fluid flow lines. Only see diffraction in the volume (nick-named the “lozenge”) defined where the detector collimator subtends onto the incident white X-ray beam Spatial Resolution inside the sample environment –Can narrow down the beam and collimator - and move the sample : thus obtaining diffraction patterns from different spatial volumes inside the sample environment Fast data collection times –minutes to fractions of a second

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 10 Energy Dispersive Diffraction Schematic of following reactions inside reaction vessels

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 11 Energy Dispersive Diffraction Beamline 16.4 at Daresbury X-ray Synchrotron, Cheshire, UK In high pressure mode and Walker Cell and Press installed All the hardware can make for a crowded and complicated environment.

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 12 Energy Dispersive Diffraction : Example of High pressure/temp. sample assembly for the multi-anvil Walker Cell

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 13 Energy Dispersive Diffraction : Example datasets at high pressure and high temperature

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 14 What do we need from the data to help us determined if there can be Oxygen in the Earth’s outer core? What do we want? –“Accurate” Unit-cell volumes to obtain equations of state (EOS) When to we want it? –Now!! (not 6 months to 5 years later!) –(far better if synchrotron beamlines offer analysis software so that problems can be defined and analysis performed in near real time) Collecting small to large amounts of diffraction data with the intention of analysing it later is a effective way of getting low productivity out of synchrotron and neutron sources.

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 15 Synchrotron Hardware Fixation Syndrome (SHFS) Diagnosis: –A neurotic spending of all effort on custom novel synchrotron hardware without consideration and similar effort put into software analysis requirements Effects: –Beamlines can have very low productivity due to data analysis being unnecessarily problematic and taking months or years of analysis (kludging together a software solution) Possible Cure: –Make sure equal amounts of effort are spent on i) hardware, ii) data collection and iii) analysis software

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 16 How can you detect if the beamline you are using suffers from SHFS If you cannot do (at the minimum), preliminary analysis of the data, it is very likely that the beamline suffers from Synchrotron Hardware Fixation Syndrome. You would want the option and ability to perform the entire data analysis in near real time. Not having an “integrated” analysis system at the beamline not only means wasting large amounts of users’ time; but that problems may only be found well after the experiment when it is too late to rectify them. (calibration problems, wrong sample inserted, flaws in experimental design, interesting occurrences that should have been immediately followed up)

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 17 Thus the next problem : Software Analysis: Difficulties that need to be considered: Energy Dispersive Diffraction setup and calibration can be very ad-hoc and problematic Possible Detector instability over short time spans Possible “other” detector problems (more neurotic of these problems only obvious when doing whole pattern Le Bail fitting)

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 18 Other Problems that need to be considered Poor resolution data with multiple sources of spurious peaks Phase transitions give unknown cells Track how diffraction patterns are changing through the experiments

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 19 3 x Problems that need to be overcome (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

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 20 Software to help Analyse the Data: XFIT, Crysfire, Chekcell and Rietica XFIT peak profiling software Crysfire powder indexing suite Chekcell powder indexing tool Rietica Rietveld for mass Le Bail fitting to obtaining cell volumes and follow reactions

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 21 Background to XFIT by Cheary and Coelho XFIT - peak profiling software for Windows – –3 peak profiling options Fundamental parameters (only applicable in XFIT for Bragg-Bretano) Pearson-7 (for assymmetric peaks) Pseudo-Voight (for symmetric peaks) –No hard limits on number of peaks that can be simultaeously profiled (except memory and time) –Can open over 100 XRD patterns for simultaneous display and peak fitting

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 22 Peak Profiling - XFIT Examples of XFIT in action:

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 23 Background to Crysfire by Robin Shirley Crysfire - powder indexing suite – –Links to 8 different indexing programs ito, dicvol, treor, taup, lzon, fjzn, kohl and losh –Simple DOS based menu system to run each program –All results are collated into a single summary file One line per solution Summary file can be used by Chekcell

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 24 Powder Indexing - the “Crysfire” suite Example of CRYSFIRE Screen prompting the saving into one of 8 different indexing program formats:

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 25 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 Incorporates Ton Spek and A. Meetsma’s Le Page *** (an addition that can really count) sub-cell / super-cell searching GUI Cell transformation New: Density / Z / Molecular Volume explorer Chekcell - Jean Laugier and Bernard Bochu

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 26 Open a data file (optional if you only have a peak listing) Routine operation of Chekcell (1 of 5)

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 27 Routine operation of Chekcell (2 of 5) Open the peak listing (In this case generated by the XFIT program)

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 28 Routine operation of Chekcell (3 of 5) Import the Crysfire summary file listing of found trial cells.

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 29 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.

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 30 Routine operation of Chekcell (5 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.

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 31 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 (1957)” Efficient Sub-cell and super-cell searching, then easy reviewing of newly derived cells within the Chekcell interface

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 32 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

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 33 Chekcell: Density / Z / Molecular Volume Explorer Easily look at effects of Z, Density and molecular volume

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 34 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

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 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

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 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)

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 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)

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 38 XFIT / Chekcell / LePage Summary: These programs give you the maximum chance of indexing unknown unit-cells from powder diffraction data, even of low data quality.

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 39 Background to Rietica by Brett Hunter Rietica Rietveld - Rietveld software – –Newish: 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

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 40 Rietica Rietveld for Mass Le Bail fitting to get cell volumes 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

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 41 Rietica Rietveld for Mass Le Bail fitting : Rietica Database of Structures 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.

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 42 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

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 43 Rietica Rietveld for Mass Le Bail fitting 1 of 10 Before the phase transition

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 44 Rietica Rietveld for Mass Le Bail fitting 2 of 10 In the phase transition No completely freestanding peak for KCl

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 45 Rietica Rietveld for Mass Le Bail fitting 3 of 10 Repeat as required No completely freestanding peak for KCl

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 46 Rietica Rietveld for Mass Le Bail fitting 4 of 10 Repeat as required No completely freestanding peak for KCl

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 47 Rietica Rietveld for Mass Le Bail fitting 5 of 10 Repeat as required Still no completely freestanding peak for KCl

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 48 Rietica Rietveld for Mass Le Bail fitting 6 of 10 Repeat as required

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 49 Rietica Rietveld for Mass Le Bail fitting 7 of 10 Repeat as required

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 50 Rietica Rietveld for Mass Le Bail fitting 8 of 10 Repeat as required

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 51 Rietica Rietveld for Mass Le Bail fitting 9 of 10 Repeat as required

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 52 Rietica Rietveld for Mass Le Bail fitting 10 of 10 Done!!!

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 53 Rietica Rietveld for Mass Le Bail : Graphing up the results Using Le Bail fittingUsing Traditional Methods

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 54 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.

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide Rietica and Le Bailing : problems with stability and calibration of the Energy Dispersive Detector(?) NaCl / Halite at Room Temperature and Pressure (thus is not crystal strain) Very nasty miss-fits on peak positions Possible instability in the detector Peaks cause detector to become unstable in the region of high counts(?) Other problems?

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide Rietica and Le Bailing : problems with stability and calibration of the 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

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 57 Using XFIT and UNITCELL for traditional Unit-cell refinement and EOS to obtained unit weighting of HKLs

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 58 Using XFIT and UNITCELL for EOS of NaCl and KCl : But:Rietica can make sure the correct HKLs are assigned to the correct peaks and phases - greater than 5 phases (spurious peaks can be easily identified)

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 59 Volume of Oxygen as a function of Pressure Energy Dispersive XRD: vol O 2 ~10 cc/mol Established vol O 2 from shockwave experiments: ~15 cc/mol (50% difference) Reasons for differences in Shockwave / Molecular Dynamics / Impulsively Stimulated Scattering Measurements (~15 cc/mol) vs Energy Dispersive Data (~10 cc/mol) beyond the scope of this talk

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 60 Chekcell and Rietica: results of the volume of Oxygen and the earth’s other core 15 cc/mol means there cannot be Oxygen (shockwave / molecular dynamics) 10 cc/mol (EDX result) means there can be Oxygen in the Earth’s outer core and has implications : –including the possibility of sensible transport mechanisms between the core mantle boundary

Using diffraction methods to solve the problems of the world Lachlan M. D. Cranswick Slide 61 Summary Hopefully show the potential power of energy dispersive diffraction And also the necessity of considering using the appropriate data analysis software to be just has important as the diffraction hardware Perhaps also the horror of SHFS (Synchrotron Hardware Fixation Syndrome) These programs (and many more) are also mirrored at the EPSRC funded CCP14 project website: Thanks: –Bob Cheary and Alan Coelho - XFIT –Robin Shirley - Crysfire –Jean Laugier and Bernard Bochu - Chekcell –Brett Hunter - Rietica Rietveld –Simon Redfern and Tony Holland - UNITCELL –Dave Walker, et al - Geosciences example