SIG_9.1: Crystallographic Computing: Advanced Computational Tools for Small Molecules and Materials...

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: [email protected]

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

ECM 2001: "New features in existing powder diffraction software"Lachlan M. D. Cranswick ([email protected]) 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.


Slide 3

Notes Free Zone - they are on the web

http://www.ccp14.ac.uk/poster-talks/ecm2001/


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


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


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


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 - 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


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)


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”


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


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


Slide 12

Open a data file

(optional if you only have a peak listing)

Routine operation of Chekcell (1 of 5)


Slide 13


Open the peak listing

(In this case generated by the XFIT program)


Slide 14


Import the Crysfire summary file listing of found trial cells.


Slide 15


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


Slide 16


•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 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


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


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


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


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)


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)


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.


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


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.


Slide 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


Slide 27

Rietica Rietveld for Mass Le Bail fitting 1 of 10

• Before the phase transition


Slide 28

Rietica Rietveld for Mass Le Bail fitting2 of 10

• In the phase transition

• No completely freestanding peak for KCl


Slide 29


• Repeat as required



Slide 30





Slide 31



• Still no completely freestanding peak for KCl


Slide 32




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Slide 36


•Done!!!


Slide 37

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


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.


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?


Slide 40

2. Rietica and Le Bailing : Short-term non-linearities of an 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 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


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/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.


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


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.


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


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)


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


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)


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.


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


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


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


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


Slide 54

GSAS: If you DON’T Use Histogram Weighting

X-ray 8.0% R(F**2) Neutron 28.1% R(F**2)


Slide 55

GSAS: If you DO Use Histogram Weighting

X-ray 8.3% R(F**2) Neutron 11.7% R(F**2)


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/


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)


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


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


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


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.


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


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.


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!


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


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


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


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.


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

x

x

x


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

x

x


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

x

x


Slide 72

GSAS: lessen the tedium: batch file control of the refinement :(EXPEDT Example: refine heavy metal framework atoms)

• File titled

ref_fmh.txt


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

x

x


Slide 73

GSAS: lessen the tedium: batch file control of the refinement :(EXPEDT Example: refine light metal framework atoms)

• File titled

ref_fml.txt


l ! least squares

a ! atom options


q ! quit atom list


q ! quit atom list


q ! quit atom list

v 1:28 x ! set framework M sites refine on coords

q ! quit atom list

x

x

x


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


l ! least squares

a ! atom options


q ! quit atom list


q ! quit atom list


q ! quit atom list

v 133:144 x ! set interstitial Met to refine



x

x

x


Slide 75

GSAS: lessen the tedium: batch file control of the refinement :(EXPEDT Example: refine oxygens)

• File titled

refoxy.txt


l ! least squares

a ! atom options


q ! quit atom list


q ! quit atom list


q ! quit atom list

v 163:324 x ! set oxygens to refine

q ! quit atom list

x

x

x


Slide 76

GSAS: lessen the tedium: batch file control of the refinement :(EXPEDT Example: refine UISO)

• File titled

refoxy.txt


l ! least squares

a ! atom options


q ! quit atom list


q ! quit atom list


q ! quit atom list

v 1:324 u ! set UISO of all atoms to refine

q ! quit atom list

x

x

x


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


expedt model < batchjob\neuonly.txt

echo step 5 NEUTRON ONLY >> autolog.txt

expedt model < batchjob\refoxy.txt

genles model


expedt model < batchjob\refuiso.txt

genles model



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


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).


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)


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


Slide 82

Ton Spek’s Platon Addsym - spectacular example

• Triclinic Cell - P1– (96 independent

Carbon atoms)


Slide 83

Ton Spek’s Platon Addsym - spectacular exampleRun 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)


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


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!


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


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.


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

SIG_9.1: Crystallographic Computing: Advanced Computational Tools for Small Molecules and Materials...

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Transcript of SIG_9.1: Crystallographic Computing: Advanced Computational Tools for Small Molecules and Materials...