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1 PDF-4+ The Powder Diffraction File Release 2006.

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Presentation on theme: "1 PDF-4+ The Powder Diffraction File Release 2006."— Presentation transcript:

1 1 PDF-4+ The Powder Diffraction File Release 2006

2 PDF-4+ 2 Index – Use direct links to skip to the section  Fundamentals Fundamentals  Design and Purpose Design and Purpose  Data sources and collaborations Data sources and collaborations  Quantitative Analysis with PDF-4+ Quantitative Analysis with PDF-4+  Material Data Sets (Entries)Material Data Sets (Entries) –Pattern Simulations –Molecular Display  Searches and Data Mining Searches and Data Mining  Pattern Fitting Pattern Fitting  Combining Tools – Analyzing polymorphs Combining Tools – Analyzing polymorphs

3 PDF-4+ 3 Notice This presentation gives an overview of features and capabilities found in the Powder Diffraction File (PDF), specifically PDF-4+ Release This presentation represents a small portion of the capabilities in the database. The presentation focuses on the database and not on the capabilities of the database when combined with the world’s leading data analysis programs. The database itself contains over 500 pages of help file documentation. This includes definitions and terms of the classifications and calculations used in the database.

4 PDF-4+ 4 Fundamentals

5 PDF-4+ 5 PDF-4+ Basic Capabilities  PDF-4+ contains 254,873 entries.  Entries contain > 85 data fields, some fields such as d, I, h,k,l and atomic parameters may contain dozens to hundreds of data points.  There are 65 different data display options.  There are 44 search options. Display and search options can be combined and permuted using a JAVA interface. This results in nearly endless combinations for data display and analysis, only a few of which are described here.

6 PDF-4+ 6 PDF Databases are designed to work with most commercial diffraction analysis software packages. The ICDD works with software distributors so that the PDF seamlessly interfaces to their software. Many features in the database are specifically designed for distributor use. A list of compatible software and distributors can be found here. Powder Diffraction File (PDF)

7 PDF-4+ 7 Diffraction Analysis Software interfaced to PDF Databases Company Software BedeBede Search/Match Bruker AXSEVA, DiffractPlus, PolySNAP, Topas Bruker AXS SASDiffractPlus, EVA (formerly Socabim) Crystal ImpactMatch, Endeavor Digital Data CorpMacPDF EDAXACT, OIM GE InspectionRayflex Search/Match GBCTraces HKL TechnologyFlamenco InelWinFit ITAL StructuresWinDust32, WinSearch32 Kratos (Shimadzu)PDF-2 Search Software Company Software MDIJADE, jPOWD RIQAS, RUBY Overseas X-rayPDF Plus Oxford InstrumentsFlamenco Oxford CryosystemsCrystallographica PANalyticalX’Pert Highscore Plus RigakuJADE, jPOWD, RIQAS, RUBY RMS KemptenADM/PADS Sine Theta2TdST STOE & Cie GmbHWinX Pow Tasker ApplicationsTXRDWIN Thermo ElectronWinXRD ZDSSEARCH/MATCH, QUANT Please check with the vendor to match their software with the specific release of the PDF database (year and type, i.e. PDF-4+ Release 2006).

8 PDF-4+ 8 Design & Purpose

9 PDF-4+ 9 All PDF Databases are designed for rapid material identification. This differentiates a PDF database from all other databases of crystallographic or physical property data. If you are working on a known material another database may be more appropriate for your work.

10 PDF Powder Diffraction File Rapid Material Identification with the PDF The database is designed to use input data and match it to candidate reference materials. Most matching is done by comparing sets of d-spacing and Intensities, however it can also be done by chemistry, properties, structural and crystallographic classifications – using dozens of different searches. All data are converted to a standardized format for rapid search. There are many embedded indexes facilitating searches. Data entries are extensively cross referenced to other entries and to physical and chemical measurements. Data are extensively classified by chemical and structural types; each classification can be searched.

11 PDF Sources of Data

12 PDF The Powder Diffraction File PDF-4+ Database Data Sources for the Database 1) Publications, journals, scientific periodicals and theses 2) ICDD Grants for new materials (~60 annual grants) 3) Data collections donated by companies or individuals 4) Data from other Database organizations that they collect from scientific publications The Powder Diffraction File contains a compilation of data from 5 global databases. PDF-4+ uses 4 database sources.

13 PDF PDF Databases – Continuous growth and change  Data on new materials are being constantly collected and published by laboratories around the world so the PDF database continually grows.  With time, data quality has steadily improved in both accuracy and precision. (Better hardware, optics, software and computational power as a function of time). This leads to improved accuracy in the database and the diffraction method of analysis. A major function of the ICDD editorial system is to evaluate quality and standardize data that has been collected by global sources over decades of time. The quality evaluations and standardization processes are also updated continually and the entire database gets reviewed each time.

14 PDF Cambridge Structural Database (CSD) Linus Pauling File (LPF) Powder Diffraction File – Database Collaborators NIST ICSD

15 PDF PDF ,873 Entries PDF-4/ Organics 312,355 Entries Release 2007 PDF-2 186,107 Entries ICDD, NIST, ICSD + LPF ICDD-organics + CSD ICDD, NIST, ICSD Each PDF database contains data from several database sources

16 PDF PDF-4+ The PDF-4+ and its subset, PDF-4/Minerals, are the only PDF databases that contains data from the Linus Pauling File (LPF). The LPF is currently the largest single global source of inorganic atomic coordinates and crystallographic parameters. It is also a large source of data on inorganic materials, many with unique compositions. This data is added to inorganic materials data from ICDD, NIST and ICSD to form the comprehensive data collection in PDF-4+.

17 PDF ,000 Material Data Sets and Growing! Data from global sources – collected, translated, edited and standardized 60 Years PDF-4/ Organics PDF-4+

18 18 PDF-4+ More Data and New Data Distribution of data by number of elements, PDF-2 and PDF-4+ Unique Formula

19 PDF Database Codes The first two digits in any PDF number contains the database Code. For example PDF is the PDF number for an Fe 3 O 4 entry that is sourced from the Linus Pauling File (04-LPF).

20 PDF Material Data Sets (Entries) Each entry contains Chemical information and nomenclature Experimental conditions Diffraction data including d,I and h,k,l listings Journal reference and bibliographic citations Crystallographic data Individual entries, such as the one for Acetaminophen, PDF , displayed on the left may contain thousands of alphanumeric data fields. Print display of a PDF entry

21 PDF Acetaminophen PDF A multi-page nested display, shown below, is used to display the data in PDF-4+. Printed Form for Data

22 PDF Quantitative Analysis with PDF-4+

23 PDF PDF-4+ The PDF-4+ database is designed for rapid identification and quantitative analysis. Quantitative analysis can be performed by any of three different methods and the database provides the properties required these analysis techniques.

24 PDF Quantitative Analysis and PDF-4+ MethodDatabase Quantity Required by of Quantitationthe Method Reference Intensity Ratio165,923 Entries with I/Ic Rietveld Analysis98,291 Structures with atomic parameters and unit cells Full Pattern Analysis254,873 entries all with full digital patterns that can be modified for wavelength, radiation (x-rays, neutrons, electrons) instrumental and specimen effects

25 PDF Full Pattern Analysis Digital patterns of ~150 A Cellulose II and Ib, with crystalline stearic acid. Experimental data on a natural product tablet in blue.

26 PDF Automated Quantitative Analysis by XRD PDF-4+ databases provide reference data, viewing software, critical physical properties and crystallographic properties required for quantitative analysis. The database is designed to work with many software packages, including those of all major global instrument manufacturers. These software packages provide the required calculations and refinements for automated quantitation utilizing the data in PDF-4+. With modern software and databases this operation is seamless and can be often be done in minutes.

27 PDF Features – The PDF Entry

28 PDF The main entry page includes several display options and data in nested display Pages. These are activated by the “point” and “click” of a mouse.

29 PDF Display Options Pattern Simulations Electron Diffraction Simulation Electron Backscatter Pattern Digital Diffraction Pattern

30 PDF Display Options Molecular Dimensions & Graphics Bond Angles & Distances Molecular Graphics

31 PDF Pattern Simulations Options for the addition of multiple phases, instrument and specimen factors, wavelengths. Options for import/export and graphic display Calculations. Crystallite size simulation

32 PDF Display Options – d,I Listings Right click Right click the mouse to Undock pattern listing and compare data with different instrument configurations. Fixed SlitVariable SlitIntegrated I Note how the intensities changes as a function of optical configuration, resolution.

33 PDF Data in Nested Display Print Forms

34 PDF Data in Nested Display – Computer Display Experimental and Bibliographic reference Structure, symmetry, atomic positions, active link to atomic environment display Editors evaluation and database cross references Subfile designations, pattern cross references (active link), Pearson symbol and prototype assignment Opening page – status, formula, quality mark

35 PDF Display Fields in PDF-4+  Fields filled in >80% of the 254,873 entries  Fields filled when the data is provided by the original source  Fields filled by an field expert editor, consultant or volunteer editorial task team  Quality indicator measurements Color Coding Key

36 PDF Display Fields Accessible from the Main Entry page through nested page displays PDF PDF# Status Quality Mark Pressure/Temperature Chemical Formula Weight % Atomic % ANX Compound Name Mineral Name Common Name Experimental Radiation Wavelength Filter d-spacing type Cutoff Intensity type I/Ic Camera Diameter Reference Title Author Citation Physical System Space Group Aspect Author Cell Volume Reference D calc D meas D structure SS/FOM Melting Pt Z R-Factor Error Crystal Space Group Z MW Crystal Cell Crystal Volume Crystal axial ratio Reduced Cell Reduced Volume

37 PDF Display Fields Accessible from the Main Entry page through nested page display Optical alpha beta gamma Sign 2V Reference Structure TF type Coordinate Table Atom Number Wyckoff Position Symmetry x,y,z SOF (Site Occupancy) ITF (Isothermal TF) AET (Atom Environment) Symmetry Operator Anisotropic Temp Factors Only in PDF-4+ 98,291 Structures in PDF-4+ Miscellaneous CAS # PDF Cross References and status Pearson Symbol Prototype Structure LPF Prototype Mineral Classification Zeolite Classification Subfiles Entry Date Last Modification Date Editorial Editors Comments -includes comments generated by statistical analysis of the data User Comments Shared Comments

38 PDF Display Fields in PDF-4+ Expanded views of the d, I, h,k,l listing and stick figure. Both are interactive displays where the user can expand, sort and scale the data.

39 PDF Searches and Data Mining

40 PDF Searches and Data Mining  ICDD problem solving software –Completely re-written in Java –Powerful search and retrieval –Numerous display options –Flexible user-interface –Features based on our extensive RDB knowledge and user feedback

41 PDF Main Search Page Searching Search Icon “Point and Click” Searches are performed by using the search option on the program DDView+. This program is embedded in the database. If you use vendor display software you may have to start the program “ICDD PDF ” from your program menu to see the options described here. Every PDF-4+ database has this program. (It is an option for PDF-2). Opening screen menu

42 PDF Search  Central input form (Main Search Page)  45 unique criteria in 7 categories  Multiple input methods: –Lists –Text –Numeric Estimated Standard Deviation (ESD) Ranges –Periodic Table –Composition Table  Logical Boolean operators  Powerful cumulative searches  Criteria selection awareness

43 PDF Searches are activated by point and click operations or alphanumeric entry. Activated fields become highlighted in red. Multiple fields can be active. In this example search fields for LPF, star quality, primary, ambient data for Si and O were activated.

44 PDF This search activated an empirical formula combined an elemental composition analysis with a specific space group and compound name. Input element composition analysis with error limits

45 PDF Search Display - Results 1 The search criteria are given in the search description. The criteria matched 1,817 entries in PDF-4 + All 1,817 entries search results can be accessed through the scroll bar. 3 2

46 PDF Search Results - User Preferences or Click on the “Preferences” Icon Use the Fields drop down menu User selection of the display fields can be done by point and click interfaces or a drop down menu. The menu above allows the user to add, drop and change the display order.

47 PDF Search Results Same search criteria as before but now the user defined order preferences are displayed: Mineral name, Quality mark, Reduced cell parameters, Pearson symbol and chemical formula. Minerals sorted Alphabetically. Reverse order by clicking on the Header.

48 PDF Search Results – Display Algorithms & Calculations  Sorting algorithms: –Alphabetical –Alphabetical Formula Index –Numerical –Proprietary  Calculations: –Mean –Median –ESD Same search, the user can highlight any numerical field and obtain a mean, median and ESD for the entries. Calculations Displayed

49 PDF Application Example 1: Phase Identification  From research we obtain the following data: –Pattern is cubic –Lattice parameter a=12.348(.010) Å –Pattern density is ρ=4.9(.1) g/cm³ –Pattern color is red –Pattern melting point is 677(5) °C  We then input these user data into DDView+ and look for possible solution(s).

50 PDF-4+ 50

51 PDF Problem 1 – Results (Answer) With the given input data there are only 2 search hits out of 254,873 entries in the database. One entry is from the experimental collection (PDF 00); the other from the LPF collection (PDF 04).

52 PDF Application: Problem 2  From research we obtain the following data: –Powder Pattern Space Group is Fm-3m –Pattern only contains elements Cu and Zn  Input user data into DDView+  Additionally: –If we measure the lattice parameter: –a=3.640 Å, what is the likely concentration of Zn in the alloy?

53 PDF Search input provide search criteria with results displayed 21 3

54 PDF Problem 2 – Results (Answer) (Obeys Vegard’s Law) Non-ideal solution behavior 4 The data from the search form were exported and plotted to identify the composition based on lattice parameter. (Composition plot not done by the database) 3

55 PDF Application Problem 3 – Answer shown, sequence described Sequence of 1) Search by composition 2) Search by temperature 3) Display results, 4) Compare cell parameter with temperature*, 5) Plot the results. * Specific temperature given in the comments section of the entry, so you would need to display the comment section. FERRO-PARA ELECTRIC TRANSITION IN BaTiO3

56 PDF Pattern Fitting and Simulations

57 PDF Pattern Simulations Point & Click Click on this icon brings up the “Preferences” menu options for display features

58 PDF Diffraction Pattern Options  Radiation Settings –Anodes X-Ray Diffraction Neutron Diffraction Electron Diffraction –Types Kα1 Kα2 Kβ Kα(avg) Kα1+2 Kα1+2+Kβ –Custom wavelength

59 PDF Diffraction Pattern Options  Geometry Settings –Bragg-Brentano –Debye Scherrer

60 PDF Diffraction Pattern Options  Profile settings –pseudo-Voigt –Modified Thompson-Cox- Hastings pseudo-Voigt –Gaussian –Lorentzian –Particle Size To change to a user defined crystallite size enter a value, hit return and then click apply.

61 PDF Graph Icon Click once Get digital pattern Click again Add, subtract, scale input other ref. patterns or experimental data Data input console, provides data input and pattern options, each pattern can be adjusted separately. 3 Crystallite size series

62 PDF Application Example 1 Pattern simulation of complex mixtures using PDF-4+, DDView+ 6 Phase solution used data from 3 different databases ICDD-powder, ICSD – single crystal, LPF- single crystal Data input console, goes to pattern options Raw Data

63 PDF Application Example 2 Full pattern analysis, mixed crystallite sizes Digital patterns of ~150 A Cellulose II and Ib, with crystalline stearic acid. Experimental data on a natural product tablet in blue.

64 PDF Combining Tools – Analyzing Polymorphs

65 PDF Example – Examining the Polymorphs of SiO 2 Execute a Search - Primary patterns, star quality, ambient conditions, 2 elements, formula SiO 2 1 1

66 PDF Display the results Search Summary 37 star quality, primary patterns 2

67 PDF Customize the results Why are there so many primary star patterns for SiO2? To study this, customize the display by selecting preferences. 3

68 PDF Customized results SiO 2 polymorphs – differences in Mineral Name, Common Names, Space Groups, Unit Cell Volumes, Pearson Symbols. 4

69 PDF Analyze SiO 2 polymorphs Highlight a selection of data entries in the results, then right click to provide a menu of options. CTRL and Shift Key can both be used to highlight user specific entries. From the menu, diffraction pattern is selected 4 5

70 PDF Polymorphs of SiO 2 All eight highlighted entries are simultaneously plotted. The data clearly show that these are polymorphic materials with different characteristic diffraction patterns for each polymorph.

71 PDF Customize the results Why are there multiple primary star quality patterns for same polymorph? To study this, use the prior results (37 SiO2 primary star patterns) and look at entries with the same space group, Pearson symbol and reduced cell volume. Three entries for Stishovite - why?

72 PDF Three entries for Stishovite - why? Examine the Comments! Single Crystal Synthetic Powder Mineral Slight difference in density, I/Ic High quality data on three different specimens taken by three different Laboratories. Mineralogists typically prefer known minerals, chemists may prefer high purity synthetic or single crystal – if different in source or properties ICDD editors will keep all entries. Examine properties

73 PDF SiO2 Why are there 37 primary, star patterns? Answer Polymorphs, a primary pattern is selected for each different polymorphic form (~24 different polymorphs). Different physical properties – the same polymorph may have slightly different physical properties or chemistry (i.e. due to calcination). This is especially common in minerals from different geographic localities. Difference source, for example mineral or synthetic, powder or single crystal.


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