presentation source

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: l.m.d.cranswick@dl.ac.uk

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

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 2

Using diffraction methods to solve the problems of the world

Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk

Notes Free Zone -

they are on the web

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

Slide 3



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 4



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

Slide 5



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 6



Energy Dispersive Diffraction

E(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 (multiwavelength) “diffracted” X-rays as a function of energy (in KeV)

– analogous to Time of Flight neutron diffraction (TOF)

Slide 7




Schematic Diagram

Collimator and

EDX detector – at a fixed angle

(stationary)

White X_ray

Beam

Slide 8

Sample

Environment

Diffraction patterns are obtained only of the volume subtended by the collimator with the incident X-ray beam



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 9




Schematic of following reactions inside reaction vessels

EDX

Detector

White X_ray

Beam

Sample

Environment

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

By moving the sample stage, the

“lozenge” can see

(possibly transient) reactant products at different times after mixing.

And/or the orientation of particles under flow – e.g., clays

Slide 10




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.

Slide 11



Energy Dispersive Diffraction :

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

Slide 12



Energy Dispersive Diffraction :

Example datasets at high pressure and high temperature

Slide 13



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 14



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 15



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 16



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 17



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 18



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 19



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 20



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 21



Peak Profiling - XFIT

Examples of XFIT in action:

Slide 22



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 23



Powder Indexing - the “Crysfire” suite

Example of CRYSFIRE Screen prompting the saving into one of 8 different indexing program formats:

Slide 24



Chekcell - Jean Laugier and Bernard Bochu http://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

• 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

Slide 25



Routine operation of Chekcell (1 of 5)

Open a data file

(optional if you only have a peak listing)

Slide 26




Open the peak listing

(In this case generated by the XFIT program)

Slide 27




Import the Crysfire summary file listing of found trial cells.

Slide 28




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

Slide 29




•

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 30



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 31



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 32



Chekcell: Density / Z / Molecular Volume Explorer

• Easily look at effects of Z, Density and molecular volume

Slide 33



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 34



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 35



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 36



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 37



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 38



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 39



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

Slide 40



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 41



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

Slide 42




1 of 10

• Before the phase transition

Slide 43



• In the phase transition


2 of 10

•

No completely freestanding peak for KCl

Slide 44




3 of 10

• Repeat as required

•


Slide 45




4 of 10


•


Slide 46




5 of 10


•

Still no completely freestanding peak for KCl

Slide 47





6 of 10

Slide 48





7 of 10

Slide 49





8 of 10

Slide 50





9 of 10

Slide 51



• Done!!!


10 of 10

Slide 52



Rietica Rietveld for Mass Le Bail : Graphing up the results

Using Le Bail fitting Using Traditional Methods

Slide 53



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 54



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 55



2. 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

Slide 56



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

Slide 57



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 58



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

Slide 59



Chekcell and Rietica: results of the volume of Oxygen

• 15 cc/mol means there cannot be and the earth’s other core

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 60



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

Slide 61



presentation source

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

Talk Aims

Notes Free Zone -

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

Is there Oxygen in the Earth’s outer core

What do we need from the data?

What do we need from the diffraction experiment

Energy Dispersive Diffraction

Energy Dispersive Diffraction

Energy Dispersive Diffraction : Advantages

Energy Dispersive Diffraction

Energy Dispersive Diffraction

Energy Dispersive Diffraction :

Energy Dispersive Diffraction :

What do we need from the data to help us determined if there can be Oxygen in the

Earth’s outer core?

Synchrotron Hardware Fixation Syndrome

(SHFS)

How can you detect if the beamline you are using suffers from SHFS

Thus the next problem :

Software Analysis:

Difficulties that need to be considered:

Other Problems that need to be considered

3 x Problems that need to be overcome

Software to help Analyse the Data:

XFIT, Crysfire, Chekcell and Rietica

Background to XFIT by Cheary and Coelho

Peak Profiling - XFIT

Background to Crysfire by Robin Shirley

Powder Indexing - the “Crysfire” suite

Routine operation of Chekcell (1 of 5)

Routine operation of Chekcell (2 of 5)

Routine operation of Chekcell (3 of 5)

Routine operation of Chekcell (4 of 5)

Routine operation of Chekcell (5 of 5)

Le Page

Chekcell: result of using Le Page

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.

Background to Rietica by Brett Hunter

• Done!!!

Volume of Oxygen as a function of Pressure

Summary

http://www.ccp14.ac.uk

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