1. A structure is not truly solved until it is refined
A structure is not truly solved until it is refined! : 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.
WWW:

2. AGU 2002: “hints and tricks for using GSAS Rietveld”
Notes Free Zone - they are on the web
Slide 2
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

3. AGU 2002: “hints and tricks for using GSAS Rietveld”
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 3
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

4. AGU 2002: “hints and tricks for using GSAS Rietveld”
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 4
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

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 5
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

6. AGU 2002: “hints and tricks for using GSAS Rietveld”
by Bob von Dreele and Alan Larsen - ftp://ftp.lanl.gov/public/gsas/
CCP14 based resources:
What may look like minor changes can result in ability to handle what were intractable problems.
Slide 6
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

7. AGU 2002: “hints and tricks for using GSAS Rietveld”
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 7
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

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.)
Slide 8
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

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 9
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

10. Brian Toby’s EXPGUI: Easy to start a new refinement (2 of 13)
When prompted, enter an experimental title then press the “Set” icon.
Slide 10
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

11. Brian Toby’s EXPGUI: Easy to start a new refinement (3 of 13)
Click on the “Phase” tab and then the “Add Phase” Icon. Input the cell and spacegroup information
Slide 11
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

12. Brian Toby’s EXPGUI: Easy to start a new refinement (4 of 13)
Click “Add” then “Continue” to the cell and spacegroup information to be incorporated into GSAS.
Slide 12
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

13. Brian Toby’s EXPGUI: Easy to start a new refinement (5 of 13)
Click “Add New Atoms” and add in the starting model either by hand or importing a PowderCell format file.
Slide 13
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

14. Brian Toby’s EXPGUI: Easy to start a new refinement (6 of 13)
Click “Add Atoms” to get the starting model into GSAS
Slide 14
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

15. Brian Toby’s EXPGUI: Easy to start a new refinement (7 of 13)
Set appropriate damping factors (I tend to like somewhere between 7 and 9)
(Lessen damping factors if parameter shifts are too small)
Slide 15
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

16. Brian Toby’s EXPGUI: Easy to start a new refinement (8 of 13)
Add the first XRD diffraction file: Select “Histogram” tab then “Add New Histogram” icon.
Slide 16
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

17. Brian Toby’s EXPGUI: Easy to start a new refinement (9 of 13)
Via the GUI, select the data file and the instrument parameter file. (in this case an XRD data file)
Slide 17
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

18. Brian Toby’s EXPGUI: Easy to start a new refinement (10 of 13)
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 18
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

19. Brian Toby’s EXPGUI: Easy to start a new refinement (11 of 13)
It is easy to add another data file. Select the “Add New Histogram” icon. (select the Bank number if this is relevant)
Slide 19
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

20. Brian Toby’s EXPGUI: Easy to start a new refinement (12 of 13)
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 20
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

21. Brian Toby’s EXPGUI: Easy to start a new refinement (13 of 13)
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 (can be preferable to use this instead of “zero offset”)
Slide 21
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

22. Brian Toby’s EXPGUI: Profile Screen in EXPGUI with shft
Slide 22
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

23. New(ish) Features in Brian Toby’s EXPGUI
Graphically define the background
Graphically exclude regions
Can export structures to Platon format (Addsym, etc)
Slide 23
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

24. 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 24
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

25. Brian Toby’s EXPGUI: Graphically Defining the Background (2 of 3)
Use the Fit icon to fit a Chebyshev function through the data points - increase number of terms as required
Slide 25
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

26. Brian Toby’s EXPGUI: Graphically Defining the Background (3 of 3)
Save into EXP file. Background is now fixed but can be refined at the click of a button. Done.
Slide 26
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

27. 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 27
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

28. Brian Toby’s EXPGUI: Graphically Excluding Regions (2 of 3)
Point and click to select excluded regions
Slide 28
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

29. Brian Toby’s EXPGUI: Graphically Excluding Regions (3 of 3)
Run powpref and genles for this to take effect
Slide 29
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

30. AGU 2002: “hints and tricks for using GSAS Rietveld”
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 30
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

31. 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 31
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

32. AGU 2002: “hints and tricks for using GSAS Rietveld”
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 32
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

33. 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 33
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

34. 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 34
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

35. AGU 2002: “hints and tricks for using GSAS Rietveld”
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 35
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

36. AGU 2002: “hints and tricks for using GSAS Rietveld”
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 36
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

37. 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 37
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

38. 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,
Slide 38
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

39. 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 39
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

40. 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 40
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

41. 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 41
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

42. GSAS: If you DON’T Use Histogram Weighting
X-ray 8.0% R(F**2)
Neutron 28.1% R(F**2)
Slide 42
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

43. GSAS: If you DO Use Histogram Weighting
X-ray 8.3% R(F**2)
Neutron 11.7% R(F**2)
Slide 43
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

44. AGU 2002: “hints and tricks for using GSAS Rietveld”
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 44
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

45. 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:
Slide 45
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

46. AGU 2002: “hints and tricks for using GSAS Rietveld”
VCT for Refinement (1 of 4) Variable Count Time data (as collected - CAD4 style)
Slide 46
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

47. AGU 2002: “hints and tricks for using GSAS Rietveld”
VCT for Refinement (2 of 4) Variable Count Time data (normalised as FCT)
Slide 47
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

48. AGU 2002: “hints and tricks for using GSAS Rietveld”
VCT for Refinement (3 of 4) Variable Count Time data (normalised as FCT)
Slide 48
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

49. AGU 2002: “hints and tricks for using GSAS Rietveld”
VCT for Refinement (4 of 4) Variable Count Time data (displayed as VCT)
Slide 49
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

50. Getting Madsen and Hill VCT data into GSAS ESD format
Mark Bowden’s VCTCONV for DOS (runs on Windows)
Download:
Slide 50
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

51. Using Nita Dragoe’s Powder v4 for Windows
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:
Open the x,y,z “free ascii” data
Save as GSAS CW ESD format
Done!
Slide 51
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

52. AGU 2002: “hints and tricks for using GSAS Rietveld”
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.
One solution is to use a spreadsheet program that allows for flexibility and extendability (MS-EXCEL for Windows)
Slide 52
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

53. Restrained refinement in GSAS: setting up an EXCEL spreadsheet
CCP14 based tutorial and example files at :
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:
Coue:
Atom constraints
Total cell contents and/or charge balance constraints
If applicable, other scripts for controlling GSAS
Slide 53
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

54. 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” (import macro file command) while in the relevant menu
Slide 54
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

55. AGU 2002: “hints and tricks for using GSAS Rietveld”
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.
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 55
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

56. AGU 2002: “hints and tricks for using GSAS Rietveld”
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:
Slide 56
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

57. AGU 2002: “hints and tricks for using GSAS Rietveld”
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 57
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

58. AGU 2002: “hints and tricks for using GSAS Rietveld”
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 58
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

59. AGU 2002: “hints and tricks for using GSAS Rietveld”
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 59
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

60. 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”:
Use - import macro file command while in the relevant menu
Done!
Slide 60
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

61. 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 61
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

62. 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
x x x ! Exit EXPEDIT menus and quit
Slide 62
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

63. 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 63
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

64. 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
Be keen to exchange experiences on this
Slide 64
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

65. AGU 2002: “hints and tricks for using GSAS Rietveld”
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)
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 65
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

66. AGU 2002: “hints and tricks for using GSAS Rietveld”
GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: script to increase the refined angular range)
p ! powder setup
h ! histogram setup
e ! edit histogram 1 (X-ray)
t ! set end of two theta
! set 70 degrees
/ ! confirm this then exit x
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.
Slide 66
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

67. AGU 2002: “hints and tricks for using GSAS Rietveld”
GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: changing the bond restraint weighting)
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
File titled bondr10.txt
Slide 67
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

68. AGU 2002: “hints and tricks for using GSAS Rietveld”
GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: only refining on neutron data) 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
File titled neuonly.txt
Slide 68
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

69. AGU 2002: “hints and tricks for using GSAS Rietveld”
GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: refine heavy metal framework atoms)
k ! don't make a backup of the file
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
v 1:324 -f ! get rid of any FRAC parameters refining
v 29:108 x ! set framework M sites refine on coords x
File titled ref_fmh.txt
Slide 69
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

70. AGU 2002: “hints and tricks for using GSAS Rietveld”
GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: refine light metal framework atoms)
k ! don't make a backup of the file
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
v 1:324 -f ! get rid of any FRAC parameters refining
v 1:28 x ! set framework M sites refine on coords x
File titled ref_fml.txt
Slide 70
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

71. AGU 2002: “hints and tricks for using GSAS Rietveld”
GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: refine interstitial metal atoms - less vacancies)
k ! don't make a backup of the file
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
v 1:324 -f ! get rid of any FRAC parameters refining
v 133:144 x ! set interstitial Met to refine
v 147:154 x ! set interstitial Met to refine
v 157:162 x ! set interstitial Met to refine x
File titled ref_int.txt
Slide 71
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

72. AGU 2002: “hints and tricks for using GSAS Rietveld”
GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: refine oxygens)
k ! don't make a backup of the file
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
v 1:324 -f ! get rid of any FRAC parameters refining
v 163:324 x ! set oxygens to refine x
File titled refoxy.txt
Slide 72
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

73. AGU 2002: “hints and tricks for using GSAS Rietveld”
GSAS: lessen the tedium: batch file control of the refinement : (EXPEDT Example: refine UISO)
k ! don't make a backup of the file
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
v 1:324 -f ! get rid of any FRAC parameters refining
v 1:324 u ! set UISO of all atoms to refine x
File titled refoxy.txt
Slide 73
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

74. AGU 2002: “hints and tricks for using GSAS Rietveld”
GSAS: lessen the tedium: batch file control of the refinement : (Create a Batch File to follow your desired command sequence)
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
echo step 4 completed >> autolog.txt
expedt model < batchjob\neuonly.txt
echo step 5 NEUTRON ONLY >> autolog.txt
expedt model < batchjob\refoxy.txt
echo step 6 completed >> autolog.txt
expedt model < batchjob\refuiso.txt
echo step 7 completed >> autolog.txt
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
Slide 74
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

75. 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 75
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

76. AGU 2002: “hints and tricks for using GSAS Rietveld”
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 76
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

77. AGU 2002: “hints and tricks for using GSAS Rietveld”
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 77
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

78. AGU 2002: “hints and tricks for using GSAS Rietveld”
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 78
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

79. AGU 2002: “hints and tricks for using GSAS Rietveld”
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 79
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

80. AGU 2002: “hints and tricks for using GSAS Rietveld”
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 80
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

81. Void checking using Platon
In the case the pink balls are showing where significant voids are in located in the structure.
Slide 81
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

82. Graphically interacting with programs that are GSAS EXP file friendly
GUI WinORTEP (
GUI WinSTRUPLO (
Slide 82
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

83. AGU 2002: “hints and tricks for using GSAS Rietveld”
Photorealistic rendering of structures GUI WinORTEP / GUI Struplo / WinGX
Can open a wide variety of file formats including GSAS!
Slide 83
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

84. AGU 2002: “hints and tricks for using GSAS Rietveld”
Ton Spek’s Platon Addsym - finding extra symmetry and exploring symmetry in simple to complex polymeric inorganics
WWW:
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 84
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

85. AGU 2002: “hints and tricks for using GSAS Rietveld”
Ton Spek’s Platon Addsym - another spectacular example
Triclinic Cell - P1
structure calculated by an-initio methods
(96 independent Carbon atoms)
Slide 85
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

86. AGU 2002: “hints and tricks for using GSAS Rietveld”
Ton Spek’s Platon Addsym - spectacular example Run 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 86
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

87. AGU 2002: “hints and tricks for using GSAS Rietveld”
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 87
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

88. AGU 2002: “hints and tricks for using GSAS Rietveld”
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 88
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick

89. AGU 2002: “hints and tricks for using GSAS Rietveld”
Summary
Help show some of the potential of using GSAS and EXPGUI for some of your mineralogical and inorganic powder samples.
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:
Thanks:
Bob von Dreele and Alan Larsen - 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
Slide 89
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick