WinPLOTR: a graphic tool for powder diffraction pattern...

$: WinPLOTR: a graphic tool for powder diffraction pattern ...w3.esfm.ipn.mx/~fcruz/ADR/Cristalografia/Roisnel-Carvajal/winplotr.… · Escuela en Ciencia e Ingenieria de Materiales,$
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


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


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


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


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


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


Miscellaneous:

space group informations: symmetry operators, Wickoff positions,extinctions rules…

unit cell volume calculation

molecular weight calculation

WinPLOTR


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


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


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


http://www-llb.cea.fr/fullweb/winplotr/winplotr.htm(Tutorials and demos, download, what’s new ?, links …)


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


winplotr.set setting file


Simple display of a diffraction pattern

‘pseudo-3D ’ mode plot

reflections fitting- handling modeautomatic mode- through a parameters file

GUI for external softwares: the cimetidine example:. FullProf. DICVOL91, TREOR90, ITO15. GFourier

WinPLOTR


1. Double click on the WinPLOTR icon on the desktop

How to display a diffraction patten with WinPLOTR ?


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 ?


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


Plotting in pseudo-3D mode:

graphical options

1- X and Y shifts 2- Hidden parts 3- Change colors / markers


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)


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


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


. Linear background

. Pseudo-Voigt function : PV = η.L + (1- η).G


( )

∆−−+=

20exp.)( H

xxIBGxG2ln2

FwhmH=∆Gaussian:

Lorentzian: ( )201)(

Hxx

IBGxL

∆−+

+= 2FwhmH=∆

IFwhm

BG

x0

x


Starting parameters for least-square refinement:

. Background points (left and right)

. Bragg Position

. Integrated intensity

. Profile parameters: FWHM, η

Handling modeAutomatic peak search



Profile fitting procedure: 1-handling modeselect reflection parameters (mgal2o4s.dat)


Profile fitting procedure: 1-handling modeenter fitting parameters


Profile fitting procedure: run and results display


Profile fitting procedure: 2-automatic modeautomatic peak search (mgal2o4s.dat)


Profile fitting procedure: 2- automatic modeenter resolution parameters


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


G42 (LLB) high resolution neutron diffractometer: Instrumental resolution (λ = 2.33 Å)

2θm

Minimum in the resolution curve for: tgθm = -V/2UG42: 2θM = 112°


Profile fitting procedure: run and results display


Profile fitting procedure: 3- edit a parameter file (.pik)


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)


GUI for WinFULLPROF: edit the PCR file (input parameters)


GUI for WinFULLPROF: select the PCR and data files


GUI for WinFULLPROF: running FullProf


GUI for WinFULLPROF: automatic plot of PRF file


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


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


( ) ( ) ( )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


(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 = ⊗


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)


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= +


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


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= + + = + +


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)


How to determine microstructural informations with FullProf ? (3)

Output microstructural file: MYFILE.MIC


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)


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


WinPLOTR setting file (winplotr.set)


1- reflection positions automatic determination (WinPLOTR: ‘automatic peak search’ menu option)


2- Creating an input file for DICVOL(WinPLOTR: ‘save as .DIC file’ menu option)


3- Launching WinDIC(WinPLOTR: ‘Run DICVOL’ menu option)


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)


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


Integrated intensities extraction:FullProf in « pattern matching » mode

WinPLOTR


- 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)


4- FullProf profile refinement («pattern matching » mode)=> Extracting integrated intensities


. 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)


Structure determination: EXPO

After relabellisationRaw results


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)


Structure Rietveld refinement: Fullprof


Gfourier: Fourier maps calculations (JFOU=4: creating an input file for Gfourier)

( )[ ]rHiHF . V (r)H

..2exp).(1 πρ −= ∑


Locating Hydrogen atoms ?


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…

WinPLOTR: a graphic tool for powder diffraction pattern...

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