tricks and hints for using alan larson and bob von dreele's gsas, and brian toby's expgui,...

Tricks and hints for using Alan Larson and Bob von Dreele's GSAS, and Brian Toby's EXPGUI, for combined X-ray / Neutron refinement and restrained Rietveld refinement of large polymeric inorganics and minerals.

Lachlan 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

AGU 2002: “hints and tricks for using GSAS Rietveld”Lachlan M. D. Cranswick ([email protected]) http://www.ccp14.ac.uk

Slide 2

Hand Written Notes Free Zonethey are on the web

http://www.ccp14.ac.uk/poster-talks/korea2002b/


Slide 3

Talk Aims

• Provide hints on performing restrained Rietveld refinement of large inorganics using GSAS including:

– Data conversion

– Histogram weighting

– Charge Balance Restraints

– Total cell composition restraints

– Bond length restraints

– Bond angle restraints

– Using Platon and WinGX to help validate the structure


Slide 4

Topics Discussed

• Converting Madsen and Hill VCT data and x,y,weight column data into GSAS format

• Using Brian Toby’s EXPGUI as a primary interface into GSAS

• Hints on using GSAS for combined X-ray / Neutron refinement

• Hints on GSAS Rietveld for restrained refinement of large inorganic polymeric framework structrures

• Using macros in GSAS


Slide 5

An initial point - computer skills

• When doing complicated (and not so complicated crystallography and powder diffraction), it is assumed the user has good general computer skills.– General program installation and configuration

– Good text editing skills

– Having multiple programs open and interacting between them

– Cut and paste using both mouse and keyboard speed keys.


Slide 6

GSAS

• by Bob von Dreele and Alan Larson - ftp://ftp.lanl.gov/public/gsas/

• 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 7

GSAS: Some Relevant Background• by Bob von Dreele and

Alan Larson

• 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 8

Brian Toby’s EXPGUI Interface for GSAS

User friendlier to start using GSAS via EXPGUI(A new combined installer makes it very easy to start using GSAS.)

http://www.ncnr.nist.gov/programs/crystallography/software/expgui/expgui_intro.html


Slide 9

Brian Toby’s EXPGUI: Easy to start a new refinement (1 of 13)

• Run EXPGUI and go to the required directory and enter a new filename (in this case pbso4) and press “read”. When prompted, then press the “Create” icon


Slide 10


• When prompted, enter an experimental title then press the “Set” icon.


Slide 11


• Click on the “Phase” tab and then the “Add Phase” Icon. Input the cell and spacegroup information

• (or import structure from Powder Cell *.cel, CIF, GSAS, MSI *.xtl, Platon *.spf)


Slide 12


• Click “Add” then “Continue” to the cell and spacegroup information to be incorporated into GSAS.


Slide 13


• Click “Add New Atoms” and add in the starting model either by hand or importing a PowderCell format file.


Slide 14


• Click “Add Atoms” to get the starting model into GSAS


Slide 15


• Set appropriate damping factors (I tend to like somewhere between 7 and 9)

• (Lessen damping factors if parameter shifts are too small)


Slide 16

Bob von Dreele’s comments on Damping

“Damping - I never use damping in any of my refinements unless I actually need it. There is an option in the LS print menu for listing the "summary table of shift/esd" that is helpful for identifying ocsillating parameters. One should first try no damping and then use it only where necessary. Invoking it early can cause trouble. Another option for atom positions is to "limit the shift" to 0.5A or whatever to keep an early refinement from going off base.”


Slide 17


• Add the first XRD diffraction file: Select “Histogram” tab then “Add New Histogram” icon.


Slide 18


• Via the GUI, select the data file and the instrument parameter file. (in this case an XRD data file)


Slide 19


• Click “Add” to add the XRD file into GSAS. Change the damping factors and fix up any incorrect diffractometer constants (I.e., the parameter file may have incorrect information in it)


Slide 20

Note from Bob von Dreele on POLA

Typically iparm files will have "incorrect" POLA values. You might suggest "good" values for graphite monochromators.

•Thus while calculated values can be determined, experimentally determined values may be recommended. Not only for laboratory systems, but also synchrotron data where ideal values might be assumed.

– In this case using cubic annealed Y2O3 (10.6Å - IA3)


Slide 21

POLA for your Diffractometer and graphite monochromator

•POLA correlates with thermals so be careful checking how robust the resulting value is. (following is determined using annealed Y2O3)


Slide 22

Another way: POLA, IPOLA and diffracted beam graphite monochromator

•Set IPOLA to 1 (POLA should now be cos2 2 of the monochromator.)

•In the case of Graphite 002 reflection: 2 = 26.603 (d=3.3480Å). cos2 2=0.80

•Mainly due to problems such as mosaic spread - POLA refines on this diffractometer (again using annealed Y2O3) to 0.911


Slide 23


• It is easy to add another data file. Select the “Add New Histogram” icon. (select the Bank number if this is relevant)


Slide 24


• Click “Add” to add the second XRD file into GSAS. Again, change the damping factors and fix up any incorrect diffractometer constants (I.e., the parameter file may have incorrect information in it)


Slide 25


• Now you are ready to run Powpref and Genles and start refining the various “relevant” parameters

• Under Profile, Powder XRD data might be happier being fitted with a type 3 profile function:– pseudo-Voight with Finger Cox Jephcoat peak asymmetry correction

• One extra hint for Bragg-Brentano XRD users - sample displacement parameter is “shft” in the profile options (is preferable to use this instead of “zero offset”)


Slide 26

Note from Bob von Dreele on shft

“Choice of "shft" vs "ZERO" is most important. Diffractometers are aligned to make ZERO=0.000 and the sample is "never" in the right place to make shft=0.0. So always refine shft for Bragg-Brentano data. Synchrotron data is different as the zero can be off and other systematic effects will look like "shft" or "trns". If sample is transparent on B-B diffractometers (especially pharmaceuticals!) then trns should be refined.”


Slide 27

Brian Toby’s EXPGUI: Profile Screen in EXPGUI with shft


Slide 28

Estimated Standard Deviations (ESD) vs Standard Deviations• An ESD is the estimated uncertainty derived from a “single

measurement”.

• A Standard Deviation is an uncertainty obtained from collecting “multiple measurements”.

• Rietveld programs ESDs are fine as ESDs go, but they can under estimate “probable error”.

• If you want to know what the “Standard Deviation” is, multiple sample preparation, packing and collection of the data a statistically valid number of times is a way to proceed.

• It helps if you refine the appropriate parameters.


Slide 29

Unit-cell “a-axis” parameter of monoclinic zirconia collected repetitively and refining zero offset

• Each sample was packed separately and run for a structure refinement quality dataset; Cu Tube, 15 to 154 at 0.025 step size on a Philips 3050/X’pert Bragg Bretano powder diffractometer.

IUCr CPD Monoclinic Zirconia

5.14400

5.14450

5.14500

5.14550

Xpert-

1

Xpert-

2

Xpert-

3

Xpert-

4

Xpert-

5

Xpert-

6

Xpert-

7

Xpert-

8

a-ax

is (

A)


Slide 30

Rietveld ESD on Unit cell parameter vs the standard deviation from multiple packings and measurements

• Rietveld ESD on the “a” unit-cell parameter: 0.00007

• Standard Deviation on the “a” unit-cell parameter: 0.00023

• Standard deviation from multiple measurements is over 3 times the estimated standard deviation (ESD) from a single measurement

• The IUCr (International Union of Crystallography) has defined various units including “standard uncertainties” but common nomenclature is being used here.


Slide 31

Unit-cell “a-axis” parameter of monoclinic zirconia collected repetitively and refining sample displacement

• Each sample was packed separately and run for a structure refinement quality dataset; Cu Tube, 15 to 154 at 0.025 step size on a Philips 3050/X’pert Bragg Bretano powder diffractometer.

IUCr CPD Monoclinic Zirconia

5.14400

5.14450

5.14500

5.14550

a-a

xis

(A

)


Slide 32

Rietveld ESD on Unit cell parameter vs the standard deviation from multiple packings and measurements

• Rietveld ESD on the “a” unit-cell parameter: 0.00008

• Standard Deviation on the “a” unit-cell parameter: 0.00008

• Standard deviation from multiple measurements is not significantly different from the estimated standard deviation (ESD) of a single measurement

• However, you can still get problems with accuracy due to misalignment in different powder diffractometers.

– Two theta offset should be a constant of the diffractometer

– Sample displacement should vary with each inserted sample

– Never refine both two-theta and sample displacement


Slide 33

Brian Toby’s EXPGUI: Writing your own importing options

• EXPGUI: customization notes on the web at– http://www.ncnr.nist.gov/programs/crystallography/software/expgui/expgui_cfg.html

• Copy over an existing import script and edit it to work with your new data format in tcl/tk.


Slide 34

New(ish) Features in Brian Toby’s EXPGUI

• Graphically define the background

• Graphically exclude regions

• Can export structures to Cif/Shelx/Platon format (Addsym, etc) / MSI *.xtl formats


Slide 35

Brian Toby’s EXPGUI: Graphically Defining the Background (1 of 3)

• After powpref, select “powder, bkgedit” and use point and click with the mouse to select background points


Slide 36


• Use the Fit icon to fit a Chebyshev function through the data points - increase number of terms as required


Slide 37


• Save into EXP file. Background is now fixed but can be refined at the click of a button. Done.


Slide 38

Brian Toby’s EXPGUI: Graphically Excluding Regions (1 of 3)

• After powpref “and” genles (0 cycles just to perform a “calculation”), select “powder, excledt”


Slide 39


• Point and click to select excluded regions


Slide 40


• Run powpref and genles for this to take effect


Slide 41

Brian Toby’s EXPGUI: If things go beserk: Backtracking through previous runs to when before things went beserk.

• Select “File, Open” and the “Include Archived Files”


Slide 42

Brian Toby’s EXPGUI: Le Bail fitting to get the whole profile fit the data before structure refinement

• Various tricks may be required.

• Fix the “Scale Factor”. It is meaningless to refine the scale factor when doing a Le Bail fit.

• Brian Toby trick: Run zero cycles until the intensities roughly match before releasing any other parameters (peak profile, unit cell, zero offset)

• Fit the background manually with Chebyshev coefficients within bkgedt instead of refining the background. This can save you a lot of pain

• Running Powpref resets the Le Bail intensities and you have to turn off all parameters and rematch the intensities with the pattern : so you would normally avoid doing this unless you make a change to the “spacegroup” or other relevant parameters such as the “peak cutoff”


Slide 43

Brian Toby’s EXPGUI: Why Isn’t this Synchrotron data fitting? - 1

• Important to know the instrumental and synchrotron beamline constants


Slide 44


• Polarization is incorrect - is zero instead of ~1 (0.9 to 1)

– Reset all synchrotron data sets / histograms to the correct value

– The beamline should determine this parameter for users


Slide 45


• With roughly correct polarization value (set at 1), things are looking better (need to get the accurate value)


Slide 46

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 47

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.– Shift Left mouse button

in Expgui’s Liveplot


Slide 48

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 99.9%

finished• Ian Grey of CSIRO Australia or Bob Roth of NIST

USA would be more appropriate to talk about the crystal chemistry and the structure itself.


Slide 49

Nuances and 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) (looks like microdomain twinning problems)

• Single Crystal Work: Gus Mumme and Ian Grey (CSIRO, Melbourne) (looks like microdomain twinning problems)

• Powder Indexing / Le Bail fitting for looking at cell and spacegroup: Lachlan Cranswick (done at 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 (done at Columbia University)

• New single crystal work based on GSAS Refined structure: Ian Grey and Pierre Bordet


Slide 50

Is GSAS the only effective program for large restrained inorganic Rietveld Refinements(?)

• Ability to handle very 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 51

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 52

GSAS - relevant newish 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 53

GSAS scales up!: to the point of refining protein data

• As cited in R. B. Von Dreele, P. W. Stephens, G. D. Smith and R. H. Blessing, "The first protein crystal structure determined from high-resolution X-ray powder diffraction data: a variant of T3R3 human insulin-zinc complex produced by grinding", Acta Cryst. (2000).

D56, 1549-1553.

http://journals.iucr.org/d/issues/2000/12/00/issconts.html


Slide 54

GSAS: Individual Histogram Weighting

• You don’t always have a choice on data collection

• Thus may need to weight histograms (diffraction data) such that they are roughly of equal weighting


Slide 55

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 56

GSAS: Individual Histogram Weighting (using 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 menus

– x !exit expedt

• Run Powpref for new weighting to take effect


Slide 57

GSAS: If you DON’T Use Histogram Weighting

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


Slide 58

GSAS: If you DO Use Histogram Weighting

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


Slide 59

GSAS: Atom shift limits(so that atoms cannot shift more than a define absolute amount (Å))

• Set via EXPEDT– y !backup

– l !least squares setup

– l !least squares controls

– a !atom shift limits

– 0.1 !set the max allowed atom shift (0.1 Å in this example)

– x x x !exit menus

– x !exit expedt


Slide 60

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 61

VCT for Refinement (1 of 4)Variable Count Time data (as collected - CAD4 style)


Slide 62

VCT for Refinement (2 of 4)

Variable Count Time data (normalised as FCT)


Slide 63


Variable Count Time data (normalised as FCT)


Slide 64


Variable Count Time data (displayed as VCT)


Slide 65

Getting Madsen and Hill VCT data into GSAS ESD format

• Mark Bowden’s VCTCONV for DOS (runs on Windows)– Download: http://www.ceramics.irl.cri.nz/Convert.htm


Slide 66

Getting ASCII x,y,weight data into GSAS ESD format

• Using Nita Dragoe’s Powder v4 for Windows– (sequel to “Convert for Windows”)– Download via: http://www.ccp14.ac.uk/tutorial/powder/

• Open the x,y,z “free ascii” data

• Save as GSAS CW ESD format

• Done!


Slide 67

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 shareware 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 68

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 69

GSAS: setting up an EXCEL spreadsheet: Example Atom Co-ordinates

• Calculate or import an atom list within Excel where it can be easily manipulated.

• In GSAS, you input the atom list via EXPEDT

– k l a

• Use Windows “cut and paste” or @r (import macro file command) while in the relevant menu


Slide 70

GSAS: setting up an EXCEL spreadsheet: ConTEXT freeware text editor and column editing

• The freeware ConTEXT editor can be very effective in getting bits of structure (or extracting HKL files) from text files using it’s “column editing” ability.– http://www.fixedsys.com/context/

• The column editor function is not on the menu but is called using [CONTROL] L. (cannot use the mouse for click and drag while in column editing mode - only the keyboard and arrow keys)


Slide 71

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

More details given at:http://www.ccp14.ac.uk/solution/gsas/restrained_inorganic.html


Slide 72

GSAS: Getting > 1600 bond restraints in a GSAS happy format In Crystals running the script to generate the list of restraints

#use struct.txt(which contains - search outward to 3.3Å to also get Oxy-Oxy bonds: and all symmetry equivalent bonds)

#rele punch lengths.txt

#DISTANCE

OUTPUT PUNCH=RESTRAIN

SELECT RANGE=LIMITS

LIM 0 3.3 0 0

end

#rele punch dummy.txt


Slide 73

GSAS: Getting > 1600 bond restraints in a GSAS happy format Use a column able editor such as ConTEXT to change to desired bond lengths and ESDs

•E.g., – Ca - O bond length = 2.3

– ESD = 0.11

– O-O bond length = 2.90

– ESD = 0.31

– (use histogram weighting on the bond restraints to tighten or loose their influence on the refinement)

[CNTRL L] in ConTEXT to go in and out of column editing mode

http://www.fixedsys.com/context/


Slide 74

GSAS: Getting > 1600 bond restraints in a GSAS happy format Use Scott Belmonte’s COUE software to convert the Crystals restraints into GSAS format

• Run Scott Belmonte’s GPL’d COUI program

• http://www.ccp14.ac.uk/ccp/web-mirrors/scott-belmonte-software/coue/

• It is possible to do Ca* to O* mass defining of restraints in GSAS’s EXPEDT program but this method gives you complete control to easily make changes and then reinsert the restraints and know what is going on.

• Show due care as problems can occur with restraints not being inserted (or wrong atoms) due to search distance (k l s d f in expedt).

Now in GSAS Macro format

I 2.300000 0.101000 2 163

Y

I 2.300000 0.101000 2 169

Y

I 2.300000 0.101000 2 175

Y

I 2.300000 0.101000 2 218

Y

I 2.300000 0.101000 2 223

Y

I 2.300000 0.101000 2 229

Y

I 2.300000 0.101000 4 170

Y

etc, etc, etc, etc


Slide 75

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 76

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 restrained to 81


Slide 77

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 78

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 “spaces”:

– 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 79

GSAS: turning off /on histograms, restraints, atoms in EXPGUI

• Histograms can be turned on and off in Brian Toby’s EXPGUI via the “histogram” menu using “Set Histogram Use Flags” Icon.


Slide 80

GSAS: turning off /on histograms, restraints, atoms in EXPEDT

• Also can be 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 81

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 82

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


Slide 83

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 go walk-about even if constrained on a problematic refinement involving lots of pseudo-symmetry.

– 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 84

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 85

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 86

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 87

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 88

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 89

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 90

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 91

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 92

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 93

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

• Extra elements in the sample - have you used a microprobe?


Slide 94

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)– Has been stated that the above can be a common

problem due to pseudo-symmetry and wrong spacegroup

– Though in this example looks like wrong chemistry and some octahedra really being tetrahedra


Slide 95

GSAS : Combined refinement on both XRD and Neutron in C1(bond length problems - “bubbles” - to stomp on)

(which imply problems with the model or symmetry).

X-ray 7.6% R(F**2)

(~3.8% R Bragg)

Neutron 4.2% R(F**2)

(~2.1% R Bragg)


Slide 96

JANA Single Crystal and Powder Diffraction Refinement

–Developed for handling inorganics / metals - commensurate and incommensurate

–by Vaclav Petricek and Michal Dusek

–http://www-xray.fzu.cz/jana/jana.html

–Single crystal and powder diffraction (not Neutron Time of Flight (TOF))

–Powder tutorial at: http://www-xray.fzu.cz/jana/Jana2000/powders.html

–UNIX, Windows and Mac Os X

–Menu driven

–Complicated inorganic solid state structure refinement

–Commensurate, incommensurate and composite structures

–Electron density and anharmonic refinement (automatically sets the required symmetry constraints for anharmonic)

–Refinement of f’ and f’’

–Equation editor based constraints make it possible to link any one parameter to another

–Can handle multiple twins

–Many other features


Slide 97

Despite a good fit : model can still have problems : wrong chemistry was defined and structure not physically reasonable.

• In this case, GSAS refined model was used to try and determine twin laws on the single crystal data using “Jana” for refinement - and Simon Parsons and Bob Gould’s “Rotax” (Fo/Fc) twinning software; and pre-defined twinning models.

• Refinement in R3 then C1 with and without various twin models gave a final R factor of 4.6%, untwinned in R3.

• Using the powder refined model as a starting point, it would seem that “Jana” was able to minimize on the single crystal data in R3 (and C1) where other programs possibly failed.


Slide 98

WinGX and Platon for validation of the structure and looking for higher symmetry

• EXPGUI can output Shelx INS and Platon SPF files.• Exporting a Shelx file can then be read by WinGX and

transferred to all its relevant callable programs– Structure plotting

– Geometry checking

– Platon


Slide 99

WinGX for Windows single crystal suite Validation and Structure Checking

• Platon (Addsym, etc)

• CIF Validation

• Parst

• GEOM

• THMA 14c

• IDEAL

• SYMMOL

• WTANAL

• R-tensor


Slide 100

Void checking using PlatonIn the case the pink balls are showing where significant voids are in located in the structure.


Slide 101

Graphically interacting with programs that are GSAS EXP file friendly

GUI WinORTEP (http://www.chem.gla.ac.uk/~louis/software/ortep3/)

GUI WinSTRUPLO (http://www.chem.gla.ac.uk/~louis/software/struplo/)


Slide 102

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 103

Ton Spek’s Platon Addsym - another spectacular example

• Triclinic Cell - P1– structure calculated

by an-initio methods

– (96 independent Carbon atoms)


Slide 104

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 atoms in the starting structure)

– Can be just as effective for ab-initio calculations on minerals.


Slide 105

Platon’s Addsym - finding extra symmetry in hand- build inorganic models

• In the GSAS refined ceramic - original starting “model” was hand-built using crystal chemical arguments 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 106

Platon’s Addsym - finding extra symmetry in powder refined structure in triclinic

• Model refined in 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.

• Got to be careful how you use this :– e.g., increasing the values for the defaults can get

you back your “ideal” non-tilt model


Slide 107

Summary • Help show some of the potential of using GSAS and EXPGUI.

• Do the Experiment with GSAS! (sample packings, different refinements)

• Show other programs that can be of assistance - Platon, WinGX, Jana, VCTCONV, Powder v 4, etc

• Many of the listed resources are available or mirrored at:

http://www.ccp14.ac.ukThanks:

– Bob von Dreele and Alan Larson - GSAS Rietveld

– Brian Tony - EXPGUI

– Ton Spek - Platon / Mark Bowden - Vctconv / Louis Farrugia - WinGX

– Ian Grey, Gus Mumme, Bob Roth, et al - High-tech ceramic example

tricks and hints for using alan larson and bob von dreele's gsas, and brian toby's expgui,...

Documents

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structure slide

web http

brian tobys expgui