® CrystalDiract Crystal Diract Interactive Powder Diraction Software
Works with CrystalMaker®: Inter Interactive active Crystal Cr ystal Structures Visualization
User’s Guide
Version V ersion 5.2 for Mac • Version 1.4 for Windows
Table T able of Contents Chapter 1: Getting Started .................................. ................ .................................... ................................... ................. 1 Using this Guide..................................................................... .................................. ......................................... ...... 1 Interface Reference Convention ................................................... ................................. .................. 2 System Requirements ................................................................... ............................... .................................... 2 Installation .................................................................. ............................... ..................................................... .................. 2 What is CrystalDiract? Cr ystalDiract? ............................................................... ................................. .............................. 3 CrystalMaker Integration Integration ............................................................. ................................ ............................. 6 Chapter 2: CrystalDiract Crys talDiract Interface ................................... ................. .................................... ....................7 ..7 Window Design ........................................................................... ....................................... .................................... 7 Displaying a Diraction Pattern ................................................... ................................. .................. 7 Scrolling and Zooming ................................................................. ................................... .............................. 9 Measuring a Pattern.......................................................... Pattern.................................................................... .......... 10 Output .................................................................. ............................... ......................................................... ...................... 10 Help and Updates ................................................................... ................................ ....................................... .... 10 Chapter 3: Simulating Diraction ................................... ................. .................................... ..................... ... 11 Calculating the Pattern ............................................................... ................................... ............................ 11 Radiation Type.................................................................. ype............................... ............................................. .......... 12 Diraction Modes .................................................................. ............................... ....................................... .... 12 Peak-Shape Functions ................................................................ .............................. .................................. 14 Peak Widths ..................................................................... .................................. ............................................. .......... 15 Editing Structural Data .............................................................. .................................. ............................ 16 Interactive Parameter Control .................................................... .............................. ...................... 17 Mixtures...................................................................... ................................... ................................................... ................ 19 Viewing Diraction Data ........................................................... ............................... ............................ 20 Chapter 4: Working with Patterns.................................... .................. .................................... ..................... ... 21 Working Working with Observed Data..................................................... Data............................... ...................... 21 Managing Multiple Patterns Patterns....................................................... ................................. ...................... 23 General Plot Settings................................. Settings.................................................................. ................................. 25 Individual Pattern Pattern Settings Settings ......................................................... ................................... ...................... 26 Customizing your Workspace Workspace ..................................................... ............................... ...................... 28 Chapter 5: Printing & Saving .................................... .................. .................................... ........................... ......... 29 Saving Your Your Work Work ................................................................... ................................ ....................................... .... 29 Saving Preferences .................................................................. ............................... ....................................... .... 29 Exporting Data ....................................................................... .................................... ....................................... .... 29 Printing ....................................................................... .................................... ................................................... ................ 30 Chapter 6: Toolbar Reference .................................... .................. .................................... ........................... ......... 31 Chapter 7: e CrystalMaker Crystal Maker ® Oce ....................................................33 Introduction to CrystalMaker.................... CrystalMaker..................................................... ................................. 33 Single-Crystal Diraction .......................................................... .............................. ............................ 34 Index
...........................................................................................35
Table T able of Contents Chapter 1: Getting Started .................................. ................ .................................... ................................... ................. 1 Using this Guide..................................................................... .................................. ......................................... ...... 1 Interface Reference Convention ................................................... ................................. .................. 2 System Requirements ................................................................... ............................... .................................... 2 Installation .................................................................. ............................... ..................................................... .................. 2 What is CrystalDiract? Cr ystalDiract? ............................................................... ................................. .............................. 3 CrystalMaker Integration Integration ............................................................. ................................ ............................. 6 Chapter 2: CrystalDiract Crys talDiract Interface ................................... ................. .................................... ....................7 ..7 Window Design ........................................................................... ....................................... .................................... 7 Displaying a Diraction Pattern ................................................... ................................. .................. 7 Scrolling and Zooming ................................................................. ................................... .............................. 9 Measuring a Pattern.......................................................... Pattern.................................................................... .......... 10 Output .................................................................. ............................... ......................................................... ...................... 10 Help and Updates ................................................................... ................................ ....................................... .... 10 Chapter 3: Simulating Diraction ................................... ................. .................................... ..................... ... 11 Calculating the Pattern ............................................................... ................................... ............................ 11 Radiation Type.................................................................. ype............................... ............................................. .......... 12 Diraction Modes .................................................................. ............................... ....................................... .... 12 Peak-Shape Functions ................................................................ .............................. .................................. 14 Peak Widths ..................................................................... .................................. ............................................. .......... 15 Editing Structural Data .............................................................. .................................. ............................ 16 Interactive Parameter Control .................................................... .............................. ...................... 17 Mixtures...................................................................... ................................... ................................................... ................ 19 Viewing Diraction Data ........................................................... ............................... ............................ 20 Chapter 4: Working with Patterns.................................... .................. .................................... ..................... ... 21 Working Working with Observed Data..................................................... Data............................... ...................... 21 Managing Multiple Patterns Patterns....................................................... ................................. ...................... 23 General Plot Settings................................. Settings.................................................................. ................................. 25 Individual Pattern Pattern Settings Settings ......................................................... ................................... ...................... 26 Customizing your Workspace Workspace ..................................................... ............................... ...................... 28 Chapter 5: Printing & Saving .................................... .................. .................................... ........................... ......... 29 Saving Your Your Work Work ................................................................... ................................ ....................................... .... 29 Saving Preferences .................................................................. ............................... ....................................... .... 29 Exporting Data ....................................................................... .................................... ....................................... .... 29 Printing ....................................................................... .................................... ................................................... ................ 30 Chapter 6: Toolbar Reference .................................... .................. .................................... ........................... ......... 31 Chapter 7: e CrystalMaker Crystal Maker ® Oce ....................................................33 Introduction to CrystalMaker.................... CrystalMaker..................................................... ................................. 33 Single-Crystal Diraction .......................................................... .............................. ............................ 34 Index
...........................................................................................35
Chapter 1: Getting Started Welcome to CrystalDiract: a program designed Welcome designed to make powder powder diraction intuitive, intuitive, interactive, and perhaps even fun! We hope you nd this program useful and entertaining. is part of the User’s 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
Searching for Topics
is User’s Guide should provide provide a very comprehensive 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:
We We have tried to provide a comprehensive comprehensive yet yet logically-structured guide. If you need to nd specic information, here are some suggestions: s uggestions:
A should browse Chapter 2: • A CrystalDiract Interface .
2. If you are viewing the guide electronically, electronica lly, you can click on the Contents or Contents or Index Index page page entries to go directly to the corresponding pages.
Tis is designed to give you a quick orientation to the program; the interface changes from version to version, and will certainly be dierent to other programs you may have have used, so it’s it’s important to to get your bearings earlier, earlier, rather than than later! •
I , we strongly recommend that you complete the Tutorial, which is available from CrystalDiract’s Help menu. Te series of short, structural exercises is designed to illustrate some of the most important program features and should address most of the the queries that you might have when using the software.
e User’s Guide describes describes the program interface, followed by sections on simulating diraction, how to put data into the program—then describing display and manipulation, before nishing with out of the program: printing and how to get data out of exporting data.
1. is guide includes a able of Contents (at Contents (at the beginning) and an Index an Index (at (at the end).
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 a bout the Demonstration Version This User’s Guide is designed for the Full-Feature version of CrystalDiffract. If you are using the free, Demonstration Version, Version, some some features may not be available: • The Demonstration Version is designed to give give you a favour of favour of the full program, using a range of examples structures. However, you cannot save les, record program settings, or specify preferences. • The Demonstration version does not let you import observed data les (although you can read such data if they have been saved in a diffraction experiment). If you are using the Demonstrat ion Version, we 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.
Chapter 1: Getting Started
1
Interface Refer Reference ence Convention
Installation
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 .
Mac and Windows versions have dierent installation procedures: •
You You will also encounter many references references to menu commands written in an abbreviated manner, such as “Edit > Copy ”, which means “from the Edit menu choose the Copy command”.
As a modern Mac application, CrystalDiract includes all its essential resources (including online help and this User’s User’s Guide), neatly packaged within the application “bundle”.
Mac & PC Shortcut Keys
Mac and Windows operating systems use dierent 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
Windows
command
control
option
alt
System Requir Requirements ements To To run CrystalDiract on a Mac, you will require Mac OS X 10.4 “Tiger” , 10.5 “Leopard”, 10.6 “Snow Leopard”, or 10.7 “Lion”. To To run CrystalDiract on a PC, you you will require Microsoft Windows XP (Service (Ser vice Pack 2), Vista or Windows 7. e program will not run on earlier versions of Windows, such as NT or 2000.
installation is a simple matter of draggingand-dropping the CrystalDiract application from the CD-ROM, to your hard disc (e.g., to your Applications your Applications folder). folder). Mac
We would also recommend that you copy the Examples Files to Files to your hard disc—possibly to your own Documents folder. Documents folder. •
Windows users
will need to run the installer program. is gives the option of installing the essential program les (application, online help, user’s guide), plus supporting resources (examples les).
Licensing your Installation
e rst time you launch CrystalDiract you are prompted to personalize your copy of the program. is process also creates a preferences preferences le. Registering Your Licence
It is very important that your licence is registered with us, as we can only provide technical technical support (and upgrades) to registered users. You You can register when you install the software, by clicking the Register button in the reminder dialog that appears following your installation. install ation. Alternatively, Alternatively, you can register later, 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 L icence, only the ofcial “keeper” of the licence needs to register with us. Once Once we have received that registration, the other users are entitled to receive technical support, within the terms of the specic licence.
2
Chapter 1: Getting Started
What is CrystalDiffract?
Crystalline Materials
CrystalDiract is a program for e starting point for simulating a diraction understanding diraction properties pattern is a crystal structure: the unique of crystals: specically, where a arrangement of atoms inside a basic building brick, powdered crystal sample (comprising or “unit cell” of material. Crystals typically contain millions of tiny crystallites ) is exposed billions of unit cells, neatly stacked in a threeto a radiation beam, resulting in patterns of dimensional lattice. scattered intensity, which can be recorded as lines on a lm, or as intensity peaks by a detector. CrystalDiract diers from its sister program, SingleCrystal, which is designed to simulate diraction patterns from a one, single crystal, when exposed to x-rays, neutrons or electrons. CrystalDiract can simulate the key powder diraction techniques used today, including traditional single (or dual-) wavelength X-ray and neutron scattering, plus newer white radiation (energy-dispersive) and time-of-ight techniques. CrystalDiract lets you manipulate diraction 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 dierent materials in the same window, and simulate multi-phase mixtures. For the experimental scientist, CrystalDiract lets you load observed data, for easy comparison with simulated data: an ideal way to characterize materials or interpret the results of synthesis experiments.
A crystal structure is derived f rom 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 diraction in the rst place. e preciselyoriented planes of atoms, repeated almost ad innitum, provide miniature diraction gratings for X-ray or neutron radiation.
Finally, CrystalDiract lets you print your diraction patterns, or export them in a range of data formats.
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?
Monochromatic Radiation
Powder diraction has a number of advantages over single-crystal techniques. Sometimes it is dicult to nd (or grow) good quality single crystals, whereas powders are much easier to manage. Single-crystal diraction (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 akes). Data collection tends to be very slow, as individual scattered beams are measured (although new, area detectors, are making this faster).
In most laboratory sources, X-rays are generated by ring a beam of electrons at a metal target—usually copper (Cu) or molybdenum (Mo). A characteristic X-ray spectrum is emitted, which is ltered, so that only the strongest, Cu K a peak emerges (this is actually a doublet, comprising K a1 and K a2 peaks, although sometimes the weaker, K a2 peak is also ltered out). is monochromatic radiation is then directed at the specimen. One typically moves the beam, relative to the sample, scanning through a range of angles, q. ere is a reciprocal relationship between q, and inter-planar distances in the crystal (“d-spacings”), which give rise to diraction peaks. is is summarized in the famous Bragg Equation:
With powder diraction, 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 diraction. Data collection times tend to be faster, since only a “onedimensional” pattern is being collected.
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.
e most-important powder diraction techniques—which can be simulated by CrystalDiract—are described below.
Derivation of the Bragg Equation
N(hkl) 1
1
2
2 θ
θ
(hkl) θ
θ
t
t
θ
d
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 ➀ and ➁ occurs when their path difference (t + t) is equal to an integral number of wavelengths.
4
Thus,
nl=2t
where: t = d sin q
hence,
n l = 2 d sin q
(the Bragg Equation).
Chapter 1: Getting Started
By measuring scattered intensity as a function of scattering angle, one is in eect measuring the scattering strengths of dierent sets of planes (with dierent d-spacings) inside the crystal. Ultimately, this scattering strength is controlled by the arrangements of atoms in dierent directions in the crystals—and hence one can learn something about the crystal structure from its diraction properties. White Radiation
Many diraction 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 diraction 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).
Time-of-Flight Diffraction
Some diraction experiments use pulses of neutrons with a range of energies. ese travel at dierent speeds, depending on the energy of the neutrons, and are directed down a long “beam line” towards a powder sample. Diraction is recorded by neutron detectors arranged around the sample, at a xed two-theta angle (2q). e number of pulses is recorded as a function of the time-of-ight of the neutrons (which is typically in the range of a few milliseconds to several hundred milliseconds). As for energy-dispersive diraction, an extended diraction pattern can be recorded at a xed Bragg angle because the sample is subjected to neutrons of dierent energies, and hence wavelengths.
Chapter 1: Getting Started
5
CrystalDiract works with CrystalMaker (left) letting you visualize crystal structures and simulate their diraction properties—in various experimental modes—in 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 CrystalDiract, 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 les from major databases and supports a wide variety of le formats. Just drag-and-drop a text le into CrystalMaker for automatic format detection and structure display. CrystalMaker lets you display a structure then, with a single menu command, see its diraction pattern appear in CrystalDiract.
6
Chapter 1: Getting Started
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 a spects of a cr ystal’s 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 is chapter provides a basic introduction to CrystalDiract’s user interface, including how to load a diraction pattern and manipulate it. Window Design
Displaying a Diffraction Pattern
CrystalDiract has a single-window program interface with a toolbar, and a Graphics pane for plotting your diraction patterns. Additional panes are available for displaying lists of Patterns or Parameters.
CrystalDiract can read from three kinds of les: text les, crystal structure les, and saved diraction session les.
At the top of each window is a toolbar with buttons/icons for measuring and manipulating diraction patterns (see Chapter 7: oolbar Reference for a description of the individual controls).
Do one of the following: •
Drag-and-drop a le onto the CrystalDiract application icon;
Mac users can toggle the toolbar on or o by clicking the lozenge-shaped button, on the right-hand side of the window’s titlebar.
•
Launch CrystalDiract, then drag-and-drop a le into the window that appears.
•
In CrystalDiract, choose File > Open then use the le dialog to specify the le(s) to be opened.
•
Drag-and-drop a le into the Patterns List, then click the new entry’s checkbox;
Toolbar
At the centre of the window is the Graphics pane, where diraction 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.
To load a le in a new window:
Graphics Pane
is is a list of experimentaland sample parameters, grouped into folder-like categories. You can edit parameters interactively, using a slider control, and observe how the diraction pattern changes. Parameters List
Each window can display a list of diraction patterns. You can drag text les, CrystalMaker binary les and folders into this list. e corresponding patterns can be displayed in the Graphics pane by clicking checkboxes. Patterns List
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).
To open a le in an existing window:
Do one of the following: •
Choose: File
> Open in Same Window .
•
Drag-and-drop your le(s) into the window. Data will be added in the form of one or more new diraction patterns.
Crystal Files
You can simulate a diraction pattern for a crystalline material, by supplying a CrystalMaker “crystal” le (le type CMDF , extension .cmdf or .crystal ). CrystalDiract will use structural data from the le to generate a diraction pattern. Please note that Demonstration Mode restricts you to reading only the latest CrystalMaker binary le format. However, the full-feature version can read from older les.
Chapter 2: CrystalDiffract Interface
7
Graphics Pane
Toolbar
Parameters List
Info Bar
Patterns Drawer
Te CrystalDiract-for-Mac program interface, showing calculated and observed diraction patterns
Patterns List
Te CrystalDiract-for-Windows interface, showing diraction patterns in “Film” mode 8
Chapter 2: CrystalDiffract Interface
Parameters Palette
Text Files
Scrolling and Zooming
You can load an observed diraction pattern, as a plain text le (le type TEXT , extension .txt or .dat) . e le should contain an xy listing of your diraction points (where the y value is the intensity), with one point per line.
You can use the horizontal scroll bar to quickly scroll through a diraction pattern. For ner control, choose the Hand tool from the toolbar then click and drag the pattern.
Session Files
e third type of le that CrystalDiract can read is its own “session le” format (letype CRDF, extension .crdf or .crystaldiffract ). A session le is a saved diraction experiment, which represents a complete record of your work in a particular window, with one or more diraction patterns, including structural data (for simulated patterns) and intensities. Sharing Data With CrystalMaker
You can also provide crystal structure data directly from within CrystalMaker, via that program’s Transform > Powder Diffraction submenu. Simply view and edit your structure in CrystalMaker; choose the relevant menu command, and then observe the diraction pattern in CrystalDiract.
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.
Arrow
Hand
Zoom
Distance
CrystalDiract’s tool buttons
Scaling Commands
e 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 t the entire diraction pattern range inside the Graphics pane). auto-scale y
x-scale
y-scale
auto-scale x & y
CrystalDiract’s axis scaling tools
Use CrystalMaker to visualize (and verify!) the structure before you proceed to simulate its diraction properties.
Chapter 2: CrystalDiffract Interface
9
Measuring a Pattern
Printing
e Arrow tool allows you to measure points on the simulated diraction 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.
e full version of CrystalDiract lets you print high-resolution diraction patterns, which are scaled to t your chosen page size.
Using the Arrow tool to measure a diraction 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).
Saving Preferences
CrystalDiract uses default settings for the window size, diraction 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 nished making your changes, click the dialog’s Save button; your settings will then be available for any new windows, and are saved in a preferences le, ready for your next session. •
To restore the program’s “Factory” settings, click the dialog’s Restore Factory Settings button.
•
To apply any saved preferences to the current window, use the Apply Preferences menu command.
Indexing a Pattern
You can display peak labels for a selected diraction pattern using the Pattern menu. Labels can contain any combination of Miller Indices, d-spacings, x-values, and so on. e Peak Threshold setting denes a minimum intensity value, below which no labels will be displayed is is useful for complex diraction patterns which may have many low-intensity peaks.
Output CrystalDiract provides a range of data output options, via the File > Export submenu. ese include exporting a complete diraction pattern, at user-dened resolution; a diraction data report (Miller indices, d-spacings, intensities, multiplicities, etc.), or a table of Structure Factors.
Help and Updates Most controls have tool tips associated with them. For detailed help, choose the Help > CrystalDiffract Help command. Help les 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 program’s Help menu. Checking for Updates
We regularly provide free, incremental program updates. ese include new features, interface enhancements and occasional bug xes. You can check whether an update is available using the Help > Check for Update command.
ere is also an option to let the program check You can also save a diraction experiment as a self- for updates automatically (Help > Check for contained “Session File”, you can print, and you can Updates Automatically ); the program will check at weekly intervals, and alert you if a newer version record your favourite settings in a Preferences le. of the software is available. You can then download this from our website. 10 Chapter 2: CrystalDiffract Interface
Chapter 3: Simulating Diffraction e Diract menu lets you alter aspects of a “virtual” diraction experiment, such as the radiation type, the experiment type (angle- or energy-dispersive), and various instrumental parameters. Calculating the Pattern CrystalDiract calculates diraction patterns using the types, and positions, of atoms in a unit cell of a crystal. e 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. CrystalDiract uses atomic scattering factors (x-ray diraction) or neutron scattering lengths for the atoms in your structure. Editing Scattering Factor Data
CrystalDiract uses a table of atomic scattering factors and neutron scattering lengths, saved as a text le called ASF.dat “ ”. CrystalDiract-for-Mac saves the ASF.dat le inside the application bundle. To view the contents of the application package, control-click on the CrystalDiract program icon and choose the Show Package Contents command from the popup menu that appears.
You can edit the ASF.dat data le if you wish to modify or add new data. e format is very simple. Each data line should contain: •
a two-character element symbol (which CrystalDiract will match with element symbols in your structure);
•
nine numbers correspond to the atomic scattering factor coecients a 1 b1 a 2 b2 a 3 b3 a 4 b4 c listed in the International Tables for Crystallography;
•
one number, corresponding to the coherent nuclear scattering length for that element.
e data le can also contain comments: these should be prefaced by an exclamation mark “!”. Note: the ASF.dat le must be a text-only le with le type TEXT . If you edit the le in a word processor, you should ensure that it is saved in a text-only format.
Locating the package contents
CrystalDiract-for-Windows has the ASF.dat le saved in the Application Data folder.
Chapter 3: Simulating Diffraction 11
Simulation Preferences
Radiation Type
You can use the Diffract menu to switch between To speed up the simulation of diraction data x-ray or neutron diraction. e diraction pattern (e.g., for massive structures such as proteins), is recalculated, using x-ray scattering factors or you can suppress all reexions below a minimum d-spacing. You can also limit the maximum number neutron scattering lengths that are stored with the program. of reexions (so that only those with the highest d-spacings are used). To set your simulation preferences:
Diffraction Modes
Choose: CrystalDiffract > Preferences (Mac), or Edit > Preferences (Windows).
CrystalDiract can simulate a number of experimental types, which cover the main techniques for powder diraction:
1
2
Navigate to the Prole tab.
group, set the Minimum d-spacing eld, enable the Limit number to option and enter a maximum number of reexions. 2
In the Generate
Reexions
Angle-Dispersive Diffraction
Traditional laboratory diractometers operate using constant radiation wavelength, with diraction measured as a function of Bragg Angle (theta, q). is is called angle-dispersive diraction. 3 Click the Save button to store your new settings. CrystalDiract allows you to simulate angle ese will apply to any new windows. dispersive diraction, plotting diracted intensity as a function of: 2q, d-spacing, or reciprocal d-spacing. You can specify the wavelength using the Diffract > Wavelength command.
Te Prole 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).
12 Chapter 3: Simulating Diffraction
Te Wavelength sheet showing CuK a1 and K a 2 radiation
e Wavelength sheet lets you specify monochromatic (single-wavelength), or dual wavelength radiation. Traditional laboratory x-ray tubes typically maximise intensity by emitting dual wavelengths, e.g., Cu K a1 and K a2 lines.
Energy-Dispersive (EDS) Diffraction
Time-of-Flight Diffraction
A relatively-new type of diraction involves using ‘white’ radiation that has a spread of wavelengths. e Bragg equation relates wavelength (l) to the d-spacing of a set of lattice planes, and the Bragg Angle (q):-
Some neutron diraction experiments use yet another kind of diraction: a neutron spallation source creates pulses of neutrons with a range of energies. ese travel at dierent speeds, depending on the energy of the neutrons, and are directed down a long “beam line” towards a powder sample.
l = 2d sin q
If l can be varied, then diraction 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 diraction from dierent d-spacings, the stationary detector must be able to discriminate between scattered radiation of dierent wavelengths. Since the wavelength of radiation is related to its energy, an energy-dispersive detector can be used to record an extended diraction pattern as a function of energy. You can specify a 2q value for this experiment, using the Diffract > Energy command.
Diraction is recorded by neutron detectors arranged around the sample, at a xed two-theta angle (2q). e number of pulses is recorded as a function of the time-of-ight, t , of the neutrons (which is typically in the range of a few milliseconds to several hundred milliseconds). As for energy-dispersive diraction, an extended diraction pattern can be recorded at a xed Bragg angle because the sample is subjected to neutrons of dierent energies, and hence wavelengths. We can analyse the time-of-ight process by combining De Broglie’s hypothesis, l = h / mn vn
Te ISIS neutron spallation source at the Rutherford-Appleton Laboratory, near Oxford, England. Neutrons are directed along beam lines, arranged radially, around the target (the cur ved light-blue chamber in the centre of the photo). ime-of ight diraction is used at one such beam line, the High-Resolution Powder Diractometer (HRPD). Chapter 3: Simulating Diffraction 13
(where h is Planck’s constant, mn is the neutron mass and vn is its velocity) with Bragg’s Law, thus: l = h / mn vn = 2 d sin q
Now, given a primary ightpath (the distance from the moderator to the sample) of L1 and a secondary ight path (sample to detector) of L2, and corresponding times of ight t 1 and t 2, we have: vn = (L1 + L2) / (t 1 + t 2) = L / t where L is the total ight path and t is the total time-of-ight. thus, h t / mn L = 2 d sin q hence: t = 2 d L (mn/h) sin q us, we have a linear relationship between the total time-of-ight, t , and the overall ight path, L. is is why the highest-resolution neutron diractometers have the longest ight paths (e.g., ~100m at the HRPD instrument in the Rutherford-Appleton Laboratory). CrystalDiract lets you specify the overall ight path, L, as well as the two theta value for the diraction experiment, using the Diffract > Time-of-Flight command.
Peak-Shape Functions In an ideal diraction experiment, the shape of a diraction peak would be determined solely by the sample, reecting its mean particle size, particle shape and structural state (including strain). In practise, for most samples the shape of diraction peaks is mainly determined by the diraction technique and geometry. For example, neutron diraction experiments tend to result in peaks with a Gaussian shape, whilst synchrotron diraction may result in a Pseudo-Voigt peak shape. CrystalDiract’s Diract menu lets you choose between dierent shape functions: •
Delta Function
•
Lorentzian
•
Gaussian
• Pseudo-Voigt e Delta Function is simply a “spike” of zero width. is provides a very quick way of showing the positions of many peaks in a complex pattern. e Lz function has a distinctive splayed appearance: peaks having very wide tails, like the mouth of a trumpet. e G function is shaped like the prole of a church bell, with a more rounded appearance
Gaussian (top) and Lorentzian (bottom) proles for the same diraction peak. Notice the lower peak maximum fo r the Lorentzian prole, 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 P-V function is a mix between the Gaussian and Lorentzian functions. It is characterized by a mixing parameter, E , which determines the Lorentzian character of the nal function:Result = E × Lorentzian + (1 – E ) × Gaussian You can edit the E parameter using the Diffract > Eta command, and entering a new value in the sheet or dialog that appears.
Peak Widths e limited resolution of a diraction experiment may result in diraction peaks that are substantially broadened. For most practical experiments, this “instrumental broadening” is the major contribution to the widths of observed diraction peaks. CrystalDiract lets you specify the amount of instrument broadening, in terms of the full width at half-maximum for a diraction peak. (e units depend on the current choice of x -axis: two-theta, d-spacing, reciprocal-d, energy in keV, or time-ofight in milliseconds.) Particle Size Broadening
e width of a diraction peak also depends on crystal size. is 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), diraction 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 dierent unit cell dimensions. In fact, there is likely to be a continuous spread of unit cell dimensions throughout the sample, resulting in a diraction pattern with a slightly “blurred” appearance. e amount of strain in the sample can be summarized by a “percent strain”. is 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.
Chapter 3: Simulating Diffraction 15
Editing Structural Data CrystalDiract lets you edit aspects of a selected pattern’s underlying crystal’s structure, so you can determine how this aects diraction. You can edit lattice parameters and site occupancies—and also omit sites from the diraction calculation. 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 crystal’s asymmetric unit. Each site row has a checkbox, which denes whether or not that site will be included in the intensity calculation. You could, for instance, decide to “turn o ” certain sites, so as to determine their inuence on the nal diraction pattern. You can edit site occupancies by typing a formula into the Site Occupancy eld. You can enter up to three element symbols and their corresponding occupancies. e total occupancy must not exceed 1.0. For example, you might enter something like:
e remaining elds cannot be edited. ey show the atom’s 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 elds, 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 nished your editing session, click the OK button to replot the diraction pattern. Tip: You can visualize atomic displacement parameters a s “thermal ellipsoids”, using recent versions of CrystalMaker.
Si 0.7 Al 0.3
or:
Ca 0.56 Mg 0.41 Al 0.03
Te 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)
16 Chapter 3: Simulating Diffraction
Interactive Parameter Control
Energy Dispersive
e Edit Crystal window lets you change multiple site occupancies and/or cell parameters, with the diraction 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 diraction pattern is replotted in real time.
If you have chosen an energy-dispersive simulation mode, then you can interactively change the two-theta angle for your sample/detector geometry.
To show the Parameters List, click the Toolbar’s Parameters button:
Time-of-Flight
For neutron diraction, in the time-of-ight simulation mode, you can interactively change the two-theta angle (for the sample/detector geometry) and the overall neutron ight path length. Instrument
Alternatively, choose: Window > Show Parameters List ; or (with the Graphics pane focussed) press the p key on your keyboard. Parameter Groups
e Parameters List contains a series of hierarchical entries, each with its own disclosure triangle, and representing dierent aspect of the diraction experiment: Angle Dispersive
is lets you interactively change the wavelength for a traditional, angle-dispersive (monochromatic radiation) experiments.
is group lets you change aspects related to your simulated diraction apparatus: the peak width (instrumental peak broadening), the “Eta” parameter—which controls the peak shape, if a “pseudo-Voigt” prole has been chosen—and 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.
Using the Parameters List to simulate an orthorhombic distortion (red pattern) in a previously-tetragonal crystal (blue pattern). Te 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 diraction pattern in real time.
Chapter 3: Simulating Diffraction 17
Background
Using the Parameters List
CrystalDiract lets you apply a basic background function to your calculated patterns. is function has the form: A + Bx + C/x. e individual parameters, A, B and C, can be adjusted interactively.
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 eld to appear below the list, allowing you to edit that item’s value. (When editing the text, press the Enter or Return keys to replot the structure.)
Sample
e full-feature version of CrystalDiract lets you simulate the eect 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
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 CrystalDiract does not perform an energy minimizations of the structure; one is simply “deforming” the unit cell, whilst keeping atoms in their existing sites, as dened by their fractional coordinates. Nevertheless, this is a useful range of settings when assessing the eect of a phase transition on the diraction properties.
Local and Global Parameters
Some Parameter entries are shown on a pink background. ese 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 aect all patterns, regardless of selection status. Examples include wavelength and peak width. Possible Applications
e Parameters List is designed to be educational as well as functional. Here are some possible uses: •
Simulating (e.g., cubic →tetragonal → orthorhombic) by changing cell parameters and watching how diraction peaks split.
•
Simulating the eect of by changing the unit cell volume (isotropic expansion/compression is assumed).
•
Visualizing the inuence of one on the nal diraction pattern, by dragging its site occupancy slider from 1 to 0.
•
Changing the x by varying the proportions of individual phases, perhaps to match an observed diraction pattern—and hence to determine its approximate composition.
Site Occupancies
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, CrystalDiract does not optimize the structure following any of these adjustments. However, it does let • you assess the chemical contribution to peak intensities. •
18 Chapter 3: Simulating Diffraction
Understanding how mean z and/or aects the diraction pattern. Fine-tuning a calculated diraction pattern to v , e.g., by changing Peak Width, Eta value, Zero Error, etc.
Mixtures CrystalDiract allows you to simulate mixtures with unlimited numbers of components, simply using the existing patterns in your diraction window. You can “create” the mixture by turning on mixture mode. To do this, use the Plot > Mixture command, or click the Toolbar’s Mix button.
To remove phases from a mixture, turn o the corresponding checkboxes in the Structures list. Tip: The Structures list’s 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 diraction patterns, just as you might do in “Separates” mode. Mixture Plot Settings oolbar Mix (left) and Unmix (right) buttons
In Mixture mode, all calculated diraction patterns are combined into a single, calculated mixture. Similarly, any observed diraction patterns are combined into a single, “observed mixture”. 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 xed, at 1.
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 diraction 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. Undoing a Mixture
You can “unmix” a mixture, and restore the display to separate diraction patterns, using the Plot > Separate command, or by clicking the Toolbar’s Unmix button.
Editing the volume fraction of Silicon in a simulated three-phase mixture
Chapter 3: Simulating Diffraction 19
Viewing Diffraction Data You can quickly view a tabulated listing of diraction data, using the Edit > Diffraction Data command:
Te Edit Diraction Data window
e 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 le, by clicking the Save button.
20 Chapter 3: Simulating Diffraction
Chapter 4: Working with Patterns CrystalDiract allows you to mix multiple simulated diraction 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 identication. 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
Applying Plot Styles
e full-feature version of CrystalDiract lets you load one or more text les in any window. ese could contain real, observed data, and you can display these will simulated (calculated) diraction patterns for easy characterization.
You adjust the plot styles for observed diraction patterns, in exactly the same way as for calculated patterns: rst select the patterns you wish to change, then choose the relevant commands from the Pattern menu.
Loading Observed Data
Observed & Calculated Data Compared
Observed datasets should be saved in plain-text les. e rst line of the le should contain a title (this is ignored by CrystalDiract). Subsequent lines should contain pairs of xy values—with one datapoint per line, for example:
When you append an observed data le to a window that already contains calculated data, CrystalDiract changes the relative scale setting for the observed data in order to best match the two patterns.
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
You can manually control the relative scaling for a selected observed pattern, using the two y-scaling buttons on the toolbar:
Note: If you are using the Mac version, it is important to check that the data le is a Mac le, with letype “TEXT”.
It is possible to reposition a selected pattern (calculated or observed), by introducing x and/ or y osets. You can use the Shift arrows on the toolbar to do this. Any osets can be reset to zero by clicking the small round button at the centre of the arrows:
To open a le in a new window:
•
Choose the File
> Open
Te oolbar’s Relative Scale buttons
command
To add les to an existing window:
Do one of the following: •
Choose: File
> Open in Same Window ,
or:
•
Drag the les into the Graphics pane, or
•
Drag the les into the Patterns List, then turn on their checkboxes.
Te oolbar’s Shift controls
You can also use the Arrow tool to click and drag a diraction pattern, when plotted in Graph mode.
Chapter 4: Working with Patterns 21
Observed and calculated time-of-ight neutron diraction patterns (top graph). Te observed data are plotted as crosses, with calculated data plotted using a smooth line. Te lower graph shows the residual func tion (observed minus calculated)
Displaying the Residual Function
Identifying an Unknown Substance
When working with observed and calculated data you have the option of displaying a separate graph or lm showing the dierence (observed minus calculated) between the two datasets: the “residual” function. is is controlled via the Plot > Show Residual or Plot > Hide Residual commands.
Being able to compare an observed diraction 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 diraction pattern, then add a sequence of CrystalMaker binary les (File > Open in Same Window ), until a good match is found.
e legend for the residual graph/lm also displays the sum-of-squares dierence between the calculated and simulated data: error =
Σ (obs - calc)2
is value corresponds only to the currentlydisplayed plot range. It can be a useful reference when attempting to ne-tune the calculated data in order to match the observed data. e 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
A more convenient way of comparing phases is to use the Patterns List, which is described next.
Managing Multiple Patterns
To rename a pattern:
e Patterns List lets you keep track of your observed and calculated diraction patterns. New patterns are automatically added to this list when you load them from crystal les, observed data les—or when you open a previously-saved session.
1
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.
Select the pattern in the list.
Press the Return or Enter keys on your keyboard (or click on the selected name). 2
When you have nished editing, press Return or Enter to nish, or click outside the selected row. (To cancel an edit, press the Escape key.) 3
To delete one or more patterns: 1
Select the relevant entries in the list.
Do one of the following:
2
Press the Delete key on your keyboard.
•
Click the Patterns icon in the Toolbar, or
To change the colour of a plotted pattern:
•
Press the s key on your keyboard, or
•
•
Choose the menu command: Window Patterns List .
To Display the Patterns List:
> Show
e Patterns list may be displayed as either a slide-out drawer (Mac), or as a window pane (Windows).
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. For more colour choices, choose the Other... command from the bottom of the menu.
Comparing Diffraction Patterns
e Patterns List can hold as many patterns as you like: you can drag les and folders—perhaps your entire CrystalMaker Structures Library—into the list. Individual patterns can be selected, and the list supports standard editing conventions, such as multiple selections (shift- and command -clicking).
e Patterns list really comes into its own when comparing an observed diraction 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 les into the Patterns list. You can then quickly compare each diraction pattern with the observed data by turning its checkbox on or o.
To plot one or more patterns:
To display only one pattern at a time:
Do one of the following:
•
Using the Patterns List
•
Check or uncheck the pattern’s checkbox.
•
Select one or more pattern(s) to be plotted or hidden, then choose the Plot or Hide commands from the Patterns List Actions menu.
Hold down the option/alt key and click a pattern’s checkbox. Any plotted patterns will be hidden, and only your clicked pattern plotted. Plot Settings
Chapter 4: Working with Patterns 23
Working with multiple patterns in the same window, using the Patterns List. Here, one item’s name is being edited.
24 Chapter 4: Working with Patterns
General Plot Settings
Stacked Graphs
e Plot menu lets you change the general way in In Graph mode you can use the Plot > Stack which all diraction patterns are displayed. You can command to stack multiple diraction patterns also customize aspects of the Graphics pane display, without danger of overlap. You can undo the including the plot range, gridlines and colours, stacking by choosing: Plot > Collapse . and so on. For specic adjustments to individual diaction patterns, use the Pattern menu. Film or Graph
You can choose to plot your diraction 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 lm. Film mode is particularly useful when comparing multiple diraction patterns: these are then stacked, making it easy to compare positions and intensities of diraction lines.
Stacked graphs showing how the diraction pattern of a crystal changes with temperature, and the progress of a displacive phase transition.
Comparing calculated and observed data in Film mode. Te central diraction 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.
Chapter 4: Working with Patterns 25
Overlaying Peak Positions
Individual Pattern Settings
For a complex diraction pattern there may be many overlapping peaks. e Plot > Overlay Peak Positions submenu allows you to identify the positions of individual diraction peaks.
e Pattern menu provides a series of commands which act upon any currently selected diraction patterns. You can change plot colours, graph attributes, such as line styles and widths, marker sizes—and control the labelling of diraction patterns.
You can superimpose a series of peak markers showing the peak centres, and their relative intensities. Alternatively, you can overlay the actual proles of individual peaks, in a choice of plot styles: solid lines, dashed lines or a “solid ll” prole.
Labelling Peaks
e Pattern menu gives you various options for labelling the peaks of selected diraction 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 prole is particularly useful for indicating dierent phases in a multi-component mixture, as illustrated above. Tweaks
You can display gridlines in the diraction 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 Strong peaks labelled with Miller Indices. Individual peak calculated data, and for mixtures, the legend lists all proles are shown by the dotted lines. Notice that only the phases and their proportions. strongest peaks are labelled in this example.
26 Chapter 4: Working with Patterns
Graph Settings
To turn labels on: 1
Select the pattern(s) you wish to label.
2
Choose: Pattern
> Show Labels .
To specify the label type:
In Graph mode, you have extensive control over the appearance of all diraction patterns. You can edit individual patterns by selecting them (individually, or collectively), and then applying settings from the Pattern menu.
Select the pattern(s) whose labels you wish to modify. 1
2 >
Choose one or more settings from the Pattern Label Style submenu.
(Note: e label text, and peak arrow, are drawn in the same colour as the host diraction pattern.) Controlling the Extent of Labelling
In order to prevent the diraction pattern from becoming too cluttered, you can suppress annotation for weak peaks. e Pattern > Label Threshold submenu lets you specify the minimum relative intensity for which annotation should be used.
Examples of dierent plot and marker styles. From bottom: solid; translucent; thick solid line; thin dashed line; lines with dots; crosses.
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. Plot Style
You can specify an explicit marker size, in pixels, or opt for an Auto setting, in which CrystalDiract scales the marker size depending on the plot size and resolution. Marker Size
You can specify an explicit line width (in pixels), or opt for an Auto setting. Line Width
You can apply dierent colours to dierent diraction patterns. Plot Colour
Tip: You can also edit plot colours using the Patterns List. Popup menus adjacent to e ach (plotted) entry let you quickly choose one of a number of preset colours.
Chapter 4: Working with Patterns 27
Customizing your Workspace
Cloning Windows (Mac)
CrystalDiract lets you open as many windows as memory permits.
You can “clone” a window, in order to preserve the original data, and give you free rein to experiment with new settings—maybe editing the structure and then wishing to compare the new diraction pattern with the old diraction pattern. Ensure that the window to be cloned is the frontmost diraction window, then choose the Window > Clone Window command.
On the Mac version, you can arrange multiple windows neatly on screen: either stacked on on top of each other, with small osets between adjacent windows, or tiled down the screen—using the Window menu’s Stack and Tile commands, respectively. Synchronizing Windows (Mac)
When comparing dierent structures in dierent windows you can use the Window> Synchronize command to adjust every window’s 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.
28 Chapter 4: Working with Patterns
Chapter 5: Printing & Saing CrystalDiract uses high-quality graphics for its on-screen drawing, and this also provides high-resolution printed output. When you have nished, you can save your “diraction experiment” in a single le, ready for immediate display next time you use the program. A tabbed dialog shows the currently-active settings; any changes you make are saved in your preferences le, and used for any new windows (existing windows retain their own settings). You can also opt to restore the original, “factory” settings.
Saving Your Work CrystalDiract allows you to save a window’s diraction experiment in a self-contained “session” le. is retains the window size and layout, your plot settings and all data required to plot the displayed diraction patterns.
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). is command will replot your current patterns, using the new, default settings. Your plot range, wavelength, diraction mode, etc., will all be reset to match your default settings.
Saving Preferences CrystalDiract uses default settings which you can inspect, edit, and save, with the Preferences command.
Exporting Data e File > Export submenu items allow you to generate text les in various dierent formats: is le contains a detailed listing of all reexions in the powder pattern(s), with their intensities, hkl values, d-spacings and multiplicities. Diffraction Data
Tip: You can quickly view and sort these diffraction data on screen, by choosing: Edit > Diffraction Data .
Te Preferences dialog.
Part of a Diraction Data le for spinel.
ref no.
(N)
h
k
l
d(hkl)
2-Theta
Intensity
[ [ [ [ [ [ [ [ [ [ [ [
3 8 11 12 16 19 24 27 32 35 36 40
1 0 1 2 0 1 2 1 0 1 2 0
1 2 1 2 0 3 2 1 4 3 4 2
1 2 3 2 4 3 4 5 4 5 4 6
4.66499 2.85671 2.43621 2.33250 2.02000 1.85368 1.64932 1.55500 1.42836 1.36577 1.34667 1.27756
19.0076 31.2843 36.8626 38.5650 44.8299 49.1048 55.6807 59.3842 65.2661 68.6613 69.7751 74.1568
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
1] 2] 3] 4] 5] 6] 7] 8] 9] 10] 11] 12]
I/Imax
m(hkl)
32.0 32.2 100.0 1.2 59.0 0.1 9.6 49.0 78.7 3.6 0.2 3.1
8 12 24 8 6 24 24 32 12 48 24 24
Chapter 5: Printing & Saving 29
is le contains a complete If multiple diraction patterns are displayed in list of reexions in three-dimensional space (this the same window, then the exported le contains is a wider range than is displayed on the screen, as multiple columns, corresponding to the y -data for the reexions have not been combined into a oneall selected diraction patterns. So, for example, if dimensional powder pattern). e intensities and three patterns, A, B and C were selected, then each the real- and imaginary parts of the structure factor row of the exported prole would contain four are included. Data are sorted in order of decreasing values: x y A y B y C. d-spacing. is simple le format can easily be imported into many graph plotting programs or spreadsheets, Profile is le is a tab-delimited listing of xy data points, corresponding to the x -range currently making it a great way of exporting high-resolution displayed. You can specify the step between diraction proles. adjacent x -axis values, allowing high-resolution output. Structure Factors
Printing x “Spinel - MgAl2O4” 18.50000 0.00000e+00 18.55000 0.00000e+00 18.60000 0.00000e+00 18.65000 2.94836e-14 18.70000 9.62476e-11 18.75000 7.98450e-08 18.80000 1.74030e-05 18.85000 1.01539e-03 18.90000 1.62704e-02 18.95000 7.37977e-02 19.00000 1.07549e-01 19.05000 3.72673e-02 19.10000 4.09937e-03 19.15000 1.25509e-04 19.20000 1.03963e-06 19.25000 2.27941e-09 19.30000 1.30270e-12 19.35000 0.00000e+00 19.40000 0.00000e+00 19.45000 0.00000e+00
e full-feature version of CrystalDiract will print the contents of the current window at the highest-possible resolution, as determined by your printer’s resolution and the available memory. If you nd 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)
CrystalDiract for Mac takes advantage of a built-in system feature: the ability to “print” to a PDF le. When you choose the Print command, the resulting Print sheet has a PDF button which, when gives the option of exporting a PDF graphics le containing your diraction pattern, scaled to t the current page size.
Part of a Prole output le for spinel.
Part of a Structure Factor output le for spinel.
ref no. [ 1] [ 2] [ 3] [ 4] [ 5] [ 6] [ 7] [ 8] [ 9] [ 10] [ 11] [ 12] [ 13]
30 Chapter 5: Printing & Saving
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
Chapter 6: Toolbar Reference Each CrystalDiract window has a horizontal toolbar at the top, which allows you to choose specic tools for manipulating or measuring a diraction pattern, and adjust the scaling settings. is chapter summarizes the various toolbar buttons or icons.
Te CrystalDiract oolbar (Mac version) Show/Hide Parameters List (p)
Tool Buttons
Show/Hide Patterns List (s)
Axis-Scaling Tools
Relative Scale
Shift Controls
Mix/Unmix Film/Graph mode
Showing the Toolbar
can then drag the cursor with the mouse.
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. You can also save your toolbar preference, with the Preferences dialog.
As you move the cursor over a diraction pattern, information about that pattern is displayed in the Info bar.
Tools
ere 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).
e Arrow tool also lets you click-and-drag a diraction prole (graph), thereby changing its xand y-axis osets. is tool lets you scroll the diraction pattern: you can click-and-drag the graphics pane, moving the diraction display to the left- or the right. is is a more precise way of repositioning the prole than using the horizontal scroll bar. Hand (h)
is “magnify” tool allows you to zoom in on a clicked point in the diraction pattern. To zoom out, hold down the option or shift keys on your keyboard as you click with this tool. Zoom (z)
e distance (“measurement”) tool has two functions: a measurement tool, and a zoom tool. To measure the distance between two points on a diraction pattern, click in the Graphics window where you want to begin measuring, then click where you want to stop. e 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 lls the window. Distance (d)
Arrow (a)
Hand (h)
Zoom (z)
Distance (d)
CrystalDiract’s tool buttons
e Arrow tool lets you measure data in the diraction 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 Arrow (a)
Chapter 6: Toolbar Reference 31
Axis Scaling Tools
Other Controls auto-scale y
x-scale
y-scale
auto-scale x & y
Clicking this icon 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 Parameters (p)
CrystalDiract’s axis scaling tools
is icon (which may be hidden if the window size is small) lets you quickly show or hide the Patterns List. is is located in either a drawer (Mac) or pane (Windows). e Patterns List lets you browse multiple diraction patterns, edit plot colours, and change the selection status of individual patterns. Show/Hide Patterns (s)
CrystalDiract provides tools for expanding or contracting the x and y axes, and for auto-scaling the display to t within the current plot range. e auto-scaling takes two forms: you can auto-scale the y-axis, so that the existing plot range ts snuggly within the vertical bounds. You can also auto-scale both x and y axes, so that all diraction patterns t entirely within the Graphics pane. Relative Scale
You can quickly toggle between “lm” and “graph”mode, by clicking this button. e icon changes, depending on which mode is currently active. Film/Graph Mode
You can adjust the y -scale for observed datasets, relative to the graph’s y -axis and any calculated data. is can be useful when trying to match calculated and observed diraction 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.
e 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.
Te “Film” and “Graph” toolbar icons
is is perhaps one of the most useful tools, allowing you to instantly toggle between display of individual diraction patterns, and a simulated multi-phase mixture. e toolbar icon changes, depending on whether or not a mixture is currently plotted: Mix/Unmix
Shift Controls
It is possible to shift selected diraction patterns horizontally, left or right, or vertically up or down. ese adjustments allow correction for zero errors in the diraction experiment, and for constant background levels. To reset any shifts to zero, click the round icon at the centre of the group of arrows.
Te oolbar’s shift controls
32 Chapter 6: Toolbar Reference
Te toolbar Mix (left) and Unmix (right) buttons
Chapter 7: The CrystalMaker® Office Dierent tasks require dierent interfaces. You wouldn’t control a train from inside a car, and you wouldn’t expect to y a plane using a steering wheel. e same applies to scientic software: our “CrystalMaker Oce” is modular, with components designed to give you the best user experience and performance, whilst ensuring a quick and easy workow.
Te crystal structure of Epidote, viewed in CrystalMaker (left). Te corresponding EM diraction pattern and stereographic projection are shown in SingleCrystal (bottom right), with a simulated x-ray powder diraction pattern in CrystalDiract (top right).
Introduction to CrystalMaker
Easy Data Processing
To really make the most of CrystalDiract, you’ll require CrystalMaker®: our agship program for building, displaying, manipulating and animating all kinds of crystal/molecular structures and their behaviour.
CrystalMaker provides drag-and-drop import of text data les in a wide range of le formats, including CIF, FDAT, GSAS, ICSD, MOL, PDB, SHELX, VASP, XYZ and many more.
CrystalMaker features an elegant and intuitive user interface, available in optimized versions for Mac and Windows (including Windows 7).
CrystalMaker can export data to a wide range of formats. You can also import/export tables of element colours & radii. is makes it easy to switch between dierent bonding topologies: from semiconductors to silicates, and from proteins to perovskite.
Chapter 7: The CrystalMaker Ofce 33
Spectacular Graphics
CrystalMaker provides superb, photo-realistic graphics, including stunning 3D stereo graphics in colour (red/blue glasses included with the program)—with exible annotation capabilities including lines, arrows, textboxes and scalebars, and high-resolution output. Animations and Video
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 les, ready for immediate display (and includes all the major rockforming minerals). Ideal for teaching and research! Diffraction Link
CrystalMaker lets you share your structural data with CrystalDiract, without the need to save les, switch applications, and load data: •
Simply choose a command from one of CrystalMaker’s Diffraction sub-menus, and CrystalDiract will generate a diraction pattern.
Single-Crystal Diffraction CrystalMaker can be extended to provide singlecrystal diraction simulation and analysis, thanks to our SingleCrystal program. is reads from CrystalMaker binary les and from graphics les (e.g., JPEG images), letting you compare images of real diraction 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 Ofce
About Us CrystalMaker Software Ltd is an award winning company, founded by two former university lecturers. Our mission is to improve the understanding of science, through the use of innovative computer software. Our company’s 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 1865–854804 +44 1865–854805
[email protected] http://www.crystalmaker.com
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
Inde A
E
Angle-Dispersive Diraction denition 12 parameter control 17 Arrow tool description 10 reference 31 Atomic Displacement Parameter 16 Atomic Scattering Factors 11 Axis Scaling Tools 32
Editing Structural Data 16 Energy-Dispersive Diraction denition 13 parameter control 17 Eta in Pseudo-Voigt function 15 Export Options 29
B
Film Mode 25
Background parameter control 18 Bragg Angle derivation of 4 for energy-dispersive diraction 12
G
C Calculating Diraction 11 Cloning Windows 28 Colour of graph 27 Crystalline Materials denition of 3
D Data displaying diraction data 20 exporting 29 Delta Function 14 Diraction angle-dispersive 12 energy-dispersive 13 time-of-ight 13 Distance Tool reference 31 D-Spacing Limit 12
F
Gaussian Function 14 Graphics Pane description 7 Graph Mode 25 Gridlines 26
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
L Licensing during installation 2 Line Width 27 Lorentzian Function 14
Index 35
M
P
Marker Size in Graph mode 27 Mixtures description 19 parameter control 18 Monochromatic Radiation 12
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 le 2 Pressure simulating eects 18 Printing 30 Prole File 30 Pseudo-Voigt Function 15
N Neutron Diraction angle-dispersive 13 scattering length data 11 time-of-ight 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 Residual Function 22
36 Index
21, 32
S
U
Sales and Ordering 34 Sample parameter control 18 Saving Your Work in a session le 29 Scaling Commands 9 Scattering Factors editing 11 Scrolling a Diraction Pattern 9 Session File 29 Shift Control 21, 32 Simulation of a powder pattern 11 Single-Crystal Diraction 34 Site Occupancies editing 16 parameter control 18 Size Eects. See Particle Size Broadening Sorting diraction 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
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 Diraction angle dispersive 12 atomic scattering factors for 11 wavelength options 12
Z Zooming a Diraction Pattern 9 Zoom Tool reference 31
T Temperature simulating eects 18 ermal Ellipsoids. See Atomic Displacement Parameter Time-of-Flight Diraction denition 13 parameter control 17 Toolbar description 7 reference 31 showing or hiding 31 Two eta 12
Index 37
38
CrystalDiract®: An interactive diraction program for Mac and Windows. Special thanks to Charles Prewitt, Gordon Nord, Yoshitaka Matsushita, Christian Baerlocher and Helge Stanjek First edition: Second edition: ird edition:
12 March 2000 7 November 2001 23 February 2002 updated for Mac version 4.1.0
Fourth edition:
20 January 2004
Fifth edition:
17 January 2005
Sixth edition:
2 January 2006 updated for Mac version 5.1
Seventh edition: Eighth edition: Ninth edition:
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 © 1995–2012 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 tness for a particular purpose, all of which are expressly disclaimed. is User’s Guide was prepared on a Mac, using Adobe InDesign and Photoshop, in combination with CrystalMaker software. e 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, CrystalDiract 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 1865–854804 • Fax: +44 1865–854805
[email protected] • http://www.crystalmaker.com
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