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.
E-mail: l.m.d.cranswick@dl.ac.uk
WWW: http://www.ccp14.ac.uk
Notes Free Zone - they are on the web
http://www.ccp14.ac.uk/poster-talks/agu2002b/
Slide 2
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
GSAS
• by Bob von Dreele and Alan
Larsen - 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 6
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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
Slide 7
• 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
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 8
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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
Slide 31
– 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
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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
Slide 36
• 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.
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 highresolution 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 38
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
GSAS: Individual Histogram Weighting
• Set via EXPEDT (using Sum(w*d**2) as a guide)
• (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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
GSAS: If you DON’T Use Histogram Weighting
X-ray 8.0% R(F**2)
Slide 42
Neutron 28.1% R(F**2)
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
GSAS: If you DO Use Histogram Weighting
X-ray 8.3% R(F**2)
Slide 43
Neutron 11.7% R(F**2)
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 45
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 50
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 51
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 52
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 53
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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
– kla
• Use Windows “cut and paste”
or @r (import macro file
command) while in the
relevant menu
Slide 54
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 55
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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:
– klsd
• More details given at:
http://www.ccp14.ac.uk/solution/gsas/restrained
_inorganic.html
Slide 56
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 60
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
GSAS: turning off /on histograms, restraints, atoms in EXPEDT
• Also can be done in GSAS’s EXPEDT
– kls
– u - The use command
• e.g., turn off X-ray data (histogram 1), turn on bond restraints (histogram
2) and neutron data (histogram 3)
kls
! Go into EXPEDT restraints menu
u1
! Use histogram 1 - X-ray Data
n
! No
u2
! Use histogram 2 - Bond Restraints
y
! Yes
u3
! Use histogram 3 - Neutron Data
y
! Yes
xxx
! Exit EXPEDIT menus and quit
Slide 62
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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
Slide 63
! last l is for list
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 65
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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.
Slide 66
p
h
e 1
t
70
/
x
x
x
x
!
!
!
!
!
!
powder setup
histogram setup
edit histogram 1 (X-ray)
set end of two theta
set 70 degrees
confirm this then exit
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
GSAS: lessen the tedium: batch file control of the refinement :
(EXPEDT Example: changing the bond restraint weighting)
• File titled bondr10.txt
Slide 67
k
!
l
!
s
!
d
!
f 10 !
x
!
x
x
x
don't make a backup of the file
least squares
soft constraints
bond length restraints
set bond restr. weighting to 10
exit expedt
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
GSAS: lessen the tedium: batch file control of the refinement :
(EXPEDT Example: only refining on neutron data)
• File titled neuonly.txt
Slide 68
k
l
s
u 1
n
u 3
y
x
x
x
!
!
!
!
!
!
least squares
soft restraints menu
use histogram 1 - X-rays
set to no
use histogram 3 - neutron
set to yes
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
GSAS: lessen the tedium: batch file control of the refinement :
(EXPEDT Example: refine heavy metal framework atoms)
• File titled
ref_fmh.txt
Slide 69
k
l
a
v
q
v
q
v
q
v
q
x
x
x
1:324 -x
1:324 -u
1:324 -f
29:108 x
!
!
!
!
!
!
!
!
!
!
!
don't make a backup of the file
least squares
atom options
get rid of any X parameters refining
quit atom list
get rid of any UISO parameters refining
quit atom list
get rid of any FRAC parameters refining
quit atom list
set framework M sites refine on coords
quit atom list
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
GSAS: lessen the tedium: batch file control of the refinement :
(EXPEDT Example: refine light metal framework atoms)
• File titled
ref_fml.txt
Slide 70
k
l
a
v
q
v
q
v
q
v
q
x
x
x
1:324 -x
1:324 -u
1:324 -f
1:28 x
!
!
!
!
!
!
!
!
!
!
!
don't make a backup of the file
least squares
atom options
get rid of any X parameters refining
quit atom list
get rid of any UISO parameters refining
quit atom list
get rid of any FRAC parameters refining
quit atom list
set framework M sites refine on coords
quit atom list
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
GSAS: lessen the tedium: batch file control of the refinement :
(EXPEDT Example: refine interstitial metal atoms - less vacancies)
• File titled
ref_int.txt
Slide 71
k
l
a
v
q
v
q
v
q
v
v
v
x
x
x
1:324 -x
1:324 -u
1:324 -f
133:144 x
147:154 x
157:162 x
!
!
!
!
!
!
!
!
!
!
!
!
don't make a backup of the file
least squares
atom options
get rid of any X parameters refining
quit atom list
get rid of any UISO parameters refining
quit atom list
get rid of any FRAC parameters refining
quit atom list
set interstitial Met to refine
set interstitial Met to refine
set interstitial Met to refine
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
GSAS: lessen the tedium: batch file control of the refinement :
(EXPEDT Example: refine oxygens)
• File titled
refoxy.txt
Slide 72
k
l
a
v
q
v
q
v
q
v
q
x
x
x
1:324 -x
1:324 -u
1:324 -f
163:324 x
!
!
!
!
!
!
!
!
!
!
!
don't make a backup of the file
least squares
atom options
get rid of any X parameters refining
quit atom list
get rid of any UISO parameters refining
quit atom list
get rid of any FRAC parameters refining
quit atom list
set oxygens to refine
quit atom list
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
GSAS: lessen the tedium: batch file control of the refinement :
(EXPEDT Example: refine UISO)
• File titled
refoxy.txt
Slide 73
k
l
a
v
q
v
q
v
q
v
q
x
x
x
1:324 -x
1:324 -u
1:324 -f
1:324 u
!
!
!
!
!
!
!
!
!
!
!
don't make a backup of the file
least squares
atom options
get rid of any X parameters refining
quit atom list
get rid of any UISO parameters refining
quit atom list
get rid of any FRAC parameters refining
quit atom list
set UISO of all atoms to refine
quit atom list
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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
Slide 74
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
echo step 4 completed >> autolog.txt
expedt model < batchjob\neuonly.txt
echo step 5 NEUTRON ONLY >> autolog.txt
expedt model < batchjob\refoxy.txt
genles model
echo step 6
completed >> autolog.txt
expedt model < batchjob\refuiso.txt
genles model
echo step 7
completed >> autolog.txt
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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)
Neutron 4.2% R(F**2)
(~3.8% R Bragg)
(~2.1% R Bragg)
Slide 77
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 predefined 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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Graphically interacting with programs that are
GSAS EXP file friendly
GUI WinORTEP
GUI WinSTRUPLO
(http://www.chem.gla.ac.uk/~louis/software/ortep3/)
(http://www.chem.gla.ac.uk/~louis/software/struplo/)
Slide 82
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
Photorealistic rendering of structures
GUI WinORTEP / GUI Struplo / WinGX
http://www.ccp14.ac.uk/tutorial/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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 84
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 abinitio calculations on
minerals.
Slide 86
AGU 2002: “hints and tricks for using GSAS Rietveld”
Lachlan M. D. Cranswick (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk
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:
http://www.ccp14.ac.uk
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 (l.m.d.cranswick@dl.ac.uk) http://www.ccp14.ac.uk