CrystalDiffract User's Guide

CrystalDiffract
Interactive Powder Diffraction Software
Works with CrystalMaker: Interactive Crystal Structures Visualization
Users 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 Users 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 Users Guide.
Using this Guide

This Users Guide should provide a very comprehensive outline of the major program features. We dont 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 its 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 CrystalDiffracts 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 Users 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 Users Guide describes the program interface, followed by sections on simulating diffraction, how to put data into the programthen 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.
Interface Reference Convention

In the following chapters we refer to elements of the programs 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 Users Guide), neatly packaged within the application bundle. We would also recommend that you copy the Examples Files to your hard discpossibly 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, users 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.
What is CrystalDiffract?
CrystalDiffract is a program for understanding diffraction properties of crystals: specifically, where a powdered crystal sample (comprising millions of tiny crystallites) is exposed to a radiation beam, resulting in patterns of scattered intensity, which can be recorded as lines on a film, or as intensity peaks by a detector. CrystalDiffract differs from its sister program, SingleCrystal, which is designed to simulate diffraction patterns from a one, single crystal, when exposed to x-rays, neutrons or electrons. CrystalDiffract can simulate the key powder diffraction techniques used today, including traditional single (or dual-) wavelength X-ray and neutron scattering, plus newer white radiation (energy-dispersive) and time-of-flight techniques. CrystalDiffract lets you manipulate diffraction patterns in real time, changing sample and instrumental parameters such as peak widths, wavelength, particle size and strain. You can measure intensities and distances on screen, compare patterns from different materials in the same window, and simulate multi-phase mixtures. For the experimental scientist, CrystalDiffract lets you load observed data, for easy comparison with simulated data: an ideal way to characterize materials or interpret the results of synthesis experiments. Finally, CrystalDiffract lets you print your diffraction patterns, or export them in a range of data formats.
Crystalline Materials
The starting point for simulating a diffraction pattern is a crystal structure: the unique arrangement of atoms inside a basic building brick, or unit cell of material. Crystals typically contain billions of unit cells, neatly stacked in a threedimensional lattice.
A crystal structure is derived from a basic unit that is tiled in three dimensions to form an extended crystal lattice.
It is the very regularity of such structures that allows diffraction in the first place. The preciselyoriented planes of atoms, repeated almost ad infinitum, provide miniature diffraction gratings for X-ray or neutron radiation.
A tiny section through the crystal lattice of sodium chloride (halite, or rock salt). Here we see a regular arrangement of chlorine ions (green) and sodium ions (yellow). Chapter 1: Getting Started 3
Why use Powder Diffraction?

Powder diffraction has a number of advantages over single-crystal techniques. Sometimes it is difficult to find (or grow) good quality single crystals, whereas powders are much easier to manage. Single-crystal diffraction (using X-rays or neutrons) is quite an arduous process, requiring precise orientation of the sample (or, in the case of electron microscopy, specially-prepared, thin crystal flakes). Data collection tends to be very slow, as individual scattered beams are measured (although new, area detectors, are making this faster). With powder diffraction, one has the advantage of speed and convenience. A powdered sample has multiple crystallites and, assuming these are randomly distributed, at least one crystal will be oriented correctly to cause diffraction. Data collection times tend to be faster, since only a onedimensional pattern is being collected. The most-important powder diffraction techniqueswhich can be simulated by CrystalDiffractare described below.
Monochromatic Radiation
In most laboratory sources, X-rays are generated by firing a beam of electrons at a metal targetusually copper (Cu) or molybdenum (Mo). A characteristic X-ray spectrum is emitted, which is filtered, so that only the strongest, Cu Ka peak emerges (this is actually a doublet, comprising Ka1 and Ka2 peaks, although sometimes the weaker, Ka2 peak is also filtered out). This monochromatic radiation is then directed at the specimen. One typically moves the beam, relative to the sample, scanning through a range of angles, q. There is a reciprocal relationship between q, and inter-planar distances in the crystal (d-spacings), which give rise to diffraction peaks. This is summarized in the famous Bragg Equation: l = 2d sin q which provides the condition for coherent scattering of the radiation (wavelength l), directed at an angle q (the Bragg Angle) with respect to the d-spacing of a set of planes in the crystal.
Derivation of the Bragg Equation
1 2
N(hkl)
1 2
(hkl)
t t
Consider a crystal with a set of planes, (hkl), shown here in blue. The interplanar spacing is denoted by d, and the plane normal is N(hkl). If a beam of monochromatic radiation (wavelength l), shown here in red, strikes these planes at a glancing angle, q, then constructive interference between adjacent wavelets and occurs when their path difference (t + t) is equal to an integral number of wavelengths. Thus, hence, nl=2t n l = 2 d sin q where: t = d sin q (the Bragg Equation).
By measuring scattered intensity as a function of scattering angle, one is in effect measuring the scattering strengths of different sets of planes (with different d-spacings) inside the crystal. Ultimately, this scattering strength is controlled by the arrangements of atoms in different directions in the crystalsand hence one can learn something about the crystal structure from its diffraction properties.
Time-of-Flight Diffraction
Some diffraction experiments use pulses of neutrons with a range of energies. These travel at different speeds, depending on the energy of the neutrons, and are directed down a long beam line towards a powder sample. Diffraction is recorded by neutron detectors arranged around the sample, at a fixed two-theta angle (2q). 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). As for energy-dispersive diffraction, an extended diffraction pattern can be recorded at a fixed Bragg angle because the sample is subjected to neutrons of different energies, and hence wavelengths.
White Radiation
Many diffraction experiments are carried out at synchrotron sources. Here, charged particles are accelerated to relativistic speeds, and emit x-rays as they travel around a curved beam path. So-called White Radiation, comprising a broad spread of wavelengths, can be generated; this is useful in diffraction experiments because it allows rapid measurements, without the need to mechanically scan a detector over a range of angles. An energydispersive detector records the scattered intensities as a function of energy (and hence wavelength).
CrystalDiffract works with CrystalMaker (left) letting you visualize crystal structures and simulate their diffraction propertiesin various experimental modesin comparison with other patterns and observed data.
CrystalMaker Integration
If you would like to be able to build your own crystals which you can load into CrystalDiffract, you will require CrystalMaker: an award-winning program for building, displaying, manipulating and animating all kinds of crystal and molecular structures. CrystalMaker provides seamless display of data files from major databases and supports a wide variety of file formats. Just drag-and-drop a text file into CrystalMaker for automatic format detection and structure display. CrystalMaker lets you display a structure then, with a single menu command, see its diffraction pattern appear in CrystalDiffract.
Further information about CrystalMaker is given at the end of this guide, or you can visit crystalmaker.com and download a free Demonstration Version.
Although CrystalDiffract allows you to edit some aspects of a crystals structure (e.g., lattice parameters and site occupancies), it does not allow you to edit atomic coordinates or to build new structures. We believe that the best way to edit these structures is via a CrystalMaker: this allows you to actually see the structure, so you can check that the coordinates and/or symmetry settings are reasonable, before you proceed to generate diffraction patterns.
Chapter 2: CrystalDiffract Interface

This chapter provides a basic introduction to CrystalDiffracts user interface, including how to load a diffraction pattern and manipulate it.
Window Design
CrystalDiffract has a single-window program interface with a toolbar, and a Graphics pane for plotting your diffraction patterns. Additional panes are available for displaying lists of Patterns or Parameters.
Toolbar At the top of each window is a toolbar
Displaying a Diffraction Pattern

CrystalDiffract can read from three kinds of files: text files, crystal structure files, 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). Mac users can toggle the toolbar on or off by clicking the lozenge-shaped button, on the right-hand side of the windows titlebar.
Graphics Pane At the centre of the window
Do one of the following: Drag-and-drop a file onto the CrystalDiffract application icon; Launch CrystalDiffract, then drag-and-drop a file into the window that appears. In CrystalDiffract, choose File > Open then use the file dialog to specify the file(s) to be opened. Drag-and-drop a file into the Patterns List, then click the new entrys checkbox;
is the Graphics pane, where diffraction patterns are plotted. Below this is a scrollbar for moving through the x-axis range, and an Info Bar which displays cursor- or status information.
Parameters List This is a list of experimental-
and sample parameters, grouped into folder-like categories. You can edit parameters interactively, using a slider control, and observe how the diffraction pattern changes.
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. Drag-and-drop your file(s) into the window. Data will be added in the form of one or more new diffraction patterns.
of diffraction patterns. You can drag text files, CrystalMaker binary files and folders into this list. The corresponding patterns can be displayed in the Graphics pane by clicking checkboxes. Displayed patterns can be selected by clicking on their Patterns List entries. Selection allows you to edit individual patterns, and move them relative to the rest of the display. You can resize the Patterns List by clicking-anddragging the drawer edge (Mac) or the pane divider (Windows).
Crystal Files
You can simulate a diffraction pattern for a crystalline material, by supplying a CrystalMaker crystal file (file type CMDF, extension .cmdf or .crystal). CrystalDiffract will use structural data from the file to generate a diffraction pattern.
Please note that Demonstration Mode restricts you to reading only the latest CrystalMaker binary file format. However, the full-feature version can read from older files.
Toolbar
Graphics Pane
Parameters List
Info Bar
Patterns Drawer
The CrystalDiffract-for-Mac program interface, showing calculated and observed diffraction patterns
Patterns List Parameters Palette
The CrystalDiffract-for-Windows interface, showing diffraction patterns in Film mode 8 Chapter 2: CrystalDiffract Interface
Text Files
You can load an observed diffraction pattern, as a plain text file (file type TEXT, extension .txt or .dat). The file should contain an xy listing of your diffraction points (where the y value is the intensity), with one point per line.
Scrolling and Zooming

You can use the horizontal scroll bar to quickly scroll through a diffraction pattern. For finer control, choose the Hand tool from the toolbar then click and drag the pattern. You can adjust the range of x-axis values by using the Zoom tool to zoom in or out around a clicked point. To enter an explicit range, use the Plot > Plot Limits command.
Session Files
The third type of file that CrystalDiffract can read is its own session file format (filetype CRDF, extension .crdf or .crystaldiffract). A session file is a saved diffraction experiment, which represents a complete record of your work in a particular window, with one or more diffraction patterns, including structural data (for simulated patterns) and intensities.
Arrow
Hand
Zoom
Distance
CrystalDiffracts tool buttons
Scaling Commands
The Toolbar includes a number of scaling tools that can be used to adjust the x- and y-axis ranges. You can adjust the x- and y-axis scales, and auto-scale the y (intensity) axis, or both the x- and y-axes (the latter option attempts to fit the entire diffraction pattern range inside the Graphics pane).
auto-scale y
Sharing Data With CrystalMaker

You can also provide crystal structure data directly from within CrystalMaker, via that programs Transform > Powder Diffraction submenu. Simply view and edit your structure in CrystalMaker; choose the relevant menu command, and then observe the diffraction pattern in CrystalDiffract.
x-scale
y-scale
auto-scale x & y
CrystalDiffracts axis scaling tools
Use CrystalMaker to visualize (and verify!) the structure before you proceed to simulate its diffraction properties.
Measuring a Pattern
The Arrow tool allows you to measure points on the simulated diffraction pattern. Choose this tool from the Toolbar, then click in the Graphics pane so that a vertical cursor appears. Information about the current point is displayed in the Info Bar at the bottom of the window.
Printing
The full version of CrystalDiffract lets you print high-resolution diffraction patterns, which are scaled to fit your chosen page size.
Saving Preferences
CrystalDiffract uses default settings for the window size, diffraction mode, plot styles, etc. Although you can edit these for individual windows, the default settings are used whenever a new window is created, or when you start up the program. You can view and edit the current program settings using a tabbed preferences dialog. To display this, choose the Preferences menu command. When you have finished making your changes, click the dialogs Save button; your settings will then be available for any new windows, and are saved in a preferences file, ready for your next session. To restore the programs Factory settings, click the dialogs Restore Factory Settings button. To apply any saved preferences to the current window, use the Apply Preferences menu command.
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, the mouse pointer changes to a double arrow ( ) to indicate that dragging is possible).
Indexing a Pattern
You can display peak labels for a selected diffraction pattern using the Pattern menu. Labels can contain any combination of Miller Indices, d-spacings, x-values, and so on. The Peak Threshold setting defines a minimum intensity value, below which no labels will be displayed This is useful for complex diffraction patterns which may have many low-intensity peaks.
Help and Updates

Most controls have tool tips associated with them. For detailed help, choose the Help > CrystalDiffract Help command. Help files are displayed in a Help Viewer application (Mac) or window (Windows). We also include a number of support topics on our website, and links to these are included on the programs Help menu.
Output
CrystalDiffract provides a range of data output options, via the File > Export submenu. These include exporting a complete diffraction pattern, at user-defined resolution; a diffraction data report (Miller indices, d-spacings, intensities, multiplicities, etc.), or a table of Structure Factors. You can also save a diffraction experiment as a selfcontained Session File, you can print, and you can record your favourite settings in a Preferences file.
Checking for Updates

We regularly provide free, incremental program updates. These include new features, interface enhancements and occasional bug fixes. You can check whether an update is available using the Help > Check for Update command. There is also an option to let the program check for updates automatically (Help > Check for Updates Automatically); the program will check at weekly intervals, and alert you if a newer version of the software is available. You can then download this from our website.
10 Chapter 2: CrystalDiffract Interface
Chapter 3: Simulating Diffraction

The Diffract menu lets you alter aspects of a virtual diffraction experiment, such as the radiation type, the experiment type (angle- or energy-dispersive), and various instrumental parameters.
Calculating the Pattern

CrystalDiffract calculates diffraction patterns using the types, and positions, of atoms in a unit cell of a crystal. The program assumes an ideal structure (although you can specify an isotropic strain). Site occupancy data and atomic displacement parameters are used to determine the amount of scattering from each site. CrystalDiffract uses atomic scattering factors (x-ray diffraction) or neutron scattering lengths for the atoms in your structure.
You can edit the ASF.dat data file if you wish to modify or add new data. The format is very simple. Each data line should contain: a two-character element symbol (which CrystalDiffract will match with element symbols in your structure); 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; one number, corresponding to the coherent nuclear scattering length for that element.
Editing Scattering Factor Data

CrystalDiffract uses a table of atomic scattering factors and neutron scattering lengths, saved as a text file called ASF.dat. CrystalDiffract-for-Mac saves the ASF.dat file inside the application bundle. To view the contents of the application package, control-click on the CrystalDiffract program icon and choose the Show Package Contents command from the popup menu that appears.
The data file can also contain comments: these should be prefaced by an exclamation mark !.
Note: the ASF.dat file must be a text-only file with file type TEXT. If you edit the file in a word processor, you should ensure that it is saved in a text-only format.
Locating the package contents
CrystalDiffract-for-Windows has the ASF.dat file saved in the Application Data folder.
Chapter 3: Simulating Diffraction 11
Simulation Preferences
To speed up the simulation of diffraction data (e.g., for massive structures such as proteins), you can suppress all reflexions below a minimum d-spacing. You can also limit the maximum number of reflexions (so that only those with the highest d-spacings are used).
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. The diffraction pattern is recalculated, using x-ray scattering factors or neutron scattering lengths that are stored with the program.
Diffraction Modes
CrystalDiffract can simulate a number of experimental types, which cover the main techniques for powder diffraction:
(Mac), or Edit > Preferences (Windows).

2 Navigate to the Profile tab.
2 In the Generate Reflexions group, set the
Angle-Dispersive Diffraction
Traditional laboratory diffractometers operate using constant radiation wavelength, with diffraction measured as a function of Bragg Angle (theta, q). This is called angle-dispersive diffraction. CrystalDiffract allows you to simulate angledispersive diffraction, plotting diffracted intensity as a function of: 2q, d-spacing, or reciprocal d-spacing. You can specify the wavelength using the Diffract > Wavelength command.
Minimum d-spacing field, enable the Limit number to option and enter a maximum number
of reflexions.
3 Click the Save button to store your new settings.
These will apply to any new windows.
The Profile pane of the Preferences dialog

Tip: If you have edited your Preferences and wish to apply the changes to an existing window, choose the Apply Preferences command, available from the CrystalDiffract menu (Mac) or the Edit menu (Windows).
The Wavelength sheet showing CuKa1 and Ka2 radiation
The Wavelength sheet lets you specify monochromatic (single-wavelength), or dualwavelength radiation. Traditional laboratory x-ray tubes typically maximise intensity by emitting dual wavelengths, e.g., Cu Ka1 and Ka2 lines.
12 Chapter 3: Simulating Diffraction
Energy-Dispersive (EDS) Diffraction

A relatively-new type of diffraction involves using white radiation that has a spread of wavelengths. The Bragg equation relates wavelength (l) to the d-spacing of a set of lattice planes, and the Bragg Angle (q):l = 2d sin q If l can be varied, then diffraction from a range of d-spacings can be recorded at the same q angle. It is therefore not necessary to mechanically scan a detector through a range of q/2q angles. However, in order to resolve diffraction from different d-spacings, the stationary detector must be able to discriminate between scattered radiation of different wavelengths. Since the wavelength of radiation is related to its energy, an energy-dispersive detector can be used to record an extended diffraction pattern as a function of energy. You can specify a 2q value for this experiment, using the Diffract > Energy command.
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. These travel at different speeds, depending on the energy of the neutrons, and are directed down a long beam line towards a powder sample. Diffraction is recorded by neutron detectors arranged around the sample, at a fixed two-theta angle (2q). The number of pulses is recorded as a function of the time-of-flight, t, of the neutrons (which is typically in the range of a few milliseconds to several hundred milliseconds). As for energy-dispersive diffraction, an extended diffraction pattern can be recorded at a fixed Bragg angle because the sample is subjected to neutrons of different energies, and hence wavelengths. We can analyse the time-of-flight process by combining De Broglies hypothesis, l = h / mn vn
The ISIS neutron spallation source at the Rutherford-Appleton Laboratory, near Oxford, England. Neutrons are directed along beam lines, arranged radially, around the target (the curved light-blue chamber in the centre of the photo). Time-offlight diffraction is used at one such beam line, the High-Resolution Powder Diffractometer (HRPD). Chapter 3: Simulating Diffraction 13
(where h is Plancks constant, mn is the neutron mass and vn is its velocity) with Braggs Law, thus: l = h / mn vn = 2 d sin q Now, given a primary flightpath (the distance from the moderator to the sample) of L1 and a secondary flight path (sample to detector) of L2, and corresponding times of flight t1 and t2, we have: vn = (L1 + L2) / (t1 + t2) = L / t where L is the total flight path and t is the total time-of-flight. thus, h t / mn L = 2 d sin q hence: t = 2 d L (mn/h) sin q Thus, we have a linear relationship between the total time-of-flight, t, and the overall flight path, L. This is why the highest-resolution neutron diffractometers have the longest flight paths (e.g., ~100m at the HRPD instrument in the Rutherford-Appleton Laboratory). CrystalDiffract lets you specify the overall flight path, L, as well as the two theta value for the diffraction experiment, using the Diffract > Time-of-Flight command.
Peak-Shape Functions
In an ideal diffraction experiment, the shape of a diffraction peak would be determined solely by the sample, reflecting its mean particle size, particle shape and structural state (including strain). In practise, for most samples the shape of diffraction peaks is mainly determined by the diffraction technique and geometry. For example, neutron diffraction experiments tend to result in peaks with a Gaussian shape, whilst synchrotron diffraction may result in a Pseudo-Voigt peak shape. CrystalDiffracts Diffract menu lets you choose between different shape functions: Delta Function Lorentzian Gaussian
The Delta Function is simply a spike of zero width. This provides a very quick way of showing the positions of many peaks in a complex pattern. The Lorentzian function has a distinctive splayed appearance: peaks having very wide tails, like the mouth of a trumpet. The Gaussian function is shaped like the profile of a church bell, with a more rounded appearance
Pseudo-Voigt
Gaussian (top) and Lorentzian (bottom) profiles for the same diffraction peak. Notice the lower peak maximum for the Lorentzian profile, with its intensity distribution spread over a wide range of x values. 14 Chapter 3: Simulating Diffraction
than the Lorentzian function, and with less extensive tails. Finally, the Pseudo-Voigt function is a mix between the Gaussian and Lorentzian functions. It is characterized by a mixing parameter, Eta, 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 entering a new value in the sheet or dialog that appears.
Peak Widths
The limited resolution of a diffraction experiment may result in diffraction peaks that are substantially broadened. For most practical experiments, this instrumental broadening is the major contribution to the widths of observed diffraction peaks. CrystalDiffract lets you specify the amount of instrument broadening, in terms of the full width at half-maximum for a diffraction peak. (The units depend on the current choice of x-axis: two-theta, d-spacing, reciprocal-d, energy in keV, or time-offlight in milliseconds.)
Particle Size Broadening

The width of a diffraction peak also depends on crystal size. This is a reciprocal relationship, so for large crystals there is very little peak broadening, but for very small crystals (fractions of a micron in diameter), diffraction peaks can become noticeably broadened. In a powder sample, we normally refer to a mean particle size, and this can be simulated using the Diffract > Particle Size command.
Strain Broadening
A strained crystal can be thought of as containing regions with slightly different unit cell dimensions. In fact, there is likely to be a continuous spread of unit cell dimensions throughout the sample, resulting in a diffraction pattern with a slightly blurred appearance. The amount of strain in the sample can be summarized by a percent strain. 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, whereas in a strained crystal there might be a normal distribution of cell parameter values, characterized by a standard deviation, ranging from zero for the ideal crystal to a few percent for a very-highly strained crystal). Use the Diffract > Percent Strain command to specify a value for the strain.
Editing Structural Data

CrystalDiffract lets you edit aspects of a selected patterns underlying crystals structure, so you can determine how this affects diffraction. You can edit lattice parameters and site occupanciesand also omit sites from the diffraction calculation.
The remaining fields cannot be edited. They show the atoms fractional coordinates (xyz) and, if available, the atomic displacement parameter data (anisotropic values and isotropic values). To view the atomic displacement parameters, you may need to resize the sheet, by clicking and dragging its size box. Alternatively, use the horizontal scrollbar to show the atomic displacement parameter fields, as the example opposite shows. You can sort your data by clicking on a column header. Click again to reverse the sort order. You can also move columns, by clicking-and-dragging their column headers. When you have finished your editing session, click the OK button to replot the diffraction pattern.
Tip: You can visualize atomic displacement parameters as thermal ellipsoids, using recent versions of CrystalMaker.
Edit Crystal Sheet

Choose the Edit > Crystal command to display the Edit Crystal window. Lattice parameters are shown at the top, with a scrolling list beneath, showing all sites in the crystals asymmetric unit. Each site row has a checkbox, which defines whether or not that site will be included in the intensity calculation. You could, for instance, decide to turn off certain sites, so as to determine their influence on the final diffraction pattern. You can edit site occupancies by typing a formula into the Site Occupancy field. You can enter up to three element symbols and their corresponding occupancies. The total occupancy must not exceed 1.0. For example, you might enter something like:
Si 0.7 Al 0.3
or:
Ca 0.56 Mg 0.41 Al 0.03
The Edit Crystal sheet can be resized horizontally and vertically, in order to show a range of sites and their atomic displacement parameter data (Uij and Uiso)
Interactive Parameter Control

The Edit Crystal window lets you change multiple site occupancies and/or cell parameters, with the diffraction pattern subsequently recalculated. A more interactive way of editing the structure is to use the Parameters List to gradually change one structural variable (e.g., unit cell angle) whilst the diffraction pattern is replotted in real time. To show the Parameters List, click the Toolbars Parameters button:
Energy Dispersive
If you have chosen an energy-dispersive simulation mode, then you can interactively change the two-theta angle for your sample/detector geometry.
Time-of-Flight
For neutron diffraction, in the time-of-flight simulation mode, you can interactively change the two-theta angle (for the sample/detector geometry) and the overall neutron flight path length.
Instrument
Alternatively, choose: Window > Show Parameters List; or (with the Graphics pane focussed) press the p key on your keyboard.
Parameter Groups
The Parameters List contains a series of hierarchical entries, each with its own disclosure triangle, 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), the Eta parameterwhich controls the peak shape, if a pseudo-Voigt profile has been chosenand the zero correction. If you are working with observed data, then you can also adjust the relative scaling (Scale Factor) between observed and calculated datasets. For example, if you have an observed dataset whose intensity range is from zero to 1000, and your calculated pattern has intensities from zero to 1, then you would want to scale your observed pattern by a factor of 0.001.
This lets you interactively change the wavelength for a traditional, angle-dispersive (monochromatic radiation) experiments.
Using the Parameters List to simulate an orthorhombic distortion (red pattern) in a previously-tetragonal crystal (blue pattern). The distortion (a b) has caused peak splitting (e.g., 400 and 040). Clicking and dragging the slider thumb continually changes the highlighted variable (the b cell edge length) and replots the diffraction pattern in real time.
Background
Using the Parameters List

You can open (expand) a hierarchical entry by clicking it, or its disclosure triangle. Individual Parameter entries can then be selected with the mouse, which causes a slider bar and a text edit field to appear below the list, allowing you to edit that items value. (When editing the text, press the Enter or Return keys to replot the structure.)
Local and Global Parameters
CrystalDiffract lets you apply a basic background function to your calculated patterns. This function has the form: A + Bx + C/x. The individual parameters, A, B and C, can be adjusted interactively.
Sample
The full-feature version of CrystalDiffract lets you simulate the effect of Particle Size and (isotropic) strain.
Mixture
If you have a multi-phase mixture (of calculated patterns), you can adjust their relative proportions using the Mixture group (this is discussed more in the next section).
Unit Cell
Some Parameter entries are shown on a pink background. These are local parameters, which relate to the currently-selected pattern, or patterns. Examples include unit cell parameters and site occupancies. Parameter entries shown on a grey background are global parameters, which affect all patterns, regardless of selection status. Examples include wavelength and peak width.
You can interactively edit the unit cell parameters (edge lengths, a, b, c; angles a, b, g) for a selected calculated pattern, using this group. Please note that CrystalDiffract does not perform an energy minimizations of the structure; one is simply deforming the unit cell, whilst keeping atoms in their existing sites, as defined by their fractional coordinates. Nevertheless, this is a useful range of settings when assessing the effect of a phase transition on the diffraction properties.
Site Occupancies
Possible Applications
The Parameters List is designed to be educational as well as functional. Here are some possible uses: Simulating structural phase transitions (e.g., cubic tetragonal orthorhombic) by changing cell parameters and watching how diffraction peaks split. Simulating the effect of pressure and temperature by changing the unit cell volume (isotropic expansion/compression is assumed). Visualizing the influence of one site occupancy on the final diffraction pattern, by dragging its site occupancy slider from 1 to 0. Changing the composition of a mixture by varying the proportions of individual phases, perhaps to match an observed diffraction patternand hence to determine its approximate composition. Understanding how mean particle size and/or sample strain affects the diffraction pattern. Fine-tuning a calculated diffraction pattern to match an observed pattern, e.g., by changing Peak Width, Eta value, Zero Error, etc.
If a calculated pattern is selected, then you can interactively adjust the occupancies of its individual sites, using this group. If a particular site is disordered (e.g., has a mixed occupancy such as Al0.5Si0.5) then the individual occupants are listed on separate lines. Please note that, as with the Unit Cell adjustments, CrystalDiffract does not optimize the structure following any of these adjustments. However, it does let you assess the chemical contribution to peak intensities.
Mixtures
CrystalDiffract allows you to simulate mixtures with unlimited numbers of components, simply using the existing patterns in your diffraction window. You can create the mixture by turning on mixture mode. To do this, use the Plot > Mixture command, or click the Toolbars Mix button.
To remove phases from a mixture, turn off the corresponding checkboxes in the Structures list.
Tip: The Structures lists Actions menu has an Equalize Phase Proportions command, which allows you to reset all volume fractions to equal values, with their sum total equal to 1.
When in Mixture mode, you can continue to edit structural data for individually-selected diffraction patterns, just as you might do in Separates mode.
Mixture Plot Settings

Toolbar Mix (left) and Unmix (right) buttons
In Mixture mode, all calculated diffraction patterns are combined into a single, calculated mixture. Similarly, any observed diffraction patterns are combined into a single, observed mixture.
In Mixture mode, you can edit the plot settings, including line style, width, colour and so on provided that at least one pattern in your mixture is selected. If both a calculated and observed mixture are displayed in the same window, you should carefully check that the appropriate pattern is selected (e.g., a calculated pattern, for the calculated mixture) to ensure that the plot settings are applied to the correct mixture. You can choose to apply labels to diffraction peaks in the mixture, in the same way that labels are applied for individual patterns. Select the patterns that you wish to label (e.g., by clicking on their entries in the Strucures list), then choose the Pattern > Show Labels command. All peak labels are colour-coded by component.
Editing Mixtures
You can edit the relative phase proportions for calculated mixtures, using the Mixture settings in the Parameters List. All calculated patterns are listed, and you can adjust the volume fractions for each component; as you do this, the volume fractions for the remaining components are automatically updated, to ensure that the overall sum of components is fixed, at 1.
Undoing a Mixture
You can unmix a mixture, and restore the display to separate diffraction patterns, using the Plot > Separate command, or by clicking the Toolbars Unmix button.
Editing the volume fraction of Silicon in a simulated three-phase mixture
Viewing Diffraction Data

You can quickly view a tabulated listing of diffraction data, using the Edit > Diffraction Data command:
The Edit Diffraction Data window
The resulting window lets you sort data, according to your chosen parameter (e.g., d-spacing or intensity). You can opt to save the sorted listing as a text file, by clicking the Save button.
Chapter 4: Working with Patterns

CrystalDiffract allows you to mix multiple simulated diffraction patterns in the same window. You can combine these with real, experimentally-observed data: useful for characterizing samples, synthesis results, checking for impurities, and even basic phase identification. You can control how individual patterns are plotted using the Plot and Pattern menus, with choice of plot type, styles, colours, line widths, markers, labels, etc.
Working with Observed Data

The full-feature version of CrystalDiffract lets you load one or more text files in any window. These could contain real, observed data, and you can display these will simulated (calculated) diffraction patterns for easy characterization.
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, then choose the relevant commands from the Pattern menu.
Loading Observed Data

Observed datasets should be saved in plain-text files. The first line of the file should contain a title (this is ignored by CrystalDiffract). Subsequent lines should contain pairs of xy valueswith one datapoint per line, for example:
Title line plus xy data 10.00 23.45 10.10 23.44 10.20 22.95 10.30 24.56 10.40 27.87
Note: If you are using the Mac version, it is important to check that the data file is a Mac file, with filetype TEXT.
Observed & Calculated Data Compared

When you append an observed data file to a window that already contains calculated data, CrystalDiffract changes the relative scale setting for the observed data in order to best match the two patterns. You can manually control the relative scaling for a selected observed pattern, using the two y-scaling buttons on the toolbar:
The Toolbars 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, or: Drag the files into the Graphics pane, or Drag the files into the Patterns List, then turn on their checkboxes.
It is possible to reposition a selected pattern (calculated or observed), by introducing x and/ or y offsets. You can use the Shift arrows on the toolbar to do this. Any offsets can be reset to zero by clicking the small round button at the centre of the arrows:
The Toolbars Shift controls
You can also use the Arrow tool to click and drag a diffraction pattern, when plotted in Graph mode.
Chapter 4: Working with Patterns 21
Observed and calculated time-of-flight neutron diffraction patterns (top graph). The observed data are plotted as crosses, with calculated data plotted using a smooth line. 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. This is controlled via the Plot > Show Residual or Plot > Hide Residual commands. 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. You can load the observed diffraction pattern, then add a sequence of CrystalMaker binary files (File > Open in Same Window), until a good match is found. A more convenient way of comparing phases is to use the Patterns List, which is described next.
(obs - calc)2
This value corresponds only to the currentlydisplayed plot range. It can be a useful reference when attempting to fine-tune the calculated data in order to match the observed data. The Plot > Data Style submenu allows you to choose how the observed data are plotted (e.g., crosses, squares, lines between points, etc.).
22 Chapter 4: Working with Patterns
Managing Multiple Patterns

The Patterns List lets you keep track of your observed and calculated diffraction patterns. New patterns are automatically added to this list when you load them from crystal files, observed data filesor when you open a previously-saved session. You can use the Patterns List to select individual patterns, show or hide them (in the Graphics pane), rename them, duplicate them, or simply to browse individual patterns from a large list.
To Display the Patterns List:
To rename a pattern: 1 Select the pattern in the list. 2 Press the Return or Enter keys on your
keyboard (or click on the selected name).
3 When you have finished editing, press Return
or Enter to finish, or click outside the selected row. (To cancel an edit, press the Escape key.)
To delete one or more patterns: 1 Select the relevant entries in the list. 2 Press the Delete key on your keyboard. To change the colour of a plotted pattern:
Do one of the following: Click the Patterns icon in the Toolbar, or Press the s key on your keyboard, or
Patterns List.
Choose the menu command: Window > Show
The Patterns list may be displayed as either a slide-out drawer (Mac), or as a window pane (Windows).
Click on the patterns colour swatch (on the right-hand side of the Pattern List) and choose a new colour from the popup menu. For more colour choices, choose the Other... command from the bottom of the menu.
Comparing Diffraction Patterns

The Patterns list really comes into its own when comparing an observed diffraction pattern with a number of calculated patterns. Having decided on a number of possible candidates to match the observed data, drag and drop their CrystalMaker binary files into the Patterns list. You can then quickly compare each diffraction pattern with the observed data by turning its checkbox on or off.
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 foldersperhaps your entire CrystalMaker Structures Libraryinto the list. Individual patterns can be selected, and the list supports standard editing conventions, such as multiple selections (shift- and command-clicking).
To plot one or more patterns:
Do one of the following: Select one or more pattern(s) to be plotted or hidden, then choose the Plot or Hide commands from the Patterns List Actions menu. Check or uncheck the patterns checkbox.
Hold down the option/alt key and click a patterns checkbox.
Any plotted patterns will be hidden, and only your clicked pattern plotted. Plot Settings
Working with multiple patterns in the same window, using the Patterns List. Here, one items name is being edited.
General Plot Settings

The Plot menu lets you change the general way in which all diffraction patterns are displayed. You can also customize aspects of the Graphics pane display, including the plot range, gridlines and colours, and so on. For specific adjustments to individual diffaction patterns, use the Pattern menu.
Stacked Graphs
In Graph mode you can use the Plot > Stack command to stack multiple diffraction patterns without danger of overlap. You can undo the stacking by choosing: Plot > Collapse.
Film or Graph
You can choose to plot your diffraction pattern as a graph of intensity versus x-value, or you can opt to display a greyscale representation which resembles a traditional photographic x-ray film. Film mode is particularly useful when comparing multiple diffraction patterns: these are then stacked, making it easy to compare positions and intensities of diffraction lines.
Stacked graphs showing how the diffraction pattern of a crystal changes with temperature, and the progress of a displacive phase transition.
Comparing calculated and observed data in Film mode. The central diffraction pattern corresponds to observed data for a mixture of analcime and silicon; the ideal calculated patterns for Silicon and Analcime are displayed above and below.
Overlaying Peak Positions

For a complex diffraction pattern there may be many overlapping peaks. The Plot > Overlay Peak Positions submenu allows you to identify the positions of individual diffraction peaks. You can superimpose a series of peak markers showing the peak centres, and their relative intensities. Alternatively, you can overlay the actual profiles of individual peaks, in a choice of plot styles: solid lines, dashed lines or a solid fill profile.
Individual Pattern Settings

The Pattern menu provides a series of commands which act upon any currently selected diffraction patterns. You can change plot colours, graph attributes, such as line styles and widths, marker sizesand control the labelling of diffraction patterns.
Labelling Peaks
The Pattern menu gives you various options for labelling the peaks of selected diffraction patterns. Labels can contain any combination of: Phase name Miller Indices (hkl) D-spacings x-axis values
Alternatively, you can opt for blank labels, where only arrows are plotted.
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, as illustrated above.
Tweaks
You can display gridlines in the diffraction window: thin lines marking the major x- and y-axis values; the colour of the gridlines is set using the Plot > Grid Colour command. You can also show or hide a legend, which acts as a key for the observed and calculated data, and for mixtures, the legend lists all phases and their proportions.
Strong peaks labelled with Miller Indices. Individual peak profiles are shown by the dotted lines. Notice that only the strongest peaks are labelled in this example.
To turn labels on: 1 Select the pattern(s) you wish to label. 2 Choose: Pattern > Show Labels. To specify the label type: 1 Select the pattern(s) whose labels you wish to
Graph Settings
In Graph mode, you have extensive control over the appearance of all diffraction patterns. You can edit individual patterns by selecting them (individually, or collectively), and then applying settings from the Pattern menu.
modify.
2 Choose one or more settings from the Pattern

> Label Style
submenu.
(Note: The label text, and peak arrow, are drawn in the same colour as the host diffraction pattern.)
Controlling the Extent of Labelling
In order to prevent the diffraction pattern from becoming too cluttered, you can suppress annotation for weak peaks. The Pattern > Label Threshold submenu lets you specify the minimum relative intensity for which annotation should be used.
Examples of different plot and marker styles. From bottom: solid; translucent; thick solid line; thin dashed line; lines with dots; crosses. Plot Style Data can be plotted using lines
between points (with a choice of smooth or dashed lines), or as individual markers (with a choice of marker styles, such as dots, squares and crosses) or you can choose a combination of lines and markers.
Marker Size You can specify an explicit marker
size, in pixels, or opt for an Auto setting, in which CrystalDiffract scales the marker size depending on the plot size and resolution.
Line Width You can specify an explicit line
width (in pixels), or opt for an Auto setting. different diffraction patterns.
Plot Colour You can apply different colours to

Tip: You can also edit plot colours using the Patterns List. Popup menus adjacent to each (plotted) entry let you quickly choose one of a number of preset colours.
Customizing your Workspace

CrystalDiffract lets you open as many windows as memory permits. On the Mac version, you can arrange multiple windows neatly on screen: either stacked on on top of each other, with small offsets between adjacent windows, or tiled down the screenusing the Window menus Stack and Tile commands, respectively.
Cloning Windows (Mac)

You can clone a window, in order to preserve the original data, and give you free rein to experiment with new settingsmaybe editing the structure and then wishing to compare the new diffraction pattern with the old diffraction pattern. Ensure that the window to be cloned is the frontmost diffraction window, then choose the Window > Clone Window command.
Synchronizing Windows (Mac)

When comparing different structures in different windows you can use the Window> Synchronize command to adjust every windows settings to match those of the current (uppermost) window. For example, the radiation type, x-axis range, y-scale, peak widths and so on, are all reset to your current settings.
Chapter 5: Printing & Saving

CrystalDiffract uses high-quality graphics for its on-screen drawing, and this also provides high-resolution printed output. When you have finished, you can save your diffraction experiment in a single file, ready for immediate display next time you use the program.
Saving Your Work

CrystalDiffract allows you to save a windows diffraction experiment in a self-contained session file. This retains the window size and layout, your plot settings and all data required to plot the displayed diffraction patterns.
A tabbed dialog shows the currently-active settings; any changes you make are saved in your preferences file, and used for any new windows (existing windows retain their own settings). You can also opt to restore the original, factory settings. If you wish to apply your changed preferences to any existing windows, use the Apply Preferences command, which is available from the CrystalDiffract menu (Mac) or the Edit menu (Windows). This command will replot your current patterns, using the new, default settings. Your plot range, wavelength, diffraction mode, etc., will all be reset to match your default settings.
Saving Preferences
CrystalDiffract uses default settings which you can inspect, edit, and save, with the Preferences command.
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), with their intensities, hkl values, d-spacings and multiplicities.
The Preferences dialog.
Tip: You can quickly view and sort these diffraction data on screen, by choosing: Edit > Diffraction Data.
Part of a Diffraction Data file for spinel.
ref no. [ [ [ [ [ [ [ [ [ [ [ [ 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) 4.66499 2.85671 2.43621 2.33250 2.02000 1.85368 1.64932 1.55500 1.42836 1.36577 1.34667 1.27756
2-Theta 19.0076 31.2843 36.8626 38.5650 44.8299 49.1048 55.6807 59.3842 65.2661 68.6613 69.7751 74.1568
Intensity 1.14849e-02 1.15645e-02 3.58979e-02 4.44064e-04 2.11695e-02 2.96662e-05 3.44335e-03 1.75771e-02 2.82416e-02 1.29683e-03 5.47933e-05 1.12600e-03
I/Imax 32.0 32.2 100.0 1.2 59.0 0.1 9.6 49.0 78.7 3.6 0.2 3.1
m(hkl) 8 12 24 8 6 24 24 32 12 48 24 24
Chapter 5: Printing & Saving 29
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, as the reflexions have not been combined into a onedimensional powder pattern). The intensities and the real- and imaginary parts of the structure factor are included. Data are sorted in order of decreasing d-spacing.
Profile This file is a tab-delimited listing of xy
If multiple diffraction patterns are displayed in the same window, then the exported file contains multiple columns, corresponding to the y-data for all selected diffraction patterns. So, for example, if three patterns, A, B and C were selected, then each row of the exported profile would contain four values: x yA yB yC. This simple file format can easily be imported into many graph plotting programs or spreadsheets, making it a great way of exporting high-resolution diffraction profiles.
data points, corresponding to the x-range currently displayed. You can specify the step between adjacent x-axis values, allowing high-resolution output.
x Spinel 18.50000 18.55000 18.60000 18.65000 18.70000 18.75000 18.80000 18.85000 18.90000 18.95000 19.00000 19.05000 19.10000 19.15000 19.20000 19.25000 19.30000 19.35000 19.40000 19.45000 - MgAl2O4 0.00000e+00 0.00000e+00 0.00000e+00 2.94836e-14 9.62476e-11 7.98450e-08 1.74030e-05 1.01539e-03 1.62704e-02 7.37977e-02 1.07549e-01 3.72673e-02 4.09937e-03 1.25509e-04 1.03963e-06 2.27941e-09 1.30270e-12 0.00000e+00 0.00000e+00 0.00000e+00
Printing
The full-feature version of CrystalDiffract will print the contents of the current window at the highest-possible resolution, as determined by your printers resolution and the available memory. If you find that line widths and/or marker sizes are too small, choose larger sizes from the Pattern > Line Width and Marker Size submenus.
Saving a PDF File (Mac)

CrystalDiffract for Mac takes advantage of a built-in system feature: the ability to print to a PDF file. When you choose the Print command, the resulting Print sheet has a PDF button which, when gives the option of exporting a PDF graphics file containing your diffraction pattern, scaled to fit the current page size.
Part of a Profile output file for spinel.
Part of a Structure Factor output file for spinel.
ref no. [ 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) 4.6650 4.6650 4.6650 4.6650 4.6650 4.6650 4.6650 4.6650 4.0400 4.0400 4.0400 4.0400 4.0400
2-Theta 19.008 19.008 19.008 19.008 19.008 19.008 19.008 19.008 21.982 21.982 21.982 21.982 21.982
Lp 35.22 35.22 35.22 35.22 35.22 35.22 35.22 35.22 26.06 26.06 26.06 26.06 26.06
F(Re) -55.70 -55.70 -55.70 -55.70 -55.70 -55.70 55.70 55.70 -0.00 -0.00 -0.00 -0.00 -0.00
F(Im) 0.00 -0.00 -0.00 0.00 -0.00 0.00 -0.00 0.00 -0.00 0.00 -0.00 -0.00 0.00
Intensity 3.99490e+02 3.99490e+02 3.99490e+02 3.99490e+02 3.99490e+02 3.99490e+02 3.99490e+02 3.99490e+02 3.61257e-11 3.67034e-11 3.67034e-11 3.53770e-11 3.61257e-11
30 Chapter 5: Printing & Saving
Chapter 6: Toolbar Reference

Each CrystalDiffract window has a horizontal toolbar at the top, which allows you to choose specific tools for manipulating or measuring a diffraction pattern, and adjust the scaling settings. This chapter summarizes the various toolbar buttons or icons.
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 windows Toolbar by clicking the lozenge-shaped button on the top right-hand side of the title bar. You can also save your toolbar preference, with the Preferences dialog.
can then drag the cursor with the mouse. As you move the cursor over a diffraction pattern, information about that pattern is displayed in the Info bar. The Arrow tool also lets you click-and-drag a diffraction profile (graph), thereby changing its xand y-axis offsets.
Hand (h) This tool lets you scroll the diffraction
Tools
There are four tool buttons, located on the left-hand side of the toolbar. Only one tool can be selected at any time, and the mouse cursor changes according to the currently-active tool. You can select a tool either by clicking its tool button, or if the Graphics pane is focussed (e.g., you recently clicked in it with the mouse), you can choose a tool by by pressing the appropriate letter on your keyboard (shown in parentheses, below).
pattern: you can click-and-drag the graphics pane, moving the diffraction display to the left- or the right. This is a more precise way of repositioning the profile than using the horizontal scroll bar.
Zoom (z) This magnify tool allows you to zoom
in on a clicked point in the diffraction pattern. To zoom out, hold down the option or shift keys on your keyboard as you click with this tool.
Distance (d) The distance (measurement) tool
Arrow (a)
Hand (h)
Zoom (z)
Distance (d)
CrystalDiffracts tool buttons Arrow (a) The Arrow tool lets you measure data
in the diffraction window, using a vertical cursor. Click once in the Graphics pane to display the cursor or to move the cursor to a new location; you
has two functions: a measurement tool, and a zoom tool. To measure the distance between two points on a diffraction pattern, click in the Graphics window where you want to begin measuring, then click where you want to stop. The region between the two points is shown highlighted, and the horizontal distance is printed in the Info bar. A Zoom button also appears: clicking this expands the scale so that the highlighted region fills the window.
Chapter 6: Toolbar Reference 31
Axis Scaling Tools

auto-scale y
Other Controls
Show/Hide Parameters (p) Clicking this icon
x-scale
y-scale
auto-scale x & y
CrystalDiffracts axis scaling tools
will show or hide the Parameters list, inside the current window. Showing the Parameters list causes the Graphics pane to shrink, so if you have a small screen you may wish to keep the list hidden until you need to use it.
Show/Hide Patterns (s) This icon (which
CrystalDiffract provides tools for expanding or contracting the x and y axes, and for auto-scaling the display to fit within the current plot range. The auto-scaling takes two forms: you can auto-scale the y-axis, so that the existing plot range fits snuggly within the vertical bounds. You can also auto-scale both x and y axes, so that all diffraction patterns fit entirely within the Graphics pane.
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). The Patterns List lets you browse multiple diffraction patterns, edit plot colours, and change the selection status of individual patterns.
Film/Graph Mode You can quickly toggle
Relative Scale
You can adjust the y-scale for observed datasets, relative to the graphs y-axis and any calculated data. This can be useful when trying to match calculated and observed diffraction patterns.
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.
between film and graphmode, by clicking this button. The icon changes, depending on which mode is currently active.
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, then adjust the Scale Factor setting, which is part of the Instrument parameter group.
useful tools, allowing you to instantly toggle between display of individual diffraction patterns, and a simulated multi-phase mixture. The toolbar icon changes, depending on whether or not a mixture is currently plotted:
Shift Controls
It is possible to shift selected diffraction patterns horizontally, left or right, or vertically up or down. These adjustments allow correction for zero errors in the diffraction experiment, and for constant background levels. To reset any shifts to zero, click the round icon at the centre of the group of arrows.
The toolbar Mix (left) and Unmix (right) buttons
The Toolbars shift controls
32 Chapter 6: Toolbar Reference
Chapter 7: The CrystalMaker Office

Different tasks require different interfaces. You wouldnt control a train from inside a car, and you wouldnt expect to fly a plane using a steering wheel. The same applies to scientific software: our CrystalMaker Office is modular, with components designed to give you the best user experience and performance, whilst ensuring a quick and easy workflow.
The crystal structure of Epidote, viewed in CrystalMaker (left). The corresponding TEM diffraction pattern and stereographic projection are shown in SingleCrystal (bottom right), with a simulated x-ray powder diffraction pattern in CrystalDiffract (top right).
Introduction to CrystalMaker
To really make the most of CrystalDiffract, youll require CrystalMaker: our flagship program for building, displaying, manipulating and animating all kinds of crystal/molecular structures and their behaviour. CrystalMaker features an elegant and intuitive user interface, available in optimized versions for Mac and Windows (including Windows 7).
Easy Data Processing
CrystalMaker provides drag-and-drop import of text data files in a wide range of file formats, including CIF, FDAT, GSAS, ICSD, MOL, PDB, SHELX, VASP, XYZ and many more. CrystalMaker can export data to a wide range of formats. You can also import/export tables of element colours & radii. This makes it easy to switch between different bonding topologies: from semiconductors to silicates, and from proteins to perovskite.
Chapter 7: The CrystalMaker Office 33
Spectacular Graphics
CrystalMaker provides superb, photo-realistic graphics, including stunning 3D stereo graphics in colour (red/blue glasses included with the program)with flexible annotation capabilities including lines, arrows, textboxes and scalebars, and high-resolution output.
Animations and Video
About Us
CrystalMaker Software Ltd is an awardwinning company, founded by two former university lecturers. Our mission is to improve the understanding of science, through the use of innovative computer software. Our companys research and development is supported by extensive international contacts and academic collaborations. Our company address is:
CrystalMaker Software Ltd Centre for Innovation & Enterprise Oxford University Begbroke Science Park Woodstock Road Begbroke Oxfordshire, OX5 1PF UK Voice: Fax: E-mail: Web site: +44 1865854804 +44 1865854805 sales@crystalmaker.com http://www.crystalmaker.com
CrystalMaker is unique in providing automatic, cross-platform QuickTime and VR output. You can easily build multi-structure/frame animations and output them as movies, or record your work using the Video Recorder palette.
Structures Library
CrystalMaker comes with a comprehensive library of over 600 fully-annotated files, ready for immediate display (and includes all the major rockforming minerals). Ideal for teaching and research!
Diffraction Link
Sales and Ordering Information

We produce and sell our own software throughout the world. Direct selling means higher-quality software at a fair price! We accept orders in U.S. dollars, Euros or British Pounds Sterling. Please refer to our web site for the latest pricing information. We accept purchase orders from universities, institutes or corporations (please fax or e-mail for fastest service), as well as credit cards. You can fax your details to us, or order online, using our new, multi-currency online ordering system:
http://www.crystalmaker.com/sales
CrystalMaker lets you share your structural data with CrystalDiffract, without the need to save files, switch applications, and load data: Simply choose a command from one of CrystalMakers Diffraction sub-menus, and CrystalDiffract will generate a diffraction pattern.
Single-Crystal Diffraction
CrystalMaker can be extended to provide singlecrystal diffraction simulation and analysis, thanks to our SingleCrystal program. This reads from CrystalMaker binary files and from graphics files (e.g., JPEG images), letting you compare images of real diffraction patterns with simulated patterns. SingleCrystal has advanced stereographic projection capabilities: display poles and traces for lattice planes or vectors, with the option of showing symmetry-related planes, with extensive customization. All graphics can be copied to the clipboard or exported to disc, with a choice of vector or pixel formats.
34 Chapter 7: The CrystalMaker Office
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, 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, 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, 32 Residual Function 22
36 Index
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, 32 Simulation of a powder pattern 11 Single-Crystal Diffraction 34 Site Occupancies editing 16 parameter control 18 Size Effects. SeeParticle 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. SeeAtomic 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
38
CrystalDiffract: An interactive diffraction program for Mac and Windows. Special thanks to Charles Prewitt, Gordon Nord, Yoshitaka Matsushita, 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 4.1.0 20 January 2004 17 January 2005 2 January 2006 updated for Mac version 5.1 25 March 2006 updated for Windows version 1.0 22 January 2007 5 November 2010 (last revised: 20 April 2012) updated for Mac version 5.2 & Windows version 1.4
Copyright 19952012 CrystalMaker Software Ltd. All Rights Reserved. No part of this manual may be reproduced, stored in a retrieval system, or transmitted, in any form, or by any means, without the prior written permission of the copyright owner. CrystalMaker Software Ltd make no representations, express or implied, with respect to this documentation or the software it describes, including without limitations, any implied warranties of merchantability or fitness for a particular purpose, all of which are expressly disclaimed. This Users Guide was prepared on a Mac, using Adobe InDesign and Photoshop, in combination with CrystalMaker software. The main fonts used were Adobe Caslon Pro and Gill Sans.
Mac is a trademark of Apple, Inc., registered in the U.S.A. and other countries. Microsoft, Windows and the Windows logo are trademarks, or registered trademarks of Microsoft Corporation. CrystalMaker, CrystalDiffract and SingleCrystal are trademarks or registered trademarks of CrystalMaker Software Ltd.
CrystalMaker
S O F T W A R E
CrystalMaker Software Limited Centre for Innovation & Enterprise Oxford University Begbroke Science Park Woodstock Road, Begbroke, Oxfordshire, OX5 1PF, UK Tel: +44 1865854804 Fax: +44 1865854805 sales@crystalmaker.com http://www.crystalmaker.com
39
CrystalMaker
S O F T W A R E
CrystalMaker Software Ltd Centre for Innovation & Enterprise Oxford University Begbroke Science Park Woodstock Road, Begbroke, Oxfordshire, OX5 1PF, UK
1994 2012 18 Years of Innovation
www.crystalmaker.com

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CrystalDiffract

Interactive Powder Diffraction Software

Works with CrystalMaker: Interactive Crystal Structures Visualization

Version 5.2 for Mac Version 1.4 for Windows

Chapter 1: Getting Started

Using this Guide

Searching for Topics

Chapter 1: Getting Started

Interface Reference Convention

Windows users will need to run the installer

Licensing your Installation

Chapter 1: Getting Started

Why use Powder Diffraction?

Derivation of the Bragg Equation

Chapter 1: Getting Started

Chapter 1: Getting Started

Chapter 1: Getting Started

Chapter 2: CrystalDiffract Interface

Displaying a Diffraction Pattern

To open a file in an existing window:

Chapter 2: CrystalDiffract Interface

Scrolling and Zooming

CrystalDiffracts tool buttons

Sharing Data With CrystalMaker

CrystalDiffracts axis scaling tools

Chapter 2: CrystalDiffract Interface

Using the Arrow tool to measure a diffraction peak

Help and Updates

Checking for Updates

10 Chapter 2: CrystalDiffract Interface

Chapter 3: Simulating Diffraction

Calculating the Pattern

Editing Scattering Factor Data

Locating the package contents

Chapter 3: Simulating Diffraction 11

(Mac), or Edit > Preferences (Windows).

2 In the Generate Reflexions group, set the

3 Click the Save button to store your new settings.

These will apply to any new windows.

The Profile pane of the Preferences dialog

The Wavelength sheet showing CuKa1 and Ka2 radiation

12 Chapter 3: Simulating Diffraction

Energy-Dispersive (EDS) Diffraction

Particle Size Broadening

Chapter 3: Simulating Diffraction 15

Editing Structural Data

Edit Crystal Sheet

Ca 0.56 Mg 0.41 Al 0.03

16 Chapter 3: Simulating Diffraction

Interactive Parameter Control

Chapter 3: Simulating Diffraction 17

Using the Parameters List

18 Chapter 3: Simulating Diffraction

Mixture Plot Settings

Editing the volume fraction of Silicon in a simulated three-phase mixture

Chapter 3: Simulating Diffraction 19

Viewing Diffraction Data

The Edit Diffraction Data window

20 Chapter 3: Simulating Diffraction

Chapter 4: Working with Patterns

Working with Observed Data

Applying Plot Styles

Loading Observed Data

Observed & Calculated Data Compared

CrystalDiffract User's Guide

CrystalDiffract User's Guide