using the latest powder diffraction methods and software to solve the problems of the world - can...

$: Using the latest powder diffraction methods and software to solve the problems of the world - can the Earth’s outer core contain Oxygen? L. M. D. Cranswick,$
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.

E-mail: [email protected]

WWW: http://www.ccp14.ac.uk

Using diffraction methods to solve the problems of the worldLachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk

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)


Slide 3

Notes Free Zone - they are on the web

http://www.ccp14.ac.uk/poster-talks/csiro2002/


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


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 - 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

Thus use powder diffraction


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.


Slide 7

Energy Dispersive DiffractionE(keV) = 6.199 / (d_space * sin(theta_angle of Energy Dispersive detector))

• Angular Dispersive Diffraction (simplification)– Roughly single X-ray wavelength (e.g., Cu k-alpha = 1.54180Å)

– 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)


Slide 8

Energy Dispersive DiffractionSchematic Diagram

White X_rayBeam

SampleEnvironment

Collimator andEDX detector – at afixed angle(stationary)

Diffraction patterns areobtained only of thevolume subtended by thecollimator with theincident X-ray beam


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


Slide 10

Energy Dispersive DiffractionSchematic of following reactions inside reaction vessels

White X_rayBeam

SampleEnvironment

(e.g., hydrothermal cell,non-ambient cell)

By moving thesample stage, the“lozenge” can see(possibly transient)reactant products atdifferent times aftermixing.And/or the orientationof particles underflow – e.g., clays

EDXDetector


Slide 11

Energy Dispersive DiffractionBeamline 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.


Slide 12

Energy Dispersive Diffraction :Example of High pressure/temp. sample assembly for the multi-anvil Walker Cell


Slide 13

Energy Dispersive Diffraction :Example datasets at high pressure and high temperature


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.


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


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)


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)


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


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


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


Slide 21

Background to XFIT by Cheary and Coelho • XFIT - peak profiling software for Windows

– http://www.ccp14.ac.uk/tutorial/xfit-95/

– 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


Slide 22

Peak Profiling - XFITExamples of XFIT in action:


Slide 23

Background to Crysfire by Robin Shirley • Crysfire - powder indexing suite

– http://www.ccp14.ac.uk/tutorial/crys/

– 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


Slide 24

Powder Indexing - the “Crysfire” suiteExample of CRYSFIRE Screen prompting the saving into one of 8 different indexing program formats:


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 Bochuhttp://www.ccp14.ac.uk/tutorial/lmgp/


Slide 26

Open a data file

(optional if you only have a peak listing)

Routine operation of Chekcell (1 of 5)


Slide 27


Open the peak listing

(In this case generated by the XFIT program)


Slide 28


Import the Crysfire summary file listing of found trial cells.


Slide 29


Play with the list of trial cells and spacegroups and hopefully obtain a good cell that is also the “true” cell.


Slide 30


•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.


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. 42-60 (1957)”

•Efficient Sub-cell and super-cell searching, then easy reviewing of newly derived cells within the Chekcell interface


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


Slide 33

Chekcell: Density / Z / Molecular Volume Explorer•Easily look at effects of Z, Density and molecular volume


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


Slide 35

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


Slide 36

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)


Slide 37

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)


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.


Slide 39

Background to Rietica by Brett Hunter • Rietica Rietveld - Rietveld software

– http://www.rietica.org/

– 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


Slide 40

Rietica Rietveld for Mass Le Bail fitting to get cell volumesExample 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


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.


Slide 42

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


Slide 43

Rietica Rietveld for Mass Le Bail fitting 1 of 10

• Before the phase transition


Slide 44

Rietica Rietveld for Mass Le Bail fitting2 of 10

• In the phase transition

• No completely freestanding peak for KCl


Slide 45


• Repeat as required



Slide 46





Slide 47



• Still no completely freestanding peak for KCl


Slide 48




Slide 49




Slide 50




Slide 51




Slide 52


•Done!!!


Slide 53

Rietica Rietveld for Mass Le Bail : Graphing up the resultsUsing Le Bail fitting Using Traditional Methods


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.


Slide 55

1. 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?


Slide 56

2. Rietica and Le Bailing : problems with stability and calibration of the Energy Dispersive Detector(?)

Le Bail fittingNon-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


Slide 57

Using XFIT and UNITCELL for traditional Unit-cell refinement and EOS to obtained unit weighting of HKLshttp://www.esc.cam.ac.uk/astaff/holland/


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)


Slide 59

Volume of Oxygen as a function of Pressure

• Energy Dispersive XRD: vol O2 ~10 cc/mol

• Established vol O2 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


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


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:

http://www.ccp14.ac.uk• 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

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