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Powder Diffraction - Max Planck Institut für Festkörperforschung

1. ai FE Di Petes Beine Bot Mel il pin ghi Sach gad Pesi cl Frese pape 4 cme nea A intensi Figure 15 Multiple pattern display An interesting feature is the ability to export an AVI film of the single patterns cycling through the selected sets and the zoomed range To do this press Export gt AVT in the context menu To make this export as versatile as possible it creates a film only of the currently selected data range intensity and selected data sets You will have to select an appropriate compression algorithm for the video In our experience DiVX4 high motion gives the best results This feature is only available on the Windows operating system Please note the installation of the library for this function are described above see Installation Normalizing Patterns Data collected using image plates generally lacks a beam decay correction This can be partially alleviated by a normalization Two or more patterns can be corrected using this function Menu Edit gt Normalize patterns Select the patterns via the list or select patterns belonging to a phase by choosing the appropriate phase Next ensure the method of normalization is correct All patterns that have been selected are superimposed over one another It is possible to zoom by dragging open a zoom box with a left click Select the region you wish to normalize the patterns with by dragging over a range with a right click
2. Fi bE Fair Tak Pia an ta Pri Tp Back gaunt Paak ahi Premion graphics A bemannen AE SER ay EEE Kin FEN akp O I TT ee 0 anti POF ii mee 6 Cnt Teese 28 e 33 Le Bail refinement Figur Peak analysis A new tool has been designed to assist in the sequential refinement of peak profiles To call it you should select the menu Tool gt Peak analysis Pattern Tools Plot Help Le Ball Peak Analysis data is RAW R Erh E Figure 34 Peak analysis menu The window in Figure 35 shall appear The pattern ranges that have been set in the main program interface are the initial ranges displayed by the peak progression tool It is therefore very useful to select the interesting range using the film plot display and the zoom function before starting the tool The rendering of a couple of hundred patterns might be slow on older hardware so it is in your own interest to reduce the amount of information The aim was to create a module which does sequential peak profile refinement in a robust manner The tools that you can select on the left are 1 azoom tool works in very much the same manner as the normal zoom tool 2 select ranges Drag this tool across a peak to select it and have the peaks displayed or found should none have been determined 3 apeak editor Add remove peaks using this tool Once you have selected a range with the range tool you
3. Center Atom No atom A b Name Type x Y zZ 1 C 8 231450 21 035601 48 083698 2 N2 N 7 811390 22 215900 47 247200 3 C3 C 6 908290 21 994101 46 270500 a N4 N 6 650100 _20 730900 46 012600 1 lt 0 Scattering Powers parameters for Cimetidine Je amp Scattering Powers AntiBump BondValence a Biso Charge Red Green Blue ML Error gho c 3 000 0 000 0 500 0 500 0 500 0 000 0 N 3 000 0 000 0 184 0 310 0 184 0 000 0 S 3 000 0 000 1 000 1 000 0 000 0 000 0 lt 4 Restraints for Cimetidine Jo amp Bond Lengths Bond Angles Dihedral Angles Rigid Groups c Atom1 Atom2 Length Restraint Sigma Delta 1 N2 1 506415 1 470000 0 010000 0 020000 2 N2 c3 1 348602 1 400000 0 010000 0 020000 3 c3 N4 1 314858 1 400000 0 010000 0 020000 4 N4 c5 1 413312 1 370000 0 010000 0 020000 5 c5 N6 1 158503 1 130000 0 010000 0 020000 6 c3 N7 1 472136 1 400000 0 010000 0 020000 7 N7 c8 1 457902 1 470000 0 010000 0 020000 8 c8 c9 1 724760 1 540000 0 010000 0 020000 9 c9 S10 1 804693 1 820000 0 010000 0 020000 10 S10 Cll 1 950899 1 820000 0 010000 0 020000 ons nm n m neh rannnan annnnnn annnannn Fig l A new tabular interface is used for a atom types ScatteringPower including access to anti bump and bond valence parameters b list of molecule atoms supporting more than 1000 atoms and c the list of molecule restraints bond length bond angle dihedral angle and rigid group A graphic d shows the evolution of
4. j 5 5 s Delete Auen q Cm E so ox Aim Mame 505 X Y z epson be F Fig 1 SARAh Representational Analysis main screen showing selection of space group propagation k vector magnetic atom coordinates entry A help window is displayed to the right explaining the input SARAh Representational Analysis uses group theory to calculate the different types of magnetic structure classified according to the symmetry of the associated irreducible representation The representations that are the starting point for these calculations are by default those collated in the tables of Kovalev and so are readily verifiable A second option based on ab inito calculations is also present if the user prefers The different possible magnetic structures are expressed using the formalism of basis vectors vector components for the atomic positions that are related by symmetry Linear combination of the basis vectors associated with an irreducible representation defines the possible magnetic structures that correspond to that symmetry type Refinement of a neutron diffraction data using SARAh Refine then corresponds to trying in turn each of the representations and refining the relative proportions of the different basis vectors 51 Central to the design of SARAH is the desire to simplify the calculations and refinement processes while making them more physically reasonable In particular the prejudices generation of trial structures as
5. Mer tii misik Pie LE Paien Aal Bot mel EE ENNE E Diren dwa or w Figure 10 The first powder pattern Data reduction Cropping tool The limits of the powder patterns generally need to be changed This is conveniently done by means of the cropping tool A click on the crop button Figure 11 draws two vertical lines which you can drag to define the desired range Figure 12 Figure 11 Crop button 14 fremir ii 7 mi E Pie bE Pien fel Fi Pet n Keen chat or Flay 5 FE F igure 12 Cropping bars On pressing the enter button the entire array is cropped to the new range Please note It is a good idea to save the data regularly to avoid possible data loss File gt Save Single pattern visualization Figure 13 Zoom button Pi bi Pattern fede Mat Hobs er TT Figure 14 Zoom tool The default tool in the 2D plot window is the zoom box Figure 14 Pull it over a region you wish to enlarge Once the enlarged window is displayed click in the borders around the plot to navigate A click to the right of the X axis moves the pattern s to the left and displays the pattern in a 20 region shifted 10 higher Clicking in the other borders works in analogous fashion A single click in the plot window resizes it to the maximum view Selecting multiple patterns from the list displays them up to 6 colour coded overlaid patterns Figure 15
6. BASE BAST BASA BASI j sewnsskorsorsen eS oo co So eo co oo oo a oo oo Soo a oo oo oo Saada So a So oo ob ee a a oe ob pe be OD j San om Sa as Sao m ba H l tom Typ Mag Ver x 7 Z Biso EI ge EZ i C4 Cs co ET Eg Eg Hagh NAL OANA 1 En Oe ee ME EIE 0 56 LEE 8 a8 1 2 2 55 Be SEE H fae S886 6 6860 6 885 48 599 9 899 48 805 na B88 888 8 88 2 2 20 5 88 2 28 MG MMHG Z G FE 0 75000 ee 2 ee er ee Ki EEE 2 5 T Li AAA mE i 65 E K 8 868 BEER ELBE S E g a g m eRe 6 66 8 88 8 88 3 89 2 23 98 5 03 gt Profile Pormeters for Pathern 2 Fig 4 The magnetic part of the FullProf input file as generated by SARAh Refine The mixing coefficients of the selected basis vectors correspond to the variables C1 C9 While representational theory is arguably the most powerful symmetry formalism for magnetic structure in general use it is important to point out that it remains incomplete Corepresentation theory is an extension of representational theory made by inclusion of antiunitary symmetry often incorrectly associated with time reversal Its use will further simplify the different symmetry allowed types of magnetic structure and reveal more about the nature of the concomitant ordering process While at present no distributed programs contain corepresentational theory its inclusion has been carried out in SARAH corepresentational theory which is due for general release in 2006 after final testing
7. a Universit Joseph Fourier Grenoble I CEA Grenoble DRFMC SP2M 17 rue des Martyrs 38054 Grenoble Cedex 9 France b Laboratoire de Cristallographie 24 quai Ernest Ansermet CH 1211 Geneve 4 Switzerland Email Vincent Favre Nicolin ujf grenoble fr WWW hitp objcryst sourceforge net Fox A new version of Fox will be available in november 2005 beta test versions are available for those interested see http objcryst sf net Fox FoxDevelopment Along with speed improvements twice faster for powder pattern calculations more on windows with the change of compiler many features have been included or improved in this new version lt Q FOX Free Objects for Xtal structures v1 6 99CVS Nov 4 2005 Jo amp Eile Objects Help Crystals Powder Diffraction Single Crystal Diffraction Global Optimization c BERN S lt Q Tracked data J oO x Cimetidjne Po wder Optimiz ation Ov erall LogLikelinood Cimetidine LogLikelihood Cimetidine BumpMergeCost 13 2 06 Cimetidine BondValenceCost Cimetidine XRay pattern LogLikelihood ScatteringPowerAtom S Sy cost 77404 570312 Best Configur cost 112733 171875 Run 1 cost 218564 796875 Run 2 cost 111049 898438 Run 3 i y 1 6e 06 cost 109065 960938 Run 4 cost 51 7326 687500 Run 5 800000 d 4 cost 1491757 250000 Run 6 o 4 t 0 50000 100000 150000 200000 x 165516 265625 y
8. i Use logarithmic axis Export to IDL Text show is Parameters Figure 47 Deleting an element We also alter X axis properties to Titel 2Q Font Symbol And the Y axis to Titel Scan number Font Times These changes give us a 20 on the X axis and a similar font for the Y axis Now we create that semi transparent 2D visualization hovering over the surface Select the menu item Insert gt Visualization Figure 48 You shall then be prompted for the type and variables defining the item We chose an Image type top right box opened the Surface branch on the left that 1s where the data is and assigned the Z value to the pixels Y values to the Y axis and X values to the X axis To do the assigning mark the data value on the left and click on the small right arrow in front of the fields you wish to be associated with the data Leave palette empty and press OK So that is done but where is the image Find your way back to the Visualization Browser or properties window as described above It shall have a new entry for the image Highlight the image and alter the Z value to well above the maximum intensity in your data array In our case it is 85000 Figure 50 Further set the transparency to 40 al Pis Sb irast Operations Wide Hie T u roe _ lek It minci fen cici and hag in aniti are im M44 Figure 48 Insert visual
9. x 1 y 1 2 z 1 3 O 0 00000 97220 0 25890 1 1 0 x 1 y 1 2 z 1 3 01 0 1 22220 0 250080 0 50899 0 O y 1 4 x 1 4 z 3 4 3 0 1 22220 0 750080 0 49110 1 y 1 4 x 3 4 z 1 4 3 O 0 22220 08 750080 0 49110 1 1 0 y 3 4 x 3 4 z 1 4 l Mn2 01 1 9301 8 Angstrom l Mn2 01 2 282 2 Angstrom L Mn2 01 2 282C2 Angstrom l Mn2 01 1 9301 8 Angstrom Mn2 01 1 9301 8 Angstrom l Mn2 01 1 9301 8 Angstrom Average bond length 2 0474 Angstrom Polyhedral volume 11 1616 Angstrom 3 Distortion index bond Length 0 07642 Quadratic elongation 1 0234 Bond angle variance 39 0014 deg 2 Input a bond valence parameter 1 76 Bond valence sum 3 014 Input an oxidation number 0 for quit 3 Expected bond Length 2 016 Angstrom Fig 2 Parts of the Output Window of VICS when selecting an MnO octahedron in Mn304 space group 4 amd a 5 765 A and c 9 442 A and calculating a bond valence sum Jahn Teller distortion in the MnO octahedron with Mn as the central cation can be quantitatively understood Other features include a addition of arrows indicating magnetic moments or positional shifts to any selected atoms b displaying X H Y hydrogen bonds and c insertion of lattice planes whose transparency and translation with a mouse are possible 3 VEND VEND can read in files storing 3D mesh data recorded with 11 formats Files output by SCAT 11 WIEN2k 12 ABINIT 13
10. COMMISSION ON POWDER DIFFRACTION INTERNATIONAL UNION OF CRYSTALLOGRAPHY http www iucr org iucr top iucr cpd html NEWSLETTER No 32 December 2005 http www fkf mpg de cpd htmI newsletter html IN THIS ISSUE 2D Powder Diffraction Robert Dinnebier Editor CPD Chairman s message Bill David Editor s message Robert Dinnebier WWW sites related to Powder Diffraction IUCr Commission on Powder Diffraction Workshop Report Watching the Action 2D Powder Diffraction In situ powder diffraction Electric Fields H Ehrenberg Datasqueeze A Software Tool for Powder and Small Angle X Ray Diffraction Analysis Paul A Heiney Powder3D A Software for tailored for in situ powder diffraction studies Bernd Hinrichsen Robert E Dinnebier and Martin Jansen Two2One Software for the analysis of two dimensional diffraction data Sven C Vogel AAND Karsten Knorr 2 Diamond Investigation and Visualization of Structural Changes H Putz K Brandenburg Detection of Ellipses in Powder Diffraction Patterns using Hough Transformation PP UU UU N N 12 23 26 2 Rajiv Paneerselvam Bernd Hinrichsen Manfred Joswig and Robert E Dinnebier Prediction of not yet synthesized phases at high and low pressures and the transitions among them using global exploration methods and ab initio calculations J C Sch n Z Cancarevic and M Jansen Computer Corner L M D Cranswick New Time of Flight Neutron To
11. Please note The assistant expects sequentially numbered Fullprof compatible data sets Please make sure that you export your patterns immediately before attempting a Le Bail fit All the data is written to that directory Sii LeBail refinement Phase information 1O x Ranges Selected phase ranges from set number 0 to 0 Current set for refinement Pattern Zero offset 0 01576 refine Import Fullprot Reset Remove HKL Cell Profile Spacegroup Pbam f refine cell a 11 2244 alpha 90 0000 b 6 25995 beta 90 0000 c 3 60249 gamma 30 0000 Import Refinement information Cancel Refine Auta Figure 31 Le Bail refinement cell parameters Once the refinements for all the data sets have been completed close the window by pressing cancel The cell dimensions can be exported to a text file by selecting the menu Refine gt Export cell data Si LeBail refinement a Phase information O x Selected phase ranges from set number 0 to 33 Current set for refinement Pattern Zero offset 0 005340 refine Import Fullprof Reset Remove HKL Cell Profile FWHM constant variable U 0 074130 y 0 03705 W 0 030701 IV refine X 0 021825 Y 10 021965 v refine Asymmetry S L 0 001730 refine D L 0 014000 refine Import Refinement information Cancel Refine Auto Figure 32 Le Bail refinement profile parameters
12. s are negative e g H Li Ti and Mn The algorithm of MEM in PRIMA is described in a document PRIMA pdf in the archive file of VENUS PRIMA makes it easier to modify a structural model during Rietveld analysis In a user input file 1ns set NMODE at 0 and NMEM at 1 and input various parameters e g numbers of pixels along a b and c axes for MEM analysis Then execute Rietveld analysis with RIETAN 2000 6 to create a MEM data set file fos F Rietveld data viz IFP s and phases recorded in this file are analyzed by PRIMA which creates a 3D density file pri and a feedback data file fba storing structure factors F MEM s obtained by the MEM analysis VEND serves to input pri to visualize 3D electron nuclear density distribution By linking RIETAN 2000 with VENUS in such a manner the structural model may be rebuilt after close checking of the density image if necessary so called MEM Rietveld method 15 MEM gives only nonnegative electron densities X ray diffraction estimates F MEM s for reflections whose intensities have not been measured and improve F MEM s for overlapped reflections Thanks to these advantages of MEM it affords much clearer density distribution with high S N ratios than Fourier synthesis from F Rietveld data Thus we now regard PRIMA as a must have item for Rietveld analysis using RIETAN 2000 The MEM Rietveld method is a halfway approach to determination of electron
13. Jansen J Chem Phys 121 2289 2004 10 J C Sch n Z Anorg Allg Chem 630 2354 2004 11 C Mellot Draznieks S Girard G Ferey J C Schon Z Cancarevic M Jansen Chem Eur J 8 4102 2002 12 N Metropolis A W Rosenbluth M N Rosenbluth A H Teller E Teller J Chem Phys 21 1087 1953 13 G Dueck and T Scheuer J Comp Phys 90 161 1990 14 S W deLeeuw J W Perram E R Smith Proc Roy Soc A 373 27 57 1980 15 R Hundt KPLOT A Program for Plotting and Investigation of Crystal Structures Univ Bonn Bonn 1979 16 J C Schon H Putz M Jansen J Phys Cond Mat 8 143 1996 17 M A C Wevers J C Schon M Jansen J Phys Cond Matter 11 6487 1999 18 Z Cancarevic J C Sch n M Jansen in Proc Progress in Materials Science and Processes Mat Sci Forum 2004 453 71 19 R Hundt J C Sch n A Hannemann M Jansen J Appl Cryst 32 413 1999 20 A Hannemann R Hundt J C Schon M Jansen J Appl Cryst 31 922 1998 21 V R Saunders R Dovesi C Roetti M Causa N M Harrison R Orlando C M Zicovich Wilson CRYSTAL2003 Univ Torino Torino 2003 22 F D Murnaghan Proc Nat Acad Sc 30 244 1944 23 J C Sch n and M Jansen Comput Mater Sci 1995 4 43 24 D Fischer Z Cancarevic J C Sch n M Jansen Z Anorg Allg Chem 630 156 2004 25 J C Schon M A C Wevers M Jansen J Mate
14. Looking to purchase software instrumentation or related services The conference also provides a venue to visit with the major vendors of X ray analysis equipment and services during the exhibition Exhibits are held concur rently with the workshops and sessions If you re working in an X ray analysis field make the Den ver X ray Conference your meeting of choice It will provide you with the opportunity to learn the latest and greatest advancements network with fellow scientists expand your knowledge and shop for your X ray analysis needs Please join us in 2006 at the Denver Marriott Tech Center Hotel eo rganics a k e Fy ge Product News o F 4 The ICDD is pleased to announce the latest l Database release of PDF 4 Organics PDF 4 Organics 2006 is designed for rapid material identification with 286 464 entries The database is produced through collaboration between the International Centre for Diffraction Data ICDD and Cambridge Crystallographic Data Centre CCDC It includes indexes display query and sorting capabilities that allow the user to data mine the database correlating diffraction bibliographic unit cell and physical property data This database is a practical results oriented product that combines the drug active compounds calcu lated from the Cambridge Structural Database CSD with the polymers including starches and celluloses excipients and pharmaceuticals in the ICDD Powder Diffraction F
15. VASP Gaussian GAMESS efc can be input directly or indirectly VEND can also input 3D density files pri created by PRIMA In principle VEND is capable of visualizing any physical quantities in parallelepipeds e g Patterson functions determined from powder diffraction data with ALBA and Laplacians of electron densities M Mizuno developed a Fortran program contrd to convert binary files FO9 and F39 output by SCAT into text files storing 3D data He has recently written its extended version called contrwd With a script wien2venus py coded by M Arai in Python 3D electron densities calculated with WIEN Kk are convertible into a text file which is in turn input by VEND to display electron density distribution in three dimensions In addition Cut3D in the ABINIT package can convert binary files output by ABINIT into text files with the XCrySDen XSF format VEND is capable of reading all of these text files With VEND electron nuclear densities as well as wave functions and electrostatic potentials obtained by molecular orbital methods are visualized as isosurfaces Fig 3 bird s eye views and two dimensional maps to learn the nature of chemical bonds Isosurfaces can be 60 expressed in three different ways smooth shading wire frame and dot surface Isosurfaces for positive and negative values e g wave functions electrostatic potentials and coherent scattering lengths b in neutron diffraction are drawn wit
16. available to the user A GSAS instrument parameter file is used to convert d spacing from the CMPR peak list into 20 values or neutron time of flight as required by RAWPLOT and add additional peaks in the neighborhood user defined in peak widths based on the instrument parameter file of the peak of interest This script can then be manually edited for extra peaks or different fit ranges Using RAWPLOT and the instrument parameter file meaningful starting values for the peak parameters can be provided A user editable template for the RAWPLOT refinement allows for maximum flexibility of the refinement strategy The output is a series of text files for each included reflection with all peak parameters and a possible external parameter such as applied stress merged into one single file These files can be conveniently plotted Conclusion We have given a brief introduction into the capabilities of our software Two2One for the analysis of 2D diffraction data It appears to be a versatile tool that allows for a variety of applications and a high degree of automation Our outlier rejection algorithm significantly improves the data quality The analysis of large amounts of data is simplified by the use of Two2One paving the way towards new insights beyond standard powder diffractometry Appendix Example script To illustrate the scripts used to control Two2One the following script provides an example This is a script file for Two2One
17. c 21 113A B 103 6 u AY heran Peder Seien Pi Ph pape Ly Pile ee FE Larch Mika ities Hie alj Pence BES Me ee Pea Pass bik gt IF Fi ER p s i tl II II Ll Pl AMM i W Ad wii JHA hi il L u J a teL le Fig 3 Dominant zone problem The first observed 20 lines are of the type hkO u Dy Glob BA inne Ur rT D Ermi TPA t B Becks j 5 D ur r amp i b SE na pm ie ee Aia on wiih ee zu om 1 E Ze ar GME AR nim Fe ee MAN MHN Bets T OM 3 E HET BH 00A AB ne FOS Tea SI an gi ar m a 1 i hie F I Tan ida hu IF ahi Pa 1 t ei ND Gwo nee iwm AMH MON Tee So rm PH 3 DB BFE 2S ciw Ee iwm ANS mow aM som r P j a SHEET Km Gi en AND SS A Se Be my hiahia IEFERRITTE AFRFEEINTFORTFERTIE ERERRTESTETDERTERRE ITTPPRETETTENDERTENTETTUPRELEERTEULBER haibi asana Bee ee De a Se es ee re ere A ae Pe eee oe eee ee 1 UE ieee eeepc peepee ere reser eee beer prereset eerste 3 rE T p a H i i E uF Ht ra Ue TAEC peas ur sit rea Ut v by Gol decry ba i fy hed hen ee i T oka 1 i Fak Hii iis J i a os WP ka Heche ane ions Je eee ai a Bn HDi Fig 4 Goodness of fit versus volume plot correct solution is ranked at position 6 Maxima correspond to V 2V 3V and 4V LP Search In the LP Search Lattice Parameter Search algorithm d spacings are not extracted and instead the whole diffraction pattern is input into the algorit
18. external conditions change e g when the temperature is raised above or below certain values Typically these phase transitions are accompanied by changes of the compound s crystal structure Studying structural changes of this kind was rather difficult until a few years ago due to the fact that the reorganisation of the structures generally crashes any original single crystals from which crystal structures could be determined leading to powders from which crystal structures could generally not be solved However this has changed in the meantime Nowadays studying phase transitions by powder diffraction methods has become a rapidly increasing field The background is that crystal structure solution from powder data has become a lot easier than a few years ago both due to progresses in hardware and software technology Nevertheless it is still not straight forward how to visually present the changes in the crystal structures obtained from these investigations Typically crystal structures are visualized using static models or pictures However this method is not really appropriate when structural changes with regard to some external parameter shall be visualized In these cases it is clearly desirable to create some sort of video sequence in which the individual pictures correspond to individual crystal structures determined at various steps of the parameter changes This presentation shows how this can be achieved using Diamon
19. range using the false color image Figure 4 b Shows the radial I q plot equivalent to a 2 Oplot showing the intensity profile of the bright ring on right in the fiber pattern in a Data were averaged over the range y 20 Red dots show the extracted data solid curve shows the results of a least squares fit Lower panel in b shows fit residuals i e model data error 7 Once extracted the x y data can be graphed saved for future analysis or compared via a least squares fit analysis to a variety of commonly used functional forms Lorentzian and Gaussian peaks power law Rayleigh and Bessel functions etc Least squares fit aficionados are provided with detailed information on multi parameter error bars correlation coefficients etc Figure 4 shows a radial plot through the bright ring on the right hand side of the fiber pattern shown in Figure 2 The data have been least squares fit to a sum of three Lorentzian functions and a linear background using the Marquard nonlinear least squares minimization algorithm 3 11 Summary Datasqueeze is a powerful tool for the analysis of 2D X ray diffraction patterns especially those arising from small angle or powder diffraction In addition to the features described above it provides facilities for pixel by pixel examination of the data extraction of statistics regarding distributions of intensities among pixels and indexing of simple powder diffraction patt
20. 1 Lattice parameters a 4 Space group preferences monoclinic axes a b c monoclinic cell choice 1 orthorhombic axes abc origin choice 2 hexagonal axes Ti 1a 0 0 0 Ba 1b 1 2 1 2 1 2 O 3d 1 2 0 0 k point R k13 1 2 1 2 1 2 Next choose an IR help R1 k13t1 R3 k13t5 Complete help file R4 k13t9 R5 k13t7 R2 k13t4 ZEN http f stokes byu edufcgi binfisofisodisplace cgi ISODISPLACE order parameter direction Space Group 221 Pm 3m Oh 1 Lattice parameters a 4 Space group preferences monoclinic axes a b c monoclinic cell choice 1 orthorhombic axes abc origin choice 2 hexagonal axes Ti 1a 0 0 0 Ba 1b 1 2 1 2 1 2 O 3d 1 2 0 0 k point R k13 1 2 1 2 1 2 IR R4 k13t10 Finish selecting your distortion mode by choosing an order parameter direction help P2 a a 0 74 Imma basis 0 2 0 1 0 1 1 0 1 origin 0 0 1 2 s 2 i 12 P3 a a 8 166 P 3m basis 1 1 0 0 1 1 2 2 2 origin 1 2 1 2 1 2 s 2 i 8 C1 ab 0 12 C2 m basis 0 0 2 0 2 0 1 0 1 origin 0 0 1 2 s 2 i 24 1 0 1 origin 0 1 2 0 s 2 i 24 Figure 2 a Here we consider the aac octahedral tilt mode of BaTiO3 which occurs at 72 42 2 in the Brillioun zone and creates a conventional supercell with Imma symmetry and four times the volume One can either specify Imma symmetry in the lower drop down menu and then search distortions at all special k poi
21. 10 The tricky things are a we must not omit group 13 here as otherwise the surface model is moved as well b after any shifts of the molecule the CCS origin should be re defined by its atoms thus the axes of rotation will still go through its center c It would be wise to frequently employ Use Outputfile here to save the different steps To avoid confusion the whole structure should at this stage only be rotated by multiples of 90 about any axis for example to look at it from the side Only when the molecule has its final orientation and position we re define the origin and tilt the whole thing to proceed to Fig 1 gt gt gt Def Origin gt gt gt Rot X 80 gt gt gt Set View 60 gt gt gt Set Light 45 90 gt gt gt Xqt Stars gt gt gt Kill Screen 3 gt gt gt Magnify Model 0 8 gt gt gt Set Origin 0 6 shade K S 3 switches automatic screen erasing off S O 0 6 shifts the whole drawing 6 cm downwards it doesn t alter the position of the atoms relative to the CCS The 6 as well as the magnification factor 0 8 depend on the size of the screen we are using Fig 1 Sulfur meets sulfur 42 2 Lachlan must have a faible for surfaces as he also mentioned the 2 surface picture on this web page Here we make an only related draw ing using the same structure as above gt gt gt Use Inputfile InpData file gt gt
22. 19 Define phase ranges Ko stripping Should you have collected laboratory data using Ka and Ka rays these can be separated using the menu Edit gt K alpha stripping Select which wavelength you wish to keep Figure 20 EEE FE Di Baten Beine Pie Me ziel pial pi _ Bigard Pred rdi Prenton antes sar Case dat bc Fa B Figure 20 Kaz stripping The following dialog Figure 21 enables you to select the sets which should be stripped The raw data is overwritten and therefore this action cannot be undone SI Apply K alpha strippin From set no fi Tosetno 200 Select phase Phase Apply Cancel Figure 21 Batch stripping Smoothing An advanced full width at half maximum FWHM optimised smoothing Figure 22 algor thm described by Dinnebier Dinnebier 2003 is implemented Edit gt Smoothing The variation of the FWHM of the peaks is generally described by the Caglioti Caglhioti er al 1958 formula FWHM xUtan 0 VtanO W This can be graphically set with aid of the function window on the left Here the function can be dragged to the desired shape with the aid of three red boxes 16 EJ ee Bi ie LE Fan cele Fit Pey la _ Ihi me _ Begard Paai pd Frems ghen A S S E Disem dwa or Fly Intensity Geunts g j WOM Ay N hak Mja A Jak Pe ob AA Figure 22 Smoothing window The correct
23. An introduction to the magnetic structures and the use of representation theory are given in The determination of magnetic structures using symmetry A S Wills Proceedings of the Ecole Magnetisme Soci t Francaise de la Neutronique J Phys IV France 11 Pr9 133 2001 and Long range orderings and representational analysis of the jarosites A S Wills Phys Rev B 63 064430 2001 A summary of the different programs that perform group theory calculations of magnetic structures is given in Symmetry and magnetic structure determination Developments in refinement techniques and examples A S Wills Appl Phys A 74 S856 S858 2002 Quantitative Rietveld analysis in batch mode with Maud and new features in Maud 2 037 Luca Lutterotti Dipartimento di Ingegneria dei Materiali e delle Tecnologie Industriali Universit a di Trento 38050 Trento Italy Email Luca Lutterotti ing unitn it WWW http www ing unitn it maud 1 Introduction Today several instruments for fast spectra recording are available In most cases the difficulty is to process and analyze the data quickly in a reliable way The Maud program in one of its many undocumented features can be used to process a list of analyses in batch mode from the console without requiring the interface This is useful to quickly process similar spectra or launch a slow time consuming refinement in a remote computer without recurring to the interface t
24. Fir Coipasa eed iene ace eect pee fee Ay Pin Views Fit Larch feck ido lint alm xi Cea ead eanele 5 Pins EL eal oy i a i Pa U 1 77 III T pees Tl IT F ol I runde p meis z hi apri pra ite i J inaani FR RAI of SAL Am Er ne v ee ee ie IE AN t i kd F J q tt wi eS Tor oo oo Lit om eS ee Fig 1 Peak fitting to T3R3 using the TOPAS direct convolution approach i RS a Bi Bal AGEL ZARAZA Al tal CL u CASE be AUU ELEU BZ Sin ee e DOW Bi OLHA Re STIS ESO Da EG gna See u De DO A a AMH BS7I0SS BEE oO DO BRAS MERI FAMA Pe z u Ben Bil IES DE ah AEST amg 4 D pet by UHI Ga decisir Seal bey Siaa Tawa bo HOW fe Pade INF lo Node Selon Fig 2 Goodness of fit versus volume for T3R3 Maxima correspond to 1 6 V 1 3V 1 2V 2 3V V 2V and 4V In contrast to T3R3 is the dominant zone problem shown in Figs 3 and 4 Data courtesy of P Stephens Stony Brook USA Sample details temporarily undisclosed to be published In this case the first observed 20 lines are of the type hkO Fig 1 A lot of noise is seen in the goodness of fit versus volume plot indicating that there is a lesser chance of the correct solution being ranked at the top of the list Here the correct solution is ranked at position 6 obscured by triclinic solutions with similar volumes and partly similar lattice parameters P21 a 23 497A b 4 773A
25. Fox nogur for servers Many laboratories have clusters Linux or MacOS X dedicated for long calculations but generally they do not have the graphical libraries required by Fox wxWidgets OpenGL glut installed and computer administrators can be reluctant to include them it It is now possible to compile Fox without the graphical interface 1 e without any library requirement which is trivially done by each user by a simple make Fox nogui command A multiple run can then be launched from the command line e g from the Fox directory after compilation src Fox i example Cimetidine powder xml nogui n 3000000 nbrun 10 silent Fox for Mac OSX The Fox and the Tiger have finally met As shown in fig 2 Fox now runs under Mac OS X with the native Aqua look 58 Fig 2 Fox running on Mac OS X Fox wiki The Fox manual has now been transfered to a wiki http objcryst sf net Fox This allows a direct editing from any web browser All users are encouraged to add their tips feature requests references to published structures Downloading Fox Fox is open source software released under the GNU General Public License It can be downloaded from http objcryst sf net Fox Precompiled versions are available for windows and MacOS X Acknowledgements The authors would like to thank all users of Fox for the feedback they provide which is used to improve the algorithm More special thanks g
26. Fullprof can handle this important feature 4 0 69956 A 7 19 29 43 The changes of diffraction patterns during charging and discharging are already described in detail 5 During charging and discharging the original phase A with maximum Li content disappears and two other phases B and C with smaller lattice parameters are formed conteracting see next figure For this sample prepared by sub solidus reaction a three phase mechanism of Li extraction and reinsertion was established However differently prepared LiMn O samples show a very distinct behaviour All three phases are of spinel type structure and differ probably in the cation distribution on the tetrahedral and octahedral interstitials The in situ technique allows to follow structural changes during operation and does not suffer from relaxations or reactions which might occur before ex situ studies after dismounting of a battery The test cell is further improved at present with respect to life time stability At least 100 charge discharge cycles are needed to investigate fatigue in the cathode This method was also successfully applied to other cathode materials Li Co Ni O 8 9 Li Mn Fe PO 10 and LiCoPO 11 Financial support from the Helmholtz Association of National Research Centres Virtual Institute VH VI 102 for the development of dedicated in situ environ
27. Mans at the LPEC laboratory of the University du Maine thanks to A Gibaud 2 1 Analysis preparation through the interface We start the Maud program and load all the datafiles together to check their integrity and to prepare a common starting analysis file A plot of all spectra and their differences is available in Figure 1 We load the two possible phases bcc iron and fcc copper from the Maud database By computing the spectra once and comparing them visually with the experimental spectra we may notice that for some samples milled at longer time an alloyed fcc phase has formed out of equilibrium and the bcc iron disappears Unluckily we could not use the copper rich 53 phase cell parameter to monitor the Fe content in it as the cell parameter tends to growth as a result probably of oxygen entrapping In a first attempt we discovered the spectra are affected by texture anisotropic crystallite sizes and microstrain as well as planar defects especially on the Cu like phase So we decide here to include also texture and anisotropic planar defect effects in the analysis For both the bcc and fcc phases we select in the proper panel the Popa model for anisotropic broadening the Warren model for planar defects and the harmonic model for texture specifying cylindrical sample symmetry and Lmax 6 in the options it is required by the experiment geometry Intensity Count 0 0 BO 2 Theta degrees Figure 1 Plot of
28. The database now contains 200 datasets 5 Each patterns is comprised of 2299 datapoints 2Theta range 0 011956500 to 54 964087 degrees Intensity range 0 0967653 to 56706 1 counts Figure 6 Import report As soon as you acknowledge the message you are displayed the first of your powder patterns Figure 10 Single pattern loading and deletion Should you wish to load a single pattern only or wish to compare a pattern to already loaded data this can be done by using the function Edit gt Add Pattern Figure 7 The pattern is added to the end of the pattern array Should the pattern differ with regard to the step width or position the intensities are interpolated to match the range and step width of the data already loaded A dialog requiring you to enter the wavelength for this pattern is displayed If a pattern needs to be deleted select it in the 2D Plot window and choose Delete pattern from the Edit menu Should you wish to delete any number of patterns select them in the pattern list and select the function Edit gt Remove Patterns from the menu bar File Edit Pattern Tools Plot Help Copy Add pattern CHI Remove Gathers at Wotmalize patterns TE eur DAT Wavelength an Figure 8 Adding a single pattern D plot aL Current data ts Aa l Mair Current set ata range Min joo 19565 Maxl54 9641 Figure 9 Pattern selection tool
29. X ray crystallographic data Although modern single crystal instrumentation software and other modern analytical techniques have made measuring this value in the lab less valuable than in years past there may be a need to bring back and improve measurements to help with identification of powdered samples With the recent increase in structure solutions from powder samples it seems that the specific gravity of a powdered sample may be more important If one knows the density then the formula of the material may be better known and increase the solution of the structure from powder data The specific gravity is tied to the volumetric relations of the X ray cell and composition of the cell w dVA w molecular weight of unit cell V volume of unit A Avogadros number d specific gravity Historically there have been many methods used to determine the specific gravity of a substance Although one must chose a method suitable for the given material the Berman method has proved successful when small quantities are required Berman in his original paper gives a good representation of the methods in use and you can find these in The International Tables of Crystallography where the techniques are describe in great detail and including methods for power samples In the paper he describes the method developed in his laboratory for the measurement of small quantity of material This method was generally well accepted and the necessar
30. an ellipse can be filtered with this method The range of a and b is determined for each ellipse by calculating the radial distances from the center These distances are found by selecting the pixels that lie with in a certain azimuthal range and finding the distance between the center and the pixels For better statistics about 16 radial lines were drawn with the azimuth range of 2 5 density 0 50 109 150 290 250 distances Figure 6 Radial distances of ellipses These two values for number of lines and azimuth range are optimized to compensate for the uncertainties caused by the beam stop shadow After computing 16 rad al distances for all the ellipses the entire array of distances is converted into a histogram which contains only the density of distances falling in certain interval Figure 6 An algorithm that scans through the entire histogram finds the starting and ending locations of filled bins These two bin locations give the approximate range of the major and minor axes of the ellipses Determination of major axis and orientation 0 In this method we assume a pair of edge pixels to be the vertices of the major axis of the ellipse 1 Their distance is calculated and if the distance lies with in the range calculated previously then the midpoint is calculated If the mid point lies with in a certain center tolerance then distance between the points and the pixel co ordinates are stored The orientation of the elli
31. atoms e g filling of cell range or neighbourhood of individual starting atom Creation of other objects e g bonds cell edges polyhedra planes or lines etc Modification of object design e g color hatching line weight etc distances define Of course this is a rather schematic representation of the actual picture creation procedure since the steps are not necessarily carried out in this order Once you have created one or even more pictures for a crystal structure they can be used for Printing Export to other programs Creation of photorealistic pictures using POV Ray Creation of video sequences That last point is the one we would like to focus on in the following 3 Visualization of Structural Changes If you would like to visualize not only a single static crystal structure but the structural changes of a compound as a function of some external parameter e g temperature the first task is to create a separate picture for each crystal structure Afterwards these pictures are composed to a video sequence using which the structural changes can be visualized The first thing to do is to define the order in which the crystal structure pictures shall appear in the video sequence The easiest way to do so is to use appropriate file names for the corresponding crystal structure data files which reflect this order For example you could use file names like 298K cif 359K cif and 60
32. can start refining those peaks The refinement will start with the strongest peak and work its way down to the smallest peak fixing the peak position automatically once the peak intensity drops below a threshold of 3 I A maximum of two ranges can be refined together This is equivalent to refining them separately should there be no overlap Should you wish to plot the peak development first select the peaks with the Select peaks Figure 38 tool Now press the plot button The main program window is brought forward and a rudimentary plot of the refined parameters is displayed Figure 39 S Analyze peak progression Be E Select pattern range and peak position Zoom 10 x C Select peaks Edit peaks Select ranges Function Foy Peakl Pseudo Voigt I Refine profile Pearson VII Tl Refine pos int Eta 10 500 Intensity 0 000 rn S L 10 025 u H L fa 025 u Refinement run Refinement progress Max cycles per tun 30 er Start Cancel Position D 000 FWHM 0 000 Plot Export Done Figure 36 Peak analysis window initial display 19 Sl Analyze peak progression 15 x Select pattern range and peak position Zoom Select ranges Select peaks Edit peaks Function Fo Peak1 Peaki Peak Pseudo Voigt IV Refine profile C Pearson VII 7 Refine pos int Intensity 1 457 74 Vv Position 1 1 53
33. com Phone 610 325 9814 eager Fax 610 325 9823 E mail info icdd com Join us for PPXRD 5 PP The 5th Pharmaceutical Powder X ray Diffraction Symposium brings XRD training to the heart of the U S A s pharmaceutical industry ICDD once again is proud to host XRD training for the pharmaceutical industry at the 5th Pharmaceutical Powder X ray Diffraction Symposium 14 16 February 2006 in Somerset New Jersey U S A This symposium is the deal training for process analytical and discovery chemists as well as pre formulation and formulation scientists Invited talks and contributed papers complete the program in areas such as X rays in Drug R amp D Formulation Product Devel opment Drug Delivery and Polymorph amp Salt Screening Patent and Regulatory Issues Process Analyt cal Tech nology Complementary Techniques XRPD Structural Techniques and New Frontiers for XRD in Pharmaceutical R amp D For even more invaluable XRD training attendees are invited to participate in an optional workshop on 13 February 2006 Covering everything from basic theories and concepts to applications and case studies this work shop entitled Characterization of Pharmaceutical Solids Crystal Studies and XRD Applications offers hands on training and a forum for round table discussions Attendees will also have the opportunity to speak with representatives from the industry s leading providers of analyti
34. gt ex2_p Enter more data gt gt gt FAce 781 Enter more data gt gt gt BOx 11 5 Enter more data gt gt gt lt Return gt Note that to obtain a surface model of reasonable thickness the 3 parameter on the BOx card referring to dhk must be much larger than before as d7g 1s much smaller than diio On the upper drawing of Fig 2 you can see that the 2D unit cell of the surface has been expanded by one full unit translation in both directions due to the two 1 on the BOx card By skipping commands to generate the background and to align the mod el by rotating it about the Z axis the following will generate the uppermost part of the picture gt gt gt Generate Ballsticks gt gt gt Mgnfy Model 0 1 gt gt gt Set Origin 0 5 0 8 gt gt gt Xqt Quick Kill Screen 3 gt gt gt Broaden All 4 3 gt gt gt Xqt Quick a a gt gt gt Brdn All 1 The positioning of the drawing with S O works only as the scale factor has been fixed by the M M p command before The last 3 lines commands emphasize the various unit cell edges gt gt gt Set Origin 0 5 0 4 varyZ uni creates the drawing in the middle which gives an impression of the depth variations within the surface Finally we want to have a side view gt gt gt Gen Cups gt gt gt Set Origin 0 5 0 1 gt gt gt Rot X 90 shade Note that the switch to cup space filling models had been performed only
35. into the program DIFFEV part of the DIFFUSE program suite 50 This program allows the user to define floating as well as real parameters to be refined Constrains may be applied for individual parameters or expressions between parameters The figure shows a fit to a powder diffraction pattern of ZnO nano particles The powder data were collected on a Philips PW diffractometer at room temperature using Cu Ka In this particular fit the nano particle was constructed in the following fashion The current set of structural parameters 1 e lattice constants atomic positions and atomic displacement parameters were used to generate large layers of half the Wurtzite structure These layers were stacked along c using the DISCUS stacking fault menu The stacking fault probability was a refined parameter The particles were cut to appropriate size here defined by two independent parameters giving the diameter in the a b plane and along c Thus a total of seven parameters were refined to describe the nano particle Member L RWERT 0 1045 0 0881 Intensity Fig 2 Powder diffraction pattern of a ZnO nano particle Observed blue and calculated red powder pattern difference green More information on the program and downloads are available at the DIFFUSE homepage at http www uni wuerzburg de mineralogie crystal discus index html or through http www totalscattering org References Kenneth Price amp Rainer Storn Diff
36. measure of its crookedness The minimization function is chosen as o MF Ym Sa 1 Em 0 Y i where Y and Y are the observed and calculated profile intensities 9 is the diffraction angle w is the weight and the sum is over the entire powder profile The derivatives are calculated by using the Savitzky Golay method The optimal convolution interval width for calculating derivatives may be either set equal to a chosen value or automatically determined by the program for each data point according to the counting statistics The background line modeling or approximations are avoided in the DDM scheme which allows increasing the precision reproducibility and comprehension of the powder diffraction analysis via the elimination of background related systematic errors 1 2 While the derivative difference method was primarily designed for cases of complex modulated background it has also been found to be advantageous in common cases of seemingly plain background line It should be noted that even when the background contribution to a powder pattern appears simple it may have and normally has some modulations hidden by the peak overlap The program includes both DDM and Rietveld refinement routines for X ray and neutron powder diffraction data as well as the Le Bail method 4 and the DDM decomposition procedure 2 for estimating the integral peak intensities Beside the crystal structure refinement the quantitative phase
37. observed is thermodynamically stable for all temperatures up to the melting point and that at high 34 pressures the CsCl type is preferred Structure candidates and barriers among them were determined using simulated annealing and the threshold algorithm The phonon contribution to the free energies was calculated using an empirical two body potential Space forbids the presentation of further examples and we refer the reader to the literature given below 5 11 17 23 26 REFERENCES 1 L Liu W A Bassett Elements Oxides and Silicates High Pressure Phases with Implications for the Earth s Interior Oxford Univ Press New York 1986 2 R J Hemley ed Ultrahigh Pressure Mineralogy Physics and Chemistry of the Earth s Deep Interior vol 37 of Reviews in Mineralogy The Mineralogical Society of America Washington DC 1998 3 D Fischer and M Jansen J Am Chem Soc 124 3488 2002 4 D Fischer and M Jansen Angew Chem 114 1381 2002 Angew Chem Int Ed 41 1755 2002 5 J C Sch n and M Jansen Angew Chem 108 1358 1996 Angew Chem Int Ed 35 1286 1996 6 J C Sch n and M Jansen Z Krist 216 307 2001 Z Krist 216 361 2001 7 J C Sch n and M Jansen in Solid State Chemistry of Inorganic Materials V Eds J Li et al 333 MRS Pitssburgh 2005 8 J C Schon M A C Wevers M Jansen J Phys Cond Mat 15 5479 2003 9 J C Sch n Z Cancarevic M
38. selection of the function shape has great effect on the smoothing efficacy Eile Demn daa br FA ae B Figure 23 Background reduction Background determination Edit gt Background can be done in two modes Either a pattern can be loaded XY format as for import or it can be calculated Figure 23 Should a pattern be loaded it is displayed as is the calculated background The normalize button then interpolates the background giving it the same number of data points as the diffraction pattern Then a linear function fitted using the least absolute deviation method is added to correct the background Should the background be higher than the powder pattern at any point it is lowered The Calculate background method utilises a robust algorithm based on an adaptive low pass filter as proposed by Briickner Briickner 2000 Select the smoothing box and number of iterations to attain an optimal background Please note that every iteration costs computing power for large data sets many iterations can make the automatic background reduction time consuming The apply button greets you with the following dialog Figure 24 SJ Apply background rede 63 From set no fi Tosetno 200 Select phase Phase Apply Cancel Figure 24 Batch background reduction To edit background points manually select the edit tool Figure 25 This can become necessary if the backg
39. temporarily by the last procedure therefore G C has to be used for another switch Fig 2 A bumpy piece of world Discussion of the Indexing algorithms within TOPAS Alan Coelho Arnt Kern Bruker AXS GmbH stliche Rheinbr ckenstra e 49 D 76187 Karlsruhe Federal Republic of Germany Email AlanCoelho optusnet com au Web http pws prserv net Alan Coelho and http www bruker axs de index php id topas TOPAS introduces two new indexing methods LSI and LP Search LSI operates on extracted d values and has been proven to be particularly strong in indexing of very large cells gt gt 100 000 A and difficult dominant zone problems On present computers LSI searches all Bravais lattices in less than 3 minutes LP Search is a Monte Carlo based whole powder pattern decomposition approach Pawley or Le Bail fitting which does not require any knowledge of d spacings Due to this LP Search is particularly suited for indexing of poor quality powder data where reliable d spacing extraction is difficult or even impossible peak overlap problems additional phases anisotropic line broadening LSI Indexing It has been reported that the Least Squares Iteration LSI indexing algorithm works and in particular it works on difficult dominant zone problems Why That question in detail is more appropriately tackled in the paper by Coelho 2003 Conceptually indexing is a simple problem whereby observed d spacings are ma
40. that they could have fully lowered the symmetry themselves The last three sliders correspond to lattice strains secondary order parameters at the I point 1 H T Stokes and D M Hatch sotropy Subgroups of the 230 Crystallographic Space Groups World Scientific Singapore 1988 Derivative Difference Minimization DDM Program Leonid A Solovyov Institute of Chemistry and Chemical Technology 660049 Krasnoyarsk Russia Email leosol icct ru Web http icct krasn ru eng content persons Sol_LA The derivative difference minimization DDM method of full profile analysis 1 s implemented in a freely available program DDM The main advantage of the DDM method is in the opportunity of powder diffraction pattern modeling independently of the background curve In this method the full profile refinement is aimed not at minimizing the absolute difference between the observed and calculated patterns but at minimizing modulations or crookedness of the difference curve The difference curve is considered as an estimation of the background which in the absence of crystalline admixtures generally varies much less rapidly along the powder pattern than the Bragg diffraction profile does Thus the DDM procedure finds such a calculated diffraction pattern that after being subtracted from the observed one gives the plainest difference In the current variant of the program the angular derivatives of the difference curve are used as a
41. the cost during the optimization After a Multiple Run optimization the obtained solutions can be browsed e by clicking on each solution 57 Better Molecule description The last version of Fox featured a new Molecule description which used a description of atomic positions from their x y z coordinates associated to bond lengths bond angles and dihedral angles restraints This description allowed a significant speed increase in the structure solution 3 times faster for cimetidine and potassium tartrate examples 1 thanks to the increased flexibility compared to the z matrix description However this involved a reduced control on the geometry of the Molecule as the algorithm forced distortions only loosely applying the specified restraints In the new version the stretch modes used to randomly alter the molecule conformation are automatically generated using the derivative of the restraints values to minimize the molecule distortion while preserving the flexibility of the random moves On average the restraint costs in the molecule during the optimization are more than ten times lower than with previous description Other new features e it is now possible to describe rigid groups of atoms within each molecule which will remain strictly rigid during the optimization e the origin of the molecule which is used as the center of rotation can now be fixed on a given atom rather than on the defaul
42. the kind of analysis to perform iterations and eventually datafile to load and name of the file were to save the analysis Additional keywords can be used to append specific results to a file for spreadsheet analysis The simplest instruction file is something containing the following First example paths for windows loop_ _riet_analysis_file _riet_analysis_iteration_number C mypathfortheanalysis analysisl par 5 C mypathfortheanalysis analysis2 par C mypathfortheanalysis analysis3 par 7 w The analysisl par or 2 or 3 are some analyses files prepared with Maud containing also the datafile spectrum already set for the parameters to be refined and saved just ready for the refinement step Maud will load each analysis starts the refinement with the number of iterations specified and save the analysis with the refined parameters under the same name The analyses can be loaded at end in Maud with the interface to see the result of the refinement In the case of the Cu Fe we need to perform some more steps first we start from one common analysis point the FeCustart par analysis file but we want to specify different datafiles second we want to perform a full automatic analysis in which Maud performs different cycles deciding which parameters to refine at each step and third we will specify the name of each analysis for the saving process and a file name were to append some selected results in a tab column
43. the simplest description of that structure in terms of symmetry operations so that each magnetic atom is generated only once The fractional occupancy of the magnetic atoms in the FullProf input pcr file should then be set to unity As with a nuclear 52 refinement only one atomic position is explicitly given and all atoms related by symmetry will be generated by the symmetry operators of the magnetic phase The relative orientations of their magnetic moments will be defined at the same time To simplify the creation of a magnetic phase in the correct format SARAh Refine can be used to generate the entire magnetic phase section of a pcr input file The relevant parts can then be substituted into the working refinement file Refinement of the mixing coefficients 1s done directly in FullProf and relations between them may be set in the normal manner Refined structured can be visualised using FPStudio Laurent Chapon and Juan Rodriguez Carvajal To facilitate the exploration of different trial structures after selection of different basis vectors SARAh Refine can be used to replace only the magnetic symmetry definitions in a working refinement file thereby enabling the rapid exploration of the different possible magnetic structures Ti lt lt HEEE grew Sye I Haye Cer Lowe Tress H Bos 3 1 2 2 Real leoginary 1 indicater far Ci t SIH X Y BASE BAST BASR BASI SYM NHL BASE BASI DASR BASI SYUM Xa gt Be
44. to known d spacings and that the rings be circular after correcting for possible detector misorientation relative to the primary beam Figure 3 Calibration using AgBe standard a The calculated rings dashed curves do not match the measured rings red and yellow b After optimization the two Sets of rings overlap Datasqueeze provides three methods for accomplishing this calibration First if the calibration parameters are already known for a particular data set the user can simply type them in Second the measured diffraction pattern can be visually compared with the predicted d spacings and the detector parameters optimized to make them overlap as shown in Figure 3 Finally program can automatically refine detector parameters using a user selected Bragg ring Data Reduction After the data set is properly cal brated one often wishes to collapse the 2D pixel array typically 10 10 pixels to a one dimensional x y list of intensities consisting of 107 10 items As discussed above this might consist of g integrated over all y for a powder diffraction measurement I q integrated over a limited range of x for a fiber measurement I y integrated over a finite range of q for a pole plot figure q integrated over a finite range of qy values etc Datasqueeze provides a variety of plotting option and in each case the user can either input the desired range and plot increment directly or graphically select the
45. 005 25 27 October 2005 MM4MX Molecular Modelling for Macromolecular Crystallographers a MAXINF2 sponsored workshop Diamond Light Source Oxfordshire UK http www diamond ac uk News LatestEvents mx_worksh op_2005 htm 30 October 2005 Recent Advances in Phasing Methods for High Throughput Protein Structure Determination an Inter national Workshop Peking University Beijing China http www ccs pku edu cn wp2005 3 5 November 2005 Pittsburgh Diffraction Conference 05 The 63rd edi tion Argonne National Laboratory Argonne IL USA http www pittdifsoc org 63rd_PDS_announce htm 27 November 2 December 2005 International Conference on Neutron Scattering 2005 Sydney Australia http www sct gu edu au icns2005 6 5 6 December 2005 WINS2005 Workshop on Inelastic Neutron Spectrome ters 2005 Cairns Australia http www iucr org cww top mtg wins2005 html 9 13 January 2006 Crystal Growth and Characterisation of Advanced Materials an international Workshop Crystal Growth Centre Anna University Chennai India http www iucr org cww top mtg chennai jpg 14 16 February 2006 PPXRD 5 The 5th Pharmaceutical Powder X ray Dif fraction Symposium Somerset New Jersey USA http www icdd com ppxrd 20 23 February 2006 RX 2006 6th Colloquium on X Rays and Matter Li moges France http www iucr org cww top mtg rx2006 pdf 2 3 March 2006 Diffraction de poudres Laboratoire L on Brill
46. 0K cif representing the ascending temperatures at which the corresponding crystal structures have been observed By doing so the crystal structure data sets can easily be sorted once they have been imported into the crystal structure visualization software Afterwards one should import the first crystal structure file check or define the interatomic distances for bonding coordinating atoms and create a first structure picture e g by filling the unit cell Once this has been achieved one should try to find the most appropriate representation of the crystal structure which emphasizes the underlying building principles Once a reasonable representation unit cell range filled connection of atoms polyhedra etc has been found it is possible to define a corresponding prescription which is able to create the structure picture automatically just from the given crystal structure data The background is that the creation of the individual structure pictures may quickly become a tedious task especially if more than just a few structures are involved Although the phases and their crystal structures are somewhat related you normally have to create a separate structure picture for each individual structure repeating practically the same steps for each of them Hence it is strongly desirable to be able to define some kind of automatic picture creation scheme for related crystal structures Diamond offers the so called Auto build schem
47. 329 A c 9 130 A within about 20 seconds on a Pentium IH 1GHz CPU Note the misfit of the observed data due to severe anisotropic line broadening as a result of lattice strain Allen et al 2003 which doesn t have an impact on indexing success as the goodness of fit is not minimized in 1 ae tira ee ee 1 2 a fir A ee FE Le Tome e ke O GF k Eg o w H jean 3HW al la ul Vek ss me Yee TA Dis EE nm RA ee jirar Fig 6 LP Search applied to LT ZrMo0 0 References Allen S Warmingham N R Gover R K B amp Evans J S O 2003 Chem Mater 15 3406 3410 Cheary R W amp Coelho A A 1992 J Appl Cryst 25 109 121 Coelho A A 2003 J Appl Cryst 36 86 95 Markvardsen A J David W I F Johnson J C amp Shankland K 2001 Acta Cryst A57 47 54 Wolff P M de 1968 J Appl Cryst 1 108 113 Structural phase transitions made easy the new ISODISPLACE software tool Branton J Campbell Harold T Stokes David Tanner and Dorian M Hatch Brigham Young University Dept of Physics amp Astronomy Email bjc79 physics byu edu Web http stokes byu edu isodisplace html ISODISPLACE http stokes byu edu isodisplace html is a new free access Internet tool for exploring structural phase transitions Parent phase structural information can either be uploaded from a CIF file or entered manually ISODISPLACE then computes the possible distortion mod
48. 4 Dinnebier R E et al 2005 Crystal Structures and Topological Aspects of the High Temperature Phases and Decomposition Products of the Alkali Metal Oxalates M C 0 4 M K Rb Cs Chem Eur J 11 1119 1129 Finger L W 1998 PROFVAL functions to calculate powder pattern peak profiles with axial divergence asymmetry J Appl Cryst 31 111 ammersley A P Svensson S O Hanfland M Fitch N and Hausermann D 1996 Two Dimensional etector Software From Real Detector to Idealised Image arson A C and Von Dreele R B 1994 GSAS General Analysis System Los Alamos National aboratory Report LAUR 86 748 e Bail A Duroy H Fourquet J L 1988 Ab initio structure determination of LiSbWO by X ray powder diffraction Mat Res Bull 23 447 452 Rodriguez Carvajal J 2001 Recent Developments of the program FULLPROF Commission on Powder Diffraction Newsletter 26 12 19 Shirley R 2002 The Crysfire 2002 System for Automatic Powder Indexing User s Manual IDL IDL VM and iTools are trademarks of Research Systems Inc Boulder CO USA Windows is a registered trademark of Microsoft Corporation Redmond WA USA Two2One Software for the analysis of two dimensional diffraction data Sven C Vogel amp Karsten Knorr l Los Alamos National Laboratory Manuel Lujan Jr Neutron Scattering Center Mail stop H805 Los Alamos NM 87545 USA sven lanl gov Christian Albrechts Unive
49. 61 B FWHM o 280262 Vv Eta 0 500000 Vv 52L 10 0140000 Vv HiL 0 0140000 7 Refinement run Max cycles per run 0 Stat DOF 28 Iterations 10 Chi2 0 099531987 Plot Export Done Figure 37 Peak analysis window range selected and peaks marked Sl Analyze peak progression Select pattern range and peak position Zoom Select ranges Select peaks Edit peaks Function FCJ Peak Pseudo Voigt 7 Refine profile Pearson Vil IV Refine pos int Eta 10 0995336 Intensity 4436 50 Vv SAL 10 0136992 u Position 11 4422 Vv H L 10 0136992 FwHM 0 184045 Iv Refinement run Max cycles per tun 0 Sat Plot Export Done Figure 38 Peak analysis window peaks selection for export plot Sj Poeder Ip als Fle dt Patter Take Mot Help eu Se e Peak Progression PEARINT Figure 39 Peak analysis a rudimentary initial plot of peak development Graphics 2D film plot This module simulates a Guinier film Figure 40 Two sliding bars enable you set the brightness and contrast of the plot Colour inversion and square root scaling can be set A tick box Interpolate allows you to do a bicubic interpolation between your patterns This smoothes plots of small data sets Of course the data range displayed can be set via the 2 and Data range fields Needless to say background corrected data has a far higher co
50. Blaha er al WIEN2k an Augmented Plane Wave Local Orbitals Program for Calculating Crystal Properties ed by K Schwarz Tech Univ Wien 2001 13 X Gonze et al Comput Mater Sci 25 478 2002 14 S Kumazawa et al J Appl Crystallogr 26 453 1993 15 M Takata et al Z Kristallogr 216 71 2001 16 K Takada et al Nature 422 53 2003 17 K Takada et al J Mater Chem 14 1448 2004 18 K Oikawa et al Mater Sci Forum 443 444 337 2004 19 M Yashima er al Chem Phys Lett 380 391 2003 20 M Yashima et al J Am Chem Soc 127 3491 2005 21 A Altomare et al J Appl Crystallogr 37 1025 2004 22 T Ikeda and K Itabashi Chem Commun 2005 27933 63 6t Who should attend Anyone who s interested n or currently using powder X ray especially if you have not received formal training in X ray powder diffraction should consider attending This includes students laboratory technicians and scientists who use powder X ray diffraction as a tool for wider research reasons The first two days concentrates on powder diffraction and Rietveld analysis using GSAS The third day focuses on PDF Pair Distribution Function Total Scattering analysis of amorphous disordered poorly crystalline or nano crystalline materials Participants Chair Professor Bruce Torrie University of Waterloo Canada Tarani faul Peay G
51. It converts an IP dataset to GSAS files All commands start with FF in the first non space character of the line All other lines are treated as comments Read a file in FIT2D binary format The filename is given by the first calling parameter of Two2One the extension is assumed to be bin ReadFit2DBinary Read the geometry correction from Two2One inf ReadGeometryFromInf Set some parameters for integration SertpslarisaticnkF ckor 1 00 25 SetIntegration2ThetaBins 1200 SetIntegration2ThetaFrom 2 Divide the full accessible range into the given number of bins Can be used to restrict automatically the 2theta range SetIntegration2ThetaStepsize AUTO SetIntegrationAzimuthFrom 80 SetIntegrationAzimuthTo 100 IntegrateNoMask IntegrateCreateOutlayerMask IntegrateWithMask WriteTwoThetaToGSAS Rename the files from raw to shell ren raw gda gda This file reads 2D data in the Fit2D binary format which can be generated using Fit2D scripts from any format Fit2D can read and applies a geometry correction based on data stored in Two2One inf It starts integration at a 20 angle of 2 calculated based on the geometry in Two2One inf such as detector to sample distance and divides the accessible 2 range into 1200 bins It selects only those pixels in the image plate for integration which correspond to an azimuth between 80 and 100 first integrates without a mask for some initialization a
52. Joerg Bergmann Germany Johannes Birkenstock Germany Bill David UK Vincent Favre Nicolin France Carmelo Giacovazzo Italy Vladimir Kogan Netherlands Vaclav Petricek Czech Republic Thomas Proffen USA Juan Rodriguez Carvajal France Leonid Solovyov Russia Matt Tucker UK Robert von Dreele USA Tentative Program Includes BGMN unter der Motorhaube BRASS unter der Motorhaube DANSE under the hood DASH under the bonnet Derivative Difference Minimization nOg KANOTOM EXPO sotto il cappuccio Fox sous le capot Fullprof and CrysFML debajo de la cap GSAS Under the hood Jana pod kapotou MAUD sotto il cappuccio Model free Aberration Correction Under the bonnet PDFFIT and Discus unter der Motorhaube PSSP under the hood RMCProfile under the bonnet TOPAS under the bonnet XND sous le capot Roundtable Discussion chaired by Robert McGreevy ISIS UK on Where does algorithm development have to go for indexing solution and refinement in powder diffraction Registration Registration for the workshop is done via the EPDIC meeting registration form Information about the EPDIC conference is on the web at http www sgk sscr ch EPDIC10 EPDIC10 html EPDIC 10 European Powder Diffraction Conference Geneva September 1 4 2006 65 News from the International Centre for Diffraction Data ICDD 12 Campus Boulevard Newtown Square PA 19073 3273 U S A www icdd com www dxcicdd
53. PL d 2 Nov 2005 http www ing unitn it maud PowderCell 7 July 2005 http www ccp14 ac uk ccp web mirrors powdcell a_v v_1 powder e_cell html and ftp ftp bam de Powder_Cell Prodd 19 August 2003 http www ccp14 ac uk ccp web mirrors prodd jpw22 Profil 24 May 2001 ftp img cryst bbk ac uk pdpl if Profil FTP site is unavailable use the CCP14 Mirrors Rietan 2000 GPL d 10 October 2005 http homepage mac com fujioizumi rietan angle_dispe rsive angle_dispersive html Winplotr Fullprof 8th July 2005 if Fullprof FTP site is unavailable use the CCP14 Mirrors http www llb cea fr winplotr winplotr htm 38 ftp charybde saclay cea fr pub divers fullprof 2k if Fullprof FTP site s unavailable use the CCP14 Mirrors Winmprof 21 June 2001 http Ipec univ lemans fr WinMProf XND 10 March 2005 http www cristallo polycnrs gre fr xnd xnd html ftp ftp grenoble cnrs fr xnd Gf XND FTP site is unavailable use the CCP14 Mirrors All the above Rietveld programs are also available via the CCP14 based mirrors in UK USA Australia and Canada http www ccp14 ac uk mirror Summary lists of some software available via the EPSRC funded CCP14 website What do you want to do lists of software by single crystal and powder methods http www ccp14 ac uk mirror want_to_do html Anharmonic Thermal Refinement Software http www ccp14 ac uk solution anharmonic Data Conversion for
54. Powder Diffraction http www ccp14 ac uk solution powderdataconv Image Plate Software http www ccp14 ac uk solution image plate Incommensurate Structure Software http www ccp14 ac uk solution incomm htm Indexing Software for Powders http www ccp14 ac uk solution indexing LeBail Method for Intensity Extraction http www ccp14 ac uk solution lebail Pawley Method for Intensity Extraction http www ccp14 ac uk solution pawley PDF High Q Powder diffraction Analys s Software http www ccp14 ac uk solution high_q_pdf Peak Find Profiling Software for Powder Diffraction http www ccp14 ac uk solution peakprofiling Pole Figure and Texture Analys s Software http www ccp14 ac uk solution pole_figure Powder Diffraction Data Visualisation http www ccp14 ac uk solution powder_data_visual Rietveld Software http www ccp14 ac uk solution rietveld_software Search Match Phase Identification Software http www ccp14 ac uk solution search match htm Single Crystal Suites linking to multiple programs relevant to Chemical Crystallography http www ccp14 ac uk solution xtalsuites Spacegroup and Symmetry operator determination software and source code http www ccp14 ac uk recomm sym_operators_to_sp acegroups html http www ccp14 ac uk recomm spacegroups_to_sym _operators html Spacegroup and Structure Transformation Software http www ccp14 ac uk solution transform Structure Conversion and Transformation http
55. The range selected in this manner is used to normalize the data By pressing Test you can preview the results of the normalization Press Cancel to discard or OK to accept the normalization i Normalize Patterns K lolx Phase 1 M Please select scaling method C Scale to maximum Scale to minimum C Scale to average Left click to zoom right to mark region OK Test Cancel Figure 16 Normalization function Wavelength The wavelength dialog accessible via the menu Edit gt Wavelength allows you to alter the radiation wavelength Figure 17 Should you wish to recalculate the pattern select the radio button recalculate patterns The 15 wavelengths for some standard anode elements have integrated in the top list S Change Wavelength x Operation corect value recalculate patterns Wavelength Theta E Dispersive fs Lambda 1 0 922400 Co Ni Lambda 2 0 000000 Cu v K alpha singlet Lambda ratio 0 000000 K alpha doublet Polarisation 0 000000 Cancel o Figure 17 Wavelength dialog Phases and ranges The increments between the patterns can be entered into a table Figure 18 which is called by Edit gt Increments and phase ranges For unvarying increments the fields on the right of the window can be used to insert values into the table Once two of the first three fields are filled the other is calculated and filled aut
56. X ray sources X ray OPTICS sample handling detectors and software all on a common platform Tw sanovations TO higher data quality and s ole Ihroughpu enhance the DS capabilities m Auto Changer for large sample batches o Effective instrumen usage without user intervention o Reflection and transmission vestigations without conversion B LynxEye and VANTEC V linear detectors o Large gt YTheta coverage TO 150 times faster easuremens Huge 12 2Theio coverage for second Snap Shot recording of kinematic processes BRUKER ADVANCED X RAY SOLUTIONS WW w bruker axs com D8 ADVA NC E Auto Changer LynxEye 1 1 02 12 2005 12 53 34 ANOTHER FIRST FROM PANALYTICAL New X Pert PRO for transmission allows for diffraction measurements on proteins The X Pert PRO MPD fitted with the focusing mirror capillary spinner and X Celerator detector Acknowledgement We thank Dr B Prugovecki University of Zagreb Croatia for the lysozyme crystallization sample preparation of capillary and stimulating discussions The Analytical X ray Company TUTE Te eae eee tera Le Bail fitting Profile function Pseudo Voigt Asymmetry correction Finger Cox Jephcoat Cell parameters a 78 99 A c 37 87A Indexing was carried out using X Pert HighScore Plus software Further processing using Le Bail fitting method provided excellent agreement with the cell parameters achieved by single crystal diffraction Using PANalytic
57. a dramatic development in the technique I believe that the trend is set to continue we have an exciting triennium ahead of us Watch the action Bill David CPD projects RIETVELD REFINEMENT OF ORGANIC STRUCTURES Increasing numbers of organic crystal structures are being solved and refined from powder diffraction data The basic ar rangement of the molecules in the structure can often be determined by direct methods or by direct space approaches How ever experience shows that problems can arise in the subsequent Rietveld refinement For example unless restrained by ap propriate bond distances and angles molecules can distort unrealistically from a reasonable molecular structure So how good are these Rietveld refinements Is the problem a fundamental one of powder diffraction eg the ambiguities and correlations caused by peak overlap or defining the background etc lead to inaccurate structures Or can some of the blame be attributed to poor refinement practice We plan to put onto the CPD web site a number of good quality powder diffraction patterns from organic compounds of known crystal structure and of different complexity These can be downloaded and powder crystallog raphers can try out their own prowess at Rietveld refinement by comparing their refined structures with the accepted single crystal structures This should be a learning exercise for us all Any suggestions as to compounds that would appear particu larly appropriate fo
58. a satellite group can be given and refined as Cartesian spherical and cylindrical coordinates The Z matrix representation is also available but presently not refinable A utility program running in console mode Mol_tpcr is now supplied with the aim of generating pieces of the PCR files Control of refinement The user can give comprehensive commands within the PCR file for controlling the refinement For doing this a section starting with the keyword COMMANDS provided just after the line giving the name of a phase can contain keywords like VARY x_Fel VARY xyz etc Improvements for creating FST file for Fp_Studio In the PCR file the user can give instructions for automatically make appropriate graphic representations of crystal and magnetic structures 56 New description of multi helical magnetic structures Multi helical magnetic structures can now be described in addition to the Fourier coefficients and basis functions formalisms in real space magnetic moments of the elliptical envelope and orientation angles of the helices are directly refinable New version of DICVOL The program DICVOL04 from A Boultif amp D Lou r J Appl Cryst 37 724 2004 is now the default indexing program of the FullProf Suite The success ratio of DICVOLO4 when running using default parameters has been highly improved Documentation Some new documents and user guides are now available as HTML and or PDF files An improved access
59. aced from the ideal 2b site 0 0 1 4 isosurfaces corresponding to M2 atoms are elongated along the c axis HO molecules are disordered on z 0 17 and z 0 33 planes encompassing the MI and M2 sites Fig 5 Electron density distribution density level 1 determined by MPF from synchrotron X ray powder diffraction data of Nav 343 H 30 o 237C002 1 19H30 Furthermore MPF has successfully been used in other studies including dynamic disordering of Cu ions in the superionic conductor RbyCuj6l72Cli2s 3 18 the conduction path and disorder in the oxide ion conductor Lao gSto 2 GaogsMgo 15C0o05 O23 19 and the migration path of Li ions in the Li ion conductor Lag 62Lio 6TiO3 20 6 ALBA ALBA is a Fortran 95 program for the MEP analysis of IFs estimated by the Le Bail method 5 from powder diffraction data and determined from single crystal diffraction data The name of the program originates from the most significant feature of the program that is MEP analysis is carried out After Le Bail Analysis using RIETAN 2000 Only one program for MEP analysis from IF l s obtained by the Pawley method has hitherto been developed 4 To our knowledge no MEP analysis program has yet been distributed on the Web We therefore built a powerful MEM engine into ALBA making alterations to that of PRIMA Thus ultra fast MEP analysis is possible with ALBA The algorithm of the MEP method in ALBA is described in a documen
60. al A graphical user interface is currently absent The program package includes a configuration for the freely available Programmer s File Editor PFE which facilitates integrating DDM with graphical utilities such as WinPLOTR and a structure viewer within the PFE shell An example of the PFE DDM interface s shown in the screenshot aj 5 r peen i Vice arg imar Ciiis in Demer maaar e Birgis Gan Fre mp wk p Mpp m jami Tram a Ta Erden E Depp Fi iu i CECT Laid O beia ii r psali Pn S een _ te Fe 1 Solovyov L A J Appl Cryst 37 2004 743 2 Solovyov L A Astachov A M Molokeev M S Vasiliev A D Acta Cryst B61 2005 435 3 Wiles D B Young R A J Appl Cryst 14 1981 149 4 Le Bail A Duroy H Fourquet J L Mater Res Bull 23 1988 447 5 Stephens P W J Appl Cryst 32 1999 281 6 Solovyov L A J Appl Cryst 33 2000 338 7 Thompson P Cox D E Hastings J B J Appl Cryst 20 1987 79 8 Roisnel T Rodriguez Carvajal J Mater Sci Forum 378 381 2000 118 Density Berman Balance Measurement Using the Richard J Staples Harvard University Department of Chemistry and Chemical Biology Cambridge Ma 02138 USA Email staples chemistry harvard edu Web http xrpc4 harvard edu staples html The Specific gravity of a substance can be of paramount importance in evaluation of
61. al s new transmission geometry with PreFIX focusing mirror in conjunction with the X Celerator detector diffraction experiments on macromolecules such as proteins can now be carried out with an X Pert PRO MPD X ray diffraction system Characterized by weak scattering and small sample volumes these materials have previously been considered difficult for X ray diffraction Instead protein structure determination traditionally relied on the use of single crystal systems or beam lines for the extraction of powder patterns Here we show for the first time that protein powder data measured on a laboratory X ray diffraction system can be used for crystallographic analysis Emphasis on the research and development of macromolecules especially in areas such as protein pharmaceutics has increased strongly in recent years By offering researchers the potential for pre screening and investigation of protein based medicines within the laboratory use of the transmission setup represents a significant technical advance As a PreFIX optic the focusing mirror is interchangeable with all other available incident optics for the X Pert PRO MPD without the need for any re alignment From a technical perspective it means e the size of the capillary tube no longer governs resolution e peaks narrower than 0 05 degrees are easily resolved Use of the X Celerator detector meanwhile ensures fast data collection Transmission experiments
62. all spectra used in this example It is possible to recognize in some samples the presence of both fcc and bcc phases but not in all Next step was to adjust the cell parameters for both bcc and fcc phases in order to get a mean starting value good for all spectra especially for the fcc and to adjust the crystallite value to a good starting point around 200A obtaining peak shapes a little sharper than in the less broadened spectrum The background constant parameter was also adjusted to the value of the spectrum with the lower background Actually only the cell parameter adjustment is critical the background one is even not necessary Finally we remove all the spectra we will specify which datafile to use for each analysis later in an instruction file and save the analysis containing everything except the spectrum a For the purpose of this article we save the analysis with the name FeCustart par 2 2 Preparation of the instruction file and batch processing To run Maud in batch we need to write an instruction file containing the list of analyses to execute one at time The file is in CIF format but containing some terms not available in the official CIF dictionary but that Maud recognize All the analyses to be performed are specified through the loop CIF instruction The first term of the loop must be the one specifying the starting analysis file to be loaded full path in unix convention and then the others to instruct Maud for
63. analysis QPA and the size strain calculations are implemented The following corrections are available e Ellipsoidal corrections for anisotropic broadening due to size and strain anisotropy e Anisotropic strain broadening correction with fourth rank hkl tensor 5 peak 47 e Selective peak broadening correction due to structural defects stacking faults etc 6 e Preferred orientation models of Rietveld Toraya March Dollase and its ellipsoidal extension e Split FWHM peak asymmetry correction for all available profile functions Lorentz Gauss pV TCH pV Pearson VII e Intensity corrections for finite sample thickness surface roughness beam overflow cylindrical sample absorption and Lorentz polarization factor The size strain calculations are performed using the TCH Pseudo Voigt profile function 7 with the allowance for the instrumental broadening and the microstructure anisotropy The DDM executable the source code based on revised DBWS 9006PC 3 a user s guide and examples are downloadable from the web at http icct krasn ru eng content persons Sol_LA The program reads parameters from input and data files and outputs results to text listings the crystallographic information file CIF the plot file readable by WinPLOTR 8 and a file with the structure factors and phases for the Fourier calculations The input files have free format and the numbering of the codewords for refinable variables is option
64. aximum entropy methods based Pattern Fitting MPF is an alternative to a classical approach i e Rietveld analysis to structure refinement from powder diffraction data 1 3 Crystal structures are represented not by structure parameters in Rietveld analysis but by electron nuclear densities in MPF A fast MEM analysis program is desired in MPF where whole pattern fitting w p f and MEM analysis are alternately iterated until convergence refer to Fig 1 in Ref 2 Before the development of PRIMA we had been utilizing MEED 14 for the MEM analysis of observed structure factors F obtained from X ray and neutron diffraction data After making every effort to speed up MEM analysis we completed our own program PRIMA It executes MEM analysis several tens times faster than MEED MEED is now obsolete because of its sluggish speed and serious bug where the total number of electrons total of b values in the unit cell deviates more or less during MEM iterations PRIMA was written from the ground up in Fortran 95 which enables us to create storage for allocatable arrays dynamically It is thoroughly optimized for PC s equipped with Intel Pentium 4 processors and operated with Windows Nonlinear single pixel approximation full use of Space group symmetry and adjustment of Lagrangian multipliers further accelerate MEM analysis PRIMA is applicable to MEM analysis from neutron diffraction data of compounds containing elements whose b
65. b beb ave Speakers Dr Robert Von Dreele Argonne National Laboratory USA Dr Angus Wilkinson Georgia Institute of Technology USA Dr Thomas Proffen Los Alamos National Lab USA Dr Ian Swainson Lachlan Cranswick National Research Council Canada Check out the CPDW webpage for further information on the workshop and information about the Waterloo area for accompanying persons or contact Lachlan Cranswick at lachlan cranswick nrc gc ca http www cins ca cpdw Canadian nstitute for Neutron Scattering Canadian Powder Diffraction Workshop Registration Costs Students Cdn 150 Academics and not for profit Cdn 180 Commercial and Industrial Cdn 210 Registration payment must be received by 14th April 2005 University of Waterloo LujanNeutron Scattering Center 64 Lecture Titles Include Sample preparation data collection considerations and phase ID using powder X ray diffraction Introduction to Powder Profile Refinement with GSAS Synchrotron Experiments Why and when to use neutron powder diffraction Freely available powder diffraction Software Measuring total scattering X ray and neutron data where and how What to do with your PDF Modeling of disordered Structures William G Davis Centre University of Waterloo Waterloo Ontario Reduced registration bursaries for students outside Ontario and Quebec are available thanks to the Canadian Inst
66. be determined by MPF 5 Application of MPF to a superconducting Co oxide hydrate Takada et al 16 prepared a layered compound Nao 343 H30 o 237C0O gt 1 19H2O space group P63 mmc a 2 8114 A and c 11 2111 A via soft chemical processing and discovered that it is a superconductor with a T of 5 K Intercalation of H O ions was overlooked at first but evidenced later by Raman spectroscopy 17 This Co oxide has aroused interest widely because it is the first superconductor where first row transition metal and oxygen atoms form layers It is interesting to note that the host in this compound is a famous thermoelectric material Na CoO To elucidate the arrangement of the guests H O H30 and Na sandwiched between two CoO layers MPF analysis from synchrotron X ray powder diffraction data with the combination of RIETAN 2000 PRIMA and 3D visualization with VEND were very effective 17 Because MEM is per se model free we could successfully find sites occupied by the guests getting rid of any preconceived ideas Fortunately this noteworthy structure refinement was the first application of PRIMA to a novel material Figure 5 illustrates isosurfaces drawn with VEND for electron densities in three unit cells Highly covalent Co O bonds are clearly visible In Rietveld analysis preceding MPF we assumed that H30 and Na ions statistically occupy MI 2 3 1 3 1 4 and M2 0 0 0 2413 sites Because M2 is slightly displ
67. c cell choe 1 orliorbombic axes abe ongm choice 2 heisagonal axes D Ta 0 0 Ba lb 2 Vee 3412 09 Mearest neighbor distances Dee 4 000 Team 34610 TiO 2 0000 Ba Bas 1 0000 Bate 2 328913 Oe 2 Ba Make shucture He _Miewporent hei Atomradue 04 Max bond length 220 Angstroms General method specify X point telp Rita a b 2K Alternate method search over all special A points help Crystal system s tnchrac O monschese C orthorhombic C tetragonal O ngonal O Hexagonal O cube C 4 z BL a E s Space group symmetry Mimma Deha H Conventional latice MECT Address http stokes byu edufcgi binfisofisodisplace cgi ISODISPLACE order parameter direction Space Group 221 Pm 3m Oh 1 Lattice parameters a 4 Space group preferences monoclinic axes a b c monoclinic cell choice 1 orthorhombic axes abc origin choice 2 hexagonal axes Ti 1a 0 0 0 Ba 1b 1 2 1 2 1 2 3d 1 2 0 0 Space group symmetry selected 74 Imma D2h 28 Finish selecting your distortion mode by choosing an order parameter direction help R4 P2 aal 74 Imma basis 1 0 1 0 2 0 1 0 1 IR5 P2 faa0 74 Imma basis f1 0 1 0 2 0 1 0 1 0 R4 P2 aal 74 Imma basis 0 2 0 1 0 1 1 0 1 in 0 0 1 2 s 2 i 12 is 0 2 0 0 0 2 2 0 0 origin 0 1 2 1 2 s 4 i http stokes byu edufcai bin isofisodisplace cgi ISODISPLACE Irreducible representation Space Group 221 Pm 3m Oh
68. cal instru mentation and services during the exhibition For more information on how to submit an abstract attend the symposium or participate in the exhibition contact Leah Mooney at ppxrd icdd com 55th Annual ag Denver X ray Conference AR Continuing its tradition of excellence MMS the 2006 Annual Denver X ray Conference will be held 7 11 August at the Denver Marriott Tech Center Hotel Denver Colorado U S A Presenting both workshops and technical sessions the conference offers something for everyone from beginners to experts DENVER X RAY CONFERENCE The Denver X ray Conference now in its 55th year offers a forum for the presentation of state of the art techniques and indications of future developments in X ray analysis This year the Plenary Session promises to be both interesting and insightful as it focuses on Medical Applications of X ray Analysis Following the Plenary session attendees to the world s largest X ray conference will choose from 16 broad range sessions Workshops are also conducted during conference week by experts who provide training and education on many practical applications of XRF and XRD techniques for the study of materials Designed to help attendees with little or many years of experience our workshops will offer suggestions and advice geared at helping attendees solve some of their most difficult problems Please visit www dxcicdd com to review the program
69. cally disordered layer structures with a Rietveld compatible approach Z Kristallogr 219 2004 519 527 41 How to add a molecule to a crystallographic surface using SCHAKAL 99 Egbert Keller Kristallographisches Institut der Universitat D 79104 Freiburg Germany Email egbert keller krist uni freiburg de Web http www krist uni freiburg de kell Lachlan Cranswick asked me to my surprise to make this contribution supposed to deal with some advanced riding of the graphics program SCHAKAL 99 note that 19 99 is a constant part of the name clearly indicating the program to be an object of the last century Just as he suggested I ll simply give some recipes on how drawings analogous to some of the more sophisticated ones on the SCHAKAL homepage see above can be generated The recipes are naturally of value only for those who happen to have some SCHAKAL experience thus to all others Have a nice day In the following I ll use mostly the good old typed commands style to save space 1 Let s start with the addition of a molecule to a crystallographic surface First we generate a 110 surface of the Pb PS structure using the file ex2_p dat which can be generated from the distributed atomic coordinates file ex2 dat using the cryst bld p procedure eryst bldtp InpData file gt gt gt ex2 Enter more Data gt gt gt OK The freshly made ex2_p dat allows to build
70. ces them with the average of their 10 neighbors Similarly if a pattern is very noisy due to low signal poor counting statistics blocks of pixels can be binned together to produce an image with lower resolution but less noise Calibration In order to quantitatively interpret an x ray scattering pattern it is necessary to map detector pixels to scattering angle units g y or g qy To accomplish this the following instrumental parameters must be known with some precision the wavelength A the pixel coordinates x Ye of the beam center the angular span of the detector as seen from the sample and the orientation of the detector relative to the primary beam The wavelength must be independently obtained it cannot be inferred from the data Since there is usually a dark patch in the image due to the beam stop it is tempting to assign xe ye to the geometric center of the beam stop image but this is almost always wrong the beam center usually differs from the beam stop center by a few pixels and misidentification of the xe Ye by even a fraction of a pixel can have significant consequences Instead by measuring a calibration sample such as silver stereate silver behenate LaBg or silicon one obtains a powder diffraction pattern consisting of a set of concentric Bragg rings The instrumental parameters can then be calibrated by requiring that xe ye be at the center of the rings the scattering angles of the rings correspond
71. cularity of the new version respect to the previous one are most of them to provide some useful routines for abinitio structure solution e Different minimization search algorithms selectable Marquardt least squares Evolutionary algorithm Simulated annealing Metadynamic search algorithm As an example the evolutionary algorithm can be used in the early steps of the refinement to select the proper starting solution and the Marquardt to drive it to convergence Possibility to use crystallites and microstrain distributions for peak shape description instead of analytical fixed shape functions e Maximum Entropy Electron Map full pattern fitting An electron map can be used for fitting instead of atoms Full pattern fitting by a list of peaks Either an arbitrary list of peaks each one with its own position intensity and shape or simply a list of structure factors to be imported instead of a list of atoms Indexing directly on the pattern selecting the Le Bail fit and the evolutionary algorithm for the cell search This may be used to improve a difficult indexing or a partly done one Introduction of fragments So fragment search can be done directly on the pattern or on a list of extracted structure factors e Energy minimization At the moment only the simple repulsion energy is completed Other energy principles are under completion e Spectra integration from image plate or CCD transmission reflection 2D images C
72. d the well known software for crystal and molecular structure visualization 2 Crystal Structure Visualization with Diamond Before the creation of video sequences is discussed in detail some general remarks and reflections concerning the creation of crystal structure pictures using Diamond shall be inserted The visualization of a crystal structure is generally achieved by creating a model of an idealized section of the structure using simple geometric objects like spheres sticks polyhedra etc based on given numerical crystal structure data like unit cell parameters space group and atomic parameters The goal is to create one or more pictures visualizing both the overall crystal structure as well as the basic construction principles e g the packing of atoms or molecules the atomic environments the building blocks and their connections among each other etc If the crystal structure has not been described before it may even be necessary to explore its construction principles before one can actually create pictures The pictures can then be used to present the structure to a scientific audience or to students Diamond offers a large variety of commands options and tools to perform these tasks 26 Typically the structure visualization consists of the following steps Input or import of the crystal structure data e g CIF file Checking of interatomic connectivity to neighbouring bonded atoms Creation of
73. d O bal c O fabe O a cb O Monoclinic cell choices 1 20 30 Orthorhombic axes abc ba c O cab O cba O bca a cb O Trigonal axes hexagonal rhombohedral O Origin choice 1 O 2 Address http stokes byu edu cgi binfisofisodisplace cgi ISODISPLACE atomic coordinates Space Group 221 Pm 3m Oh 1 Lattice parameters a 4 Space group preferences monoclinic axes a b c monoclinic cell choice 1 orthorhombic axes abc origin choice 2 hexagonal axes Enter the unique atomic positions help Atomic position 1 Identity of atom Ti Atomic position 3 Identity of atom 0 Atomic position 2 Identity of atom Ba Position 1a 0 0 0 iv Position 1b 172 172 172 E Position 3d 1 200 I x L x L y LL yl wal z z 6f 1 2 1 2 Figure 1 a When entering the parent structure manually the space group can either be entered using a drop down number or by entering its number from the International Tables Only the unique and non trivial unit cell parameters are required Non standard settings are available and apply to both parent cell and supercell b Atomic coordinates are entered via menus and fields for the non trivial components The example shown is a cubic barium titanate perovskite hiies fsboker bu euer ISODISPLACE k point Space Grea 221 Pm S Oh Lathes piane a Spate group preferences monockes aves abie moneta
74. detection plate Distortion by the focusing optics can induce nonlinearities in measured peak positions the quality of these optics is one of the primary differences between expensive and very expensive X ray CCD cameras Data from image plates can also suffer from distortions caused by waviness in the collecting plate or irregularities in the scanning hardware Data Input Most commonly the scientist will be analyzing a single data set at a time but sometimes they are combined One common situation is where many frames are collected under the same conditions Datasqueeze can add up to eleven such files to produce a single composite dataset while keeping track of counting statistics etc A somewhat more complicated situation 1s encountered when the user has collected a background data set for example air scattering with no sample in place Under these circumstances the natural tendency is to perform a one to one subtraction of the background data from the sample data but this is almost always incorrect It 1s important to understand all the possible sources of background There may be a constant source of readout noise as discussed above in the case of CCD detectors This should clearly just be subtracted from each data file independent of count time There may be background scattering that originates from the primary beam after it passes through the sample This scattering will be proportional to the integration time but also de
75. ds accelerating the OpenGL API e g those powered by GeForce and RADEON graphic processing units Four different modes of rotating objects are supported drag push click and automatic In addition to crystallographic and electronic state studies and education we will take pleasure in manipulating 3D objects on personal computers PC s 59 PRIMA is a MEM analysis program to calculate electron densities from X ray diffraction data and nuclear densities from neutron diffraction data 1 It was designed with MEM based Pattern Fitting MPF 1 3 in mind as can be inferred from its name ALBA is a program for the Maximum Entropy Patterson MEP method 4 whereby Patterson functions in the unit cell can be determined from observed integrated intensities resulting from Le Bail analysis 5 The VENUS package is distributed free of charge on a Web site http homepage mac com fujioizumi 2 VICS VICS can read in 23 kinds of crystal data files such as CIF PDB and ICSD Users of a multi purpose pattern fitting system RIETAN 2000 6 will be pleased to learn that VICS can read and write standard input files ins of RIETAN 2000 After Rietveld analysis using RIETAN 2000 it updates lattice and structure parameters in an input file vcs with the VICS format if vcs shares the same folder with ins Crystal structures are represented by ball and stick space filling polyhedral wireframe stick dot surface and thermal
76. e 30000 t OkV mm iR 5 5 kV mm 20000 ran 10000 The pictures show a PZT ceramic with sputtered Pt electrodes as used in the in situ device left and the whole device mounted on the diffractometer B2 1 at HASYLAB middle The position sensitive detector OBI 2 can also be seen and covers the whole 20 range simultaneously For more information on the specific sample see reference 3 A section of two diffraction patterns A 0 49975 A is shown on the right hand side for different states of poling The effects of microstructural changes are clearly reflected in the different profiles The evolution of these profiles along hystereses loops is reversible and has to be correlated with the underlying microstructure these analyses are still in progress 4 Two different test cells for in situ studies of the electrochemical Li extraction and insertion have been developed 5 6 Teflon Stainless Steel Spring O Rings Lithium Foil KM Swagelok housing Al J caros mix Cu Beam Sealings The following figure shows the complete diffraction pattern for LiMn O as observed before charging and calculated by the Rietveld method using the program package Winplotr 7 Note that phase specific sample shifts from the diffractometer centre have to be taken into account because of the sequential arrangement of Al current collector cathode and Li anode along the beam direction The newer versions of
77. e Fock calculations and other DFT approximations Due to the approximations inherent in the ab initio calculations and numerical errors the locations of the transition pressures are only accurate to about 5 GPa e g when employing DFT LDA LYP the range of the PbCl type phase in Cs2S includes standard pressure 0 GPa as observed in experiment 32 The threshold algorithm has been designed to y eld estimates of energy and entropy barriers around local minima on a general energy landscape Starting points of the explorations are the local minima of the energy landscape One then proceeds by selecting a sequence of energy lids thresholds above the energy of the local minimum For each lid one performs many random walks starting at the minimum where each move is accepted as grouped into several classes according to their structural similarity using the algorithm CMPZ implemented in KPLOT The ab initio calculations are performed on Hartree Fock and or DFT level using the program CRYSTAL2003 21 For the local optimization of the structure candidates the heuristic algorithm HARTREE 18 9 1s employed which E V curves for Cu N system 4970 8 4970 85 4970 9 T u m 4970 95 ey ak U 4971 Structure Types Ipha UO LiaN 4971 05 I K3N RbaN 4971 1 30 40 50 long as the energy of the new state does not exceed the threshold energy Along these random walks one periodically performs stochastic quench
78. e happy with your selection a click on Presentation graphics copies the data over to the iSurface programme It is always possible to further reduce the displayed data in the iTools programme suite should you find it necessary A right click on the data opens a context menu which lets you select the properties of the view Figure 46 Pie Dat iiet Gperations window hep Diaa lee frome fy ae AlSlololele Fi igure 46 The iTools property window pen the properties window to the full extent by pressing an unobtrusive left arrow in the top left corner of the window Figure 46 left 21 In the left side of Visualisation Browser Figure 46 You see the various elements that make up the image Once an element is highlighted its properties are displayed in the right part of the window We shall change the surface values to the following Color 145 145 145 Fill shading Gouraud Draw method Triangles The last two changes make the rendering slower but the picture better We open up the Axes branch and delete the Z axis by a right click and delete Figure 47 SI IDL iTool Yisualization Browser window 8 0 View 1 2 2 Visualization Layer iE Data Space Surface EE Axes E Axis 0 E Axis 1 Axis 2 P E Annotation Layer Axis plus labels Right Above False True Belows left
79. ed a real application of some of these techniques within the novel image plate integration soft ware Powder3D IP Arndt Kern focused on laboratory experiments giving a detailed view of the challenges facing the experimentalist during high temperature experiments He wowed the crowd with some novel applications of the Rietveld re finement software Topas The remaining working day was spent practicing data re duction and presentation using the software Powder3D http www fkf mpg de xray Dr J A Kaduk Jim BP Chemicals 150 W Warrenville Rd P O Box 3011 MC F 9 Naperville IL 60566 USA Telephone 1 630 4204547 Fax 1 630 4205252 e mail James Kaduk innovene com Dr Irene Margiolaki ESRF BP220 F 38043 Grenoble Cedex France Telephone 33 476 88 21 48 Fax 33 476 88 29 07 e mail margiolaki esrf fr Prof P Scardi Paolo Dipartimento di Ingegneria dei Materiali e Tecnologie Indu striali Universita di Trento 38050 Mesiano TN Italy Telephone 39 0461 882417 67 Fax 39 461 881977 e mail Paolo Scardi ing unitn it Dr M Yashima Tokyo Inst of Technology Grad School of Sci amp Engn Dpt of Matls Sci amp Engn Nagatsuta cho 4259 J 1 4 Midori ku Yokohama 226 8502 Japan e mail yashima masatomo mail goo ne jp The evening program consisted of a wine tasting of se lected German produce A delicious buffet dinner com plemented the wines all hand picked by Robert Dinnebier pe
80. ed to the distribution and the web page In addition the graphic user interface referred to as BGMNwin was improved to allow a more user friendly handling of the program A context sensitive help was introduced in both the sav and the str file editors By placing the cursor on a keyword or variable and pressing Fl a pop up window containing the description of the item will appear A complete list of variables and keywords for the BGMN files is also provided by this function A new window show device function see Fig 1 has been introduced In a simple and intuitive way one may now inspect the device function as used by BGMN The function show database lines was added to the window displaying the measured and calculated diffraction patterns This function refers to the 415 structures stored in the structures subdirectory of BGMNwin By choosing one of these structure files the line positions will be displayed together with the measured diffraction pattern Users can easily add structure files to the structures subdirectory to allow their use in BGMNwin The new function show calculated profile displays the calculated profile pattern of a selected phase within the Rietveld plot This feature is particularly useful for the inspection of the refinement progress Figure 2 shows the graphic window of BGMNwin with the functions show database lines and show calculated profile being enabled SUMMARY The pres
81. ellipsoid models Ball and stick and stick models may be enclosed in dot surface spheres of van der Waals radii With translucent coordination polyhedra atoms and bonds inside them are visible Needless to say VICS expresses anisotropic thermal motion by 3D graphics Fig 1 whereas ORTEP III 7 has no 3D graphics capability Fig 1 Monoclinic unit cell of Rb2Al B O7 drawn with VICS Its structure consists of Rb ions AlO tetrahedra and BO triangles VICS supports automatic atom search on the basis of bond specifications including minimum and maximum bond lengths Boundaries for drawing structures can be specified in sophisticated ways similar to convoluting and reiterative convoluting spheres in ORTEP III For example we can readily find all the atoms in a molecule starting from only one atom inside it Selection of objects atoms bonds and coordination polyhedra makes it possible to obtain fractional coordinates symmetry operations translation vectors interatomic distances bond angles torsion angles and information on coordination polyhedra including volumes Baur s distortion indices 8 quadratic elongations 9 bond angle var ances 9 bond valence sums 10 of central metals and bond lengths expected from bond valence parameters 10 Fig 2 2 Mn2 Mn 9 020000 0 00000 9 50000 1 1 x 1 y 1 2 z 1 3 01 0 22220 8 25000 0 50899 1 y 3 4 x 1 4 z 3 4 3 0 0 00000 0 02780 0 25890 1 1
82. em3b uhp nancy fr nancy2006 1 4 September 2006 EPDIC 10 European Powder Diffraction Conference University of Geneva Geneva Switzerland http www sgk sscr ch EPDIC10 EPDIC10 html 13 15 September 2006 ECRS 7 The 7th European Conference on Residual Stresses Berlin Germany http www ecrs7 de 17 November 2006 Protein crystallization Present and future Crystallisa tion Workshop EMBL Hamburg Outstation Hamburg Germany http www embl hamburg de workshops 2005 htx 18 19 November 2006 Theoretical Crystallography and Materials Science Satellite Conference of the AsCA 06 CrSJ meeting Tsu kuba Japan http www lcem3b uhp nancy fr mathcryst asca2006 htm 7 17 June 2007 Engineering of Crystalline Materials Properties State of the Art in Modelling Design and Applications the 39th crystallographic course at the Ettore Majorana Cen tre Erice http www crystalerice org futuremeet htm How to receive the IUCr CPD Newsletter The best and fastest way to receive the CPD Newsletter is to download it in electronic format as a pdf file from the CPD web site If you wish to be added to the mailing list for the Newsletter of the IUCr Commission on Powder Diffraction or have changed address please contact the Chairman Bill David bill david rl ac uk Call for contributions to the next CPD Newsletter No 33 The next issue of the CPD Newsletter will be edited by Miguel Delgado to appear
83. en after measurement This information along with other analytical techniques Mass Spec and NMR has proven effective Our standard palladium complex gave a measured density of 2 101 g cm compared to the value received by the solution of the X ray structure from the crystal at 60 C 2 113 g cm from Cambridge Structural Data Base 2 113 g cm at room temperature Acknowledgements The author would like to thank the Berman Laboratory for supplying the Berman balance and Dr William Croft for much of the related information regarding the procedure 1 General survey of Acta Crystallogr shows that until 1970 s the measured density was generally given in the structure reports published in the journal 2 Harry Berman American Mineralogist 1939 24 434 440 3 International Tables For Crystallography Vol C 1995 ed A J C Wilson pages 141 143 by F M Richards describes various methods for the determination of the density for a solid compound 4 Complete description resides in reference 2 5 International Critical Tables 3 1928 28 29 6 The Cambridge Structural Database F H Allen Acta Crystallogr B58 380 388 2002 49 Fitting of nano particle structures to powder diffraction pattern using DISCUS R B Neder and T Proffen Institut f r Mineralogie Am Hubland 97074 W rzburg Germany Lujan Neutron Scattering Center LANL MS H805 Los Alamos NM 87545 USA E mail reinhard neder mail uni wuer
84. en construct the landscape of free energy at temperature T which consists of locally ergodic regions that are separated by generalized barriers We note that this information also allows us to make statements about the metastable phases in the system that can be of importance in real life applications and phase diagrams where the specific synthesis methods employed might yield a metastable and not the thermodynamically stable phase As mentioned in the introduction we deal with non zero pressures by studying the properties of the enthalpy landscape H Epot pV 5 6 9 10 leading to the construction of free enthalpy landscapes 7 The locally ergodic regions discussed so far exhibit various degrees of order However at very high temperatures the local free energies of such ordered regions become unfavorable compared to the free energy of the set of states associated with the melt Then the free energy landscape becomes in a certain sense trivial since now the ordered phases are only stable on relatively short observational time scales and all these locally ergodic regions are directly connected to the region representing the melt at essentially the same value of free energy Finally we need to deal with variation in composition in the chemical system The prescription given above for constructing a free energy enthalpy landscape assumed that the composition of the system was kept fixed The next step is the analysis of landscapes that i
85. ent analys s The Rwp value for each analysis is reported in the second column and the biggest value found was 5 6 as an indication of the success of the analysis As an example we report in Figure 2 the graphical correlation of the copper rich phase percentage and its mean crystallite value as found in the analysis versus the sample number The files and examples used in this articles will be uploaded in a tutorial in the Maud web page along with some additional files with the batch mode commands for an easier use 250 T T T 1 j 1 7 T m Vol 200 x Size Angstrom 2 a a 1 gt 100 2 m a mu T i a BEW 50 pa rnnga m a m Eg 0 ii i Dr er A PR ec f i ti 0 5 10 15 20 25 30 Analysis Figure 2 Copper rich phase volumetric content and mean crystallite size vs sample number as obtained by the automatic batch mode analysis The plot has been created from the results file saved by Maud 3 How to get Maud 2 0 and new features For this analysis we need Maud version 2 037 or later and it can be freely downloaded from the Maud web page at http www ing unitn it maud for the preferred platform There are two archives for Windows and Mac OS X plus a generic Unix version that can be used for Linux Solaris or every Unix based system with a Java 2 virtual machine installed The new version 2 0 has a new interface focused on reducing the effort of a new user and simplifying the most common tasks Some parti
86. ent report describes the progress in the development of the BGMN package achieved over the last three years BGMN has been designed for quantitative phase analysis but it may also be used as a full featured Rietveld program for structure analysis A restricted demo version of the program is available at http www bsmn de The full featured version is specifically discounted for academic use ben BGHNwin File Run Tools Configuration Windows Help BoA gt 8 SON Fig 2 Graphic window of BGMNwin showing database line positions and calculated individual phase profiles ACKNOWLEDGEMENTS Thanks to Douglas McCarty and Chevron Texaco for providing the synchrotron data Use of the Advanced Photon Source was supported by the U S Department of Energy Office of Science Office of Basic Energy Sciences under Contract No W 31 109 Eng 38 The Java GUI was written by Robert Henschel The new spacegrp dat could not have been prepared without the help of Gert Nolze BAM Berlin REFERENCES 1 J Bergmann R Henschel and R Kleeberg The new BGMN and its use in quantitative phase analysis of mineralogical multiphase samples CPD Newslett 27 2002 26 27 2 L A Solovyov Full profile refinement by derivative difference minimization J Appl Cryst 37 2004 743 749 3 K Ufer G Roth R Kleeberg H Stanjek R Dohrmann J Bergmann Description of X ray powder pattern of turbostrati
87. entre tilting errors and distance from sample can be refined in the spectra fitting Bugs and errors should be reported to the author through the bug reporter web page questions in the Maud forum accessible from the Maud web page In a future article we will report the instructions on how to modify extend the program by little Java programming or provide a new alternative model plug in for the instrument or the structure microstructure or datafile importing References 1 D L Bish and S A Howard J Appl Cryst 21 86 91 1988 2 R J Hill and C J Howard J Appl Cryst 20 467 474 1987 3 L Lutterotti and S Gialanella Acta Mater 46 1 101 110 1998 4 B E Warren X ray Diffraction Addison Wesley Reading MA 1969 99 Update of the FullProf Suite and CrysFML Juan Rodriguez Carvajal Laboratoire L on Brillouin CEA CNRS CEA Saclay 91191 Gif sur Yvette Cedex France Institut Laue Langevin BP 156 38042 Grenoble Cedex France Email Juan Rodriguez Carvajal cea fr WWW http www Ilb cea fr fullweb powder htm and http www ccp14 ac uk ccp ccp 14 ftp mirror fullprof During the last year the FullProf Suite and the set of Fortran 95 modules constituting the Crystallographic Fortran Modules Library CrysFML have been extensively modified and updated In this short note I summarize the list of programs and the most important changes in the FullProf Suite as well as the available modules of C
88. eo sequence the structural changes as a function of the external parameter can now be viewed and understood much more intuitively 27 Detection of Ellipses in Powder Diffraction Patterns using Hough Transformation Rajiv Paneerselvam Bernd Hinrichsen Manfred Joswig and Robert E Dinnebier l Max Planck Institute for solid State Research Heisenbergstra e 1 70569 Stuttgart Germany 2 Institute for Geophysics Stuttgart University Richard Wagner Str 44 70184 Stuttgart Germany Introduction To gain structural information from image plate data it is essential to know the experimental configuration This information is contained in ellipses detected by an image plate Cystallographically speaking they are the intersection of the Bragg cone with a 2D detector Automatic recognition and refinement of the parameters describing the concentric ellipses is fundamental to modern powder x ray diffraction This is generally a very time consuming 4 operation We present a robust method for the automatic detection and characterization of ellipses using a modified Hough transformation Our method involves no mathematical complexity and exhibits excellent overall efficiency Overview An ellipse can be described by five parameters the major axis a minor axis b center co ordinates X and Yo and angle of orientation a Computing all five parameters simultaneously using Hough transformation by constructing a huge quan
89. erential Evolution http www icsi berkeley edu storn code html Magnetic Rietveld and single crystal refinement with SARAh Representational Analysis and SARAh Refine for the MS Windows Andrew S Wills Department of Chemistry University College London Christopher Ingold Laboratories 20 Gordon Street London WCIH OAJ United Kingdom Email a s wills ucl ac uk WWW http www chem ucl ac uk people wills and ftp ftp ill fr pub dit sarah The SARAh suite of programs was created to enable unspecialised users to use symmetry arguments to refine and understand magnetic structures The package contains two programs SARAh Representational Analysis which performs the group theory calculations of the different symmetry types and SARAh Refine a program that enables the results to be used directly in refinements using GSAS and FullProf Through this structure SARAR enables the analys s of both powder and single crystal neutron diffraction data using programs already familiar to the user The formalisms used in SARAJ are designed to educate the user with regards to magnetic structures their definition their types and their phase transitions Ka 1 fe Please reference che use of SANAR as Bills fhysica D 276 500 2000 4 3 Fi Progoee avallable Frou bid Ems pu LESS zosedinates Tri Enter ti rt amd poesaa Tah Enter the position coordinates spare delimited Click Add Edi Mom Arcem Change
90. ergy landscape is large compared to the observation time For such a locally ergodic region R we can apply standard statistical mechanical methods 1 e we can calculate the time averages of observables along trajectories within the region by evaluating the ensemble averages restricted to the region instead In particular we can compute the local free energy via the sum over states taken over the region R For very low temperatures both conditions for local ergodicity are usually fulfilled for regions that correspond to the neighborhood of local minima of the potential energy At elevated temperatures our general approach to identifying regions that can locally equilibrate and are sufficiently stable on time scales of interest focuses on the flow of probability on the energy landscape For this purpose we employ various indicator observables such as the potential energy or the radial distribution function averaged over time intervals of varying length along stochastic trajectories at constant temperature T By comparing these averages and their fluctuations we can identify candidates for locally ergodic regions The generalized barriers comprising the effects of energetic entropic and dynamical barriers on the energy landscape 8 31 which separate these locally ergodic regions can be found by measuring the amount of probability flowing away from the region as function of time at temperature T Based on this information we can th
91. erns using a graphical interface In addition to the graphical interface the program can run in a batch mode for automated processing of many files A particular strength of the program is that it is still evolving A new version is released every 2 4 months generally incorporating improvements or new features suggested by users Anticipated upgrades to the program include support for yet more data formats more options for 2D to 1D data reduction and improved support for non English speaking readers References 1 The description of Datasqueeze in this article does not constitute or imply an endorsement by the University of Pennsylvania Datasqueeze can be obtained from hrtp datasqueezesoftware com A manual with more detailed information on the program is available as a free download from the same site 2 The instrumentation 1S described at http www lrsm upenn edu lrsm facMAXS html 3 D W Marquardt J Soc Ind Appl Math II 2 431 441 1963 Powder3D A Software for tailored for in situ powder diffraction studies Bernd Hinrichsen Robert E Dinnebier and Martin Jansen Max Planck Institute for Solid State Research Heisenbergstrasse 1 Stuttgart Introduction Powder3D is a program for data reduction and publication quality visualisation aimed specifically at large data sets collected in time resolved powder diffraction experiments The program is in ongoing development so there shall be regular upda
92. es for this task Having defined the new scheme the remaining crystal structure data sets are imported and sorted so that their order is equivalent to the one of the pictures in the video sequence which shall be created Afterwards the Auto build scheme is applied to all crystal structure datasets to create the corresponding pictures in a single step In a so called thumbnail representation of all created structure pictures it is now easily possible to get an overview over the structural changes fig 1 If in some cases the changes between two neighbouring pictures are rather large due to a complete rearrangement of the crystal structure it may be necessary to create and apply a new Auto build scheme for the corresponding group of crystal structures o Hamas aan a a F r ES Yes Store Prhe fell Chidi Meee Tem Wire Heip 0x 0D a il BD i E oo BEIEIL BRE E 8 a H BHEILI i j j i i te E eii a mr 4 ee tS BE Figure 1 The Diamond software displaying a series of crystal structure pictures ready for the creation of a video sequence Once the individual crystal structure pictures have been created they are assembled to the final video sequence using the corresponding Diamond command The video sequence is written to an AVI file which can be used in other software packages e g in RealPlayer for viewing or in Microsoft PowerPoint for presentation purposes Using this vid
93. es that end in either the starting configuration or other local minima on the landscape The thresholds where new minima are found for the first time constitute upper bounds of the barriers separating the local minima from the remainder of the landscape The frequency with which such neighboring regions are reached as function of lid energy are a measure of the entropic and dynamical barriers surrounding given minimum This procedure is then repeated until all known and newly found minima have been explored From this information one can construct a lumped tree graph representation of the energy landscape Further details regarding the threshold algorithm can be found in the literature Refinement stage of candidates associated with unique local minima 18 9 With the help of the program LOAD 18 the several thousand minimum configurations and other structure candidates generated during the global optimization stage and the constant temperature runs are analyzed regarding their symmetries using the algorithms SFND 19 and RGS 20 implemented in the program KPLOT 15 and 33 BO r BO 90 Volume A Figure 2 E V curves for structure candidates in the Cu3N system At standard pressure the experimentally observed ReO3 type is found while at pressures above ca 30 GPa most likely the a UO3 or the Li3P structure type will occur consists of a nested sequence of line searches in the cell parameters for fixed and variable v
94. es that satisfy any user specified constraints and finally allows the user to interactively view and manipulate the 3D superstructure via a server based Java applet requires SunJava 1 4 2 or later and to save the distorted structure as a CIF file Topic specific links to the help pages are available throughout the ISODISPLACE site and should serve to answer many common questions Specifically the ISODISPLACE GUI interfaces to the subroutines of the ISOTROPY software suite Stokes and Hatch http stokes byu edu isotropy html which it uses to compute all of the isotropy subgroups of the parent space group symmetry 1 It then chooses those isotropy subgroups that correspond to structural phase transitions displacive order disorder and or strain and makes them 45 available to the user via drop down menus After a distortion mode has been selected using these menus a second window pops up containing the corresponding 3D superstructure along with one interactive slider bar for each free order parameter primary and secondary Once the free parameter values have been adjusted individually to obtain an interesting structure the overall amplitude of the mode can be varied with a master slider bar The structure can be zoomed and rotated arbitrarily using the mouse and the keyboard and the view direction can also be set precisely using either direct or reciprocal lattice coordinates The unique atoms in the supercell that split
95. ethod The convolution range is set via the Caglioti diagram the threshold and minimum distance between peaks can be set via the sliding bar The radio buttons under the Caglioti diagram determine if a new peak list is written with every run or the current peak list appended with the newly found peaks 17 a pit ri en Paa rd Preumtster papes AA Tumen den RW e E r F F F F F F t P F M n a nl Figure 26 Peak searching The peak positions and intensities can be saved to a Crysfire Shirley 2002 format file via the button Save on the Peak search tab Peaks can be added and removed manually by selecting the edit button as with the background points Single peak fitting Once the peaks have been found their position can be Figure 27 using a pseudo Voigt function corrected for axial divergence Finger 1998 All refined values are stored for later use You can select the peak by dragging over it A light blue box fills the border of the selection Pressing enter starts the refinement with the default values The fit is overlaid in blue for visual inspection Please note The FWHM Caglioti function has a profound effect on the convergence of the fit Should the procedure fail ensure the FWHM distribution is set to realistic values Peak markers can be added and removed manually by returning to the peak search window Figure 25 the modus operandi is identical to the additi
96. etter 67 Calls for contributions to CPD Newsletter 33 67 CPD Chairman s Message It is my privilege and pleasure as the incoming chair of the Commission on Powder Diffraction to write the introduction to this newsletter edited by the outgoing chair Robert Dinnebier The CPD was founded almost 20 years ago in 1987 and had its first meeting as a satellite to the main IUCr congress in Perth Australia in that year It is interesting to review progress over the past twenty years within the context of the reasons cited for the establishment of the CPD One of the most fundamental arguments for the formation of the commission was the unique position of international re search using powder diffraction as its main technique In almost all cases in the field of crystallography there is consid erably more activity in published material from academic institutions than from industry This position is exactly reversed in the field of powder diffraction and it is one of the major purposes of the commission to provide an information link be tween the very large industrial community and the more academic less applied aspects of the subject I would like to think that the boundaries between industry and academia have blurred a little over the past 20 years Many of the most important advances have been pioneered by industry and particularly by the diffractometer companies Faced with the phenomenal capabilities of powder diffractometers at synchrotron sou
97. etween the calculations for histogram step widths of 0 025 A and 0 010A No damping of the powder pattern is observed even at 20 140 The calculations were carried out for ZnO nano particles with 50x34 A diameter and 100 78 A diameter The powder calculations may be carried out for X ray and neutron diffraction data The user can define the section of reciprocal space for which the powder pattern is to be calculated on an angular as well as a q 4T sin O A scale The DISCUS commands to calculate and store a powder pattern are described in the following macro This macro reads the asymmetric unit of the quartz structure ans expands this to a small crystal of 5x5x5 unit cells No defects are introduced in this short example In the powder menu the calculation mode is set to debye Another option allows full integration of reciprocal space this option is better suited to large crystals where he integration can be limited to non zero regions of reciprocal space Reciprocal space is defined in units of q and the calculation is carried out from q 0 5 to 7 0 in steps of 0 01 The atomic displacement parameters are used while anomalous dispersion is switched off No instrumental broadening is done by setting delta to 0 0 A non zero value would instruct DISCUS to convolute the diffraction pattern with a Gaussian function The wave length is defined and the calculation run with X ray form factors The powder pattern is stored as an ASCII f
98. f parameters e s d s determined by least squares analysis are influenced by the intensity uncertainties via error propagation through the weighting scheme used Correct assignments of statistical uncertainties for each bin need to take into account that 20 values at a larger radius are measured more frequently than on inner rings This is of importance in particular for sealed tube X ray studies due to the lower brilliance of the source and the related poor peak background ratio During the integration step also an outlier rejection single crystal spots from diamond anvil cells shadows dark current noise can dramatically improve the data quality as shown below It should be pointed out that Two2One is not intended to replace Fit2D but rather to add functionality not found in Fit2D to the data reduction and analysis process For instance the parameters required for the geometry correction are obtained in Fit2D Two2One provides also automation of single peak fitting as frequently required during deformation studies Two2One Two2One is written in C making it in principle available on any platform but currently only executables for Windows are available upon request from the authors It is 23 always called with a data filename and a script applied to this data file e g for data reduction from a 2D data set to a 20 scan or single peak fits of selected peaks The scripts are s mple ASCH files an example of a script file is gi
99. f the most used parameters and results It is possible to specify the parameters we want in output using the CIF word riet append result to in addition or as an alternative but in the preparation of the starting analysis file in the Maud interface the parameters to be added to the results must be specified by turning to true the switch in the output column of the parameter list window or panel Now 54 to run Maud in batch in the console or DOS window we type in the directory or folder where the Maud jar is located the following DOS everything in the same line java mx512M cp Maud jar lib mischlib jar lib JSginfo jar lib jgae c jar lib ij jar it unitn ing rista MaudText f fecu ins Unix everything in the same line java mx512M cp Maud jar lib miscLib jar lib JSgInfo jar lib Jjgaec Jar 116 17 Jar it unitn ing rista MaudText f fecu ins For Mac OS X it is advised to use the generic Unix Maud installation or to change the path to the jar files Before running Maud in batch mode it s important to run Maud interactive with the interface at least once to create and extract the databases examples and preferences folder 2 3 Analysis of results After running Maud in batch mode we can check quickly the results by loading the results file FECUresults txt in a spreadsheet program The results are arranged in rows and separated by tabs The first row contains the column titles each subsequent row a differ
100. f trapped solvent molecules Procedure Procedure is very simple and at one time was taught in mineralogy courses here at Harvard University To calculate the specific gravity the general formula is used S Wd S Specific Gravity of solid W W balance W Weight of solid in air as determined by the W Weight of solid in liquid of density d d Density corrected for temperature of solution The true density of the liquid is temperature dependant so the temperature needs to be recorded The variation of the specific gravity by temperature is expressed as follows di d 10 a t t 10 B t t 10 y t t Where d 0 70048 a 0 8476 B 0 1880 y 5 23 t 0 C In practice the largest errors come from bubbles or surface tension effect which hold the basket and help contribute to air bubbles on the powder or crystal Example Common practice is to measure a standard mineral prior to determination of the specific gravity of an unknown material We use a piece of quartz and then measure the specific gravity for a single crystal and then compare that to the reported value when a unit cell or structural solution is completed We have used this information to help identify potential solvent trapped in the lattice when the solvent is disordered Care must be taken when choosing liquid to use since the solvent can be removed from the lattice It is best if you can confirm a unit cell before measurement and th
101. format for subsequent easy loading in a spreadsheet program Cu Fe example loop_ _riet_analysis_file _riet_analysis_iteration number _riet_analysis_wizard index _riet_analysis_fileToSave _riet_meas_datafile name _riet_append_simple_result_to mypath FeCustart par 7 13 mypath FECU1010 par mypath FECU1010 UDF mypath FECUresults txt mypath FeCustart par 7 13 mypath FECU1O11 par mypath FECU1011 UDF mypath FECUresults txt Sones lines with all the other 23 datafiles omitted for brevity mypath FeCustart par 7 13 mypath FECU1LO38 par mypath FECU1038 UDF mypath FECUresults txt With this instruction file that we save under the name fecu ins we specify for example that as a first analysis Maud has to load the FeCustart par file then to load in the analysis the FECU1010 UDF datafile to perform the automatic analys s number 13 in the wizard panel of Maud the automatic analys s number 13 is the texture analysis we need to refine also the texture parameters along with phase analys s and microstructure and to use 7 iterations for each cycle the texture automatic analysis is composed by 4 cycles to ensure sufficient convergence At the end the analysis is saved with the name FECU1010 par and simple selected results will be appended in the file FECUresults txt The simple results saved in the spreadsheet like file are some o
102. from the same parent cell site may also be separately highlighted in the structure For distortions that occur at special reciprocal space k points e g I R M etc the isotropy subgroups have been precomputed making it possible to simultaneously search all of the special k points for relevant distortions The search can further be constrained by choice of crystal system conventional lattice basis and or final space group symmetry Distortions occurring at non special k points can also be explored one k point at atime After entering the k point as a rational fraction incommensurate wavevectors are have not yet been implemented subsequent drop down menus allow the user to specify an irreducible representation of the parent space group and an order parameter direction in abstract representation space which uniquely identify a given distortion mode Because each distortion mode can be explored and evaluated interactively in the viewer it is not necessary to thoroughly understand the group theoretical concepts behind this approach Address _ http stokes byu edu iso isodisplacemanual html ISODISPLACE parent structure Space group help 221 Pm 3m Oh 1 J 221 Lattice parameters Angstroms and degrees help a 40 b c alpha beta gamma Number of unique atomic positions help 3 Space group preferences the defaults are typically OK help Monoclinic axes afb c c bjaO abc
103. g 5 shows the result for LP Search applied to Cimetidine data taken from www ccpl4 ac uk Input for indexing comprised the Bravais lattice and minimum maximum values for the lattice parameters and volume The top plot shows the Rwp values as a function of refinement iteration here 21 Pawley refinements were performed the total time take was approximately 1 minute Larger lattice parameters and volume ranges increases the time taken to solution TOPAS eh her mer lp wearch cneikine gpro cin ook ig x SCH TEE lei D a eB co nn iu it li Fame oa wv all oe A a SE gt how MK eG os gt 90 sn Rwp for Pawley refinements Lu a i Tod h hl h i hi gp Wi N l i i i 4 L I 1 soll Tka i AU Ru e e aA or bu Fe 30 20 o 50 100 4150 200 250 300 350 Iteration hie Finase 0 00 9 10 12 14 16 18 20 22 24 26 20 30 32 2Th Degrees Ress Say seer Fig 5 LP Search applied to Cimetidine Important to realize here is that peak positions were not extracted This makes LP Search particularly suitable for poor quality powder diffraction data where reliable peak extraction is difficult or even impossible e g due to peak overlap problems additional phases or anisotropic line broadening This is shown in Fig 6 for orthorhombic LT ZrM0 O data courtesy of S Allen Durham UK This example was indexed to a 5 879 A b 7
104. ground intensity of X ray images is high near the incident beam and decreases towards higher 20 angles 6 Subtracting the background for such images with non uniform intensity distribution is crucial The entire image is divided into radial segments The average intensity of each segment differs from the others Background reduction is accomplished by subtracting twice the median from all the pixels of a segment Figure 5 Bit scaled images before a and after b background reduction After background subtraction the image is converted into a binary image through thresholding Here we set the pixels of high intensity to 1 and the rest to 0 by applying a suitable threshold A conversion 1s necessary for an efficient Hough transformation 2 It 1s extremely important for non uniform images to be subjected to background reduction in order to choose a single optimal threshold value for the entire image The comparison between the binary images obtained without background reduction Figure 5a and with background reduction Figure 5b3 is shown A lot of noise has accumulated near the center of the pattern in the image without background reduction After experimenting with many values we have chosen 10 as the optimal value for threshold 29 Range of major and minor axes of ellipse To put some geometric restrictions on major and minor axes we need to find the approximate range of a and spurious pixels that are unlikely to be of
105. h two different colors Fig 3a a ib Fig 3 Isosurfaces of a the wave function of HOMO and b electron densities calculated for the Cd SMo Hnta 3 gt ion with SCAT Isosurface levels a 0 002a and b O 08a where a denotes the Bohr radius VEND also has a feature of surface colorization to show the electrostatic potential value at each point on isosurfaces Isosurfaces can be smoothed by spline interpolation Clicking a More button doubles pixel numbers along a b and c directions whereas clicking a Less button half them One of great advantages of VEND over other visualization tools is a feature to overlap translucent isosurfaces as well as slices with ball and stick and stick models drawn with VICS Fig 3a Drawing boundaries are specified using the numbers of unit cells along a b and c directions as well as a pair of cross sections inside a unit cell Unit cell edges and or cross sections are colorized according to values of physical quantities on them to learn their distribution inside isosurfaces Fig 3b As Fig 4 shows we can insert up to three slices i e planes colorized with an equation relating values to colors Fig 4 Isosurfaces of electron densities density level 0 7 A calculated for a superconductor MgB by an augmented plane wave method with WIEN2k 100 and 002 planes where Mg and B atoms are located are inserted as slices 4 PRIMA and its use in MPF M
106. hat would need to open a session involving the remote display setting The overall procedure is to prepare the analysis locally using the interface or to prepare a starting point for a series of spectra one common starting point also using the interface then to prepare an instruction file in CIF like format to specify the analyses the spectra and the kind of refinement to conduct and finally to run Maud in batch mode providing the instruction file previously prepared The program will run and process one analysis at time and prepare an output file extracting some key information either the default or some to be specified in a format suitable to be imported in spreadsheet or graphical programs to analyze the results As an example we will show the procedure to analyze a series of ball milled Cu Fe mixed powders in which two different phases may form with a different composition By an automatic Rietveld analysis performed in batch mode we will extract information about phase content 2 1 crystallite and microstrain for each sample spectrum The analysis is further complicated from the fact that the powders milled at higher energy show the presence of planar defects 4 and texture arising from sample preparation and the platelet like shape of the grains 3 2 Analysis and procedure In this section we will present the procedure to analyze 25 spectra of Cu Fe different samples The spectra were collected on a Philips X pert system in Le
107. hip I decided to incorporate the full papers into the newsletter which explains the slight oversize of this issue Supplementary material additional tutorials and many abstracts can also be found at http www fkf mpg de xray Robert Dinnebier WWW sites related to powder diffraction The Commission on Powder Diffraction CPD http www ucr org iucr top iucr cpd html The International Union of Crystallography IUCr http www ucr org The International Centre for Diffraction Data ICDD http www icdd com The International X ray Analysis Society IXAS http www ixas org CCP 14 http www ccp14 ac uk Submitting a proposal for neutron diffraction or synchrotron radiation X ray diffraction is possible at many publicly funded large scale facilities in the world It represents an important and frequently unique opportunity for powder diffraction experi ments A useful guide and information can be accessed through the following web site maintained by R Dinnebier at http www fkf mpg de xray This list s far from being complete and needs input from users and readers of the CPD Newsletter Please send comments to R Dinnebier r dinnebier fkf mpg de THE IUCR COMMISSION ON POWDER DIFFRACTION TRIENNIUM 2005 2008 Chairman Prof W I F David Bill Rutherford Appleton Laboratory CCLRC Chilton Oxon OX11 OQX United Kingdom Telephone 44 1235 445179 Fax 44 1235 445643 e mail bill david
108. hm An input set of lattice parameters is varied until Eq 1 is minimized where N is the number of calculated peaks 26 are the calculated peak positions Y 2 the observed intensity at 20 and V the volume of the unit cell formed by the lattice parameters n is set to 2 3 for triclinic lattices 1 2 for monoclinic lattices and 1 3 otherwise 1 44 20 f 20 20 Y 20 d20 20 20p1 2 29 20 12 f 20 20 Y 20 d20 20 p 1 Np FOM V gt Eq 1 is minimized using an iterative mechanism whereby at each iteration a particular length lattice parameter is varied between 50 of its value Angle lattice parameters are varied within 10 A Pawley Le Bail refinement is then performed with starting lattice parameters corresponding to the minima of Eq 1 Eq 1 performs the task of getting close to a set of lattice parameters that would give a good Pawley Le Bail fit The process of minimization of Eq 1 and then a Pawley Le Bail refinement is repeated with random sets of starting lattice parameters Resulting solutions are ranked by Rwp values with smaller values being superior Critical to the success of LP Search algorithm is the speed to which Eq 1 can be calculated In TOPAS highly optimized code is used whereby monoclinic lattices can be solved in a few minutes Triclinic lattices can take as much as 15 minutes on today s laptop computers LP Search Indexing Examples Fi
109. hus of the stability of the region Further analysis steps usually follow such as local quenches from points within the candidate region in order to decide whether the region is associated with one or many local minima In order to gain better estimates of the escape times as function of temperature we perform an ensemble of Monte Carlo runs for a set of trajectories starting from the locally ergodic regions Finally we employ the structure comparison algorithm CMPZ implemented in the program KPLOT 15 for the analysis of the structural relationships among the various candidates We note that there exist several classes of chemical systems where the high temperature structure candidates imply a peculiar structure of the energy landscape Examples are quasi ionic compounds where one of the cations or anions participating constitutes a complex ion such as the NO group in KNO or chemical systems where alloy formation is to be expected To deal with these types of systems we have developed specific methodologies 7 however since the focus here is on high pressure effects we are not going to discuss these in further detail Threshold algorithm to measure generalized barriers via probability flow 16 17 8 Legend ME CaCl WE Car BE Poci BEE Ni In distorted Chemical System Pressure GPa Figure 1 Pressure phase diagrams for the alkali metal sulfides DFT B3LYP level Similar results are found for Hartre
110. ile Further Information To learn more about the ICDD its products and services please visit our web sites www icdd com and www dxcicdd com ICDD the ICDD logo and PDF are registered in the U S Patent and Trademark Office Powder Diffraction File and Denver X ray Conference are NAR cl of the JCPDS International Centre for Diffraction Data What s On 19 21 September 2005 SES IH Synchrotron Environmental Science III Upton NY USA http www cems stonybrook edu ses 1i index html 22 24 September 2005 7th International Meeting on Single Nucleotide Poly morphism and Complex Genome Analysis Hinckley Leicestershire UK http snp2005 nci nih gov 3 7 October 2005 4th NCCR Practical Course Synchrotron Data Acqui sition Techniques in Macromolecular Crystallography Swiss Light Source Villigen Switzerland http www structuralbiology unizh ch course05 asp 6 7 October 2005 Watching the Action Powder Diffraction at non ambient conditions Max Planck Institute for Solid State Research Stuttgart Germany http www fkf mpg de xray 10 14 October 2005 Autumn School Application of Neutron and Synchro tron Radiation in Engineering Materials Science Ham burg Germany http www tu berlin de pnam 17 19 October 2005 3rd MECA SENS Conference on Stress Evaluation by Neutron and Synchrotron X Ray Radiation Bishop s Lodge Resort Santa Fe New Mexico USA http www lansce lanl gov mecasens2
111. ile with columns q and intensity read cell quartz cell 5 5 5 powder set calc debye set ax1s q set qmin 0 5 set qmax 7 0 set dg 0 01 set temp use set disp off set delta 0 0 set wvle 1 54056 xray run exit output form powder q outfile quartz q run exit Intensity Fig 1 Powder pattern of a small quartz particle Powder pattern fitting The calculation of the powder pattern of nano particles based on a single simulated particle is a valid solution only if all particles are assumed to be identical in size and structure Usually nano particles will be subject to a particle size distribution and the presence of structural defects such as stacking faults or twinning In this case the powder diffraction pattern must be averaged from powder diffraction pattern calculated for a distribution of several particles The individual particles within this distribution are simulated by randomly placing defects within the particle structure The refinement of the corresponding structural parameters that define the crystal structure and especially the defect structure are not straightforwardly implemented into a least squares refinement since the derivatives of the individual parameters are lost in the averaging We therefore use a differential evolutionary algorithm Storn amp Price to refine the parameters The differential evolutionary algorithm is considered a very effective genetic algorithm This algorithm has been encoded
112. in June 2006 Miguel will greatly appreciate contributions from readers on matters of interest to the powder diffraction community e g meeting reports future meetings developments in instruments techniques and news of general interest Please contact him for sending articles and suggestions Software developments can be directly addressed to Lachlan Cranswick or to the Editor of Newsletter No 33 Prof Miguel Delgado Laboratorio de Cristalografia Departamento de Quimica Facultad de Ciencias La Hechicera Universidad de Los Andes M rida 5101 Venezuela Telephone 58 274 240 13 72 e mail migueld ula ve 68 Dr Lachlan M D Cranswick Neutron Program for Materials Research National Research Council Canada Building 459 Chalk River Laboratories Chalk River ON Canada KOJ 1J0 Phone 1 613 584 8811 ext 3719 C2 ext 3039 Fax 1 613 584 4040 E mail lachlan cranswick nrc gc ca http neutron nrc gc ca
113. ing isaw 2 Tao et al Nuc Instr Meth submitted New Features of the BGMN Rietveld program J Bergmann R Kleeberg Ludwig Renn Allee 14 D 01217 Dresden Technical University Bergakademie Freiberg Institute of Mineralogy Brennhausgasse 14 D 09596 Freiberg Germany Email email jbergmann de kleeberg mineral tu freiberg de Web http www bgmn de The present article describes the modification of the Rietveld program BGMN since its last presentation in this newsletter in 2002 1 The following minor revisions of the refinement kernel as well as extensions of the program code have been introduced The new version of BGMN supports the refinement of synchrotron data For example the key SYNCHROTRON 0 079 serves a sharp delta function for the synchrotron wavelength distribution function 0 079 nm for use in the profile convolution Because of the unknown geometric parameters and the uncertainties of the detector resolution function the learnt profiles method for getting the instrumental contribution is recommended The program VERZERR was modified accordingly for the application of learnt profiles from synchrotron data Figure 1 shows a learnt instrumental profile of the device attached at sector 32 of the Advanced Photon Source in Argonne IL A mixture of LaB6 NIST SRM 660a and Si NIST SRM 640c was used as profile standard The model describing the preferred orientation correction was revised In additi
114. ional Add further lighting via Insert gt Light The mouse has two modes while manipulating lights positional and rotational Change between the two by selecting the pointer or the circled arrow Figure 52 alm oz RSS EEE jis Al al lt Figure 52 Mouse modus buttons This should be the last fine tuning the image needs When complete export the image via File gt Export Select To a file in the following dialog When questioned whether 22 or TwoTheta Scan High Pressure Research 14 235 248 Structure Window View or Data are to be exported either Window or View shall suffice Next specify your export file name and type and resolution References When publishing please give reference to Powder3D in the following manner Hinrichsen B Dinnebier R E and Jansen M 2004 Powder3D An easy to use program for data reduction and graphical presentation of large numbers of powder diffraction patterns Z Krist Suppl in press Briickner S 2000 Estimation of the background in powder diffraction patterns through a robust smoothing procedure J Appl Cryst 33 977 979 Caglioti G Paoletti A Ricci F P 1958 Choice of collimators for a crystal spectrometer for neutron diffraction Nucl Instr 3 223 228 Dinnebier R E 2003 FWHM optimised polynomial smoothing filters A practical approach Powder Diffraction 18 3 199 20
115. ioned because none of them have been updated for quite a long time K Momma and one of the authors F I have been developing successors to VICS and VEND using wxWidgets as a C GUI framework The new software has tabbed multiwindow browsing as the most pronounced feature A B version of the structure drawing program VICS II 1S available for download on http www geocities jp kmo_mma crystal en vics html This next generation 3D visualization software will be reported elsewhere Acknowledgment We wish to thank H Ohki of Shinshu University and K Momma of Tohoku University for their assistance in improving VENUS References 1 F Izumi and R A Dilanian Recent Research Developments in Physics Vol 3 Part II Transworld Res Network Trivandrum 2002 pp 699 726 2 F Izumi and T Ikeda Comm Powder Diffr UCr Newslett No 26 7 2001 3 F Izumi Solid State Ionics 172 1 2004 4 W I F David J Appl Crystallogr 20 316 1987 5 A Le Bail et al Mater Res Bull 23 447 1988 6 F Izumi and T Ikeda Mater Sci Forum 321 324 198 2000 7 M N Burnett and C K Johnson Oak Ridge Natl Lab Report ORNL 6895 1996 8 W H Baur Acta Crystallogr Sect B 30 1195 1974 9 K Robinson et al Science 172 567 1971 10 I D Brown and D Altermatt Acta Crystallogr Sect B 41 244 1985 11 H Adachi et al J Phys Soc Jpn 45 875 1978 12 P
116. is commonly the case is prevented SARAA is written in native Windows code and the input process is as intuitive as possible To perform the symmetry calculations the user must input the space group of the chemical structure before the ordering process the propagation vector of the resultant magnetic structure use of a propagation vector is core to the correct and simplest definition of a magnetic structure and the atomic coordinates of each site occupied by a magnetic ion After initialisation a default course for the calculations is created by the program that depends on the particular input and the user only has to press lt Return gt to complete them The listing files show the calculations of the irreducible representations the Istl file and the associated basis vectors the lst2 file Two additional files are created The first is written in LaTeX and contains a summary of the calculations including formatted tables in the form of a report that can be read normally Citations are given to key references and a brief introduction to the use of representation theory is given The second file with the extension mat is used by SARAh Refine Element Rotation matrix IT notation Kovalev notation Jones symbol g R Im R T gr halt 100 913 010 o 0 0 0 001 1 0 0 gis wu o 000 0 0 1 D 1 8 915 gu Oda 00 0 0 Ui bay 2E 20 Gis 100 oal 000 0 1 haz 000 2 y 2 has 000 2 Y 2 ha
117. is methods have been introduced which greatly extend the range of thermodynamic conditions under which compounds can be studied and generated In particular synthesis at very high pressures 1 2 and even effective negative pressures 3 4 has become an important area of investigation in many research groups around the world However in spite of highly improved experimental techniques the in situ measurements of the structure of these compounds are still far from trivial and in many instances the only reliable information obtained are the cell constants of the modification under investigation Thus it would be very helpful in the identification of newly generated phases if one could complement the experimental results by theoretical investigations on the same system In the following we are going to present our general approach to structure prediction for given thermodynamic boundary conditions 5 7 We describe the current implementation and illustrate the various aspects of our approach at the example of several chemical systems Quite generally at non zero temperatures a structure candidate corresponds to a locally ergodic region on the energy enthalpy landscape with sufficiently low local free energy A locally ergodic region equals a set of states on the energy landscape that fulfills two conditions 6 the system can equilibrate on time scales small compared to the observation time and the escape time from this region on the en
118. it Help Open ru my De Y Print XYE DAT Le La A gg ge Figure 3 Import menu Six different formats are available although XY and Chi formats are identical You shall be prompted to select a file Figure 4 Standard versions of GSAS GDA Fullprof DAT Bruker UXD and DASH XYE data files are imported 2x Suchen in 5 chi files lt e c Ea Fy E 8 012 chi a 023 chi a 034 chi a 002 chi a 013 chi a 024 chi a 035 chi Verlauf 003 chi 014 chi 9 025 chi 036 chi 4 004 chi 015 chi 026 chi 037 chi G f 005 chi 8 016 chi 027 chi 038 chi Desktop a 006 chi 017 chi a 028 chi 9 039 chi EN 007 chi 018 chi 029 chi 040 chi ER a 008 chi 013 chi a 030 chi 041 chi eee ey fa 009 chi 020 chi 031 chi 042 chi 010 chi 021 chi 032 chi a 043 chi 011 chi a 022 chi a 033 chi 38 044 chi Arbeitsplatz 4 gt A Jo Dateiname oot chi v Netzwerkumg Dateityp chi epf v Abbrechen Figure 4 Select import files Select any file of your set Once you press open a search for all files with a suffix identical to the selected file within the given directory is started Beware th s search is recursive if you have further file in subdirectories matching the search pattern these shall also be loaded The files are sorted according to the
119. ither by additional disturbing signals or hide the object of interest by not transparent shieldings A promising approach to in situ materials characterisation has to follow three steps 1 identification of a suitable probe 11 design of an operating test cell 411 combination with an adapted dector system For structural studies of polycrystalline materials under operation the use of synchrotron radiation can overcome most of the limitations High energetic radiation short wavelength has a very good penetration capability the high intensity allows fast data collection with good time resolution and the low vertical divergence can reveal also subtle details by the small and in most cases neglectable instrumental contribution to the observed reflection profiles in powder diffraction In this contribution two examples for the characterisation of materials driven in operation by electric fields are shown 1 Piezoelectric Pb Zr T O ceramics are polarized by electric fields and the resulting strain is used in actuators 2 Li Co Ni O allows to extract and reinsert Li ions This reversible process is exploited in the cathode of rechargeable Li ion batteries During charging the electric field of the external charger pumps electrons from the cathode to the anode and induces for charge compensation a movement of one Li ion per electron from the cathode to the anode through a Li conducting but for electrons insulating electrolyt
120. itute for Neutron Scattering and University of Waterloo As well as similar bursaries for US based students thanks to the Lujan Neutron Scattering Center Pr H vo L ha ie fe z E 2 po Mr Preliminary Announcement t Under the Bonnet a Powder Diffraction Software Workshop 8 50am to 6 00pm Friday Ist September 2006 Uni Mail University of Geneva Br Geneva Switzerland just prior and in the same venue as the EPDIC 10 European powder diffraction conference http www pa msu edu cmp billinge group Geneva2006 Use Software for Powder diffraction Want to know which program to use for a particular application Want to hear from the developers what great engine they have got hiding under that pretty GUI Get direct feedback to your questions from the Developers themselves Contribute to the discussion of code extensions and the next generation School Organisers Simon Billinge Michigan State University USA Lachlan Cranswick NRC Chalk River Canada Workshop Aims To have powder diffraction software developers present the advanced features in their indexing solution and refinement programs To help participants answer the following questions about the programs what does it do why when should I use it how where can I use get it what is under the bonnet Confirmed Presenters As of mid November 2005 the following speakers have been confirmed e Michael Aivazis USA
121. ization Sl Insert Visualization xj amp Data Manager image 7 Image Parameters IMAGEPIXELS PALETTE PALETTE Z PALETTE FAG Surface parameters PALETTE nz x 010 x 010 Y x Ebe Plot Profile sR o gt gt Y xf gt Import Variable Import File Type IDLPALETTE Description BYTE 3 256 OK Cancel Figure 49 Define the type and variables for the visualization 15 x Image Si IDL iTool Yisualization Browser Window BO view E E Visualization Layer i E Data Space E pA Surface mage Image Image True Edit color table Nearest Neighbor 85000 0 023913 1 7 99891 0 a Lights Annotation Layer Image transparency 0 Row order Bottom to top Z value for image plane Figure 50 Correcting the height of the image Now our image is complete All that remains to be done is to improve the lighting and export a high resolution image You might have become aware of the Lights branch on the left in the Visualization Browser Figure 50 Open this branch and select the directional light You should observe something like Figure 51 0 pr Figure 51 Lighting in iTools Now you can manipulate the geometric coordinates with the mouse and alter the intensity in the properties window This you can do three different light types ambient positional and direct
122. k current or electrical noise in CCD area detectors resulting in more or less arbitrary intensities across the image contributing more noise the more points contribute to a 2 bin Figure 2 Intensity Uncertainties During the integration process correct intensity uncertainties have to be assigned to the histogram data points During the least squares e g Rietveld analysis 24 these uncertainties allow to compute statistical not experimental uncertainties for resulting parameters such as lattice parameters or bond lengths Unrealistic uncertainties may result if this is not treated correctly Other indicators of wrong intensity uncertainties are the goodness of fit indicators such as the reduced x that may be too large gt 10 for an almost perfect fit or too small lt 1 As was shown in 7 the intensity uncertainty of a 2 bin is given by c 4 N where is the mean intensity for a given integration ring and N is the number of contributing pixels This results in a smaller uncertainty for rings with greater radius since those peaks are measured more often than 20 bins resulting from rings with smaller radius This effect compensates partially for the decrease in peak intensity due to atomic displacement factors atomic form factor etc Figure 3 Hass tk ah HE tia Bi I id aD ee Ma a i lO Y E fi to K i alL oe vo tM donate eee ee eee BEEN 7 ONEENS OAE EEan A Figure 3 2D diffraction data
123. kolowski M Hinterstein H Ehrenberg Electrochem Solid State Lett 8 2005 A379 A381 11 N N Bramnik K G Bramnik C Baehtz H Ehrenberg J Power Sources 145 2005 74 81 Datasqueeze A Software Tool for Powder and Small Angle X Ray Diffraction Analysis Paul A Heiney Department of Physics and Astronomy University of Pennsylvania 209 S 33 St Philadelphia PA 19104 U S A heiney sas upenn edu Introduction A substantial portion of X ray Diffraction XRD research is today performed using two dimensional 2D positional detectors also known as area detectors Such detectors measure the scattered intensity over a surface and save the data as an array of pixel intensities The researcher must then interpret this array of intensities to obtain a structural model for the system of interest Typically the detector manufacturer supplies software for reading the obtained data files and performing some kind of primary data processing However this software varies in quality and even when it is well designed it may not suit the needs of the user For example the scientist may be performing small angle x ray scattering SAXS using an instrument that the manufacturer had intended for use with single crystal structure refinement The hardware itself could be perfectly adequate for the purpose but the manufacturer s software ineffective at extracting the kind of information desired Furthermore the supplied sof
124. l co za Dr R E Dinnebier Robert Max Planck Institut f r Festk6rperforschung Heisenbersstrasse 1 D 70569 Stuttgart Germany Telephone 49 711 689 1503 Fax 49 711 689 1502 e mail r dinnebier fkf mpg de home www fkf mpg de xray Workshop Report Watching the Action An international workshop on in situ powder diffraction organized by Robert E Dinnebier Bernd Hinrichsen and Martin Jansen was held in Stuttgart in the first week of October The Max Planck Institute for Solid State Re search hosted the event spanning two days organized un der the auspices of the DGK CPD and MPG Various aspects of this fascinating experimental method were presented during the morning sessions the afternoons being reserved for hands on tutorials in data reduction presentation and Rietveld refinement Twelve participants contributed short presentations detailing their current re search in the field and also presenting experimental facili ties The opening presentation by Paul Norby went directly to the heart of the matter giving insight into novel high speed synchrotron experiments aimed at studying chemical reac tions Christian Schoen showed us what we are looking for in his talk on structure prediction of new high and low pressure phases After the coffee break image analysis filled the rest of the morning session Some general aspects of image filtering techniques were introduced by Manfred Joswig Bernd Hinrichsen present
125. last number in the file names A specific suffix is not necessary Powder3D does however filter for the endings according to the selected file format in the file selection dialog Should your files have a different suffix type lt your suffix here gt lt Enter gt in the File name field to display them Upon pressing enter the file names in the directory are read and sorted then the first file is loaded and the theta range read The next window prompts you for the wavelength and the two theta range and increment The increment entered can not be altered later The range can only be cropped Should the range of your files differ from the set values the intensities are interpolated using the selected function linear quadratic or spline The entries correspond to the values of the sample data provided 13 x Set wavelength Theta Lambda 1 0 9224 Lambda 2 0 000000 Lambda ratio 0 000000 00 Polarization 0 300000 00 New polarisation om Cancel OF H Imported files gj Setwavelength Theta Min theta 0 011 9565 Be quadrati Max theta 54 3590 Interpolation method nn spline Step width 0 0239130 t linear Cancel UK Figure 5 Import settings After the files have been read a message displays a few details on the array Figure 6 There is no set limit to the number of files that can be read the only limitation is the available memory Database information a x d A i
126. ments for the characterisation of polycrystalline materials using high energetic synchrotron radiation is gratefully acknowledged Electrical fatigue in functional materials is investigated in the frame of the DFG Collaborative Research Centre SFB 595 Experiments and analyses on PZT ceramics are performed by K A Sch nau M Knapp and H Fue on Li ion battery materials by N N Bramnik K Nikolowski and C B htz 1 M Knapp C Baehtz H Ehrenberg H Fuess J Synchrotron Rad 11 2004 328 334 2 M Knapp V Joco C Baehtz H H Brecht A Berghaeuser H Ehrenberg H von Seggern H Fuess Nucl Instrum Meth A 521 2004 565 570 3 K A Sch nau M Knapp N Balke H Ehrenberg H Fuess Z Kristallogr Suppl 22 2005 127 4 K A Sch nau PhD Thesis Materials Science Darmstadt University of Technology 5 C Baehtz Th Buhrmester N Ni5Bramnik K Nikolowski H Ehrenberg Solid State Ionics 176 2005 1647 1652 6 K Nikolowski C Baehtz N N Bramnik H Ehrenberg J Appl Cryst 38 2005 851 853 7 T Roisnel J Rodriguez Carvajal Mater Sci Forum 378 381 2001 118 123 8 T Gross T Buhrmester K G Bramnik N N Bramnik K Nikolowski C Baehtz H Ehrenberg H Fuess Solid State Ionics 176 2005 1193 1199 9 H Ehrenberg K Nikolowski N N Bramnik C Baehtz T Buhrmester T Gross Adv Eng Mater in print 10 N N Bramnik K G Bramnik K Ni
127. n cell q are the ionic charges of the ions o the sum of the ionic radii and amp quantifies the strength of the atom atom repulsion and polarization terms The sum in the Coulomb term is performed either with the aid of a convergence factor exp arj or via the DeLeeuw method 14 If the composition is to be varied during the exploration we add a term Z u N to H where u is the chemical potential of atoms of type 1 and N the total number of atoms of type 1 in the simulation cell General search algorithm to find locally ergodic regions 7 In order to identify locally ergodic regions at non zero temperatures we analyze the probability flow on the landscape This flow is represented by stochastic random walkers at constant temperature employing the Metropolis acceptance criterion For a given random trajectory we register the fluctuation and average value of indicator variables over time intervals of length Tin such as the potential energy or enthalpy if p 0 or radial distribution functions When starting from a random atom arrangement the difference in average energy between two consecutive intervals will exceed the fluctuation within the two intervals and the system is not in equilibrium However once this difference falls below the fluctuations we have detected a candidate for a locally ergodic region By registering when the system falls out of equilibrium again we can gain a first estimate of the escape time and t
128. nces e g when analyzing systems with complex ions we include building units that contain several atoms in a fixed spatial arrangement 11 and optimize the units positions and orientations as part of the global exploration procedure Global optimization to identify local minima A central element of the study of the energy landscape of a chemical system is the determination of the local minima since most locally ergodic regions even at elevated temperatures are associated with one or many such minima We usually employ a stochastic search algorithm such as simulated annealing with a variety of acceptance rules of the moves e g the Metropolis criterion 12 or threshold accepting 13 The moveclass employed for the generation of neighbor configurations during the stochastic walk allows the free variation of cell parameters of atom unit positions and orientation shift of single atoms or groups of atoms rotation of atom groups and exchange of atoms or groups of atoms and of ionic charges In addition the composition of the cell can be changed but as mentioned above we usually keep the composition fixed For the global exploration of the enthalpy landscape described by H E pV we employ an empirical potential energy function usually in the form Epo 2 Bion Zij qi qty j o t oy r Here Eion is the ionization energy or electron affinity of the ions being formed V is the volume of the simulatio
129. nclude not only the pressure via a term pV but also the chemical potential of species 1 via a term uN We have performed such simulations in the past however we found it to be more efficient to keep the composition fixed within one set of investigations and to repeat the global exploration for many different compositions But no matter how one decides to deal with the issue of varying composition once the free energy enthalpy landscapes of a chemical system have been constructed as function of temperature pressure and composition one can deduce many features of the system s phase diagram at least at low temperatures the exact location of the transition between melt and the various solid phases is still not easily determined from first principles METHODS The implementation of the general approach described in the previous section consists of several algorithms that can be put together in a modular fashion depending on the type of question asked In all instances the starting point is the energy landscape i e the hypersurface of the potential energy over the configuration space of the system Here a configuration is defined by the cell parameters of the simulation cell plus the electronic state charge and positions of the atoms in the cell Since we are in most cases interested in ordered crystalline compounds we usually employ periodic boundary conditions and between 10 and 40 atoms per simulation cell In certain insta
130. nd the other for the horizontal points are fitted separately The point of intersection of these lines gives the approximate center of the ellipse Bei rr ee TAF sc ir W af Ay ah Difference 7 Paai a a I F m Pixels i Figure 4 Difference histogram of profile This algorithm for approximate center determination robust against the outliers in the image and also against the geometric position of the ellipses with respect to the image center Masking of high intensity spikes Powder diffraction images are often disturbed by the high intensity outliers formed due to high grain dispersion in the sample These high intensity pixels must be masked out to enhance the accuracy in the determination of the ellipse parameters The masking is done by capping the intensities six times the median of the entire image The influence of the outliers to the center determination is very moderate and unpredictable due to the randomness of the spikes in the image The slight uncertainties caused by them are further minimized by a statistically reliable least absolute deviation fit function used to fit lines along the mid points of the grids Background reduction and thresholding Background reduction and thresholding are an important step in preparing the image for Hough transformation The diffraction images are surrounded by cloudy background formed due to the scattering of X rays by air molecules Hence the back
131. nd then generates an outlier mask with 7o around the mean of each ring After integration which takes into account this mask the data is written in GSAS format References 1 Hammersley A P Svensson S O amp Thompson A 1994 Nucl Instr Meth A346 312 321 2 Vogel S C High Pressure and Texture Measurements with an Imaging Plate diploma thesis at the institute for Earth Sciences Christian Albrechts University Kiel Germany 2001 3 Vogel S C Ehm L Knorr K amp Braun G 2002 Advances in X Ray Analysis 2002 45 31 33 4 Lutterotti L Matthies S Wenk H R Schultz A S amp Richardson J W 1997 J Appl Phys 81 594 600 5 Matthies S Pehl J Wenk H R Lutterotti L amp Vogel S C 2005 J Appl Cryst 38 462 475 6 Knorr K Ehm L Hytha M Winkler B amp Depmeier W 2001 phys stat sol b 223 435 440 7 Chall M Knorr K Ehm L amp Depmeier W 2000 High Press Res 17 315 323 8 Ehm L Vogel S C Knorr K Schmid Beurmann P amp Depmeier W 2002 J Alloy Comp 339 30 34 9 Toby B H 2001 http www ncnr nist gov programs crystallography software cmpr Diamond Investigation and Visualization of Structural Changes H Putz K Brandenburg Crystal Impact GbR Bonn Germany E mail info crystalimpact com http www crystalimpact com 1 Introduction Most compounds undergo phase transistions when the
132. nd up two graphics programs taking full advantage of the OpenGL technology These two bear the bell in three dimensional 3D visualization rendering and manipulation of crystal structures and electron nuclear densities determined not only by X ray neutron diffraction but also by electronic structure calculations With VENUS visualization of electrostatic potentials and wave functions calculated with part of these programs is also possible Further VENUS includes two programs for Maximum Entropy Methods MEM They allow us to determine electron nuclear densities and Patterson functions which are readily visualized as described above 1 Four components of VENUS The VENUS package comprises four independent programs VICS Visualization of Crystal Structures VEND Visualization of Electron Nuclear Densities PRIMA PRactice Iterative MEM Analyses ALBA After Le Bail Analysis VICS and VEND visualize crystal structures and electron nuclear densities respectively They have been written in ANSI C for cross platform portability which enabled us to port them from Microsoft Windows to UNIX Linux Their Graphical User Interface GUI was constructed with a combination of GLUT and GLUI They can output 10 kinds of image files such as TIFF EPS including pixel or vector data JPEG and JPEG 2000 With VICS and VEND objects are rotated expanded shrunken and translated fast in three dimensions particularly in the presence of video car
133. nsform for 2 D grayscale object detection Proceedings of International Conference on Pattern Recognition Volume 2 511 515 1996 3 Lei Y Wong K C Ellipse detection based on symmetry Pattern Recognition Letters 20 41 47 1999 4 Bennett N Burrigge R Saito N A method to detect and characterize ellipses using Hough Transform IEEE 30 Transactions on Pattern analysis and Machine Intelligence 21 7 1999 5 Dammer C Leleux P Villers D Dosiere M Use of Hough Transform to determine the center of digitized X ray diffraction patterns Nuclear Instruments and Methods in Physics Research B132 214 220 1997 6 R Fisker H F Poulsen J Schou J M Carstensen S Garbe Use of Image Processing Tools for Texture Analysis of High Energy Synchrotron Data J Appl Cryst 31 647 653 1998 7 Kanatani K Ohta N Automatic detection of circular objects by Ellipse growing Memoirs of the Faculty of Engineering Okayama University 36 107 116 2001 8 Feng L Fainman Y Detection of a general ellipse by an optical Hough Transform Applied Optics 31 1992 Prediction of not yet synthesized phases at high and low pressures and the transitions among them using global exploration methods and ab initio calculations J C Sch n Z Cancarevic and M Jansen Max Planck Institute for Solid State Research D 70569 Stuttgart Germany INTRODUCTION AND GENERAL APPROACH In recent decades new synthes
134. ntrast The zoom and pan tools are available for this display ie Ein Pater Katee Fi Py Daer daii Aii EEE E a Fir K zao e Temperature K ut Figure 40 2D film plot 3D line plot alfa x fame eds he deem oe Figure 41 3D line plot By clicking the 3D plot button the default 3D line plot is displayed Figure 41 The data range can be set as with the 2D film plot Rotation around X and Y axes can be controlled via slides Two preset views are stored and can be accessed via the buttons Top and Slant Mouse rotation is enabled by default pressing the appropriate radio buttons activates translation and scaling modes Finally the line plot can be immediately changed to a rendered surface plot by selecting the Surface radio button 3D surface plot The surface plot Figure 42 is identical to the line plot in handling As rendering the surface can be a slow process 20 dependant on the amount data displayed the surface mode requires more patience while adjusting the view All images can be exported either by copying to the clipboard Edit gt Copy exporting to an image file File gt Export gt Image or printing File gt Print For the latter two Operations the image is rendered from scratch and dependant on the resolution of the image file or printer can take a considerable amount of time Lights The 2nd
135. nts or else specify the R point in the upper menu b The special k point approach leads directly to a list of distortions with the 46 specified symmetry along with their respective IRs and OPDs as well as other useful descriptive information c d The general k point approach involves two steps First specify the IR in panel c and then select from its OPDs in panel d to uniquely identify the distortion mode of interest Pe O Wem fota tock W Pete 110 25 eat econ ISODISPLACE view distortion Geaphecal rendenng of selected crymal bei Weed View Coor dinates Spk SAW ParHKL Dann o 05 85 1 tu mode 1 3 04 Pde Gu made 1 G A O 2 ne lt D Input View Coordinates SupHKL SuplvwW ParHKL Partin I 0 5 Rot iT 1u mode 1 mo fo 9 0 45 R4 Eu mode 1 Se nn o R5 Eu mode 2 a 0 GM4 strain 1 gt 0 GM3 strain 2 OO seme 0 15 GMS strain 3 Figure 3 The ISODISPLACE viewer applet with expanded view of the sliders The example shown here is a well known perovskite tilt mode aa c induced by the R i irrep along the P2 a a 0 order parameter direction The distortion has a v2xv2x2 supercell and spacegroup symmetry Imma See that the parent oxygen site has split into two sites with separate checkboxes The first oxygen slider is the primary order parameter though the other two Ba and O parameters irrep R are actually co primary in
136. nuclear densities from X ray neutron powder diffraction data because the 61 F Rietveld s are more or less biased toward the structural model in the Rietveld analysis For this purpose MPF is far superior to the MEM Rietveld method Nothing is so difficult as MPF At first w p f is carried out from the F MEM data in fba Simply set NMODE at 2 and NMEM at 1 in ins and then run RIETAN 2000 Note that all the structure parameters in ins must have been updated on the analysis of X ray diffraction data because contributions of anomalous scattering to structure factors need to be calculated from them On repartition of observed diffraction intensities after w p f the improvement of structure factors for the overlapped reflections effectively reduces the bias toward the structural model in the Rietveld analysis F w p f data in the resultant file fos are analyzed by PRIMA to get fba as well as pri In such a way w p f and MEM analysis are alternately repeated until R factors usually Rwp in the former no longer decrease REMEDY cycles The bias to the structural model reduces with increasing number of cycles Throughout the REMEDY cycles the total number of electrons X ray diffraction or the total of b values neutron diffraction in the unit cell is fixed at that evaluated from the chemical formula and Z Thus electron nuclear density distribution affording the best fit to the observed diffraction pattern can
137. o 000 y 2 2 har 000 y z 2 Table 5 Symmetry operators of the space group I4 m mm The notations used are of the International Tables where the elements are separated into rotation 3 and translation components and the Jones faithful representations 10 Element Rotation matrix IT notation Kovalev notation Jones symbol R ga R T gon ha 7 9 Wr g 010 E 000 hy 000 2 Y 2 001 L UoD g5 0 2 0 C2 0 0 0 hs 000 2 y 2 G i Table 6 Symmetry elements of the little group Gg The notations used are of the International Tables where the elements are separated into rotation 3 and translation components and the Jones faithful representations 10 Fig 2 A tables from the LaTeX summary file generated by SARAh Representational Analysis DO ATE T i Select Bane ectora helen al Wrede All MAT fin c ee h E mat EP bie cgpa aai A a p ar eu Ri Cpi Conan Dami Chem D Sui Oo Fig 3 SARAh Refine main screen showing selection of basis vectors to be tested Refinement is started using a button in the Refinement Controls Tab A help window at the side gives general advice SARAh Refine should be invoked once the user has created a working magnetic refinement in either GSAS or FullProf In GSAS the user should enter a magnetic only phase with the symmetry Pl A magnetic atom should be entered into this phase and profile parameters set up according to the nuclear
138. o be excluded is laborious and automation therefore desirable Using the fact that the frequency of intensities on a powder ring of constant diffraction angle 2 is Poisson distributed for a random sample texture such pixels can be identified by computing the difference of the pixel intensity to the mean intensity I on a ring This difference can be normalized by the width o I of the measured distribution for a particular ring and the number of o width away from the mean outside which a pixel is identified to be an outlier is an adjustable parameter in the Two2One script Single crystal spots etc result in intensities appearing as outliers in the intensity distribution and therefore can be readily identified and rejected from the integration Figure 1 shows an example of the automated masking Masks generated this way by Two2One may be inspected using Fit2D ALOE 2 i kooman i m bep I j eal 4 I 7 tU 50 W ha woeOne from CeQ2_int OO bir Scan te Lambda lamboac 0190 Observed Profile ALOE r i e 1 A M i Ze ar ka Wintin POT eels pel lpi i 1 1 0 1 0 7 0 Figure 2 Raw data of Ceria powder left measured using a Bruker SMART1500 CCD area detector at the 13 BM D beam line GSECARS at the Advanced Photon Source Argonne National Laboratory Data integrated over a 20 degree azimuth section with Two2One without center and with outlier rejection of 70 right Another source of noise is dar
139. o to Thierry Bataille ongoing tests with bond valence Christian Baerlocher Mac OS X testing Mark Pitt neutron TOF Michal Husak many tests and Jan van Mechelen large molecules testing 1 Z Kristallogr 219 2004 847 http dx doi org 10 1524 zkri 219 12 847 55869 2 J Appl Cryst 2001 34 318 http dx doi org 10 1107 S0021889801004332 3 Acta Cryst 2002 A58 316 http dx doi org 10 1107 S010876730200510X VENUS a 3D Visualization System for Crystal Structures and Electron Nuclear Densities Fujio Izumi amp Ruben A Dilanian a Advanced Materials Laboratory National Institute for Materials Science 1 1 Namiki Tsukuba Ibaraki 305 0044 Japan b School of Physics Monash University Clayton Melbourne Victoria Australia 3800 Email IZUMI Fujio nims go jp WWW hittp homepage mac com fujioizumi Despite the availability of many structure drawing programs cross platform free software to visualize both crystal and electronic structures in three dimensions are relatively few We should understand structural details and space distribution of various physical quantities not two dimensionally but three dimensionally No whole picture of the complex space distribution is obtainable from contour maps that are often plotted To improve such a situation we developed our own software package VENUS Visualization of Electron NUclear densities and Structures We designed from the grou
140. of FeosNbS2 8 left measured with a laboratory X Ray source and a MAR image plate detector and the integrated data with the GSAS Rietveld fit The applied intensity uncertainties force the fit to a better agreement with the measured data in the high 20 large radius range as is evident by the inset Integration The integration in Two2One can be performed using arbitrary azimuth ranges and the output can be either plain ASCII files with 26 intensity and uncertainty in 3 columns or GSAS format Azimuth ranges are for instance used to analyze deformation anisotropy having a vertical load axis the grains resulting in diffraction close to the vertical exhibit a larger elastic deformation longitudinal to the load axis than the grains resulting in diffraction to the horizontal plane transverse to the load axis Another application of azimuth integration is quantitative texture determination The intensity distribution on a Debye Scherrer ring is converted to a trace in a pole density figure Diffraction patterns taken at several sample orientations allow filling the pole density figure and the reconstruction of the orientation distribution function from a set of incomplete pole density figures Single Peak Fit Automation Two2One allows automatically generating scripts for single peak fits based on peak lists generated by CMPR 9 The GSAS program RAWPLOT is used for this process making all peak profile functions included in GSAS
141. of the ease with which it can be implemented in this type of software ALBA allows us to improve IF l s of overlapped reflections adding value to them Ikeda and Itabashi 22 have recently determined the structure of a new zeolite RMA 3 from X ray powder diffraction data measured with Cu Ka radiation Integrated intensities resulting from Le Bail analysis with RIETAN 2000 were improved with ALBA and analyzed by the direct method using EXPO to give an initial structure model Subsequent Rietveld and MPF analyses based on this model revealed a novel framework topology containing two eight membered ring pore openings with dimensions of 4 9 x 0 37 A and 3 4 x 3 8 A 7 Concluding remarks The development of VENUS was motivated by a desire to present the poor with the advanced graphics software neither expensive graphics workstations nor commercial programs are now necessary for 3D visualization As described above VENUS has superior features compared with existing commercial software VENUS will contribute to a wide variety of studies as a tool for understanding the crystal and electronic structures of materials three dimensionally to enhance the creativity of researchers VENUS may be able to prevent phase separation between experimental and theoretical approaches Because VENUS is free software it is ideal for education of crystal and electronic structures for various compounds Now the GUI in GLUT and GLUI is rather old fash
142. olume together with line search optimizations of free atom position parameters as the innermost loop Unless specific stability analyses are performed the space groups of the structure candidates remain fixed For more details we refer to the literature Fitting the data points obtained from these optimizations results in E V curves for the various structure candidates where we have employed a standard Murnaghan fit 22 Since the pressure for a given volume equals the negative slope of the E V curve one can compute the transition pressures between two modifications by calculating the slope of the common tangent if it exists The result can then be depicted in form of a so called 1d pressure phase diagram EXAMPLES An example of a 1d pressure phase diagram is shown below for the structure family of the alkali sulfides 9 An example of the E V curves for several structure candidates is given in Fig 2for the system Cu3N 27 G eV Atom 150 750 1050 1 00 1350 4 20 1650 1950 2250 2850 4 00 a 4 20 4 60 4 80 Sphal 5 00 p BeO Wurtz 5 20 5 40 NiAs 5 60 Tip 5 80 NaCl a G eV Atom s CsCl 0 b Figure 3 Free enthalpy landscapes for the system SrO at standard pressure a and 160 GPa b Fig 3 shows the free enthalpy landscapes in the SrO system for standard and very high pressures 10 7 One clearly sees that at standard pressure the rock salt type experimentally
143. omatically Should all fields contain values no updating takes place Pressing the Insert button fills the table with the calculated values These values are used for labelling purposes only Sj Set increments and phase ranges loj x Increments Phase ranges Set increment values 154 000 Ik Poo 2 00000 158 000 gl Increment 4 K 3 00000 162 000 i IE 4 00000 166 000 First value E K 5 00000 170 000 6 00000 174 000 Last value 466 000 K 7 00000 178 000 O _ 8 00000 182 000 rom set no 9 00000 186 000 a CE o set no 190 000 v gt Insert Done Cancel Figure 18 Insert increments Adding phase ranges can either be done manually by editing the fields of the range table Figure 19 Please note while editing you have to leave the cell you are editing for the values to be read properly by the Insert command The aid for entering the values at the bottom of the window works in the same fashion as that used in the increment window These values are necessary for the Le Bail Rietveld assistant of which a first version is included Sj Set increments and phase ranges Increments Phase ranges Dataset No K Phasel Phase2 Phase3 Phase4 Phase5 32 32 278 000 xyz aj 33 33 282 000 xyz a fa 286 000 xyz waf 35 35 290 000 xyz 2x 35 Is 294 000 zyx 5 4 gt Phase2 Kane evs From set no 35 To set no 79 Insert Done Cancel Figure
144. omineralogicoVia Orabona 4 Bari I 70125 Italy map Telephone 39 80 5442624 Fax 39 80 5442591 e mail rosanna rizzi ic cnr it Prof Dr P W Stephens Peter Peter W Stephens Professor Department of Physics amp Astronomy State University of New York Stony Brook NY 11794 3800 USA Telephone 1 631 632 8156 Fax 1 631 632 4977 e mail pstephens stonybrook edu home powder physics sunysb edu Dr Pamela Whitfield Pam CChem MRSC Energy Materials Institute for Chemical Process and Environmental Technol ogy Building M12 National Research Council Canada 1200 Montreal Road Ottawa ON K1A OR6 CANADA Telephone 613 998 8462 Fax 613 991 2384 Email pamela whitfield nrc cnrc gc ca home http icpet itpce nrc cnrc gc ca ICDD Representative Prof R L Snyder Bob Department of Materials Science amp Engineering Georgia Institute of Technology Columbus 771 Ferst Dr N W At lanta GA 30332 0245 USA Telephone 1 404 894 2888 Fax 1 404 894 2888 e mail bob snyder mse gatech edu Consultants Dr James Cline Jim Ceramics Division National Insititute of Standards and Te chnology 100 Bureau Dr Stop 8523 Gaithersburg Maryland 20899 USA e mail cline nist gov Dr Johan Pieter Roos De Villiers Mineralogy Division MINTEK Private Bag X3015 Ran dburg 2125 South Africa Telephone 27 11 7094745 Fax 27 11 7094564 e mail jpdev postino up ac za johandev globa
145. on 3 Christoph Dammer and Pol Leleux used Hough transformation to determine the center of X ray diffraction patterns 5 Mummar et al combined tangents of pair of edge points to find the center and orientation of ellipse 3 In most of the above mentioned methods there exists either a lack of accuracy or usage of huge amount of memory We propose a generic two step approach to determine the center co ordinates of an ellipse In the first step we find the approximate center by using the intensity patterns of vertical and horizontal grids Figure 2 drawn on the image In the next step we find the exact co ordinates of center using some geometric constraints of the major axis a of the ellipse Figure 2 Center detection grid 28 Py pee HEINE 0 60 Pal Pixels Figure 3 Profile along a grid line The intensities of all pixels in the image along a grid are plotted Figure 3 The peaks Bragg peaks in Figure 4 correspond to the edge pixels with very high intensity The center of symmetry the midpoint of this distribution is detected by finding the absolute difference in intensities between left and right parts of the pattern This difference is plotted Figure 5 and the lowest point in this difference plot gives the maximum overlap of Bragg peaks This is the approximate symmetric Many such points are obtained for vertical and horizontal grids along the ellipses Two lines one for the vertical points a
146. on and removal of background points Data export By pressing the export button you are able to export the peak data of the pattern in a variety of methods The positions and heights can be exported to Crysfire format file cdt The refined values can be exported to text file Should you have refined more than six peaks an instrument resolution file in Fullprof format irf can be exported remir m al x fie De Amer jene Ao Fe Det Due nesmund Meet Ammsionginnen 4 AED Figure 27 Peak refinement Peak Indexing Powder3D has no own indexing capabilities but does provide a simple interface to the powerful indexing suite Crysfire http www ccp14 ac uk ccp web mirrors crys r shirley Two very similar methods can be chosen for interaction 1 Save the peak file in the Crysfire format and start Crysfire manually 2 Should Crysfire be installed only Windows operating systems according to the installation instructions in the Crysfire manual it can be called by pressing the Crysfire button The file is exported to the current working directory and Crysfire is started in there A message is displayed with the name of the file that has been exported g z0 30 ET 2T heta Dvermrite Append Crystre Search Figure 28 Crysfire button Le Bail refinement assistant Selecting Refine gt Le Bail via the menu opens the following window Figure 31 Here y
147. on hen egg white lysozyme using an X Pert PRO MPD fitted with the new mirror and the X Celerator detector provided high resolution data sufficient to enable cell searching indexing and unit cell refinement The lattice parameters determined were in good agreement with literature data obtained from single crystal measurements To find more about PANalytical s X Pert PRO for transmission contact PANalytical PANalytical B V P O Box 13 7600 AA Almelo The Netherlands t 31 546 534444 f 31 546 534598 e info panalytical com www panalytical com N S PANalytical in situ powder diffraction Electric Fields H Ehrenberg Materials Science Darmstadt University of Technology Petersenstr 23 D 64287 Darmstadt The investigation of materials under real operation conditions is of primary importance for materials science From a more basic research point of view the underlying working principles can be elucidated guiding the route to advanced functionalized materials On the other hand degradation mechanisms can also be revealed allowing a goal aimed optimization of cycle stability in long time operation by minimizing fatigue Two main challenges for such studies can be summarized 1 Materials are normally multi phase components combined in a specific way to form highly inhomogeneous devices far away from ideal crystal structures 2 in situ conditions require sample environments which restrict the observations e
148. on to the phase intensity the number of peaks in the measuring range was introduced as a criterion to automatically reduce the PO correction model The new feature prevents that over parameterized PO correction models are used for high symmetric phases which is especially helpful in routine phase analysis of complicated mixtures o DD Fe alal F r Fum Tob Conlgquaion Winders Help AGa aG 8 Fig l Graphic window showing the learnt geometric profile of the APS BL32 instrument The DDM method 2 is implemented as a option for the refinement The switch is DDM Y in the control file sav 40 A new and much larger file spacegrp dat containing more non conventional spacegroup settings was prepared Currently more than 730 settings are supported without need of conversion into standard settings In the new version the GSAS formats STD and ESD are supported for direct use in BGMN in addition to val raw and rd The wavelength keyword LAMBDA CU or CO FE CR and MO respectively or SYNCHROTRONS can be used for supplying the wavelength information lacking in the GSAS files New structure files for quantitative phase analysis were added to the BGMN distribution as well as to www bsmn de download structures html Currently 415 structures are available that mostly represent naturally occurring minerals The modeling of profiles for disordered clay minerals 3 has been improved and some examples have been add
149. orial analysis 3 Computer Corner Updates on Available Crystallographic and Powder Diffraction Software Suggestions corrections comments and articles on new or updated software are appreciated especially if you know of new program features program updates and announcements that should be mentioned here Lachlan M D Cranswick Canadian Neutron Beam Centre CNBC National Research Council NRC Building 459 Station 18 Chalk River Laboratories Chalk River Ontario Canada KOJ 1J0 Tel 613 584 8811 ext 3719 Fax 613 584 4040 E mail Lachlan Cranswick nrc gc ca WWW http neutron nrc gc ca Rietveld Software Updates as of 4th November 2005 Hugo Rietveld website http home wxs nl rietv025 Armel Le Bail website http sdpd univ lemans fr BGMN 1 Sep 2005 http www bgmn de BRASS 24 Mar 2005 http www brass uni bremen de DBWS 22 February 2000 http www physics gatech edu downloads young downl oad_dbws html DDM 4 Nov 2005 http icct krasn ru eng content persons Sol_LA ddm ht ml Debvin 25 May 2001 http users uniud it bruckner debvin html GSAS 2 Nov 2005 http www ccp14 ac uk ccp ccp 14 ftp mirror gsas public gsas EXPGUI 6 August 2005 http www ncnr nist gov programs crystallography Jana 23 February 2005 http www xray fzu cz jana jana html LHPM Rietica 27 November 2001 ftp ftp ansto gov au pub physics neutron rietveld Rieti ca_LHPM95 MAUD for Java G
150. ort relatively low count rates they are commonly employed in laboratory settings fixed tube or rotating anode generators CCD detectors are the most expensive They do not have a count rate limitation but tend to have a fairly high readout noise on the order of tens of counts per pixel they are most often used in synchrotron applications From the user s point of view however the data from all three detector types once obtained look quite similar an array of pixel intensities generally in a file format unique to the manufacturer of that detector In the analysis of XRD images considerable attention is often paid to questions of instrumental resolution how does the width of a diffraction peak depend on the physical size and divergence of the incident beam the sample size the sample detector distance the pixel by pixel resolution of the detector etc Less attention is sometimes paid to the angular linearity of the detector itself In wire detectors for example the positions of the wires within the detector may very from nominal values and parallax corrections of the photon path through the detector can be substantial In our experience this can lead to discrepancies between measured and calculated peak positions on the order of lAg q I 2 4 even after linearity corrections are applied by the data gathering program Similarly CCD detectors generally consist of a fluorescent screen focusing optics and the actual CCD
151. ou can set up the starting values for a Le Bail refinement Le Bail 1988 using Fullprof Should a single pattern format PCR file exist you can load it by pressing the button Import Fullprof All the values displayed in the window are then imported n Tools Plot Help Peak Analysis Export cell data Figure 29 Le Bail menu The cell dimensions can alternatively be imported from a Crysfire summary file Pressing Import in the cell frame does this You can select a SUM file and the cell dimensions are displayed in a table Select the desired cell by marking the entry Figure 30 The lengths and angles are imported on clicking OK RR 90 0000 755 463 0 740000 5245 2 300000 107 679 es 008 8 i BE i 112794 s0 0000 Figure 30 Crysfire import The peak shape descriptors can also be imported if a peak refinement has been done for the pattern Otherwise enter your desired starting values Figure 32 The background correction is integrated into the refinement if a background was defined using the background function The space group should be entered and then you can start the refinement by pressing Refine If the refinement is 18 successful some statistics of the refinement are displayed at the bottom of the window The button Reset sets the phase information back to zero The button Remove HKL removes all HKL files for this pattern and forces Fullprof to recalculate them
152. ouin France http www llb cea fr SOLEIL LLB DiffractionPoudres diffractionpoudres html March 6 8 and October 23 25 2006 Basic and Advanced X Ray Powder Diffraction Pharmaceutical Applications Part I Basic crystallogra phy and its application in X ray powder diffractometry sample preparation and measurement strategies Stamford Connecticut US http www assainternational com March 9 10 and October 26 27 2006 Basic and Advanced X Ray Powder Diffraction Pharmaceutical Applications Part II Basic and ad vanced structure solving solutions from X ray powder patterns Stamford Connecticut US http www assainternational com April 10 13 2006 Crystallographic Textures basic course Prof H G Brokmeier Texturschule Agricolastrabe 6 IWW TU Clausthal 38678 Clausthal Zellerfeld Germany 28 May 3 June 2006 SRI2006 Ninth International Conference on Synchrotron Radiation Instrumentation Daegu Exco Korea http sri2006 postech ac kr 9 13 July 2006 SAS2006 The XIII th International Conference on Small Angle Scattering Kyoto Japan http www2 scphys kyoto u ac jp sas2006 index html 22 27 July 2006 ACA 2006 The American Crystallographic Association Annual Meeting Honolulu Hawaii USA http www hwi buffalo edu aca 28 August 2 September 2006 Analyse structurale par diffraction des rayons X cristallographie sous perturbation Summer School Ecole thematique Nancy France http www l
153. pend on how much the primary beam was attenuated by the sample Background originating upstream of the sample on the other hand will not be affected by sample attenuation Datasqueeze can accomplish all of these manipulations i e addition or subtraction of a constant term subtraction of a background file multiplied by a scaling term depending on the sample attenuation but it is important for the user to clearly understand the source of the background scattering rather than simply blindly subtracting a background file Data Display and Processing The scientist generally wants to visualize the data before performing quantitative analysis Datasqueeze presents the data as a false color image with tunable maximum minimum and contrast To locate features of interest a polar or Cartesian grid can be superimposed on the data as shown in Figure 2 Figure 2 False color image of a fiber diffraction pattern showing superimposed qx q Cartesian grid Data collected at the University of Pennsylvania 2 Note that because the scattering plane is not identical to a reciprocal space plane the Ewald sphere is projected onto a plane the constant q q or curves are not straight lines Further manipulations can be performed at this stage Data from CCD cameras often contain isolated bad pixels arising from electronic noise the dezing feature searches for pixels that are astatistically different from their neighbors and repla
154. program for single crystals Prepares files to be used by FullProf Indexing programs SuperCell WDICVOL04 WTREOR and WITOIS Utilities Mendel and Mol_tpcr A part of correcting bugs a list of the most important changes in the FullProf Suite during the current year is the following for details the user can consult the file fp2k inf accessible from the Help WinPLOTR news FullProf news menus of WinPLOTR Code ef files pcos cf Werking D fp2kk Directory titie CrL file imported fren CIF SpeceGroup HH or Hall symbol p gt Cell parameters i 2 9151 98 Sigms are op n furm 0 91 204 s s tional Hunder of Atons da en reed Title Eik gt tile inperted from Eif file ue2s cit Unit cell parameters a4 Alpha Beta Canna Write item in the Cell 5 50200 6 7508 9 29708 90 60000 9A 59000 Space Grou ton 4 aton 2 cn2 H Atom strings in the order Label Species x aton 3 en a 4 2 Biso 0 273080 2 2200 0 50758 0 14 1 c Ca 8 09760 0 79818 1 i 8 23248 8 178140 0 58170 6 34 Aton 04 u 0 700688 8 013950 0 55990 8 30 o u 07070 e 74920 69 a 0 0 485098 0 668320 0 63810 0 27 0 0 15588 or u0 0 472648 0 28 Buspar m wetions mx 3 200 0 008 to 70 00 Fig 2 Snapshot showing the use of Bond_Str by importing a CIF file Extension of the rigid body representations At present internal coordinates of a rigid body or
155. pse is calculated 1 The distances of all the pairs of pixels satisfying the above conditions are stored in an array and the maximum value in that array gives the most probable value of major axis of the ellipse and the corresponding orientation a for this maximum is calculated 1 We can also assume that the two points Al and A2 to be the vertices of minor axis the ellipse but it would increase the complexity of the problem 1 This method extracts the parameter by using pairs of pixels without evaluation of the edge contours Hence it is insensitive to image noises 3 moreover it can represent the global information of a contour more stably We consider the pairs of pixels with in a certain distance range very close pixels which are noise sensitive 3 are ignored Determination of b using Hough transformation Hough transformation is a standard tool in image analysis which is used to detect shapes by the recognition of points in a new transformed space called Hough parameter space The transformation is implemented by quantizing the Hough space in to finite intervals After processing all the edge points in the image the local maxima in the accumulator array corresponds to the parameter of specified shape After finding the length of major axis we choose a third pixel in the image and find its distance from the center We restrict this distance to be less than a Calculate the length of the minor axis from 1 The accumula
156. r Chem 11 69 2001 26 H Putz J C Schon M Jansen Z Anorg Allgem Chem 625 1624 1999 27 Z Cancarevic J C Sch n M Jansen Z Anorg Allgem Chem 631 1167 2005 35 Rigaku Advanced X ray Diffraction Measurements Simple operation SmartLab X RAY DIFFRACTOMETER SmartLab makes powder diffraction easy thin film analysis flexible and SAXS simple Reciprocal space map SiGe Si 224 Rigaku Corporation Rigaku Americas Corporation 4 14 4 Sendagaya Shibuya ku Tokyo 151 0051 Japan 9009 New Trails Drive The Woodlands TX 77381 USA Phone 81 3 3479 0618 Fax 81 3 3479 6112 e mail rinttyo rigaku co p Phone 281 362 2300 Fax 281 364 3628 e mail info rigaku com http www rigaku com 36 a S OE a STOE STADI P was Mo radiation High resolution yielding well defined peak Powder diffractometer fie Transmission Debye Scherrer or Bragg Brentano mode Analysis of air moisture sensitive and micro Samples closing control and evaluation software package Winx ij Sample changers writ ade Aura 4 J bad appt el ba atl Fy be wl I Scintillation counter okiti nlsatlhiye and l j n det baka ANY WAU YY yy Ue MTN STOE amp Cie GmbH PO Box 101302 D 64213 Darmstadt imagi ap ate eetors Phone 49 6151 98870 Fax 49 6151 988788 E mail stoe stoe com Homepage http www stoe com Inden high and low ae systems High throughput and combinat
157. r this project are very welcome Please contact the CPD chairman TEXTBOOK ON POWDER DIFFRACTION R Dinnebier and S Billinge are editing a textbook targeted at graduate students to be published by the Royal Society of Chem istry 2 3 of the contributions have been received The final deadline has been extended to early 2006 From the Editor of Newsletter 32 2D POWDER DIFFRACTION As one of my last duties as leaving chairman it is my pleasure to edit this last issue of our CPD newsletter for the triennium 2002 2005 Powder Diffraction is an active field of research and it is exciting to watch new developments becoming routine This is in particular true for in situ powder diffraction employing fast 2 dimensional detectors which is also the main topic of this newsletter Before a exciting new technique really becomes routine a lot of hardware and software development in combination with teaching is required As an example in order to handle hundreds or even thousands of high resolution powder diffraction patterns simultaneously new generally available software must be developed and debugged Hands on workshops are required which not only reflect the state of the art but also teach students how to handle challenging problems One of these workshops called Watching the Action Powder Diffraction at non ambient conditions was recently held at the MPI in Stuttgart In order to make the proceeding to this workshop available to a broader readers
158. rarily chosen direction The scattering angle is often characterized using the momentum transfer g 47 A sin 0 which can also be represented using Cartesian coordinates Gx q COS X Gy g Sin Y Scattered Beam Detector Transmitted Beam Incident Beam Sample Figure 1 Schematic of a typical XRD experiment employing an area detector Depending on the experiment being performed the user will wish to extract different information In a typical SAXS or powder diffraction experiment the quantity of interest is the radial dependence of the intensity g integrated over all y If the sample is a fiber or liquid crystal the user may wish to obtain g profiles evaluated at different values of y If the material is a partially oriented polymer or poorly ordered crystal the quantity of interest may be the mosaic obtained by plotting I y at a chosen value of g this is sometimes known as a pole figure The most commonly employed detector technologies are image plates gas wire detectors and charge coupled device CCD cameras Each has its advantages and disadvantages Image plates are often the least expensive They offer high dynamic range in intensity but the duty cycle can be low due to the time required to read the data and prepare the plate for the next image Wire detectors in which crossed wires are embedded in an ionizable gas offer fast readout and very low background noise but can only supp
159. rces these companies have risen to the challenge and developed machines that are able to tackle some of the most challenging topics in powder diffraction today You will for ex ample find seminal contributions from both academic and industrial researchers in this newsletter On the other hand academ ics have been able to focus more on the crystallography of real materials that are of importance to industrial sectors ranging from pharmaceuticals to energy and the environment These are exciting times for powder diffraction and we can expect to see significant growth over the next few years This newsletter gives a glimpse of some of the challenges that lie ahead of us It is also my privilege and pleasure to thank the outgoing members of the Commission for their participation over their terms of office they are Rob Delhez Cam Hubbard Davor Balzar and Gert Kruger many thanks You will find the list of current CPD members on the next page of this newsletter I am pleased to welcome Simon Billinge David Rafaja Rosanna Rizzi Pe ter Stephens and Pam Whitfield as new members Do feel free to e mail us with your thoughts and suggestions Finally I would like to thank Robert Dinnebier the outgoing Chair of the Commission for his immense energy and great dedi cation in fulfilling the varied roles of newsletter editor workshop organiser general CPD fund raiser and passionate advocate of powder diffraction His three years as CPD chair have witnessed
160. refinement As GSAS is only capable of analysing commensurate magnetic structures the lattice parameters of the magnetic cell must be integer multiples of the nuclear cell and the phase fraction for the magnetic phase must be set accordingly Once the magnetic refinement runs SARAh Refine can be used to input all of the magnetic atoms into the magnetic phase This step greatly facilitates the analysis of complex structures Before SARAh Refine can be used to start the refinement it should be pointed out that the orientation of the magnetic moments will be defined using unit vectors and their magnitude is refined using the fraction occupancy FRAC Appropriate constraints should be set up to allow related moments to be of the same size The refinement process now corresponds to selecting the different basis vectors of a given representation from by checking a list table deciding the number of reverse Monte Carlo refinement steps required and launching the refinement The magnetic structures associated with the different irreducible representations can be tried in turn Landau theory limits a second order phase transition to involving only a single irreducible representation by simply unselecting and selecting different basis vectors If several atomic sites are involved in the same second order transition a result of Landau theory can be invoked that the same representations should be involved on the different sites to further reduce the n
161. rfectly This social event was only possible due to the friendly support of our industrial sponsors The next day started with as much fervour as the previous had ended Ulrich Schwarz teaching us the intricacies of high pressure powder diffraction experiments Gaining a better understanding of batteries motivates the electrical field in situ studies of Holger Ehrenberg His presentation of the Hasylab beamline B2 dedicated to in situ experiments proved the high level of dedication and specialization in the field Holger Putz presented the powerful capabilities of Dia mond when visualizing structural changes The capability to create films easily being responsible for the greatest interest The rest of the day was spent following the incomparable Juan Rodriguez Carvajal during his presentation and tuto rial of Fullprof The cyclic mode making structural analy sis of large in situ data collections much more manageable Late Friday afternoon saw the last of the ninety partici pants leave for home weighed down by the workshop manuscript but certainly inspired to take up the in situ challenge The organizers would like to thank the DGK for the gener ous financial support of the event this allowed the regis tration fees to be waived The workshop manual and some impressions are available http www fkf mpg de xray online under Ds DIFFRACI D DIFFRACTION SOLU NS stands for continual progress in all Aray core technologies
162. rl ac uk Secretary Prof A N Fitch Andy ESRF BP220 F 38043 Grenoble Cedex France Telephone 33 476 88 25 32 Fax 33 476 88 25 42 e mail fitch esrf fr Prof Dr S Billinge Simon Department of Physics and Astronomy 4268 Biomed Phys Sciences Building Michigan State University East Lansing MI 48824 Telephone 1 517 355 9200 x2202 Fax 1 517 353 4500 email billinge pa msu edu home http www totalscattering org Prof M Delgado Miguel Laboratorio de Cristalografia Departamento de Quimica Facultad de Ciencias La Hechicera Universidad de Los Andes M rida 5101 Venezuela Telephone 58 274 240 13 72 e mail migueld ula ve Dr I Madsen Ian CSIRO Minerals Box 312 Clayton South 3169 Victoria Australia Telephone 61 3 9545 8785 Fax 61 3 9562 8919 e mail Ian Madsen csiro au Prof N Masciocchi Norberto Dipartimento di Scienze Chimiche e Ambientali Universita dell Insubria via Valleggio 11 22100 Como Italy Telephone 39 031 326227 Fax 39 031 2386119 norberto masciocchi uninsubria it http scienze como uninsubria it masciocchi Prof Dr D Rafaja David Institute of Physical Metallurgy TU Bergakademie Freiberg Gustav Zeuner Str 5 D 09599 Freiberg Germany e mail rafaja ww tu freiberg de Telephone 49 3731 392299 Fax 49 3731 393657 e mail rafaja ww tu freiberg de home www tu freiberg de mk Dr R Rizzi Rosanna CNR IC c o Dip Ge
163. round varies strongly from pattern to pattern You can now remove background points with a shift click left click while pressing the shift button and add background points with a click Figure 25 The edit tool You can cycle through the patterns in the usual fashion either by selecting the next and previous buttons in the context menu or by pressing the arrow buttons on the Main tab If a background has been calculated for the pattern it will be displayed Should phases have been defined it is possible to select the data sets associated to the phase by choosing the appropriate phase The Fullprof Rodriguez Carvajal 2001 format is a simple XY ASCII file containing 20 values in the first column and intensities in the second The GSAS Larson et al 1994 format contains four columns the first contains a single 1 the second contains 2 values the third the intensities and the fourth the standard errors Peak hunting By selecting the menu Edit gt Peak search and clicking the search button you shall see the following window Figure 26 Changing the mouse to edit mode enables you to remove peaks with a right click and add peaks with the left click You can drag the borders of the peak search to encompass all important areas of the powder pattern by selecting the range tool in the context menu right click on the image Peaks are searched by a multiple pass variable FWHM second derivative m
164. rsit t zu Kiel Institut f r Geowissenschaften Olshausenstra e 40 D 24098 Kiel Germany knorr min uni kiel de Introduction Powder diffraction data from 2D area detectors such as image plates or CCD detectors are typically integrated into 1D 2 scan powder diffraction patterns for further crystal structure strain or texture investigations During the integration process the diffraction angle 20 is calculated for every 2D detector pixel the intensity sorted into intervals bins determined by the step width chosen for the 1D pattern and usually averaged by normalization to the number of intensities N contributing to a bin Software typically applied for this process is e g Fit2D 1 However several desired features are unavailable in Fit2D and led to the development of the software Two2One 2 3 described in this paper Only the Rietveld program MAUD 4 5 allows skipping of the integration step and refinement of the 2D data directly for the analysis of crystal structures texture and strain This approach requires significant computing power and again may not be applicable in all cases e g to study the anisotropy of plastic deformation due to the lack of appropriate analytical models Integration is done either over the full Debye Scherrer ring or partially over a given azimuth range over ring segments The amount of data per image and frequent parametric studies call for automation of the integration process The uncertainties o
165. rysFML FullProf Suite eee Stanie zu ah el a a BSS Fig 1 Snapshot of a session on magnetic structure refinement using WinPLOTR FullProf and Fp_Studio Today several instruments for fast spectra recording are available In most cases the difficulty is to process and an The present list of executable programs available in the FullProf Suite is the following WinPLOTR General purpose program able to represent many formats of powder diffraction patterns as well as single crystal peak profiles WinPLOTR can access the other programs of the FullProf Suite and it can be used for automatic peak search for indexing profile fitting running FullProf in sequential mode etc FullProf Determination by simulated annealing and refinement of crystal and magnetic structures for powder and single crystals Generates files for other programs EdPCR Friendly edition of the input control file PCR file for FullProf Imports CIF and SHELX files Fp_Studio Automatic graphic representation after running FullProf of crystal and magnetic structures using OpenGL Fourier and GFourier Fourier maps calculations and graphic representation Visualisation of apparent average crystallite shapes and anisotropic strains BasIreps and GBasireps Calculation of irreducible representations of space groups and basis functions Bond_Str and GBond_Str Distances angles and bond valence calculations Import CIF files DataRed Data reduction
166. sections of the crystal structure with all thiophosphate ions intact i e complete We reload this file and generate a 110 surface of some dimensions defined in relation to the surface s 2D unit cell see below gt gt gt Use Inputfile InpData file gt gt gt ex2_p Enter more Data gt gt gt FAce 11 Enter more Data gt gt gt BOx 1 5 Enter more Data gt gt gt OK Now we ass gn all atoms to group 1 and move the surface model by enough down the Z axis i e away from the origin of the Cartesian coordinate system CCS 0 0 gt gt gt Define Group 1 gt gt gt Translate Z 8 We re now ready to add a penicillin molecule which will be centred at the origin of the CCS gt gt gt Add Inputfile InpData file gt gt gt ex4 Now we switch to space filling models suppress unit cell edges and check the group numbers of the new atoms gt gt gt Generate Cups Unitcell 1 gt gt gt Xqt gt gt gt Write Groupnumbers All new atoms have been assigned the group number 13 We will therefore be able to address them by the common atom code gg13 Next we will have to adjust the new molecule relative to the surface e g by some rotations or translations shifts To be able to do this we first have to unlock the model gt gt gt Unlock Model gt gt gt Define ggl3 gt gt gt Trans Y 5 gt gt gt Trans 255 gt gt gt Define Origin gt gt gt Rotate Z
167. sed to determine the correct space group from an already determined set of solutions It is further anticipated that progress on ranking solutions is possible when intensities amongst a set of hkl s are placed on a probabilistic basic In other words what is the probability of a set of hkl s having intensities as observed 43 LSI Indexing Examples Figs 1 and 2 show indexing of T3R3 human insulin zinc complex data taken at the LSLS Brookhaven with 1 4011A data courtesy of B Von Dreele Argonne USA Individual peaks are first fitted using a direct convolution approach Cheary amp Coelho 1992 With this approach an appropriate modelling of the observed line profile shapes is achieved furthermore intrinsic peak shifts due to axial divergence are corrected Fig 1 Indexing is then initiated using the extracted d spacings and intensities After an indexing run a Goodness of fit versus Volume plot is obtained Fig 2 These plots are very useful for visually determining the quality of the solution where each point corresponds to an indexing solution as returned by the LSI indexing algorithm Here it is seen that the solution is well defined with sharp maxima corresponding to the correct solution and pseudo solutions with fractional or multiple volumes of the correct solution T3R3 indexes easily to R3 a 81 3010A c 73 0522A Vol 418173 without any need to rescale the wavelength to cope with the large cell volume
168. t ALBA_manual pdf in the archive file of VENUS Integrated intensities of overlapped reflections in powder diffraction data are more or less improved by the sophisticated MEP method which is favorable for ab initio structure analysis from powder diffraction data ALBA is used in combination with RIETAN 2000 6 or EXPO2004 21 for ab initio structure analysis from powder diffraction data by a direct method Fig 6 Such a collaborative analysis is particularly effective for deriving 62 initial structural models for relatively heavy atoms compounds containing RIETAN format Gedata jump Intensity data Le Bail analysis EXTRA data frecycle odata frecycle Introduction of a partial structure MEP a nalysis ALBA sal IZ 3D visualization VICS VEND SUI MEP analysis PRIMA Rietveld analysis RIETAN 2000 Fig 6 Flow chart of ab initio structure analysis with RIETAN 2000 EX PO2004 VENUS ALBA outputs a binary file pri storing 3D Patterson functions which are in turn visualized with VEND refer to Sect 3 The resulting 3D images in the unit cell serve for construction of an initial structural model by the heavy atom method However the direct method is preferred to the heavy atom method because the number of experts in the latter is decreasing more and more Most Rietveld analysis programs have the feature of Le Bail analysis because
169. t geometrical center of the molecule e the list of atoms is now presented using a tabular view which supports a much larger number of atoms tested with gt 1000 atoms and is much faster e the list of restraints bond lengths angles dihedral angles rigid groups are now presented in a single window using the same tabular view for a fast display Multiple Solutions The Parallel Tempering PT method used in Fox ensures that the algorithm will always get out of any local minimum to find the global one so that a single run is required to ensure finding the global minimum However it is often convenient to be presented with several solutions to choose from if only to have a better feeling of how stable the solution is This option is now available and it is recommended to launch a Multiple Runs optimization this will do PT optimizations for a given number of trials 100 000 to 10 000 000 user chosen depending on the complexity of the structure and re start from a random configuration At the end of the optimization the list of solutions can be browsed and clicking in the list will update the display 3D Crystal view powder pattern for each solution Bond Valence One key difficulty when solving the a structure is the validation of the structure particularly for high symmetry compounds it can be difficult to assert whether the solution has been reached To help with this Bond Valence calcula
170. tab on the 3D display control board is Lights Figure 43 Four light sources can be controlled One ambient and three positional light sources can be manipulated Mi Dt Pacer Gatien Mot tei ajel Dei Wie Beid ioi O ee ach 44 Comet data ac Ra H Lights ste F Potone Perel D Fria FAE ne ne e AT Figure 43 Lights control panel iTools presentation graphics For the very ambitious there is the extremely powerful data visualisation and manipulation software iTools that is called by pressing the button Presentation Graphics Figure 44 iTools has been developed by RSI Inc and is a completely independent of Powder3D Powder3D passes on the data to iTools and is free for user interaction again ei i ee See He Dham ein Er I E Lj i ala Dn pies ee en Zim Figure 44 iTools The iTools do represent an excellent set of programmes and contain complex architecture For this reason I shall extend the tutorial to cover the creation of an image like that in Figure 26 First we shall have to subtract the background from all the data sets so that we rid ourselves of the undulations of background intensity visible in Figure 26 A value of 1 smoothing box and 3 iterations worked well for this data set It is convenient to decide on with part of the pattern array you wish to use by previewing it in the 3D surface mode in Powder3D Once you ar
171. tabulating meta data The top menu View provides visualization tools called viewers such as those on display in figure 2 Operations and Macros menus allow various data and function operations which are implemented in concrete Java classes called operators Data visualization reduction and analysis tasks are typically implemented in a sequence of such operations and called scripts The Scripts pane allows input edit open save and execution commands GUIs for operators and scripts are identical and automatically generated by the ISAW Figure 2 top left window shows a 3 D viewer top right the image viewer graphing all pixels bottom left shows the 39 table viewer generating and exporting data tables at the bottom middle is an example of the generated intensity vs TOF table bottom right shows a block of data with the graph viewer The typical GLAD analysis script GUI is shown in the left of the figure 3 In terms of the functional steps involved in the total scattering data analysis process raw neutron scattering data count rate corrections i e detector dead time delayed neutron detector efficiency are applied first Rebinning and normalization procedures were employed using ISAW operators and methods Absorption and multiple scattering correction routines were slightly modified from their ISIS versions in Fortran to be executed by ISAW behind the scenes A vanadium normalization proced
172. tal Scattering Data Analysis Software at IPNS 31 38 39 J Taoa T G Worltona J Hammondsa C J Benmorea D Mik kelson R Mikkelsonb New Features of the BGMN Rietveld program J Bergmannl R Kleeberg2 ISSN 1591 9552 40 How to add a molecule to a crystallographic surface using SCHAKAL 99 Egbert Keller Discussion of the Indexing algorithms within TOPAS 43 Alan Coelho Arnt Kern Structural phase transitions made easy the new ISODISPLACE software tool 45 Branton J Campbell Harold T Stokes David Tanner and Dorian M Hatch Derivative Difference Minimization DDM Program 41 Leonid A Solovyov 41 Density Measurement Using the Berman Balance 48 Richard J Staples Fitting of nano particle structures to powder diffraction pattern using DISCUS R B Nederl and T Proffen2 Magnetic Rietveld and single crystal refinement with SARAh Representational Analysis and SARAh Refine 49 for the MS Windows 51 Andrew S Wills Quantitative Rietveld analysis in batch mode with Maud and new features in Maud 2 037 53 Luca Lutterotti Update of the FullProf Suite and CrysFML 55 Juan Rodr guez Carvajal FOX Free Objects for Xtallography version 1 7 november 2005 57 Vincent Favre Nicolin amp Radovan Cerny VENUS a 3D Visualization System for Crystal Structures and Electron Nuclear Densities 59 Fujio Izumi amp Ruben A Dilanian News from the ICDD 66 What s On 67 How to receive the CPD Newsl
173. tched against calculated d spacings The problem can be divided into two parts 1 finding a set of possible solutions 2 ranking these solution in order of fitness As has been shown in Coelho 2003 the correct solution for a particular problem is found by the TOPAS LSI algorithm However placing the correct solution at the top of the list is dependent upon the precision of the data For poor data the LSI algorithm may place the correct solution down the list This is no surprise as the figure of merit function is based on that of de Wolff 1968 Algorithms that find the correct solution even when the correct solution is not ranked at the top of the list have not failed On the contrary an algorithm that excludes solutions that ranks higher than the correct solution has in fact missed solutions Thus success or failure needs to be qualified An algorithm can be deemed a failure if in fact it misses a possible solution as determined by its figure of merit function The most important part of indexing therefore becomes one of ranking the solutions All methods that use d spacings as input and a ranking similar to that of de Wolff is likely to suffer from the problem of obtaining many solutions with the correct solution ranked down the list for data of poor quality Improving this situation can only be brought about by the use of further information There has been some success reported by Markvardsen et al 2001 where Wilson Statistics are u
174. tes and extensions to the present functionality For comments or suggestions please contact r dinnebier fkf mpg de Getting Started Installation The latest version of Powder3D can be downloaded from http www fkf mpg de xray As Powder3D is written in the programming language IDL you will need to install the IDL virtual machine IDL VM before being able to run Powder3D Virtual machines for various platforms can be downloaded from the RSI website http www rsinc com idlvm free of charge When you have installed IDL VM unpack Powder3D into a directory of your choice and double click on the file Powder3D sav After dismissing the IDL VM current version 6 1 only splash screen the following window Figure 1 should welcome you Please note the libraries necessary for the AVI export and peak refinement namely IDLtoAV1 dll IDLtoAVI dlm p3d dlm and p3d dll should be in the same directory as Powder3D The functions only work on the Windows operating system Other operating systems are not supported UNC unmapped network paths will cause the program to fail The sample data set The data set that is the basis for the graphics displayed in the manual is available for download from http www fkf mpg de xray The data stems from an experiment carried out at the X7B beamline of the NSLS Dinnebier et al 2005 The wavelength was 0 9224 The initial substance was Rb C 0 Se
175. tions have been added using tabulated Ro values for pairs of elements or ions the valence can be calculated for all or part of the atoms and compared to the expected formal charge It is also possible to use the bond valence calculations as a cost function provided that Ro values have been added for all couples of elements ions but this is still experimental Automatic Background using the Bayesian David Sivia algorithm Following the algorithm which was proposed by David amp Sivia 2 using a Bayesian approach the background can be automatically estimated the user only has to choose the number of points Either linear or cubic spline interpolation can be used And the background points can finally be edited from the interface Time Of Flight and reflection profiles Time Of Flight neutron powder patterns are now supported in Fox along with an adequate double exponential pseudo Voigt DE PV profile thanks to Mark Pitt For this the description of profiles has been entirely changed and asymmetric profiles are now also available in the pseudo Voigt profile used for monochromatic patterns Maximum Likelihood Maximum likelihood 3 principles have been included in Fox this allows to tell the algorithm that some atoms are blurred i e are evaluated as if their position is only approximately known In some cases this can improve the convergence 2 but this is still experimental Fox without graphical interface
176. tized 5D parameter space is very memory time consuming 7 Reduction of resolution Approximate center determination Background reduction and Threshold Range ofa and b a alpha center determination b using HT Figure 1 Flowchart of ellipse detection algorithm In practice the transformation scales to the number of dimensions in parameter space In order to overcome the complexity of the problem the complete process of ellipse detection is decomposed into different modules Figure 1 Hough transformation is used for the calculation of the parameter b alone Hence we require only a one dimensional parameter space for voting This is advantageous for the accuracy of estimation of the parameter 3 Reduction of resolution The spatial resolution of digitized powder diffraction images is normally in the order of a few thousand pixels squared Manipulation such a huge amount of data is impractical The computational complexity of an image of size N x N is N x N 8 Moreover the implementation of standard Hough transformation requires an accumulation memory in the order of approximately N To improve the execution speed the image is squeezed by a factor of 5 Approximate center determination Many methods have been used for the determination of the center of an ellipse Yiwu Lei used symmetry of ellipses to determine the center 3 Kimmel et al made ellipse detection more effective by using local edge orientati
177. to the documentation is now possible through the Help menu of WinPLOTR In particular to access the PDF manual for Fp_Studio the use of FullProf for time of flight and for flipping ratio refinements polarised neutrons The preparation of several tutorials concerning different aspects of the use of the FullProf Suite is under way CrysFML The current Fortran 95 modules available for distribution are concerned with the following topics Chemical and Physical tables scattering factors etc Mathematical methods for Crystallography Symmetry Fast Fourier transforms and convolutions global and local optimization procedures string utilities handling of formats CIF etc managing refinement codes and names of parameters reflection utilities geometrical and bond valence calculations structure factors profile functions including TOF reading powder diffraction patterns in different formats etc Some examples of main programs using the library are also available In the forthcoming months the FullProf Suite and CrysFML will be both available at the Diffraction Group site of the Institute Laue Langevin At present the people wishing to obtain CrysFML must contact the author by e mail The whole FullProf Suite can be obtained from the CCP14 site at http www ccp14 ac uk ccp ccp 14 ftp mirror fullprof FOX Free Objects for Xtallography version 1 7 november 2005 Vincent Favre Nicolin amp Radovan Cerny
178. tor array is incremented for all the pixels satisfying this constraint After processing all the points in the image the local maxima of the accumulator array is the minor axis length Figure 7 We only use Hough transformation to determine the minor axis of ellipses Only a 1D accumulator array is required for voting This ensures less memory usage since the dimension of accumulator array is directly related to the usage of memory 7 LELEI LEELLLLE Lars s La S Lu LES LEI ILL IE J Accumulator Figure 7 The accumulator array i r bee Ei In the process of ellipse detection we determine the parameters of the innermost ellipse first and then proceed outwards The reason for this is that the x ray images have high intensity gradients with the maximum near the center of diffraction pattern There are fewer pixels in outer ellipses than in inner ones This results in better statistics for inner ellipses The influence of high intensity inner ellipses on other ellipses is minimized After detecting an ellipse its pixels are removed from the image the rest of the ellipses are detected iteratively As a result the computational time for b decreases with every detected ellipse References 1 Chellali R Fremont V Ellipse detection using Hough Transform 13 International Conference on Artificial reality and Telexistence Japan 2003 2 Fung P F Lee W S King I Randomized generalized Hough Tra
179. tware often runs only on the computer used for collecting the data The scientist may have obtained the data at a central facility or synchrotron and wish to analyze the data back at his or her own desk Here we describe a software application Datasqueeze 1 that can be used to analyze data from a wide variety of x ray area detectors Datasqueeze runs on Windows Linux and Macintosh OS X It is particularly useful for the analysis of powder diffraction data diffuse scattering from polymers or liquid crystals or small angle scattering from colloids polymers or gel solutions Datasqueeze is not well suited for analysis of single crystal diffraction patterns with many sharp Bragg peaks This article discusses the capabilities of Datasqueeze and also reviews some common problems and concerns encountered when analyzing data from area detectors X ray Detector Properties Figure 1 shows a schematic of a typical XRD experiment using an area detector The incident beam which is monochromatic with wavelength and collimated strikes a sample The transmitted beam is blocked by a beamstop to avoid damaging the detector The scattered radiation strikes the detector The detector records the integrated intensity in each pixel but the quantity of interest is generally the scattered intensity measured as a function of 20 the angle between the primary beam and the scattered beam and y the orientation on the detector relative to an arbit
180. umber of trial structures Data files _rmc dat are generated which list the values of 7 against the relative proportions termed mixing coefficients of the different selected basis vectors The least squares aspects of the refinement can be controlled in GSAS as normal and the resultant structure drawn using DRAW lt xtl Larry Finger Martin Kroeker and Brian Toby One of the main reasons behind this operation of SARAh Refine is that GSAS defines magnetic symmetry in terms of Shubnikov groups The author argues that this is an unwieldy technique and less general than the use of representation theory By being a clip on program SARAh Refine facilitates use of the results of representation theory to the extent that the scientist need not even enter a structure by hand Instead they are encouraged to look at the basis vectors and work to understand the types of magnetic structure they represent and indeed the intimate nature of the magnetic phase transition The philosophy for the use of SARAh Refine with FullProf is quite different FullProf accepts magnetic structures defined using basis vectors and the use of a propagation vector For this last reason the magnetic positions that are required as input are restricted to those of the chemical or zeroth unit cell Just as was explained previously refinement involves selection of the different basis vectors associated with the trial structure that is being tested SARAh Refine then creates
181. ure subsequently yields the differential scattering cross section do dQ do dQ yey 40 AQ isini 2 Cab P Q 0 I Q where P Q is the inelastic contribution and Q is the interference function arising from the distinct scattering contribution C is the atomic concentration and b the scattering length of isotope a By way of example the Q of a carbon nanotube is plotted as a function of scattering vector Q in the bottom right of figure 3 A Fourier transform routine converts the scattering function S Q to various radial distribution functions for further interpretation une hT rriet ime daa yare tipi bp rm DL 4 de iM IM nn nn n a a 15 Li 26 7 mi g isli One significant improvement over the previous software is that the analysis is now carried for each data group pixel by pixel with data merging only performed at the last step to produce a single I Q vs Q that s 1 6 million points while the old code regrouped and averaged the raw data twice in the very beginning of data treatment As a result the ISAW analyzed data is more accurate and the low Q limit of GLAD has been extended from 0 325 to 0 175 The new software also enables irregular detector groupings for orientated samples Finally we note that it should be relatively straightforward to implement this software on a similar neutron instrument at a different facility References 1 http www pns anl gov comput
182. ven n the appendix The parameters for the geometry correction for integration of 2D datasets obtained using calibration routines in FIT2D need to be stored in another ASCII file named TWO2ONE INF In the following sections applications of Two2One are described Ae cI 1 800 500 me No Mask With Mask Difference 700 600 500 Counts 400 300 200 5 10 5 9 20 25 30 Figure 1 Raw data of SnS in a diamond anvil pressure cell left 6 measured using a laboratory X ray source and a MAR image plate detector and the mask generated by Two2One after an outlier analysis center The single crystal spots the diffraction from the gasket with a different diffraction geometry and the rings from secondary excitation opened to the bottom of the picture are identified in the mask and excluded from the integration process The integrated patterns with and without outlier rejection and the difference between the two are shown to the right Automated outlier rejection masking Measured intensities resulting from beam stop shadow single crystal spots secondary excitations and other intensity not resulting from diffraction by the sample itself but from for instance high pressure cells needs to be rejected from further analysis Such intensities reduce the quality of 2 scan patterns especially single crystal spots would appear as weak peaks Manual identification of regions or points t
183. ven phases can be identified and are tabulated below 12 CSS I nll u E Ale DE We imk Mi Helgi wu JEEE Figure 1 Welcome screen Table 1 Phases identified in the sample data set Pbam 11 29 6 29 3 62 ak P2 c 10 45 0 63k Rb C204 Pnma 10 9 Rb C2014 r IK P6 m 6 4 Rb C204 me ia q 5 89 7 80 Be FE 10 14 RhiCO sok Rb CO3 The temperature ramp was set to 298 gt 838 gt 298 K The sample was heated at a rate of 2 8 Kmin and cooled at a rate of 4 8 Kmin Considering the exposure and development time this leads to a heating rate of 4 2 Kframe and a cooling rate of 7 62 Kframe l Rb C O II Rb CO Volume A hy 3 B 3 aa tn a 4 T 7 6 i I a er Mi a ewe a Pham F2 Phina Pesan p ci2 ala o2 a G 4 i ra F i i ta le oa t en ne Da liag Il i een 45 i Pome P mme Pama amp 12 16 E 500 400 300 soo so00 700 600 Temperature K Figure 2 Powder diffraction patterns lattice parameters and cell volumes of Rb2 C204 and Rb CO as a function of temperature in the range from 298 to 838 K 2 4 K min and back down to 298 K 4 8 K min Taken from Dinnebier et al 2005 300 400 500 600 700 Import One of the first things you shall want to do is to import data To do that press the import button Figure 3 or select File gt Import Fie Edt Patten Toole P
184. www ccp14 ac uk solution structconv Structure Drawing and Visualisation http www ccp14 ac uk solution structuredrawing Unit Cell Refinement of Powder Diffraction Data http www ccp14 ac uk solution unitcellrefine New Time of Flight Neutron Total Scattering Data Analysis Software at IPNS J Tao T G Worlton J Hammonds C J Benmore D Mikkelson R Mikkelson Intense Pulsed Neutron Source Argonne National Laboratory Argonne IL 60439 USA Department of Mathematics Statistics and Computer Science University of Wisconsin Stout Menomonie WI 54751 USA Email Benmore anl gov Web http www pns anl gov computing isaw New total scattering data analysis code has been written within the SAW framework 1 lifting constraints on the functionality of the Glass Liquid and Amorphous materials Diffractometer GLAD imposed by legacy code SAW stands for Integrated Scattering Analysis Workbench and is a completely free fully open java based working and development environment It provides the data structures basic data operations visualization tools and user interfaces for the new GLAD software Due to the nature of object oriented programming and Java s syntax being much like C the code is highly structured and easy to port if the need rises file Co view Operations Macros Wirards Help Figure 1 The ISAW main GUI listing data in a tree structure with an Attributes display pane
185. y items were sold by various companies including Roller Smith Company and Federal Pacific Electric Company 1961 which sold all the accessories for The Berman Density Balance The intent of this brief article is to present the basics of the technique and a simple example The Berman balance consists of a torsion balance Figure 1 which has a maximum weighting capacity of 25 mg A platinum wire double weighing pan or a platinum wire hook and a coarse wire mesh basket for powder weighing Below the hook resides a glass dish which can be raised and lowered so that the hook or basket can become submerge in the solution Figure 1 Berman Balance 48 Figure 2 Lab balance in operation Figure 3 Baskets available to crystal or powders Liquid is placed in the dish The liquid choice can be critical Toluene was seen as the best for many mineral studied in Berman s lab The liquid must have a low surface tension small variation of the density with temperature and inert to the material in question We have found that for measuring single crystals of small molecules that the liquid of choice is heptane although pentane and n hexane work also These liquids however are harder to use in that the exact position of the weight in liquid is harder to determine than in toluene Harassed of liquid choice also include the possibility that the liquid dissolves the compound or effect the crystal structure generally by loss o
186. zburg de and tproffen lanl gov Web http www uni wuerzburg de mineralo gie crystal discus index html The authors have been developing the DIFFUSE programming suite which contains programs for the simulation of crystal structures especially disordered structures In this contribution we present current developments of the DIFFUSE program suite which are of special interest to powder diffraction experiments These developments include an efficient algorithm for the calculation of powder pattern from finite particles as well as a refinement algorithm to fit the corresponding structural parameters The Debye formula is an algorithm to calculate the powder pattern of randomly oriented finite objects In this algorithm one sums over the contribution of all atom pairs with the finite object Thus this algorithm is very well suited to be used for the refinement of nano particle structures DISCUS realizes this algorithm by sorting the interatomic distances into partial distance histograms By binning the interatomic distances into histograms with equal and constant width Ar each interatomic distance may be misrepresented by a value of Ar 2 This is effectively a displacement of the atoms and results in a decrease of the calculated intensities just as the Debye Waller factor Several trial calculations were carried out with different step width for the histogram ranging from 0 10 down to 0 01 A It turns out that there is hardly any difference b

Powder Diffraction - Max Planck Institut für Festkörperforschung

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Powder Diffraction - Max Planck Institut f&uuml;r Festk&ouml;rperforschung

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Powder Diffraction - Max Planck Institut für Festkörperforschung