V
V
ersion 5.2 for Mac •
ersion 5.2 for Mac •
V
V
ersion 1.4 for
ersion 1.4 for
Windows
Windows
User’s Guide
User’s Guide
Crystal
Crystal
Diract
Diract
®
®
Interactive
Interactive
P
P
owder Diraction
owder Diraction
Software
Software
W
T
Table of Contents
able of Contents
ChapterChapter 1: 1: Getting Getting Started Started ... 11 Using this
Using this Guide Guide ... 11 Interface
Interface Reference Reference Convention Convention ... 22 System
System Requirements Requirements ... 22 Installation
Installation ... 22 What is Cr
What is CrystalDiract? ystalDiract? ... 33 CrystalMaker Inte
CrystalMaker Integration gration ... 66 Chapter
Chapter 2: 2: CrysCrystalDiract talDiract Interface Interface ...7..7 Window Design ...
Window Design ... 77 Displaying a Diraction
Displaying a Diraction Pattern Pattern ... 77 Scrolling and
Scrolling and Zooming Zooming ... 99 Measuring
Measuring a a Pattern...Pattern... 1010 Output
Output ... 1010 Help and
Help and Updates Updates ... 1010 Chapter
Chapter 3: 3: Simulating Simulating Diraction Diraction ... 1111 Calculating the
Calculating the Pattern Pattern ... 1111 Radiation
Radiation TType...ype... 1212 Diraction
Diraction Modes Modes ... 1212 Peak-Shape
Peak-Shape Functions Functions ... 1414 Peak
Peak Widths Widths ... 1515 Editing
Editing Structural Data Structural Data ... 1616 Interactive
Interactive Parameter Parameter Control Control ... 1717 Mixtures
Mixtures ... 1919 Viewing Diraction
Viewing Diraction Data Data ... 2020 Chapter
Chapter 4: 4: WWorking orking with with Patterns Patterns ... 2121 W
Working with Observed Data...orking with Observed Data... 2121 Managing Multiple P
Managing Multiple Patterns atterns ... 2323 General Plot Settings
General Plot Settings... 2525 Individual P
Individual Pattern Settattern Settings ings ... 2626 Customizing your W
Customizing your Workspace orkspace ... 2828 Chapter
Chapter 5: 5: Printing Printing & & Saving Saving ... 2929 Saving Y
Saving Your Woour Work rk ... 2929 Saving
Saving Preferences Preferences ... 2929 Exporting
Exporting Data Data ... 2929 Printing
Printing ... 3030 Chapter
Chapter 6: 6: TToolbar oolbar Reference Reference ... 3131 Chapter
Chapter 7: 7: e e CrystalCrystalMaker Maker ®®Oce ...33Oce ...33
Introduction
Introduction to to CrystalMaker...CrystalMaker... 3333 Single-Crystal
Single-Crystal Diraction Diraction ... 3434 Index ...35 Index ...35
T
Table of Contents
able of Contents
ChapterChapter 1: 1: Getting Getting Started Started ... 11 Using this
Using this Guide Guide ... 11 Interface
Interface Reference Reference Convention Convention ... 22 System
System Requirements Requirements ... 22 Installation
Installation ... 22 What is Cr
What is CrystalDiract? ystalDiract? ... 33 CrystalMaker Inte
CrystalMaker Integration gration ... 66 Chapter
Chapter 2: 2: CrysCrystalDiract talDiract Interface Interface ...7..7 Window Design ...
Window Design ... 77 Displaying a Diraction
Displaying a Diraction Pattern Pattern ... 77 Scrolling and
Scrolling and Zooming Zooming ... 99 Measuring
Measuring a a Pattern...Pattern... 1010 Output
Output ... 1010 Help and
Help and Updates Updates ... 1010 Chapter
Chapter 3: 3: Simulating Simulating Diraction Diraction ... 1111 Calculating the
Calculating the Pattern Pattern ... 1111 Radiation
Radiation TType...ype... 1212 Diraction
Diraction Modes Modes ... 1212 Peak-Shape
Peak-Shape Functions Functions ... 1414 Peak
Peak Widths Widths ... 1515 Editing
Editing Structural Data Structural Data ... 1616 Interactive
Interactive Parameter Parameter Control Control ... 1717 Mixtures
Mixtures ... 1919 Viewing Diraction
Viewing Diraction Data Data ... 2020 Chapter
Chapter 4: 4: WWorking orking with with Patterns Patterns ... 2121 W
Working with Observed Data...orking with Observed Data... 2121 Managing Multiple P
Managing Multiple Patterns atterns ... 2323 General Plot Settings
General Plot Settings... 2525 Individual P
Individual Pattern Settattern Settings ings ... 2626 Customizing your W
Customizing your Workspace orkspace ... 2828 Chapter
Chapter 5: 5: Printing Printing & & Saving Saving ... 2929 Saving Y
Saving Your Woour Work rk ... 2929 Saving
Saving Preferences Preferences ... 2929 Exporting
Exporting Data Data ... 2929 Printing
Printing ... 3030 Chapter
Chapter 6: 6: TToolbar oolbar Reference Reference ... 3131 Chapter
Chapter 7: 7: e e CrystalCrystalMaker Maker ®®Oce ...33Oce ...33
Introduction
Introduction to to CrystalMaker...CrystalMaker... 3333 Single-Crystal
Single-Crystal Diraction Diraction ... 3434 Index ...35 Index ...35
1 1
Using this Guide
Using this Guide
is User’s Guide should pris User’s Guide should provide a very ovide a very comprehensiv
comprehensive outline of the e outline of the major programmajor program
features. We don’t expect you to read it from features. We don’t expect you to read it from cover-to-cover, but would recommend the following key to-cover, but would recommend the following key sections:
sections:
•• A A should browse should browse Chapter 2:Chapter 2: CrystalDiract Interface
CrystalDiract Interface .. Tis is designed to give you
Tis is designed to give you a quick orientation toa quick orientation to the program; the interface changes from version the program; the interface changes from version to version, and will certainly be dierent to other to version, and will certainly be dierent to other programs you may hav
programs you may have used, so it’e used, so it’s important ts important too get your bearings ea
get your bearings earlier, rlier, rather trather than later! han later! •
• I I , , we we strongly strongly
recommend that you complete the Tutorial, recommend that you complete the Tutorial, which is available from CrystalDiract’s Help which is available from CrystalDiract’s Help
menu. menu.
Te series of short, structural exercises is designed Te series of short, structural exercises is designed to illustrate some of the
to illustrate some of the most important programmost important program features and should address most of t
features and should address most of the queries that he queries that you might have when using the
you might have when using the software.software. e User’s Guide d
e User’s Guide describes the program interface,escribes the program interface, followed by sections
followed by sections on simulating diraction, how on simulating diraction, how to put data
to put data intointo the program—then describingthe program—then describing display and manipulation, before nishing with display and manipulation, before nishing with how to get data
how to get data out out of the program: printing andof the program: printing and exporting data.
exporting data.
Searching for
Searching for TTopicsopics
W
We have tried to provide a coe have tried to provide a comprehensive yemprehensive yett logically-structured guide. If you need to logically-structured guide. If you need to ndnd specic information, here are some s
specic information, here are some suggestions:uggestions: 1.
1. is is guide guide includes includes aa able of Contents able of Contents (at the(at the beginning) and an
beginning) and an Index Index (at the end).(at the end). 2.
2. If you If you are viewing the are viewing the guide electronicaguide electronically, lly, youyou can click on the
can click on the Contents Contents oror Index Index page entriespage entries to go directly to the
to go directly to the corresponding pages.corresponding pages. 3.
3. If you If you need to need to search for a search for a keyword keyword or phrase,or phrase, you should be able to use the
you should be able to use theSearchSearch commandcommand
in a PDF viewer such as Adobe (Acrobat) in a PDF viewer such as Adobe (Acrobat) Reader or Apple Preview.
Reader or Apple Preview.
A Note a
A Note about the Demonstration Versionbout the Demonstration Version This User’s Guide is designed for the
This User’s Guide is designed for the Full-Feature versionFull-Feature version of CrystalDiffract. If you are using the free,
of CrystalDiffract. If you are using the free, DemonstrationDemonstration Version
Version, som, some features e features may not be may not be available:available: •
• The Demonstration The Demonstration VVersion is designed to giversion is designed to give you ae you a favour
favour of the full program, using a range of of the full program, using a range of examplesexamples structures. However, you cannot save les, record structures. However, you cannot save les, record program settings, or specify preferences.
program settings, or specify preferences. •
• The Demonstration The Demonstration version version does not does not let you let you importimport observed data les (although you can read such data if observed data les (although you can read such data if they have been saved in a diffraction
they have been saved in a diffraction experiment).experiment). If you
If you are using are using the Demonstratthe Demonstrat ion ion VVersion, wersion, we e stronglystrongly recommend that you explore the
recommend that you explore the saved diffractionsaved diffraction experiments provided:
experiments provided: these demonstrate a these demonstrate a range of range of features that are possible with the full version of the features that are possible with the full version of the program.
program.
Chapter 1: Getting Started
Chapter 1: Getting Started
W
W
elcome to CrystalDiract:
elcome to CrystalDiract:
a program design
a program design
ed to make pow
ed to make pow
der diraction intu
der diraction intu
itive,
itive,
interactive, and perhaps even fun! We hope you nd this program useful and entertaining.
interactive, and perhaps even fun! We hope you nd this program useful and entertaining.
is part of the Us
is part of the Us
er’s Guide
er’s Guide
is designed to give
is designed to give
a quick overview of what the program is,
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
its scope, plus information on how to install the program, followed by tips on using the rest
of this User’s Guide.
of this User’s Guide.
Chapter 1: Getting Started Chapter 1: Getting Started
2
2 Chapter 1: Getting StartedChapter 1: Getting Started
Interface
Interface
Refer
Refer
ence Convention
ence Convention
In the following chapters we refer to elements of In the following chapters we refer to elements of the program’the program’s interface (such s interface (such as button names,as button names, menu commands and keys on your keyboard) using menu commands and keys on your keyboard) using aa typewriter fonttypewriter font..
Y
You will also encounter many rou will also encounter many references to menueferences to menu commands written in an abbreviated manner, such commands written in an abbreviated manner, such as “
as “Edit > CopyEdit > Copy”, which means “from the”, which means “from the EditEdit
menu choose the
menu choose the CopyCopy command”.command”.
Mac & PC Shortcut Keys
Mac & PC Shortcut Keys
Mac and Windows operating systems use
Mac and Windows operating systems use dierentdierent key combinations for menu
key combinations for menu shortcuts (“acceleratorshortcuts (“accelerator keys”). In this guide we make repeated reference to keys”). In this guide we make repeated reference to
command
command andand optionoption keys, which are included onkeys, which are included on
the standard Mac keyboard Windows users should the standard Mac keyboard Windows users should use the following translation:
use the following translation: Mac
Mac Windows Windows
c
coommmmaanndd ccoonnttrrooll o
oppttiioonn aalltt
System
System
Requir
Requir
ements
ements
TTo run CrystalDiract on a Mac, o run CrystalDiract on a Mac, you will requireyou will require Mac OS X 10.4 “Tiger” , 10.5 “Leopard”, 10.6 Mac OS X 10.4 “Tiger” , 10.5 “Leopard”, 10.6 “Snow Leopard”, or 10.7 “Lion”.
“Snow Leopard”, or 10.7 “Lion”. T
To run CrystalDiract on a PC, yo run CrystalDiract on a PC, you will requireou will require Microsoft Windows XP (Ser
Microsoft Windows XP (Service Pack 2), vice Pack 2), Vista orVista or Windows 7.
Windows 7. e program will not run on earliere program will not run on earlier versions of Windows,
versions of Windows, such as NT or 2000.such as NT or 2000.
Installation
Installation
Mac and Windows versions have
Mac and Windows versions have dierentdierent installation procedures:
installation procedures:
•• MacMac installation is a simple matter of dragging-installation is a simple matter of
dragging-and-dropping the CrystalDiract application and-dropping the CrystalDiract application from the CD-ROM, to your hard disc (e.g., to from the CD-ROM, to your hard disc (e.g., to your
your Applications Applications folder).folder). As a
As a modern Mac application, CrystalDiract modern Mac application, CrystalDiract includes all its essential resources (including online includes all its essential resources (including online help and this
help and this User’User’s Guide), neatly packaged withins Guide), neatly packaged within the application “bundle”.
the application “bundle”.
We would also recommend that you copy the We would also recommend that you copy the Examples Files
Examples Files to your hard disc—possibly toto your hard disc—possibly to your own
your own Documents Documents folder.folder.
•• WindowsWindowsusers will need to run the installerusers will need to run the installer
program.
program. is gives the is gives the option of installingoption of installing the essential
the essential program les (application, onlineprogram les (application, online help, user’s guide), plus supporting resources help, user’s guide), plus supporting resources (examples les).
(examples les).
Licensing your Installation
Licensing your Installation
e rst time you launch CrystalDiract you are e rst time you launch CrystalDiract you are
prompted to personalize your copy of the program. prompted to personalize your copy of the program. is process also creates a pre
is process also creates a preferences le.ferences le.
Registering Your Licence
Registering Your Licence
It is very important that
It is very important that your licence is registeredyour licence is registered with us,
with us, as we can only provide teas we can only provide technical supportchnical support (and upgrades) to registered users.
(and upgrades) to registered users. Y
You can register when you install the software,ou can register when you install the software, by clicking the
by clicking the RegisterRegister button in the reminderbutton in the reminder
dialog that appears following your install
dialog that appears following your installation.ation. Alternatively
Alternatively, , you can register lateryou can register later, , by choosing theby choosing the
Help > Register CrystalDiffract
Help > Register CrystalDiffract command.command.
Multi-User Licence Registration
Multi-User Licence Registration
We only require one registration per licence. So, if you We only require one registration per licence. So, if you have a multi-user licence, such as a Research Group, have a multi-user licence, such as a Research Group, Classroom or Site L
Classroom or Site L icence, only the ofcial “keeper”icence, only the ofcial “keeper” of the licence
of the licence needs to register needs to register with us. Owith us. Once we havence we have received that registration, the other users are entitled to received that registration, the other users are entitled to receive technical support, within the terms of the
receive technical support, within the terms of the specicspecic licence.
3
What is CrystalDiffract?
CrystalDiract is a program for understanding diraction properties of crystals: specically, 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 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.
Finally, CrystalDiract lets you print your
diraction patterns, or export them in a range of data formats.
Crystalline Materials
e starting point for simulating a diraction 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 three-dimensional lattice.
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 precisely-oriented planes of atoms, repeated almost ad
innitum, provide miniature diraction 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).
4
N(hkl)
θ θ θ θ θ t t(hkl)
d
1
1
2
2
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 wavelets➀ and➁occurs when their path difference (t + t) is equal to an integral number of wavelengths.
Thus, n l = 2 t where: t = d sin q hence, n l = 2 d sin q (the Bragg Equation).
Derivation of the Bragg Equation
Why use Powder Diffraction?
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).
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 “one-dimensional” pattern is being collected.
e most-important powder diraction techniques—which can be simulated by CrystalDiract—are described below.
Monochromatic Radiation
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 a1and K a2peaks, although sometimes the weaker, K a2peak 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 betweenq, and
inter-planar distances in the crystal (“d-spacings”), which give rise to diraction peaks. is is
summarized in the famous Bragg Equation:
l= 2d sin q
which provides the condition for coherent
scattering of the radiation (wavelengthl), directed at an angle q(the Bragg Angle) with respect to the d-spacing of a set of planes in the crystal.
5
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 energy-dispersive 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.
6
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.
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.
7
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
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.
Toolbar 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).
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.
Graphics Pane 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.
Parameters List is 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 diraction pattern changes.
Patterns 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.
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-and-dragging the drawer edge (Mac) or the pane divider (Windows).
Displaying a Diffraction Pattern
CrystalDiract can read from three kinds of les: text les, crystal structure les, and saved diraction session les.
To load a le in a new window:
Do one of the following:
• Drag-and-drop a le onto the CrystalDiract application icon;
• Launch CrystalDiract, then drag-and-drop a le into the window that appears.
• In CrystalDiract, chooseFile > 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;
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.
8
Te CrystalDiract-for-Windows interface, showing diraction patterns in “Film” mode
Toolbar Parameters List Graphics Pane Patterns Drawer Info Bar Parameters Palette Patterns List
Te CrystalDiract-for-Mac program interface, showing calculated and observed diraction patterns
9
Text Files
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.
Session Files
e third type of le that
CrystalDiract can read is its own “session le” format (letypeCRDF,
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.
Use CrystalMaker to visualize (and verify!) the structure before you proceed to simulate its diraction properties.
Scrolling and Zooming
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.
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).
x-scale y-scale
auto-scale y
auto-scale x & y
CrystalDiract’s axis scaling tools
10
Measuring a Pattern
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.
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).
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. You can also save a diraction experiment as a
self-contained “Session File”, you can print, and you can record your favourite settings in a Preferences le.
Printing
e full version of CrystalDiract lets you print high-resolution diraction patterns, which are scaled to t your chosen page size.
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 thePreferences 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.
Help and Updates
Most controls have tool tips associated with them. For detailed help, choose theHelp >
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 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.
11
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.
Locating the package contents
CrystalDiract-for-Windows has the ASF.datle
saved in the Application Data folder.
You can edit the ASF.datdata 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 b1a 2 b2a 3b3 a 4b4c 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.
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Simulation Preferences
To speed up the simulation of diraction data (e.g., for massive structures such as proteins), you can suppress all reexions below a minimum
d-spacing. You can also limit the maximum number of reexions (so that only those with the highest d-spacings are used).
To set your simulation preferences:
1 Choose:CrystalDiffract > Preferences
(Mac), or Edit > Preferences (Windows).
2 Navigate to the Prole tab.
2 In the Generate Reexions group, set the Minimum d-spacing eld, enable theLimit number to option and enter a maximum number
of reexions.
3 Click theSave button to store your new settings.
ese will apply to any new windows.
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).
Radiation Type
You can use the Diffract menu to switch between
x-ray or neutron diraction. e diraction pattern is recalculated, using x-ray scattering factors or neutron scattering lengths that are stored with the program.
Diffraction Modes
CrystalDiract can simulate a number of experimental types, which cover the main techniques for powder diraction:
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. CrystalDiract allows you to simulate
angle-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 Wavelength sheet showing CuK a1and 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 a1and K a2lines.
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Energy-Dispersive (EDS) 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
):-l= 2d sin q
If lcan 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.
Time-of-Flight Diffraction
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. 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).
14
(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 sinq
Now, given a primary ightpath (the distance from the moderator to the sample) of L1and 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 sinq
hence:
t = 2 d L (mn/h) sinq
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 for the Lorentzian prole, with its intensity distribution spread over a wide range of x values.
15
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 theDiffract
> 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-of-ight 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 theDiffract > Percent Strain command
to specify a value for the strain.
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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 theSite 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:
Si 0.7 Al 0.3
or: Ca 0.56 Mg 0.41 Al 0.03
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.
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)
17
Interactive Parameter Control
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.
To show the Parameters List, click the Toolbar’s
Parameters button:
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.
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 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
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.
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Background
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.
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.
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.
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 eld to appear below the list, allowing you to edit that item’s value. (When editing the text, press the
Enteror Return keys to replot the structure.)
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.
• 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.
19
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.
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.
Editing the volume fraction of Silicon in a simulated three-phase mixture
To remove phases from a mixture, turn o the corresponding checkboxes in the Structures list.
Tip: The Structures list’s Actionsmenu 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
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 thePlot > Separate command, or by clicking the Toolbar’s Unmixbutton.
20
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.
21
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
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.
Loading Observed Data
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:
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 le is a Mac le, with letype “TEXT”.
To open a le in a new window:
• Choose theFile > Open 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.
Applying Plot Styles
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.
Observed & Calculated Data Compared
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.
You can manually control the relative scaling for a selected observed pattern, using the two y-scaling buttons on the toolbar:
Te oolbar’s Relative Scale buttons
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:
Te oolbar’s Shift controls
You can also use the Arrow tool to click and drag a diraction pattern, when plotted in Graph mode.
22
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
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.
e legend for the residual graph/lm also displays the sum-of-squares dierence between the
calculated and simulated data:
error =
Σ
(obs - calc)2is value corresponds only to the currently-displayed plot range. It can be a useful reference when attempting to ne-tune the calculated data in
order to match the observed data.
ePlot > Data Style submenu allows you to
choose how the observed data are plotted (e.g., crosses, squares, lines between points, etc.).
Identifying an Unknown Substance
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.
A more convenient way of comparing phases is to use the Patterns List, which is described next.
23
Managing Multiple Patterns
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. 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:
Do one of the following:
• Click the Patterns icon in the Toolbar, or • Press the s key on your keyboard, or
• Choose the menu command:Window > Show Patterns List.
e Patterns list may be displayed as either a slide-out drawer (Mac), or as a window pane (Windows).
Using the Patterns List
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).
To plot one or more patterns:
Do one of the following:
• 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.
To rename a pattern:
1 Select the pattern in the list.
2 Press the Return orEnter keys on your
keyboard (or click on the selected name).
3 When you have nished editing, pressReturn
or Enter to nish, 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:
• 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 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 display only one pattern at a time:
• 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
24
Working with multiple patterns in the same window, using the Patterns List. Here, one item’s name is being edited.
25
General Plot Settings
ePlot menu lets you change the general way in
which all diraction patterns are displayed. You can also customize aspects of the Graphics pane display, including the plot range, gridlines and colours, 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.
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.
Stacked Graphs
In Graph mode you can use the Plot > Stack
command to stack multiple diraction patterns without danger of overlap. You can undo the
stacking by choosing: Plot > Collapse.
Stacked graphs showing how the diraction pattern of a crystal changes with temperature, and the progress of a displacive phase transition.
26
Overlaying Peak Positions
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. 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.
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 thePlot > 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.
Individual Pattern Settings
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.
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.
Strong peaks labelled with Miller Indices. Individual peak proles are shown by the dotted lines. Notice that only the
strongest peaks are labelled in this example.
27 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
modify.
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.
Graph Settings
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.
Examples of dierent 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 CrystalDiract 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.
Plot Colour You can apply dierent colours to
dierent diraction patterns.
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.
28
Customizing your Workspace
CrystalDiract 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 osets between
adjacent windows, or tiled down the screen—using the Window menu’sStackand Tile commands,
respectively.
Synchronizing Windows (Mac)
When comparing dierent structures in dierent windows you can use theWindow> 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.
Cloning Windows (Mac)
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.
