CrystalDiffract User's Guide

® CrystalDiffractInteractive Powder Diffraction Software Works with CrystalMaker®: Interactive Crystal Structures Visualization User’s Guide Version 5.2 for Mac • Version 1.4 for Windows Table of Contents Chapter 1: Getting Started .....................................................................1 Using this Guide........................................................................... 1 Interface Reference Convention ................................................... 2 System Requirements ................................................................... 2 Installation .................................................................................... 2 What is CrystalDiffract?............................................................... 3 CrystalMaker Integration ............................................................. 6 Chapter 2: CrystalDiffract Interface .......................................................7 Window Design ........................................................................... 7 Displaying a Diffraction Pattern ................................................... 7 Scrolling and Zooming ................................................................. 9 Measuring a Pattern.................................................................... 10 Output ........................................................................................ 10 Help and Updates ....................................................................... 10 Chapter 3: Simulating Diffraction ........................................................ 11 Calculating the Pattern ............................................................... 11 Radiation Type............................................................................ 12 Diffraction Modes ...................................................................... 12 Peak-Shape Functions ................................................................ 14 Peak Widths ............................................................................... 15 Editing Structural Data .............................................................. 16 Interactive Parameter Control .................................................... 17 Mixtures...................................................................................... 19 Viewing Diffraction Data ........................................................... 20 Chapter 4: Working with Patterns......................................................... 21 Working with Observed Data..................................................... 21 Managing Multiple Patterns ....................................................... 23 General Plot Settings.................................................................. 25 Individual Pattern Settings ......................................................... 26 Customizing your Workspace ..................................................... 28 Chapter 5: Printing & Saving ............................................................... 29 Saving Your Work ....................................................................... 29 Saving Preferences ...................................................................... 29 Exporting Data ........................................................................... 29 Printing ....................................................................................... 30 Chapter 6: Toolbar Reference ............................................................... 31 Chapter 7: The CrystalMaker® Office .................................................... 33 Introduction to CrystalMaker..................................................... 33 Single-Crystal Diffraction .......................................................... 34 Index ........................................................................................... 35 Chapter 1: Getting Started Welcome to CrystalDiffract: a program designed to make powder diffraction intuitive, interactive, and perhaps even fun! We hope you find this program useful and entertaining. This part of the User’s Guide is designed to give a quick overview of what the program is, its scope, plus information on how to install the program, followed by tips on using the rest of this User’s Guide. Using this Guide This User’s Guide should provide a very comprehensive outline of the major program features. We don’t expect you to read it from coverto-cover, but would recommend the following key sections: • All users should browse Chapter 2: CrystalDiffract Interface. Searching for Topics We have tried to provide a comprehensive yet logically-structured guide. If you need to find specific information, here are some suggestions: 1. This guide includes a Table of Contents (at the beginning) and an Index (at the end). • This is designed to give you a quick orientation to the program; the interface changes from version to version, and will certainly be different to other programs you may have used, so it’s important to get your bearings earlier, rather than later! 2. If you are viewing the guide electronically, you can click on the Contents or Index page entries to go directly to the corresponding pages. If you are a new user, we strongly recommend that you complete the Tutorial, which is available from CrystalDiffract’s Help menu. 3. If you need to search for a keyword or phrase, you should be able to use the Search command in a PDF viewer such as Adobe (Acrobat) Reader or Apple Preview. A Note about the Demonstration Version This User’s Guide is designed for the Full-Feature version of CrystalDiffract. If you are using the free, Demonstration Version, some features may not be available: • The Demonstration Version is designed to give you a flavour of the full program, using a range of examples structures. However, you cannot save files, record program settings, or specify preferences. • The Demonstration version does not let you import observed data files (although you can read such data if they have been saved in a diffraction experiment). If you are using the Demonstration Version, we strongly recommend that you explore the saved diffraction experiments provided: these demonstrate a range of features that are possible with the full version of the program. The User’s Guide describes the program interface, followed by sections on simulating diffraction, how to put data into the program—then describing display and manipulation, before finishing with how to get data out of the program: printing and exporting data. The series of short, structural exercises is designed to illustrate some of the most important program features and should address most of the queries that you might have when using the software. Chapter 1: Getting Started 1 Interface Reference Convention In the following chapters we refer to elements of the program’s interface (such as button names, menu commands and keys on your keyboard) using a typewriter font. You will also encounter many references to menu commands written in an abbreviated manner, such as “Edit > Copy”, which means “from the Edit menu choose the Copy command”. Mac & PC Shortcut Keys Installation Mac and Windows versions have different installation procedures: • Mac installation is a simple matter of dragging- and-dropping the CrystalDiffract application from the CD-ROM, to your hard disc (e.g., to your Applications folder). Mac and Windows operating systems use different key combinations for menu shortcuts (“accelerator keys”). In this guide we make repeated reference to command and option keys, which are included on the standard Mac keyboard Windows users should use the following translation: Mac command option As a modern Mac application, CrystalDiffract includes all its essential resources (including online help and this User’s Guide), neatly packaged within the application “bundle”. We would also recommend that you copy the Examples Files to your hard disc—possibly to your own Documents folder. • Windows users will need to run the installer Windows control alt program. This gives the option of installing the essential program files (application, online help, user’s guide), plus supporting resources (examples files). Licensing your Installation System Requirements To run CrystalDiffract on a Mac, you will require Mac OS X 10.4 “Tiger” , 10.5 “Leopard”, 10.6 “Snow Leopard”, or 10.7 “Lion”. To run CrystalDiffract on a PC, you will require Microsoft Windows XP (Service Pack 2), Vista or Windows 7. The program will not run on earlier versions of Windows, such as NT or 2000. The first time you launch CrystalDiffract you are prompted to personalize your copy of the program. This process also creates a preferences file. Registering Your Licence It is very important that your licence is registered with us, as we can only provide technical support (and upgrades) to registered users. You can register when you install the software, by clicking the Register button in the reminder dialog that appears following your installation. Alternatively, you can register later, by choosing the Help > Register CrystalDiffract command. Multi-User Licence Registration We only require one registration per licence. So, if you have a multi-user licence, such as a Research Group, Classroom or Site Licence, only the official “keeper” of the licence needs to register with us. Once we have received that registration, the other users are entitled to receive technical support, within the terms of the specific licence. 2 Chapter 1: Getting Started or “unit cell” of material. CrystalDiffract lets you load observed data. or “rock salt”). CrystalDiffract can simulate the key powder diffraction techniques used today. including traditional single (or dual-) wavelength X-ray and neutron scattering. which is designed to simulate diffraction patterns from a one. which can be recorded as lines on a film. wavelength. particle size and strain. or export them in a range of data formats. Finally. Chapter 1: Getting Started 3 . resulting in patterns of scattered intensity. neutrons or electrons. changing sample and instrumental parameters such as peak widths. A crystal structure is derived from a basic unit that is tiled in three dimensions to form an extended crystal lattice. where a powdered crystal sample (comprising millions of tiny crystallites) is exposed to a radiation beam. when exposed to x-rays. CrystalDiffract lets you print your diffraction patterns. You can measure intensities and distances on screen. and simulate multi-phase mixtures.What is CrystalDiffract? CrystalDiffract is a program for understanding diffraction properties of crystals: specifically. A tiny section through the crystal lattice of sodium chloride (“halite”. for easy comparison with simulated data: an ideal way to characterize materials or interpret the results of synthesis experiments. compare patterns from different materials in the same window. Crystals typically contain billions of unit cells. SingleCrystal. plus newer white radiation (energy-dispersive) and time-of-flight techniques. The preciselyoriented planes of atoms. repeated almost ad infinitum. Crystalline Materials The starting point for simulating a diffraction pattern is a crystal structure: the unique arrangement of atoms inside a basic building brick. CrystalDiffract lets you manipulate diffraction patterns in real time. neatly stacked in a threedimensional lattice. or as intensity peaks by a detector. For the experimental scientist. provide miniature diffraction gratings for X-ray or neutron radiation. Here we see a regular arrangement of chlorine ions (green) and sodium ions (yellow). CrystalDiffract differs from its sister program. It is the very regularity of such structures that allows diffraction in the first place. single crystal. The interplanar spacing is denoted by d. shown here in red. (hkl). then constructive interference between adjacent wavelets ➀ and ➁ occurs when their path difference (t + t) is equal to an integral number of wavelengths. This is summarized in the famous Bragg Equation: l = 2d sin q which provides the condition for coherent scattering of the radiation (wavelength l). The most-important powder diffraction techniques—which can be simulated by CrystalDiffract—are described below. so that only the strongest. With powder diffraction. Data collection tends to be very slow. 4 Chapter 1: Getting Started . One typically moves the beam. Derivation of the Bragg Equation 1 2 N(hkl) 1 2 (hkl) θ θ θ t t θ θ d Consider a crystal with a set of planes. which is filtered. one has the advantage of speed and convenience. There is a reciprocal relationship between q. nl=2t n l = 2 d sin q where: t = d sin q (the Bragg Equation). and the plane normal is N(hkl). scanning through a range of angles. shown here in blue. and inter-planar distances in the crystal (“d-spacings”). Thus. which give rise to diffraction peaks. Cu Ka peak emerges (this is actually a doublet. as individual scattered beams are measured (although new. Sometimes it is difficult to find (or grow) good quality single crystals. Monochromatic Radiation In most laboratory sources. q. are making this faster). requiring precise orientation of the sample (or. in the case of electron microscopy.Why use Powder Diffraction? Powder diffraction has a number of advantages over single-crystal techniques. Ka2 peak is also filtered out). assuming these are randomly distributed. specially-prepared. A characteristic X-ray spectrum is emitted. Single-crystal diffraction (using X-rays or neutrons) is quite an arduous process. strikes these planes at a glancing angle. although sometimes the weaker. If a beam of monochromatic radiation (wavelength l). comprising Ka1 and Ka2 peaks. Data collection times tend to be faster. since only a “onedimensional” pattern is being collected. area detectors. This monochromatic radiation is then directed at the specimen. whereas powders are much easier to manage. thin crystal flakes). relative to the sample. A powdered sample has multiple “crystallites” and. directed at an angle q (the Bragg Angle) with respect to the d-spacing of a set of planes in the crystal. hence. at least one crystal will be oriented correctly to cause diffraction. X-rays are generated by firing a beam of electrons at a metal target—usually copper (Cu) or molybdenum (Mo). q. By measuring scattered intensity as a function of scattering angle. and emit x-rays as they travel around a curved beam path. this scattering strength is controlled by the arrangements of atoms in different directions in the crystals—and hence one can learn something about the crystal structure from its diffraction properties. one is in effect measuring the scattering strengths of different sets of planes (with different d-spacings) inside the crystal. can be generated. Ultimately. Time-of-Flight Diffraction Some diffraction experiments use pulses of neutrons with a range of energies. Here. and are directed down a long “beam line” towards a powder sample. charged particles are accelerated to relativistic speeds. White Radiation Many diffraction experiments are carried out at synchrotron sources. An energydispersive detector records the scattered intensities as a function of energy (and hence wavelength). The number of pulses is recorded as a function of the time-of-flight of the neutrons (which is typically in the range of a few milliseconds to several hundred milliseconds). So-called “White Radiation”. and hence wavelengths. this is useful in diffraction experiments because it allows rapid measurements. These travel at different speeds. an extended diffraction pattern can be recorded at a fixed Bragg angle because the sample is subjected to neutrons of different energies. at a fixed two-theta angle (2q). comprising a broad spread of wavelengths. As for energy-dispersive diffraction. Diffraction is recorded by neutron detectors arranged around the sample. Chapter 1: Getting Started 5 . depending on the energy of the neutrons. without the need to mechanically scan a detector over a range of angles. before you proceed to generate diffraction patterns.. Just drag-and-drop a text file into CrystalMaker for automatic format detection and structure display.CrystalDiffract works with CrystalMaker (left) letting you visualize crystal structures and simulate their diffraction properties—in various experimental modes—in comparison with other patterns and observed data. manipulating and animating all kinds of crystal and molecular structures. Although CrystalDiffract allows you to edit some aspects of a crystal’s structure (e. CrystalMaker lets you display a structure then. CrystalMaker provides seamless display of data files from major databases and supports a wide variety of file formats. with a single menu command. you will require CrystalMaker®: an award-winning program for building. so you can check that the coordinates and/or symmetry settings are reasonable. Further information about CrystalMaker is given at the end of this guide.g. it does not allow you to edit atomic coordinates or to build new structures. CrystalMaker Integration If you would like to be able to build your own crystals which you can load into CrystalDiffract. see its diffraction pattern appear in CrystalDiffract. We believe that the best way to edit these structures is via a CrystalMaker: this allows you to actually see the structure. displaying. lattice parameters and site occupancies). or you can visit crystalmaker.com and download a free Demonstration Version. 6 Chapter 1: Getting Started . Chapter 2: CrystalDiffract Interface This chapter provides a basic introduction to CrystalDiffract’s user interface. Parameters List This is a list of experimental- • and sample parameters. and an Info Bar which displays cursor. on the right-hand side of the window’s titlebar. Patterns List Each window can display a list To open a file in an existing window: Do one of the following: • • Choose: File > Open in Same Window. Window Design CrystalDiffract has a single-window program interface with a toolbar. Drag-and-drop a file into the Patterns List. where diffraction patterns are plotted. Below this is a scrollbar for moving through the x-axis range. extension . then drag-and-drop a file into the window that appears. However. and move them relative to the rest of the display. You can drag text files. In CrystalDiffract. The corresponding patterns can be displayed in the Graphics pane by clicking checkboxes. crystal structure files.cmdf or . choose File > Open then use the file dialog to specify the file(s) to be opened. by supplying a CrystalMaker “crystal” file (file type CMDF. Crystal Files You can simulate a diffraction pattern for a crystalline material. Additional panes are available for displaying lists of Patterns or Parameters. CrystalDiffract will use structural data from the file to generate a diffraction pattern. You can resize the Patterns List by clicking-anddragging the drawer edge (Mac) or the pane divider (Windows). Selection allows you to edit individual patterns.crystal). grouped into folder-like categories.or status information. is the Graphics pane. the full-feature version can read from older files. Drag-and-drop your file(s) into the window. and a Graphics pane for plotting your diffraction patterns. and saved diffraction session files. To load a file in a new window: with buttons/icons for measuring and manipulating diffraction patterns (see Chapter 7: Toolbar Reference for a description of the individual controls). including how to load a diffraction pattern and manipulate it. then click the new entry’s checkbox. Displayed patterns can be selected by clicking on their Patterns List entries. You can edit parameters interactively. and observe how the diffraction pattern changes. of diffraction patterns. Mac users can toggle the toolbar on or off by clicking the lozenge-shaped button. Toolbar At the top of each window is a toolbar Displaying a Diffraction Pattern CrystalDiffract can read from three kinds of files: text files. Please note that Demonstration Mode restricts you to reading only the latest CrystalMaker binary file format. using a slider control. Data will be added in the form of one or more new diffraction patterns. Chapter 2: CrystalDiffract Interface 7 . Launch CrystalDiffract. CrystalMaker binary files and folders into this list. Graphics Pane At the centre of the window Do one of the following: • • • Drag-and-drop a file onto the CrystalDiffract application icon. showing diffraction patterns in “Film” mode 8 Chapter 2: CrystalDiffract Interface . showing calculated and observed diffraction patterns Patterns List Parameters Palette The CrystalDiffract-for-Windows interface.Toolbar Graphics Pane Parameters List Info Bar Patterns Drawer The CrystalDiffract-for-Mac program interface. and auto-scale the y (intensity) axis. with one point per line. which represents a complete record of your work in a particular window. Chapter 2: CrystalDiffract Interface 9 .txt or . extension . choose the relevant menu command. including structural data (for simulated patterns) and intensities. use the Plot > Plot Limits command. Simply view and edit your structure in CrystalMaker. Session Files The third type of file that CrystalDiffract can read is its own “session file” format (filetype CRDF. The file should contain an xy listing of your diffraction points (where the y value is the intensity).and y-axis ranges. via that program’s Transform > Powder Diffraction submenu.dat).crystaldiffract). Arrow Hand Zoom Distance CrystalDiffract’s tool buttons Scaling Commands The Toolbar includes a number of scaling tools that can be used to adjust the x. To enter an explicit range.and y-axis scales. with one or more diffraction patterns. choose the Hand tool from the toolbar then click and drag the pattern.crdf or .and y-axes (the latter option attempts to fit the entire diffraction pattern range inside the Graphics pane). x-scale y-scale auto-scale x & y CrystalDiffract’s axis scaling tools Use CrystalMaker to visualize (and verify!) the structure before you proceed to simulate its diffraction properties.Text Files You can load an observed diffraction pattern. You can adjust the x. Scrolling and Zooming You can use the horizontal scroll bar to quickly scroll through a diffraction pattern. auto-scale y Sharing Data With CrystalMaker You can also provide crystal structure data directly from within CrystalMaker. You can adjust the range of x-axis values by using the Zoom tool to zoom in or out around a clicked point. or both the x. and then observe the diffraction pattern in CrystalDiffract. extension . as a plain text file (file type TEXT. A session file is a saved diffraction experiment. For finer control. Output CrystalDiffract provides a range of data output options. the mouse pointer changes to a double arrow ( ) to indicate that dragging is possible). use the Apply Preferences menu command. Labels can contain any combination of Miller Indices. You can then download this from our website. you can print. the default settings are used whenever a new window is created. Indexing a Pattern You can display peak labels for a selected diffraction pattern using the Pattern menu. d-spacings. the program will check at weekly intervals. When you have finished making your changes. via the File > Export submenu. or a table of Structure Factors. intensities. at user-defined resolution. To display this. and are saved in a preferences file. These include new features. below which no labels will be displayed This is useful for complex diffraction patterns which may have many low-intensity peaks. or when you start up the program. The Peak Threshold setting defines a minimum intensity value. 10 Chapter 2: CrystalDiffract Interface . Checking for Updates We regularly provide free. etc. You can also save a diffraction experiment as a selfcontained “Session File”. Choose this tool from the Toolbar. and you can record your favourite settings in a Preferences file. etc. There is also an option to let the program check for updates automatically (Help > Check for Updates Automatically). then click in the Graphics pane so that a vertical cursor appears. We also include a number of support topics on our website. Printing The full version of CrystalDiffract lets you print high-resolution diffraction patterns. and so on. Help and Updates Most controls have tool tips associated with them. and alert you if a newer version of the software is available. Help files are displayed in a Help Viewer application (Mac) or window (Windows). plot styles. x-values. which are scaled to fit your chosen page size. You can check whether an update is available using the Help > Check for Update command. ready for your next session. Although you can edit these for individual windows. Information about the current point is displayed in the Info Bar at the bottom of the window. a diffraction data report (Miller indices. and links to these are included on the program’s Help menu. For detailed help. You can view and edit the current program settings using a tabbed preferences dialog. choose the Help > CrystalDiffract Help command. choose the Preferences menu command. Saving Preferences CrystalDiffract uses default settings for the window size. To apply any saved preferences to the current window.Measuring a Pattern The Arrow tool allows you to measure points on the simulated diffraction pattern. d-spacings. Using the Arrow tool to measure a diffraction peak You can move the vertical cursor by clicking and dragging it with the Arrow tool (note that when the Arrow tool is placed over the vertical cursor. These include exporting a complete diffraction pattern. incremental program updates. your settings will then be available for any new windows. interface enhancements and occasional bug fixes.). diffraction mode. • • To restore the program’s “Factory” settings. click the dialog’s Save button. multiplicities. click the dialog’s Restore Factory Settings button. one number. you should ensure that it is saved in a text-only format. If you edit the file in a word processor. saved as a text file called “ASF. Calculating the Pattern CrystalDiffract calculates diffraction patterns using the types.or energy-dispersive). such as the radiation type. Each data line should contain: • a two-character element symbol (which CrystalDiffract will match with element symbols in your structure). CrystalDiffract-for-Mac saves the ASF. You can edit the ASF.dat file saved in the Application Data folder. CrystalDiffract uses atomic scattering factors (x-ray diffraction) or neutron scattering lengths for the atoms in your structure. Note: the ASF. Chapter 3: Simulating Diffraction 11 . Site occupancy data and atomic displacement parameters are used to determine the amount of scattering from each site. corresponding to the coherent nuclear scattering length for that element. The format is very simple.dat file inside the application bundle. control-click on the CrystalDiffract program icon and choose the Show Package Contents command from the popup menu that appears.dat”. and positions. and various instrumental parameters. To view the contents of the application package.dat file must be a text-only file with file type TEXT. • The data file can also contain comments: these should be prefaced by an exclamation mark “!”. The program assumes an ideal structure (although you can specify an isotropic strain). nine numbers correspond to the atomic scattering factor coefficients a1 b1 a2 b2 a3 b3 a4 b4 c listed in the International Tables for Crystallography. Locating the package contents CrystalDiffract-for-Windows has the ASF.Chapter 3: Simulating Diffraction The Diffract menu lets you alter aspects of a “virtual” diffraction experiment. the experiment type (angle. of atoms in a unit cell of a crystal.dat data file if you wish to modify or add new data. • Editing Scattering Factor Data CrystalDiffract uses a table of atomic scattering factors and neutron scattering lengths. you can suppress all reflexions below a minimum d-spacing. or Edit > Preferences (Windows). d-spacing. choose the Apply Preferences command.. for massive structures such as proteins). The Profile pane of the Preferences dialog Tip: If you have edited your Preferences and wish to apply the changes to an existing window. set the Angle-Dispersive Diffraction Traditional laboratory diffractometers operate using constant radiation wavelength. CrystalDiffract allows you to simulate angledispersive diffraction. Diffraction Modes CrystalDiffract can simulate a number of experimental types. using x-ray scattering factors or neutron scattering lengths that are stored with the program. which cover the main techniques for powder diffraction: (Mac).Simulation Preferences To speed up the simulation of diffraction data (e. Cu Ka1 and Ka2 lines. e. Minimum d-spacing field. 2 In the Generate Reflexions group. The Wavelength sheet showing CuKa1 and Ka2 radiation The Wavelength sheet lets you specify monochromatic (single-wavelength). You can also limit the maximum number of reflexions (so that only those with the highest d-spacings are used).. or dualwavelength radiation. Traditional laboratory x-ray tubes typically maximise intensity by emitting dual wavelengths. with diffraction measured as a function of Bragg Angle (theta. q). 3 Click the Save button to store your new settings. enable the Limit number to option and enter a maximum number of reflexions. 2 Navigate to the Profile tab. or reciprocal d-spacing.g. available from the CrystalDiffract menu (Mac) or the Edit menu (Windows). These will apply to any new windows. This is called angle-dispersive diffraction. To set your simulation preferences: 1 Choose: CrystalDiffract > Preferences Radiation Type You can use the Diffract menu to switch between x-ray or neutron diffraction. 12 Chapter 3: Simulating Diffraction .g. You can specify the wavelength using the Diffract > Wavelength command. plotting diffracted intensity as a function of: 2q. The diffraction pattern is recalculated. Diffraction is recorded by neutron detectors arranged around the sample. Time-offlight diffraction is used at one such beam line. The Bragg equation relates wavelength (l) to the d-spacing of a set of lattice planes. These travel at different speeds. and are directed down a long “beam line” towards a powder sample. and hence wavelengths. near Oxford.Energy-Dispersive (EDS) Diffraction A relatively-new type of diffraction involves using ‘white’ radiation that has a spread of wavelengths. You can specify a 2q value for this experiment. We can analyse the time-of-flight process by combining De Broglie’s hypothesis. Neutrons are directed along beam lines. and the Bragg Angle (q):l = 2d sin q If l can be varied. Chapter 3: Simulating Diffraction 13 . Since the wavelength of radiation is related to its energy. using the Diffract > Energy command. at a fixed two-theta angle (2q). arranged radially. However. the High-Resolution Powder Diffractometer (HRPD). an energy-dispersive detector can be used to record an extended diffraction pattern as a function of energy. an extended diffraction pattern can be recorded at a fixed Bragg angle because the sample is subjected to neutrons of different energies. Time-of-Flight Diffraction Some neutron diffraction experiments use yet another kind of diffraction: a neutron spallation source creates pulses of neutrons with a range of energies. then diffraction from a range of d-spacings can be recorded at the same q angle. l = h / mn vn The ISIS neutron spallation source at the Rutherford-Appleton Laboratory. England. in order to resolve diffraction from different d-spacings. t. As for energy-dispersive diffraction. around the target (the curved light-blue chamber in the centre of the photo). It is therefore not necessary to mechanically scan a detector through a range of q/2q angles. The number of pulses is recorded as a function of the time-of-flight. the stationary detector must be able to discriminate between scattered radiation of different wavelengths. of the neutrons (which is typically in the range of a few milliseconds to several hundred milliseconds). depending on the energy of the neutrons. 14 Chapter 3: Simulating Diffraction . and corresponding times of flight t1 and t2. as well as the two theta value for the diffraction experiment. h t / mn L = 2 d sin q hence: t = 2 d L (mn/h) sin q Thus. reflecting its mean particle size.(where h is Planck’s constant. t. given a primary flightpath (the distance from the moderator to the sample) of L1 and a secondary flight path (sample to detector) of L2. L. and the overall flight path. using the Diffract > Time-of-Flight command. particle shape and structural state (including strain). This is why the highest-resolution neutron diffractometers have the longest flight paths (e. ~100m at the HRPD instrument in the Rutherford-Appleton Laboratory). CrystalDiffract lets you specify the overall flight path. with its intensity distribution spread over a wide range of x values. The Gaussian function is shaped like the profile of a church bell. Peak-Shape Functions In an ideal diffraction experiment. for most samples the shape of diffraction peaks is mainly determined by the diffraction technique and geometry. Notice the lower peak maximum for the Lorentzian profile. neutron diffraction experiments tend to result in peaks with a Gaussian shape. whilst synchrotron diffraction may result in a Pseudo-Voigt peak shape. like the mouth of a trumpet. with a more rounded appearance Pseudo-Voigt Gaussian (top) and Lorentzian (bottom) profiles for the same diffraction peak.. CrystalDiffract’s Diffract menu lets you choose between different shape functions: • • • • Delta Function Lorentzian Gaussian The Delta Function is simply a “spike” of zero width. the shape of a diffraction peak would be determined solely by the sample. we have: vn = (L1 + L2) / (t1 + t2) = L / t where L is the total flight path and t is the total time-of-flight. The Lorentzian function has a distinctive splayed appearance: peaks having very wide tails. This provides a very quick way of showing the positions of many peaks in a complex pattern. mn is the neutron mass and vn is its velocity) with Bragg’s Law. In practise.g. L. thus. we have a linear relationship between the total time-of-flight. For example. thus: l = h / mn vn = 2 d sin q Now. than the Lorentzian function. In fact. so for large crystals there is very little peak broadening. or time-offlight in milliseconds. (The units depend on the current choice of x-axis: two-theta. Peak Widths The limited resolution of a diffraction experiment may result in diffraction peaks that are substantially broadened. there is likely to be a continuous spread of unit cell dimensions throughout the sample. CrystalDiffract lets you specify the amount of instrument broadening. characterized by a standard deviation. The amount of strain in the sample can be summarized by a “percent strain”. reciprocal-d. resulting in a diffraction pattern with a slightly “blurred” appearance. in terms of the full width at half-maximum for a diffraction peak. this “instrumental broadening” is the major contribution to the widths of observed diffraction peaks. whereas in a strained crystal there might be a normal distribution of cell parameter values. Finally. d-spacing. the Pseudo-Voigt function is a mix between the Gaussian and Lorentzian functions. but for very small crystals (fractions of a micron in diameter). Strain Broadening A strained crystal can be thought of as containing regions with slightly different unit cell dimensions. This is the standard deviation for the variation of cell parameters in the sample (in an ideal crystal there would be one unique cell parameter. diffraction peaks can become noticeably broadened. which determines the Lorentzian character of the final function:Result = Eta × Lorentzian + (1 – Eta) × Gaussian You can edit the Eta parameter using the Diffract > Eta command. and with less extensive “tails”. This is a reciprocal relationship. ranging from zero for the ideal crystal to a few percent for a very-highly strained crystal). In a powder sample. For most practical experiments. It is characterized by a mixing parameter. and this can be simulated using the Diffract > Particle Size command.) Particle Size Broadening The width of a diffraction peak also depends on crystal size. and entering a new value in the sheet or dialog that appears. Use the Diffract > Percent Strain command to specify a value for the strain. energy in keV. we normally refer to a mean particle size. Chapter 3: Simulating Diffraction 15 . Eta. in order to show a range of sites and their atomic displacement parameter data (Uij and Uiso) 16 Chapter 3: Simulating Diffraction . if available. use the horizontal scrollbar to show the atomic displacement parameter fields. you may need to resize the sheet. Edit Crystal Sheet Choose the Edit > Crystal command to display the Edit Crystal window. you might enter something like: Si 0. for instance.7 Al 0. so you can determine how this affects diffraction. You can edit lattice parameters and site occupancies—and also omit sites from the diffraction calculation. Alternatively. To view the atomic displacement parameters.0. When you have finished your editing session. Each site row has a checkbox. You can enter up to three element symbols and their corresponding occupancies.3 or: Ca 0. You can sort your data by clicking on a column header. You could.56 Mg 0. You can also move columns. by clicking and dragging its size box. Tip: You can visualize atomic displacement parameters as “thermal ellipsoids”. Lattice parameters are shown at the top. The remaining fields cannot be edited. They show the atom’s fractional coordinates (xyz) and.03 The Edit Crystal sheet can be resized horizontally and vertically. Click again to reverse the sort order. For example. so as to determine their influence on the final diffraction pattern. with a scrolling list beneath. the atomic displacement parameter data (anisotropic values and isotropic values). decide to “turn off ” certain sites. The total occupancy must not exceed 1. You can edit site occupancies by typing a formula into the Site Occupancy field.41 Al 0. by clicking-and-dragging their column headers. using recent versions of CrystalMaker. click the OK button to replot the diffraction pattern.Editing Structural Data CrystalDiffract lets you edit aspects of a selected pattern’s underlying crystal’s structure. as the example opposite shows. showing all sites in the crystal’s asymmetric unit. which defines whether or not that site will be included in the intensity calculation. .g. To show the Parameters List. you can interactively change the two-theta angle (for the sample/detector geometry) and the overall neutron flight path length.Interactive Parameter Control The Edit Crystal window lets you change multiple site occupancies and/or cell parameters. and your calculated pattern has intensities from zero to 1. Using the Parameters List to simulate an orthorhombic distortion (red pattern) in a previously-tetragonal crystal (blue pattern). unit cell angle) whilst the diffraction pattern is replotted in real time. with the diffraction pattern subsequently recalculated. For example. if a “pseudo-Voigt” profile has been chosen—and the zero correction. in the time-of-flight simulation mode. then you can interactively change the two-theta angle for your sample/detector geometry. This lets you interactively change the wavelength for a traditional. Clicking and dragging the slider thumb continually changes the highlighted variable (the b cell edge length) and replots the diffraction pattern in real time.g. if you have an observed dataset whose intensity range is from zero to 1000. then you can also adjust the relative scaling (Scale Factor) between observed and calculated datasets. the “Eta” parameter—which controls the peak shape. Instrument Alternatively. A more interactive way of editing the structure is to use the Parameters List to gradually change one structural variable (e. Time-of-Flight For neutron diffraction.. then you would want to scale your observed pattern by a factor of 0. Parameter Groups The Parameters List contains a series of hierarchical entries. The distortion (a ≠ b) has caused peak splitting (e. each with its own disclosure triangle. angle-dispersive (monochromatic radiation) experiments. choose: Window > Show Parameters List.001. click the Toolbar’s Parameters button: Energy Dispersive If you have chosen an energy-dispersive simulation mode. or (with the Graphics pane focussed) press the p key on your keyboard. Chapter 3: Simulating Diffraction 17 . 400 and 040). and representing different aspect of the diffraction experiment: Angle Dispersive This group lets you change aspects related to your simulated diffraction apparatus: the peak width (instrumental peak broadening). If you are working with observed data. b. allowing you to edit that item’s value. • If a calculated pattern is selected. • • • • 18 Chapter 3: Simulating Diffraction . g) for a selected calculated pattern. this is a useful range of settings when assessing the effect of a phase transition on the diffraction properties.g. can be adjusted interactively. it does let you assess the chemical contribution to peak intensities..g. You can interactively edit the unit cell parameters (edge lengths.) Local and Global Parameters CrystalDiffract lets you apply a basic background function to your calculated patterns. angles a. Please note that CrystalDiffract does not perform an energy minimizations of the structure. B and C.g. cubic → tetragonal → orthorhombic) by changing cell parameters and watching how diffraction peaks split. by dragging its site occupancy slider from 1 to 0. However. Simulating the effect of pressure and temperature by changing the unit cell volume (isotropic expansion/compression is assumed). which causes a slider bar and a text edit field to appear below the list. etc. which relate to the currently-selected pattern. Unit Cell Some Parameter entries are shown on a pink background. regardless of selection status. using this group. or patterns. which affect all patterns. Mixture If you have a multi-phase mixture (of calculated patterns). CrystalDiffract does not optimize the structure following any of these adjustments. c. perhaps to match an observed diffraction pattern—and hence to determine its approximate composition. whilst keeping atoms in their existing sites. you can adjust their relative proportions using the Mixture group (this is discussed more in the next section).. then you can interactively adjust the occupancies of its individual sites. If a particular site is disordered (e. These are local parameters.. Examples include wavelength and peak width. Parameter entries shown on a grey background are global parameters.5) then the individual occupants are listed on separate lines. Zero Error. (When editing the text. Nevertheless. as with the Unit Cell adjustments. Please note that. has a mixed occupancy such as Al0. Examples include unit cell parameters and site occupancies. e. Visualizing the influence of one site occupancy on the final diffraction pattern. by changing Peak Width.5Si0. Sample The full-feature version of CrystalDiffract lets you simulate the effect of Particle Size and (isotropic) strain. Fine-tuning a calculated diffraction pattern to match an observed pattern. a. as defined by their fractional coordinates. The individual parameters. Individual Parameter entries can then be selected with the mouse.Background Using the Parameters List You can open (expand) a hierarchical entry by clicking it. using this group. This function has the form: A + Bx + C/x. Eta value. Changing the composition of a mixture by varying the proportions of individual phases. Here are some possible uses: • Simulating structural phase transitions (e. Understanding how mean particle size and/or sample strain affects the diffraction pattern. press the Enter or Return keys to replot the structure. b. A. or its disclosure triangle. Site Occupancies Possible Applications The Parameters List is designed to be educational as well as functional. one is simply “deforming” the unit cell. by clicking on their entries in the Strucures list). and restore the display to separate diffraction patterns. any observed diffraction patterns are combined into a single. using the Mixture settings in the Parameters List. using the Plot > Separate command. To remove phases from a mixture. width. with their sum total equal to 1. To do this. If both a calculated and observed mixture are displayed in the same window. you can continue to edit structural data for individually-selected diffraction patterns. to ensure that the overall sum of components is fixed. as you do this. which allows you to reset all volume fractions to equal values. just as you might do in “Separates” mode. turn off the corresponding checkboxes in the Structures list. calculated mixture.g. Undoing a Mixture You can “unmix” a mixture. Similarly. or by clicking the Toolbar’s Unmix button. colour and so on— provided that at least one pattern in your mixture is selected. then choose the Pattern > Show Labels command. Select the patterns that you wish to label (e. for the calculated mixture) to ensure that the plot settings are applied to the correct mixture. All peak labels are colour-coded by component. Mixture Plot Settings Toolbar Mix (left) and Unmix (right) buttons In Mixture mode.. and you can adjust the volume fractions for each component. use the Plot > Mixture command. simply using the existing patterns in your diffraction window. When in Mixture mode. Editing the volume fraction of Silicon in a simulated three-phase mixture Chapter 3: Simulating Diffraction 19 . you can edit the plot settings. all calculated diffraction patterns are combined into a single. Editing Mixtures You can edit the relative phase proportions for calculated mixtures. You can “create” the mixture by turning on mixture mode. “observed mixture”. at 1. Tip: The Structures list’s Actions menu has an Equalize Phase Proportions command. in the same way that labels are applied for individual patterns. including line style.Mixtures CrystalDiffract allows you to simulate mixtures with unlimited numbers of components. you should carefully check that the appropriate pattern is selected (e. All calculated patterns are listed.. the volume fractions for the remaining components are automatically updated. In Mixture mode. You can choose to apply labels to diffraction peaks in the mixture. or click the Toolbar’s Mix button.g. a calculated pattern. using the Edit > Diffraction Data command: The Edit Diffraction Data window The resulting window lets you sort data. d-spacing or intensity). by clicking the Save button.g.Viewing Diffraction Data You can quickly view a tabulated listing of diffraction data. 20 Chapter 3: Simulating Diffraction .. according to your chosen parameter (e. You can opt to save the sorted listing as a text file. experimentally-observed data: useful for characterizing samples. Chapter 4: Working with Patterns 21 . synthesis results. These could contain real.44 10. and you can display these will simulated (calculated) diffraction patterns for easy characterization. etc. CrystalDiffract changes the relative scale setting for the observed data in order to best match the two patterns.00 23. it is important to check that the data file is a Mac file.95 10. or: Drag the files into the Graphics pane. You can manually control the relative scaling for a selected observed pattern. Any offsets can be reset to zero by clicking the small round button at the centre of the arrows: The Toolbar’s Shift controls You can also use the Arrow tool to click and drag a diffraction pattern. checking for impurities. You can combine these with real. labels. when plotted in Graph mode. You can use the Shift arrows on the toolbar to do this. or Drag the files into the Patterns List. Loading Observed Data Observed datasets should be saved in plain-text files. line widths. Subsequent lines should contain pairs of xy values—with one datapoint per line.10 23. colours. styles. then choose the relevant commands from the Pattern menu. observed data. for example: Title line plus xy data… 10. then turn on their checkboxes. Observed & Calculated Data Compared When you append an observed data file to a window that already contains calculated data. with choice of plot type.20 22. Applying Plot Styles You adjust the plot styles for observed diffraction patterns. in exactly the same way as for calculated patterns: first select the patterns you wish to change.45 10. with filetype “TEXT”. and even basic phase identification.40 27.87 Note: If you are using the Mac version. It is possible to reposition a selected pattern (calculated or observed). markers.56 10. by introducing x and/ or y offsets. The first line of the file should contain a title (this is ignored by CrystalDiffract). using the two y-scaling buttons on the toolbar: The Toolbar’s Relative Scale buttons To open a file in a new window: • Choose the File > Open command To add files to an existing window: Do one of the following: • • • Choose: File > Open in Same Window. You can control how individual patterns are plotted using the Plot and Pattern menus.Chapter 4: Working with Patterns CrystalDiffract allows you to mix multiple simulated diffraction patterns in the same window. Working with Observed Data The full-feature version of CrystalDiffract lets you load one or more text files in any window.30 24. g. crosses. which is described next. The observed data are plotted as crosses. Σ (obs .Observed and calculated time-of-flight neutron diffraction patterns (top graph). The legend for the residual graph/film also displays the sum-of-squares difference between the calculated and simulated data: error = Identifying an Unknown Substance Being able to compare an observed diffraction pattern with one or more calculated patterns for known substances can be very useful when trying to identify an unknown substance.calc)2 This value corresponds only to the currentlydisplayed plot range. The Plot > Data Style submenu allows you to choose how the observed data are plotted (e. then add a sequence of CrystalMaker binary files (File > Open in Same Window). with calculated data plotted using a smooth line. This is controlled via the Plot > Show Residual or Plot > Hide Residual commands. You can load the observed diffraction pattern. squares. until a good match is found. It can be a useful reference when attempting to fine-tune the calculated data in order to match the observed data. A more convenient way of comparing phases is to use the Patterns List. lines between points. The lower graph shows the residual function (observed minus calculated) Displaying the Residual Function When working with observed and calculated data you have the option of displaying a separate graph or film showing the difference (observed minus calculated) between the two datasets: the “residual” function.). 22 Chapter 4: Working with Patterns . etc.. and only your clicked pattern plotted.) To delete one or more patterns: 1 Select the relevant entries in the list. or click outside the selected row. or simply to browse individual patterns from a large list. To display only one pattern at a time: Using the Patterns List The Patterns List can hold as many patterns as you like: you can drag files and folders—perhaps your entire CrystalMaker Structures Library—into the list. and the list supports standard editing conventions. You can then quickly compare each diffraction pattern with the observed data by turning its checkbox on or off. Click on the pattern’s colour swatch (on the right-hand side of the Pattern List) and choose a new colour from the popup menu. To change the colour of a plotted pattern: Do one of the following: • • • Click the Patterns icon in the Toolbar.. observed data files—or when you open a previously-saved session. Individual patterns can be selected. show or hide them (in the Graphics pane). press the Escape key. or Patterns List. 2 Press the Return or Enter keys on your keyboard (or click on the selected name). then choose the Plot or Hide commands from the Patterns List Actions menu. To Display the Patterns List: To rename a pattern: 1 Select the pattern in the list. You can use the Patterns List to select individual patterns. or Press the s key on your keyboard. Comparing Diffraction Patterns The Patterns list really comes into its own when comparing an observed diffraction pattern with a number of calculated patterns.. To plot one or more patterns: Do one of the following: • • Select one or more pattern(s) to be plotted or hidden. rename them. New patterns are automatically added to this list when you load them from crystal files. Check or uncheck the pattern’s checkbox. duplicate them. or as a window pane (Windows). Plot Settings Chapter 4: Working with Patterns 23 . command from the bottom of the menu. • Hold down the option/alt key and click a pattern’s checkbox. drag and drop their CrystalMaker binary files into the Patterns list. Having decided on a number of possible candidates to match the observed data. Choose the menu command: Window > Show • The Patterns list may be displayed as either a slide-out drawer (Mac). 3 When you have finished editing. (To cancel an edit. such as multiple selections (shift. Any plotted patterns will be hidden.and command-clicking). For more colour choices. choose the Other. 2 Press the Delete key on your keyboard. press Return or Enter to finish.Managing Multiple Patterns The Patterns List lets you keep track of your observed and calculated diffraction patterns. one item’s name is being edited. Here.Working with multiple patterns in the same window. using the Patterns List. 24 Chapter 4: Working with Patterns . Chapter 4: Working with Patterns 25 . Film or Graph You can choose to plot your diffraction pattern as a graph of intensity versus x-value. use the Pattern menu. gridlines and colours. and so on. You can also customize aspects of the Graphics pane display. making it easy to compare positions and intensities of diffraction lines. You can undo the stacking by choosing: Plot > Collapse.General Plot Settings The Plot menu lets you change the general way in which all diffraction patterns are displayed. For specific adjustments to individual diffaction patterns. Stacked graphs showing how the diffraction pattern of a crystal changes with temperature. or you can opt to display a greyscale representation which resembles a traditional photographic x-ray film. The central diffraction pattern corresponds to observed data for a mixture of analcime and silicon. Stacked Graphs In Graph mode you can use the Plot > Stack command to stack multiple diffraction patterns without danger of overlap. the “ideal” calculated patterns for Silicon and Analcime are displayed above and below. including the plot range. Film mode is particularly useful when comparing multiple diffraction patterns: these are then stacked. Comparing calculated and observed data in Film mode. and the progress of a displacive phase transition. dashed lines or a “solid fill” profile. You can superimpose a series of peak markers showing the peak centres. Individual peak profiles are shown by the dotted lines. Individual Pattern Settings The Pattern menu provides a series of commands which act upon any currently selected diffraction patterns.and y-axis values. You can also show or hide a legend. Alternatively. you can opt for “blank” labels. as illustrated above. Labelling Peaks The Pattern menu gives you various options for labelling the peaks of selected diffraction patterns.Overlaying Peak Positions For a complex diffraction pattern there may be many overlapping peaks. Tweaks You can display gridlines in the diffraction window: thin lines marking the major x. and their relative intensities. Notice that only the strongest peaks are labelled in this example. Labels can contain any combination of: • • • • Phase name Miller Indices (hkl) D-spacings x-axis values Alternatively. marker sizes—and control the labelling of diffraction patterns. The Plot > Overlay Peak Positions submenu allows you to identify the positions of individual diffraction peaks. the colour of the gridlines is set using the Plot > Grid Colour command. You can change plot colours. 26 Chapter 4: Working with Patterns . in a choice of plot styles: solid lines. the legend lists all phases and their proportions. which acts as a key for the observed and calculated data. where only arrows are plotted. Strong peaks labelled with Miller Indices. graph attributes. you can overlay the actual profiles of individual peaks. such as line styles and widths. Analysing a simulated mixture. by overlaying the peak positions for individual phases Overlaying peak positions using a solid profile is particularly useful for indicating different phases in a multi-component mixture. and for mixtures. or as individual markers (with a choice of marker styles. The Pattern > Label Threshold submenu lets you specify the minimum relative intensity for which annotation should be used.To turn labels on: 1 Select the pattern(s) you wish to label. (Note: The label text. 2 Choose one or more settings from the Pattern > Label Style submenu. such as dots. you have extensive control over the appearance of all diffraction patterns. thin dashed line. To specify the label type: 1 Select the pattern(s) whose labels you wish to Graph Settings In Graph mode. Chapter 4: Working with Patterns 27 . thick solid line. in pixels. squares and crosses)— or you can choose a combination of lines and markers. You can edit individual patterns by selecting them (individually. or opt for an Auto setting. Line Width You can specify an explicit line width (in pixels). modify. different diffraction patterns. translucent. or collectively). and peak arrow. Plot Style Data can be plotted using lines between points (with a choice of smooth or dashed lines). Popup menus adjacent to each (plotted) entry let you quickly choose one of a number of preset colours. or opt for an Auto setting.) Controlling the Extent of Labelling In order to prevent the diffraction pattern from becoming too cluttered. lines with dots. Examples of different plot and marker styles. Marker Size You can specify an explicit marker size. are drawn in the same colour as the host diffraction pattern. you can suppress annotation for weak peaks. Plot Colour You can apply different colours to Tip: You can also edit plot colours using the Patterns List. in which CrystalDiffract scales the marker size depending on the plot size and resolution. crosses. and then applying settings from the Pattern menu. 2 Choose: Pattern > Show Labels. From bottom: solid. For example. Ensure that the window to be cloned is the frontmost diffraction window. respectively. On the Mac version. 28 Chapter 4: Working with Patterns . with small offsets between adjacent windows. and give you free rein to experiment with new settings—maybe editing the structure and then wishing to compare the new diffraction pattern with the old diffraction pattern. then choose the Window > Clone Window command. the radiation type. or tiled down the screen—using the Window menu’s Stack and Tile commands. peak widths and so on. x-axis range. Synchronizing Windows (Mac) When comparing different structures in different windows you can use the Window> Synchronize command to adjust every window’s settings to match those of the current (uppermost) window. are all reset to your current settings. in order to preserve the original data.Customizing your Workspace CrystalDiffract lets you open as many windows as memory permits. y-scale. Cloning Windows (Mac) You can “clone” a window. you can arrange multiple windows neatly on screen: either stacked on on top of each other. 1 9. Tip: You can quickly view and sort these diffraction data on screen. d-spacings and multiplicities. [ [ [ [ [ [ [ [ [ [ [ [ 1] 2] 3] 4] 5] 6] 7] 8] 9] 10] 11] 12] (N) 3 8 11 12 16 19 24 27 32 35 36 40 h 1 0 1 2 0 1 2 1 0 1 2 0 k 1 2 1 2 0 3 2 1 4 3 4 2 l 1 2 3 2 4 3 4 5 4 5 4 6 d(hkl) 4. edit. and used for any new windows (existing windows retain their own settings).82416e-02 1.47933e-05 1.11695e-02 2.6 0. and this also provides high-resolution printed output. you can save your “diffraction experiment” in a single file.29683e-03 5.58979e-02 4.6807 59.55500 1.0076 31.3842 65.15645e-02 3.36577 1.12600e-03 I/Imax 32. This command will replot your current patterns.7 3. The Preferences dialog.2843 36. default settings.34667 1.42836 1.2 3.2 59. use the Apply Preferences command.64932 1.96662e-05 3.1 m(hkl) 8 12 24 8 6 24 24 32 12 48 24 24 Chapter 5: Printing & Saving 29 .0 78.0 32.33250 2.43621 2. wavelength. your plot settings and all data required to plot the displayed diffraction patterns.66499 2.14849e-02 1.6 49. diffraction mode. by choosing: Edit > Diffraction Data. Part of a Diffraction Data file for spinel.1568 Intensity 1. Saving Your Work CrystalDiffract allows you to save a window’s diffraction experiment in a self-contained “session” file. with their intensities.27756 2-Theta 19.6613 69. This retains the window size and layout.8299 49. ready for immediate display next time you use the program. You can also opt to restore the original.1048 55.02000 1.85671 2.2661 68.44335e-03 1.44064e-04 2. will all be reset to match your default settings. Exporting Data The File > Export submenu items allow you to generate text files in various different formats: Diffraction Data This file contains a detailed listing of all reflexions in the powder pattern(s).8626 38..0 0.5650 44. any changes you make are saved in your preferences file.75771e-02 2. When you have finished. ref no.0 1. Saving Preferences CrystalDiffract uses default settings which you can inspect. with the Preferences command. which is available from the CrystalDiffract menu (Mac) or the Edit menu (Windows). using the new. If you wish to apply your changed preferences to any existing windows.Chapter 5: Printing & Saving CrystalDiffract uses high-quality graphics for its on-screen drawing.7751 74. A tabbed dialog shows the currently-active settings.85368 1. Your plot range. etc. and save. “factory” settings. hkl values.2 100. 06 26.00000e+00 2.0400 4.6650 4.99490e+02 3.27941e-09 1.008 19.74030e-05 1.00 -0.008 19.40000 19.00000 19.Structure Factors This file contains a complete list of reflexions in three-dimensional space (this is a wider range than is displayed on the screen.70000 18.67034e-11 3.6650 4.65000 18.07549e-01 3.and imaginary parts of the structure factor are included. for example.98450e-08 1.982 21. When you choose the Print command.22 35.25000 19.00 -0. Saving a PDF File (Mac) CrystalDiffract for Mac takes advantage of a built-in system feature: the ability to “print” to a PDF file.06 26.008 19.008 19. If you find that line widths and/or marker sizes are too small.22 26.10000 19.37977e-02 1.982 Lp 35.6650 4.00 -0.22 35.99490e+02 3.00000e+00 0.008 19. You can specify the step between adjacent x-axis values.60000 18. scaled to fit the current page size.70 -55.00 -0.99490e+02 3.00000e+00 Printing The full-feature version of CrystalDiffract will print the contents of the current window at the highest-possible resolution.70 55.008 19. The intensities and the real.00 0.70 -55.06 26.0400 4. choose larger sizes from the Pattern > Line Width and Marker Size submenus.99490e+02 3.67034e-11 3.50000 18.99490e+02 3.008 21.982 21. Part of a Profile output file for spinel.00 0.22 35. ref no.06 F(Re) -55.22 35.00 -0. then each row of the exported profile would contain four values: x yA yB yC.MgAl2O4” 0.99490e+02 3.22 35.30270e-12 0. then the exported file contains multiple columns. as determined by your printer’s resolution and the available memory.62704e-02 7.72673e-02 4.22 35.00 F(Im) 0.61257e-11 30 Chapter 5: Printing & Saving .0400 4.0400 2-Theta 19.00 0.61257e-11 3.00000e+00 0.6650 4.15000 19.55000 18. allowing high-resolution output.6650 4.00 -0.6650 4.62476e-11 7.20000 19. So.70 -55.95000 19.03963e-06 2.008 19.6650 4.70 -55.35000 19.70 -0. This simple file format can easily be imported into many graph plotting programs or spreadsheets.00000e+00 0.45000 .22 35.00 Intensity 3.30000 19.00 -0.70 -55.25509e-04 1.53770e-11 3. A.06 26.99490e+02 3.982 21. x “Spinel 18.00 0. the resulting Print sheet has a PDF button which.0400 4. Data are sorted in order of decreasing d-spacing.85000 18. if three patterns.90000 18.982 21. making it a great way of exporting high-resolution diffraction profiles.05000 19.75000 18. [ 1] [ 2] [ 3] [ 4] [ 5] [ 6] [ 7] [ 8] [ 9] [ 10] [ 11] [ 12] [ 13] h -1 -1 1 1 1 -1 -1 1 -2 0 0 0 2 k -1 1 -1 -1 1 1 -1 1 0 0 0 -2 0 l 1 1 1 -1 -1 -1 -1 1 0 2 -2 0 0 d(hkl) 4.00 -0.09937e-03 1.00 -0.6650 4. Profile This file is a tab-delimited listing of xy If multiple diffraction patterns are displayed in the same window. Part of a Structure Factor output file for spinel. corresponding to the x-range currently displayed.00000e+00 0. data points.00 -0.99490e+02 3.94836e-14 9.80000 18. as the reflexions have not been combined into a onedimensional powder pattern).00 0. corresponding to the y-data for all selected diffraction patterns. when gives the option of exporting a PDF graphics file containing your diffraction pattern.01539e-03 1. B and C were selected.00 -0.70 55. click in the Graphics window where you want to begin measuring. thereby changing its xand y-axis offsets. below). Chapter 6: Toolbar Reference 31 . The Arrow tool also lets you click-and-drag a diffraction profile (graph). You can select a tool either by clicking its tool button. Distance (d) The distance (“measurement”) tool Arrow (a) Hand (h) Zoom (z) Distance (d) CrystalDiffract’s tool buttons Arrow (a) The Arrow tool lets you measure data in the diffraction window. using a vertical cursor.g. Hand (h) This tool lets you scroll the diffraction Tools There are four tool buttons. This chapter summarizes the various toolbar buttons or icons. pattern: you can click-and-drag the graphics pane. The CrystalDiffract Toolbar (Mac version) Show/Hide Parameters List (p) Show/Hide Patterns List (s) Tool Buttons Axis-Scaling Tools Relative Scale Shift Controls Mix/Unmix Film/Graph mode Showing the Toolbar You can show or hide a window’s Toolbar by clicking the lozenge-shaped button on the top right-hand side of the title bar. This is a more precise way of repositioning the profile than using the horizontal scroll bar. can then drag the cursor with the mouse. information about that pattern is displayed in the Info bar. and the horizontal distance is printed in the Info bar. Zoom (z) This “magnify” tool allows you to zoom in on a clicked point in the diffraction pattern. You can also save your toolbar preference.or the right. and adjust the scaling settings. Click once in the Graphics pane to display the cursor or to move the cursor to a new location. The region between the two points is shown highlighted. you has two functions: a measurement tool. located on the left-hand side of the toolbar. To measure the distance between two points on a diffraction pattern. or if the Graphics pane is focussed (e. and a zoom tool. you can choose a tool by by pressing the appropriate letter on your keyboard (shown in parentheses. Only one tool can be selected at any time. A “Zoom” button also appears: clicking this expands the scale so that the highlighted region fills the window.. To zoom out. moving the diffraction display to the left. with the Preferences dialog.Chapter 6: Toolbar Reference Each CrystalDiffract window has a horizontal toolbar at the top. As you move the cursor over a diffraction pattern. which allows you to choose specific tools for manipulating or measuring a diffraction pattern. you recently clicked in it with the mouse). and the mouse cursor changes according to the currently-active tool. then click where you want to stop. hold down the option or shift keys on your keyboard as you click with this tool. edit plot colours. This can be useful when trying to match calculated and observed diffraction patterns. left or right. The toolbar icon changes. The “Film” and “Graph” toolbar icons Mix/Unmix This is perhaps one of the most The y-scale values can also be adjusted using the Parameters list: select the (observed) datasets you wish to edit. The auto-scaling takes two forms: you can auto-scale the y-axis. and change the selection status of individual patterns. may be hidden if the window size is small) lets you quickly show or hide the Patterns List. This is located in either a drawer (Mac) or pane (Windows). which is part of the Instrument parameter group. The icon changes. depending on which mode is currently active. The Patterns List lets you browse multiple diffraction patterns. so that the existing plot range fits snuggly within the vertical bounds. or vertically up or down. Note: when observed data are appended to a graph of calculated data (or vice versa) the relative scale for the observed data is adjusted to give the best match with the y-axis range for the calculated data. so that all diffraction patterns fit entirely within the Graphics pane. so if you have a small screen you may wish to keep the list hidden until you need to use it. and for auto-scaling the display to fit within the current plot range. depending on whether or not a mixture is currently plotted: Shift Controls It is possible to shift selected diffraction patterns horizontally. These adjustments allow correction for zero errors in the diffraction experiment. useful tools. The toolbar Mix (left) and Unmix (right) buttons The Toolbar’s shift controls 32 Chapter 6: Toolbar Reference . Show/Hide Patterns (s) This icon (which CrystalDiffract provides tools for expanding or contracting the x and y axes. click the round icon at the centre of the group of arrows. inside the current window. by clicking this button. To reset any shifts to zero. and for constant background levels. Film/Graph Mode You can quickly toggle Relative Scale You can adjust the y-scale for observed datasets. You can also auto-scale both x and y axes. then adjust the Scale Factor setting. between “film” and “graph”mode. Showing the Parameters list causes the Graphics pane to shrink. allowing you to instantly toggle between display of individual diffraction patterns. and a simulated multi-phase mixture. relative to the graph’s y-axis and any calculated data.Axis Scaling Tools auto-scale y Other Controls Show/Hide Parameters (p) Clicking this icon x-scale y-scale auto-scale x & y CrystalDiffract’s axis scaling tools will show or hide the Parameters list. GSAS. The same applies to scientific software: our “CrystalMaker Office” is modular. with a simulated x-ray powder diffraction pattern in CrystalDiffract (top right). XYZ and many more. MOL. manipulating and animating all kinds of crystal/molecular structures and their behaviour. and from proteins to perovskite. and you wouldn’t expect to fly a plane using a steering wheel. FDAT. displaying. Chapter 7: The CrystalMaker Office 33 . with components designed to give you the best user experience and performance. This makes it easy to switch between different bonding topologies: from semiconductors to silicates. Easy Data Processing CrystalMaker provides drag-and-drop import of text data files in a wide range of file formats. available in optimized versions for Mac and Windows (including Windows 7). whilst ensuring a quick and easy workflow. viewed in CrystalMaker (left). ICSD.Chapter 7: The CrystalMaker® Office Different tasks require different interfaces. Introduction to CrystalMaker To really make the most of CrystalDiffract. CrystalMaker features an elegant and intuitive user interface. The corresponding TEM diffraction pattern and stereographic projection are shown in SingleCrystal (bottom right). VASP. SHELX. You wouldn’t control a train from inside a car. PDB. The crystal structure of Epidote. you’ll require CrystalMaker®: our flagship program for building. You can also import/export tables of element colours & radii. CrystalMaker can export data to a wide range of formats. including CIF. 34 Chapter 7: The CrystalMaker Office . and high-resolution output. without the need to save files. Structures Library CrystalMaker comes with a comprehensive library of over 600 fully-annotated files. OX5 1PF UK Voice: Fax: E-mail: Web site: +44 1865–854804 +44 1865–854805 sales@crystalmaker. You can fax your details to us.com/sales CrystalMaker lets you share your structural data with CrystalDiffract. founded by two former university lecturers. Direct selling means higher-quality software at a fair price! We accept orders in U.g. Animations and Video About Us CrystalMaker Software Ltd is an awardwinning company. as well as credit cards. Our company address is: CrystalMaker Software Ltd Centre for Innovation & Enterprise Oxford University Begbroke Science Park Woodstock Road Begbroke Oxfordshire. arrows. thanks to our SingleCrystal program. Our company’s research and development is supported by extensive international contacts and academic collaborations. including stunning 3D stereo graphics in colour (red/blue glasses included with the program)—with flexible annotation capabilities including lines. All graphics can be copied to the clipboard or exported to disc.com http://www. or order online. dollars. Euros or British Pounds Sterling. SingleCrystal has advanced stereographic projection capabilities: display poles and traces for lattice planes or vectors.com CrystalMaker is unique in providing automatic. We accept purchase orders from universities. with the option of showing symmetry-related planes.S. institutes or corporations (please fax or e-mail for fastest service). letting you compare images of real diffraction patterns with simulated patterns. with a choice of vector or pixel formats. You can easily build multi-structure/frame animations and output them as movies. ready for immediate display (and includes all the major rockforming minerals).crystalmaker. and load data: • Simply choose a command from one of CrystalMaker’s Diffraction sub-menus. Our mission is to improve the understanding of science. Single-Crystal Diffraction CrystalMaker can be extended to provide singlecrystal diffraction simulation and analysis. This reads from CrystalMaker binary files and from graphics files (e. textboxes and scalebars.. JPEG images). multi-currency online ordering system: http://www. using our new. Please refer to our web site for the latest pricing information. cross-platform QuickTime and VR output. photo-realistic graphics. with extensive customization. through the use of innovative computer software. Ideal for teaching and research! Diffraction Link Sales and Ordering Information We produce and sell our own software throughout the world.crystalmaker. and CrystalDiffract will generate a diffraction pattern.Spectacular Graphics CrystalMaker provides superb. or record your work using the Video Recorder palette. switch applications. Index A Angle-Dispersive Diffraction definition 12 parameter control 17 Arrow tool description 10 reference 31 Atomic Displacement Parameter 16 Atomic Scattering Factors 11 Axis Scaling Tools 32 E Editing Structural Data 16 Energy-Dispersive Diffraction definition 13 parameter control 17 Eta in Pseudo-Voigt function 15 Export Options 29 F Film Mode 25 B Background parameter control 18 Bragg Angle derivation of 4 for energy-dispersive diffraction G 12 Gaussian Function Graphics Pane description 7 Graph Mode 25 Gridlines 26 14 C Calculating Diffraction 11 Cloning Windows 28 Colour of graph 27 Crystalline Materials definition of 3 H Hand tool reference 31 I Identifying an Unknown Substance 22 Indexing a Pattern displaying peak labels 10 Instrument parameter control 17 Instrumental Broadening 15 D Data displaying diffraction data exporting 29 Delta Function 14 Diffraction angle-dispersive 12 energy-dispersive 13 time-of-flight 13 Distance Tool reference 31 D-Spacing Limit 12 20 L Licensing during installation 2 Line Width 27 Lorentzian Function 14 Index 35 . M Marker Size in Graph mode 27 Mixtures description 19 parameter control 18 Monochromatic Radiation P Parameters List description 7 examples of use 18 Particle Size Broadening 15 Patterns List 7. 32 Residual Function 22 36 Index . 29 Preferences file 2 Pressure simulating effects 18 Printing 30 Profile File 30 Pseudo-Voigt Function 15 12 N Neutron Diffraction angle-dispersive 13 scattering length data 11 time-of-flight 13 Neutron Scattering Length 11 O Observed Data 21 Opening a Crystal 7 R Radiation Type 11 Registration of licence 2 Relative Scaling of observed and calculated patterns 21. 23 deleting an entry 23 renaming a pattern 23 Peak Positions indicating with markers 26 overlaying 26 Peak-Shape Functions 14 Peak Widths instrumental broadening 15 particle size broadening 15 strain broadening 15 Personalize dialog 2 Phase Transitions simulating 18 Plot Range setting explicitly 9 Plot Settings 23 Plot Style in Graph mode 27 Portable Data Format (PDF) 30 Preferences 10. See Atomic Displacement Parameter Time-of-Flight Diffraction definition 13 parameter control 17 Toolbar description 7 reference 31 showing or hiding 31 Two Theta 12 Index 37 . See Particle Size Broadening Sorting diffraction data 20 Stacked Graphs 25 Strain Broadening 15 Structure Factors File 30 Superimpose peak markers 26 Synchronizing Windows 28 System Requirements for running CrystalMaker 1 U Unit Cell parameter control 18 Unmix Button 19 Updates automatic update checking 10 W Wavelength specifying 12 Windows cloning 28 synchronizing 28 X X-ray Diffraction angle dispersive 12 atomic scattering factors for 11 wavelength options 12 Z Zooming a Diffraction Pattern Zoom Tool reference 31 9 T Temperature simulating effects 18 Thermal Ellipsoids. 32 Simulation of a powder pattern 11 Single-Crystal Diffraction 34 Site Occupancies editing 16 parameter control 18 Size Effects.S Sales and Ordering 34 Sample parameter control 18 Saving Your Work in a session file 29 Scaling Commands 9 Scattering Factors editing 11 Scrolling a Diffraction Pattern 9 Session File 29 Shift Control 21. 38 . or registered trademarks of Microsoft Corporation. CrystalMaker® S O F T W A R E CrystalMaker Software Limited Centre for Innovation & Enterprise Oxford University Begbroke Science Park Woodstock Road. Microsoft.0 22 January 2007 5 November 2010 (last revised: 20 April 2012) updated for Mac version 5. express or implied. Begbroke. or transmitted. All Rights Reserved. CrystalMaker.0 20 January 2004 17 January 2005 2 January 2006 updated for Mac version 5. without the prior written permission of the copyright owner. any implied warranties of merchantability or fitness for a particular purpose. including without limitations. all of which are expressly disclaimed. Christian Baerlocher and Helge Stanjek First edition: Second edition: Third edition: Fourth edition: Fifth edition: Sixth edition: Seventh edition: Eighth edition: Ninth edition: 12 March 2000 7 November 2001 23 February 2002 updated for Mac version 4. Oxfordshire. Gordon Nord. CrystalMaker Software Ltd make no representations.com 39 . Windows and the Windows logo are trademarks. in combination with CrystalMaker software. Mac is a trademark of Apple. Inc.S.1 25 March 2006 updated for Windows version 1. stored in a retrieval system.2 & Windows version 1.com • http://www. CrystalDiffract and SingleCrystal are trademarks or registered trademarks of CrystalMaker Software Ltd. in any form. The main fonts used were Adobe Caslon Pro and Gill Sans.crystalmaker. using Adobe InDesign and Photoshop. and other countries. OX5 1PF. This User’s Guide was prepared on a Mac. with respect to this documentation or the software it describes.. registered in the U.4 Copyright © 1995–2012 CrystalMaker Software Ltd.1. UK Tel: +44 1865–854804 • Fax: +44 1865–854805 sales@crystalmaker. Special thanks to Charles Prewitt. No part of this manual may be reproduced. or by any means.CrystalDiffract®: An interactive diffraction program for Mac and Windows.A. Yoshitaka Matsushita. Oxfordshire. UK 1994 – 2012 18 Years of Innovation www.CrystalMaker® S O F T W A R E CrystalMaker Software Ltd Centre for Innovation & Enterprise Oxford University Begbroke Science Park Woodstock Road.com . OX5 1PF. Begbroke.crystalmaker.