Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
WinPLOTR: a graphic tool for powder diffraction pattern analysis
T. Roisnel1 and J. Rodriguez-Carvajal2
1- Laboratoire de Chimie du Solide et Inorganique Moléculaire(UMR CNRS 6511), Institut de Chimie de Rennes,
Université de Rennes 135042 Rennes Cedex (France)
2- Laboratoire Léon Brillouin (CEA-CNRS), C.E. Saclay91191 Gif sur Yvette Cedex (France)
[email protected]://www-llb.cea.fr/fullweb/winplotr/winplotr.htm
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
computer system:. Windows 9x (x=5,8),2k ,NT. Color screen resolution (1024 x 768)
language: Fortran 90 (www.lahey.com)RealWin (www.indowsway.com) as Windows interface
==> windows, menus, dialog boxes, mouse …
WinPLOTR
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
WinPLOTR T.R. , J.R.C.
MENDEL periodic table T.R. , J.R.C.
DICVOL indexation D. Louër(Rennes)
TREOR indexation P.E. Werner (Stokholm)
ITO indexation J. Visser (Delft)
SUPERCELL supercell determination J. R.C.incommensurate propagationvector components
WinPLOTR installation ftp://ftp.cea.fr/pub/llb/divers/winplotr/winplotr.zipftp://ftp.cea.fr/pub/llb/divers/fullprof.2k/Windows/setup_FullProf_Suite.exe
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
FULLPROF L.S. refinement of powder J.R.C.and/orsingle crystal dataexamples, user’s guide …
EdPCR GUI to edit, modify PCR J. Gonzalez-PlatasFullProf input files (Tenerife)Files conversion: CIF to PCR J.R.C
INS to PCR
GFOURIER Fourier maps (calculation and J.G.P., J.R.C.graphics)
install.exe: . automatic installation of WinPLOTR and its tools. WinPLOTR and FullProf environment variables
WinPLOTR installation
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Plotting powder diffraction patterns:
raw data, normalized ou refined data:
neutrons, X-Rays (conventional or synchrotron)
constant wavelength, dispersive energy, time of flight
a large number of data file formats coming from several kinds of diffractometers
scattering space: - 2θ(°)/time of flight (µsec.)/energy (KeV)- Q (Å-1) , 1/d (Å-1), sinθ/λ (Å-1)- d (Å)
Intensity scale: linear, log(Y), SQRT(Y)
WinPLOTR
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Calculations facilities:
automatic search procedures: background, reflections
background substraction
fit procedure (interactif / automatic)
single line micro-structural analysis
smoothing, normalization, difference …
resolution curve (Caglioti, IRF file)
WinPLOTR
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Miscellaneous:
space group informations: symmetry operators, Wickoff positions,extinctions rules…
unit cell volume calculation
molecular weight calculation
WinPLOTR
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Graphical capabilities:
graphical options: zoom, shift/offset, pseudo-3D, error barrs …
Create BMP, PostScript files
Change markers symbols, colors, styles (non-continuous / continuous,dashed lines, histograms …)
change text fonts
…
WinPLOTR
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Graphical User Interface for powder diffraction analysis programs:
FullProf (JRC): profile refinement (Rietveld, whole pattern fitting) . PCR file editing. FullProf launching. PRF file plotting (Rietveld plot)
automatic indexing of powder diffraction patterns: DICVOL (D. Louër), TREOR (P.E. Werner), ITO (Visser):
. Peak search
. Input file creating (help of a dialog box)
. WinDICVOL/WinTREOR90/WiTO launching
. Automatic creation of a PCR file for FullProf (« pattern matching » mode)
WinPLOTR
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
SuperCELL (JRC): determination of a super unit cell or thecomponents of an incommensurate propagation vector
EdPCR (J. Gonzalez-Platas, JRC):
user’s defined program (winplotr.set)
WinPLOTR
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
http://www-llb.cea.fr/fullweb/winplotr/winplotr.htm(Tutorials and demos, download, what’s new ?, links …)
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
The setting file winplotr.set:
adapt WinPLOTR capabilities to the user needs
Definition of:
Arrays dimensionsPrograms launched by WinPLOTRExternal applications: editor, browser, PDF and PS readers, …Graphical options: colors, markers, fonts …Instrumental parameters: wavelength, resolution functionData files extensions
…
WinPLOTR
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Simple display of a diffraction pattern
‘pseudo-3D ’ mode plot
reflections fitting- handling mode- automatic mode- through a parameters file
GUI for external softwares: the cimetidine example:. FullProf. DICVOL91, TREOR90, ITO15. GFourier
WinPLOTR
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
1. Double click on the WinPLOTR icon on the desktop
How to display a diffraction patten with WinPLOTR ?
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
2. Launch WinPLOTR through a command line:
. Open a DOS console (Start / Execute / cmd)
. Go to the working directory:c:\> cd d:\Docs\Conferences2004\Mexico-Unam\Thierry\MgAl2O4
. Run WinPLOTR:
d:\Docs\Conferences2004\Mexico-Unam\Thierry\MgAl2O4> winplotr 3 mgal2O4s.dat
Program to be launched format File name
How to display a diffraction patten with WinPLOTR ?
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Plotting in pseudo-3D mode:
reading the data
1- Edit a buffer file 2- Open the buffer file 3- Select the common format
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004Laffargue et al, J. Alloys and Compounds 262-263(1997) 219-224
Plotting in pseudo-3D mode
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Plotting in pseudo-3D mode:
graphical options
1- X and Y shifts 2- Hidden parts 3- Change colors / markers
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Typical diffraction patterns of magnetic ordering (G4.1, LLB)
Laffargue et al, J. Alloys and Compounds 262-263(1997) 219-224
Paramagnetic phask = (kx kx ½)
k = (0 0 ½)
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Save the pattern plot as .PGF file
Laffargue et al, J. Alloys and Compounds 262-263(1997) 219-224
Save:
. Graphical options: . Graduations. Colors. Markers. Text. fonts …
. X,Y data
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
The profile can be modelled using the calculated counts yci at the ithstep by summing the contribution from neighbouring Bragg reflections plus the background.
The model to calculate a powder diffraction pattern is (for a single phase):
( )= + Ω −∑ h hh
ci i iy b I T T
background
integratedintensity of Bragg reflection h
Normalized profilefunction (at point i for reflection h)
calculated intensityat the point i
WinPLOTR: profile fitting procedure
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
. Linear background
. Pseudo-Voigt function : PV = η.L + (1- η).G
WinPLOTR: profile fitting procedure
( )
∆−−+=
20exp.)( H
xxIBGxG2ln2
FwhmH=∆Gaussian:
Lorentzian: ( )201)(
Hxx
IBGxL
∆−+
+= 2FwhmH=∆
IFwhm
BG
x0
x
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Starting parameters for least-square refinement:
. Background points (left and right)
. Bragg Position
. Integrated intensity
. Profile parameters: FWHM, η
Handling modeAutomatic peak search
WinPLOTR: profile fitting procedure
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Profile fitting procedure: 1-handling modeselect reflection parameters (mgal2o4s.dat)
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Profile fitting procedure: 1-handling modeenter fitting parameters
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Profile fitting procedure: run and results display
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Profile fitting procedure: 2-automatic modeautomatic peak search (mgal2o4s.dat)
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Profile fitting procedure: 2- automatic modeenter resolution parameters
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Instrumental resolution of a neutron 2 axis diffractometer
Caglioti formula: Fwhm2 = U.tg2θ + V.tgθ + WInstrumental ressolution parameters U, V, W = f(αi, βM, θM)
Ref.:- Caglioti et al, Nuclear Instruments 3 (1958) 223-228- Hewatt, Nuclear Instruments and Methods 127 (1975) 361-370
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
G42 (LLB) high resolution neutron diffractometer: Instrumental resolution (λ = 2.33 Å)
2θm
Minimum in the resolution curve for: tgθm = -V/2UG42: 2θM = 112°
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Profile fitting procedure: run and results display
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Profile fitting procedure: 3- edit a parameter file (.pik)
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
GUI for FullProf
WinPLOTR
Edit PCR file (input parameters)Select PCR and DAT files to launch FullProfPlotting the PRF file (Yobs, Ycalc, Yobs-Ycalc, Bragg positions)
Winplotr (mgal2o4s)
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
GUI for WinFULLPROF: edit the PCR file (input parameters)
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
GUI for WinFULLPROF: select the PCR and data files
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
GUI for WinFULLPROF: automatic plot of PRF file
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
GUI for FULLPROF: refinement of CeO2 (particle size round robin)
Xray data: D500 Siemens diffractometer (Rennes Univ.)λ = 1.54056 A (Ge111)
Sample: CeO2 F m 3 m (a=5.412 A)
Microstructural analysis:. Voigt function analysis (NPROF=7). Use of IRF file
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
The profile function is characterized by:
Full Width at Half Maximum: H (in deg. for cwl data)
Integral breath β or β* (β* = β2θ.cosθ/λ)
Profil parameter (form factor) φ = H/β
The profile function Ω(x)
( ) ( ) ( )x f x g xΩ = ⊗
Observed profile Instrumental profile(diffractometer setup + wavelength dispersion)Intrinsic profile
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
( ) ( ) ( )x f x g xΩ = ⊗(1) ( ) ( )H g H f Ω ≈( ) ( )x g x
“Instrumental” profile is preponderant:* low resolution diffractometer (neutrons)* “perfect” sample (infinite coherent domain size)
(2) ( ) ( )H f H g ( ) ( )x f xΩ ≈
Sample profile is preponderant:* nanocristalline powders
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
(3) ≈( ) ( )H g H f
Separation of instrumental and sample contributions needs a perfect knowledge of the g(x) function. f(x) will be obtain through a mathematical deconvolution
( ) ( ) ( )x f x g xΩ = ⊗
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
The Voigt function
Voigt function : convolution of Gauss function and Lorentz function
( , ) ( , ) ( , , )⊗ =L LG GG x H L x H V x H H
1 21 1 2 2( , , ) ( , , ) ( , , )⊗ = G LG L G LV x H H V x H H V x H H2 2 2
1 2
1 2
= += +
G G G
L L LH H HH H H
( ) ( ) ( )x f x g xΩ = ⊗If Ω and g are Voigtian: f is Voigtian (f contains micro-structural features)
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Micro-structural features (size, strains) are separated through different angular dependences of the Gauss part and the Lorentz part of the Voigt function used to described the sample profile.
(1) Particle size effects: H(g) = f(1/cosθ)
Gaussian component:
Lorentzian component:
2 22
_ 2
( ( ))cos
isoG size
G F S zH γθ
+=
( )_
1 ( ( ))cos
isoL size
Y F S zH
γθ
+ −=
(2) Microstrain effects: H(g) = f(tgθ)
Gaussian component:
Lorentzian component:
( )( )2 2 2 2_ 1 . .G strain str isoH D U tgξ θ= − +
( )_ . .L size iso strH X D tgξ θ= +
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Diffraction peaks profile analysis (microstructural parameters determination –particles size, microstrains)- needs a good knowledge of theInstrumental Resolution Function ( )instrH f θ=
Sample under study and reference sample has to be measured in the same experimentalconditions (diffractometer setup, slits, sampleholder …)
Reference sample: * standart NBS (LaB6, Si …)* strainless and well cristallized sample
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
How to determine microstructural informations with FullProf ? (1)
The selected profile function:NPROF = 7: Voigt function approximated by a pseudo-Voigt function through
T.C.H. approximations ( , ) ( , )G L PV VH HH ηReference sample data analysis (use Voigt function)
Instrumental Resolution Function (FullProf, WinPLOTR)
Broadened pattern analysis: IRF is fixed through IRESO parameter
and read in the FILERES file (free format)
IRESO = 1,2,3:
IRESO = 1
IRESO = 2
IRESO = 3
IRESO = 4 list of 2 (2 ) (2 )LGH Hθ θ θ
, , , , ,i i i i i iU V W X Y Z2 2tan tan tan cosG i i i L i i iH U V W H X Y Zθ θ θ θ= + + = + +
( )2 2tan tan 2 2G i i i L i i iH U V W H X Y Zθ θ θ θ= + + = + +
( ) ( )2 2 2 2 2G i i i L i i iH U V W H X Y Zθ θ θ θ= + + = + +
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
How to determine microstructural information with FullProf ? (2)
Control parameters:
isotropic effects:* crystallite size : IG YL
* strain effects : UG XL
anisotropic effects:* crystallite size (lorentzian component) :
ISTR, SZ, hkl, ISizeModel
* strain effects (gaussian component) :ISTR, STRAIN-MODEL,hkl, strain_parameters (Stephens notation)
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
How to determine microstructural informations with FullProf ? (3)
Output microstructural file: MYFILE.MIC
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
GUI for FULLPROF: refinement of CeO2 (particle size round robin)
PCR file:
Run #1:. IRESO = 4 (use of IRF file). Broadening parameters fixed to 0. . Refine cell parameters. Fixed background points
Run #n:. + refine size isotropic broadening parameters
Winplotr (ceo2dl)
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Ex: Cimetidine S4C40N24H64 (J. Appl. Cryst. (1991), 24, 222-226)
Structure determination from synchrotron powder diffraction data (λ=1.52904Å,Daresbury,UK):
1- Unit cell determination DICVOL, TREOR, ITO2- Integrated intensities
extraction FullProf in pattern matching mode3- Structure determination EXPO (C. Giacovazzo)4- Structure refinement FullProf in Rietveld mode 5- Fourier maps Gfourier
WinPLOTR: GUI for several cristallographic softwares
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
1- reflection positions automatic determination (WinPLOTR: ‘automatic peak search’ menu option)
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
2- Creating an input file for DICVOL(WinPLOTR: ‘save as .DIC file’ menu option)
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
3- Launching WinDIC(WinPLOTR: ‘Run DICVOL’ menu option)
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
4- Creating an input PCR file for FullProf (« pattern matching »mode)
. Instrumental parameters: (dialog box). Wavelength. Resolution parameters (U, V, W). Peaks profile
. Structural parameters: (through WinDICVOL). Unit cell parameters. Space group (point group)
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Extinctions analysis:100 not observed : h00 h=2n001 not observed : 00l l=2n030 not observed : 0k0 k=2n20-1 not observed : h0l h+l=2n101 observed : h0l h+l=2n
P21/n
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Integrated intensities extraction:FullProf in « pattern matching » mode
WinPLOTR
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
- Extand the 2θ range to the whole diffraction pattern
- Refine: - cell parameters, zero shift- peaks profile (shape, FWHM, asymetry)- background- JHKL=-2 (create output HKL file for EXPO)
WinPLOTR:edit the PCR file (input parameters for FullProf)
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
4- FullProf profile refinement («pattern matching » mode)=> Extracting integrated intensities
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
. EXPO input file
%struct cime%job cimetidine -- Synchrotron data%init%data
cont S 4 C 40 N 24 H 64wave 1.52904cell 10.6986 18.8181 6.8246 90.000 111.284 90.000space p 21/nref2 pm2.hkl
%continue
Structure determination: EXPO(http://www.irmec.ba.cnr.it)
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Structure determination: EXPO
After relabellisationRaw results
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Rietveld refinement
- Structural parameters:. Atomic positions (previously determined by EXPO). Isotropic thermal parameters. Cell parameters, zero shift
- Profile parameters:. peaks profile (shape, FWHM, asymetry). background
WinPLOTR:edit the PCR file (input parameters for FullProf)
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
Gfourier: Fourier maps calculations (JFOU=4: creating an input file for Gfourier)
( )[ ]rHiHF . V (r)H
..2exp).(1 πρ −= ∑
Escuela en Ciencia e Ingenieria de Materiales, Mexico, 2004
WinPLOTR Web site: http://www-llb.cea.fr/fullweb/winplotr.htm
FullProf Web site: http://www-llb.cea.fr/fullweb/fp2k/fp2k.htmftp://ftp.cea.cea.fr/pub/llb/divers/
- FullProf Suite, winplotr.zip, user ’s guide, demos, news, tutorials …
LLB powder diffraction Web site: http://www-llb.cea.fr/fullweb/powder.htm
- WinPLOTR, PLOTR, plotrHKL- FULLPROF, FOURIER- BONDSTR ...
Interesting Web sites:
CCP14: http://www.ccp14.ac.ukSoftwares web-mirrors, tutorials …
SINCRIS:http://www.lmcp.jussieu.fr/sincris-topCrystallographic software database
IUCr: http://www.iucr.org/iucr-top/comm/cpd/Commission on powder diffraction
LeBail: http://pcb4122.univ-lemans.fr/tutorials, course, ESPOIR…