Jade 5.

Jade
5.0

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Jade 5.0

Jade's Main Window

An example of Jade's main window is given below with identification of its main interface components:

The Main Toolbar provides instant access to routine functions of XRD pattern processing. You can
perform most of the toolbar functions from the main menu as well. But with the toolbar, you can bypass
the menu dialogs that allow you to change the default parameters of the functions.
Most of the toolbar buttons in Jade respond to the right mouse button as well as the left, to provide
related or opposite functions on a single toolbar button, and the yellow tooltips use the notation 'L> ... |
R> ...' to indicate actions associated with the left and right mouse buttons. Throughout Jade's help
system, the following terms are used to describe the operations of a mouse: 'Left-Click' means to click
with the left mouse button, 'Right-Click' means with the right mouse button, 'Left-Drag' means click and
drag with the left mouse button, etc.
You can promote most of the 2nd-level menus to the main menu bar for easier access by using the
toggle switch '||' after the Help menu. They behave as pop-up menus on the main menu bar, and some
are also accessible with right-clicks at the relevant places in the main window. The Load menu appears
only if you have saved work into *.SAV files. The Print menu appears only if you have saved print
settings from the Print Setup window; these print items are called 'preset prints'.
The top (pattern) window always displays the pattern in full range. The bottom (zoom) window is
highlighted with a rubber-band or opaque box if it's less than 80% of the full data range in either

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intensity or angle. You can alter the heights of these two windows by dragging the boundary between
them up or down. You can hide the top window with a double-click above it (just below the main
toolbar, where the scan setting is displayed) if you need a larger zoom window.
The Zoom Window:
The zoom window is where most of the pattern processing is carried out. There are several ways you
can zoom & pan the pattern (we call it focusing the zoom window) besides using the Zoom & Pan
Toolbar along the right side of the zoom window:
Drag out a rubber-band box in the zoom or the pattern window any way you like. Tip: It's easier to
drag from top down rather than from bottom up, and you can drag to the left or to the right when you
need to reach the very beginning or ending of the pattern.
Double-click almost anywhere in the zoom or the pattern window (such as on top of a peak).
With the Shift key down, left- or right-click anywhere in the zoom or the pattern window for instant
vertical zoom.
Use the Home & End, Page-Up & Page-Down, and arrow keys when the zoom window has the
keyboard focus (i.e., after you have clicked in the zoom window). Jade also transfers the keyboard
focus to the zoom window after you have used the zoom & pan toolbar.
Focusing the zoom window is a flexible and effective way for Jade to carry out certain tasks for which
only a limited range of your data may be required or desired. These tasks include search/match, plot
printing, statistics, and pattern data output, among others.
The pattern & zoom windows and their surroundings also respond to the right mouse click for quick
access to some routine operations. Experiment and discover for yourself! For detailed information on
the toolbars, refer to the following topics: Edit & Cursor Toolbar, Scan Overlay Toolbar, PDF Overlay
Toolbar, Quick Annotation Toolbar. The overlay toolbars can be placed just below the main toolbar or
above the status bar, and are accessible only after you add scan patterns or PDF overlays in the zoom
window. The quick annotation toolbar appears only after you have done a peak search and/or overlaid
PDF d-I lines. You can hide most of the toolbars from the 'View | Hide Toolbars' menu should you be
overwhelmed by them. You can learn a great deal about Jade just by reading the tooltips that appear
when you leave the mouse pointer over a screen object such as a tool button. In addition to what you
can do from the 'Properties' dialog of Windows desktop, you can customize most of the display colors in
Jade from the 'View | Customize Colors...' menu.
The Status Bar:

Besides providing information on various data items, the bottom status bar also serves as an array of
toggle switches that can be used to turn on/off the individual items with a simple click of the mouse.
You may not see all the items on the status bar if your screen is less than 1024 pixels in width. If you
have done analyses on a pattern and saved results to files, some of the 3-letter items (file extensions)
will light up to indicate the presence of companion files to the pattern file being displayed. If you hold
the mouse pointer over them, Jade will tell you what type of files they are. There are two kinds of
companion files created by Jade: (a) those that can be restored in the zoom window (*.SAV, *.PKS,
*.DSP, *.PDF, *.PFT, *.RPT); (b) those that can't (*.PID, *.SZS, *.KSI, *.FIT...). The (a) files are in
general written as binary files, and the (b) files as plain text files for reports. You can restore or browse
these files simply by clicking their extension items. Notice that you can create more types of report files
in Jade than can be indicated by the 3-letter items on the status bar. You can find and browse all report
files from the 'View | Reports & Files | Browse Report Files' menu. Similar arrays of the 3-letter items
are provided on the Read Pattern Files Dialog and Thumbnail Browsing Dialog for easy recall of
analysis results produced by Jade.
If you turn on the processing logs from the User Preferences dialog, you can browse it simply by
clicking the 'LOG-ON' item on the status bar. Otherwise you can right-click it to bring up the

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preferences dialog.
Close Jade down - Exit from Jade: There are three ways to close Jade down:
Choose the 'File | Save & Exit' menu: save the current work (if any) as well as the program settings
before closing Jade down. Jade will automatically restore the saved work on its subsequent start-up.
See File Output topic for more information on saving work.
Choose the 'File | Exit' menu: save the current program settings but prompt to save the current work
(if any) before closing Jade down. This option is the same as double-clicking the small icon on the
upper-left corner of the main window (Alt+F4).
Choose the 'File | Quit' menu: close Jade down without saving the current work as well as the
program settings. This option is usefull if you have loaded an old saved file '*.sav', which overwrites
the current program settings.
Tip 1: You can drop output files written by Jade as well as pattern files onto the zoom window from the
Explorer or from the Read Pattern Files Dialog.
Tip 2: You can change the font (type style & size) used to display the text in the main window (such as
axis labels and scaling) from the User Preferences dialog.
Tip 3: You can resize the main window by pressing the Ctrl+J key repeatedly.

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Jade's Dialog Windows

Jade's user interface is pattern-centric and non-hierarchical in task execution. There is no predefined
path for pattern processing in general. Basic pattern processing tasks can largely be accomplished with
the drop-down menus and the toolbars. More advanced tasks may require working with function dialog
windows that interact with the zoom window.
There are two kinds of dialog windows in Jade with regard to their behavior: (a) modal dialog windows,
and (b) modeless dialog windows. A modal dialog window requires you to close it down in order to
interact with its parent window. When you click outside the frame of such a dialog window, you will hear
a beep from the PC speaker telling you that the click is invalid and thus ignored. A modeless dialog
window has no such restriction, behaves very much like a toolbar or toolbox, and usually has no OK and
Cancel buttons to dismiss it. The word 'modeless' means that the program is not constrained into a
particular mode of operation which it needs to be released from. Note that dialog windows are often
called dialog boxes or just dialogs in this on-line help.

Jade implements many modeless dialogs to augment the flexibility of its user interface. You can tell
one of them easily by the thumbtack icon on its title bar. An example of such a dialog window is the
Background Fitting dialog. When you make a change on such a dialog, it is carried out immediately by
Jade and new results may appear in the zoom window. You can then use the zoom & pan tools to
examine the changes without having to close the dialog, and to try other changes if necessary. This
immediate feedback greatly speeds up the data analysis. With experience you should find you can get
things done much faster in Jade.
You should also realize that most of the dialog windows that show a list of items are resizable, as
indicated by the little square button at the right end of the title bar. An example is the Read Pattern Files
dialog shown above. In general you can sort the list by clicking the desired column header, reverse the
sorting by clicking the same column header again, change the widths of columns by dragging in
between their headers, and even swap them by dragging their headers to the left or right. Jade will
remember width changes of certain columns it deems important (such as those for file names, scan id's,
phase id's). Any width changes made to the columns of numbers will not be remembered by Jade, nor

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will be the column order you may swap. However, Jade will utilize the current column widths in printing
some lists (such as file list and PDF list) so that you have some control over how to fit the text on the
printed page. You can also change the printing orientation and font of most reports on the Report tab of
the User Preferences dialog.
Note that some dialogs may not display the sizing grip at the lower right corner even though they are
resizable. Jade utilizes the title bar of dialog windows to display relevant information (such as file name
of the pattern being processed for the sake of screen capture). Should the caption overflow the title bar,
you can get around it either by resizing the dialog window if it's resizable or by changing the font type
(such as using non-bold type face) or font size of the 'Active Title Bar' item on the Appearance tab of
desktop setting.
Tip 1: You can press the ESC key to close most of the dialog windows in Jade.
Tip 2: You can bring up context-sensitive help by pressing the F1 key or the Help button on the dialog.
Tip 3: You can copy the active dialog window to the clipboard by pressing the Alt+Print-Screen keys.
Tip 4: You can place the active dialog to another monitor using the Alt+Arrow keys instead of dragging if
you have multiple monitors supported on Windows 98. Jade will remember where to display the dialog
next time you show it.

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Jade's Main Toolbar

The following diagram identifies the button groups on the toolbar:

The main toolbar provides instant access to routine functions of XRD pattern processing. You can
perform most of the toolbar routines from the main menu as well. But with the toolbar, you can bypass
the function dialog windows that allow you to change the default parameters of the functions (which you
often won't need to do).
Most of the toolbar buttons in Jade respond to the right mouse button as well as the left, to provide
related or opposite functions on a single toolbar button, and the yellow tooltips use the notation 'L> ... |
R> ...' to indicate actions associated with the left and right mouse buttons. You can get a lot of ideas
about Jade's interface from these tooltips; sometimes you need to wait momentarily for them to appear
when you point the mouse cursor at a screen object.

Buttons to Access & Read Pattern Files:

The 1st button finds and reads the latest or newly created pattern file in the folder being pointed to on
the Read Pattern Files dialog. If it is your data acquisition folder, the newly acquired pattern file will be
displayed, and the existing data in the zoom window will be cleared away. But if you want to overlay the
latest file in the zoom window, you can hold down the Ctrl key while you left-click the 1st button. You
can also instruct Jade to read the latest pattern file automatically on start-up (see the option on the Misc
tab of the User Preferences dialog). You can fetch a pattern file by its name if you right-click the 1st
button, causing an input box to appear, for example:

You don't need to enter the file extension if it's the same file type as the one being displayed. You can
include a folder name in the input if you want to fetch a pattern file from a different folder.
The 2nd button reads and displays the next (left-click) or previous (right-click) pattern file on the sorted
list of files in the current data folder.
The 3rd button brings up the Read Pattern Files dialog for pattern file listing and selection. If you hold
down the Ctrl key while left-clicking, Jade brings up the Thumbnail Browsing dialog instead. If you
right-click this button, Jade brings up the Window's file-open dialog for you to read output files saved
from Jade as well as all pattern files available on the read pattern files dialog. An example is shown
below:

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Tip: You can overlay a pattern file from this dialog if you hold down the Ctrl key while selecting it.
The 4th button provides quick access to the floppy disk. If you left-click on it, Jade brings up the Read
Pattern Files dialog to list all pattern files on the floppy. Although we don't encourage you to use
removable media such as floppies for routine analysis, this button makes it easy for casual users such
as students to process their data. There is an option on the Misc tab of the User Preferences dialog to
tell Jade to copy the pattern file to the current User/Project folder whenever a new pattern file is read
from the floppy. Therefore the same file can be accessed again from the hard drive without the need to
keep the disk in the floppy drive. The same is also true if you access pattern files over the local
network. If you right-click on the floppy button, Jade brings up the Copy File dialog for easy data
archival.
MRU File List: Jade maintains a list of Most Recently Used (MRU) pattern files for quick recalls.
Although you can access this list from the Read Pattern Files dialog, it's also conveniently displayed
below the four buttons just described (e.g., ). By default Jade shows the last eight
pattern files on this drop-down list, but you can see more or fewer of them using the up-down button
next to the list. Tip: You can select a pattern file from the MRU list to overlay if you hold down the Ctrl
key.

Buttons to Print and Save Data:

The 1st button will print the current display in the zoom window to the default printer. If you hold down
the Ctrl key while left-clicking, the Print Preset list (if any) will appear. If you right-click this button, Jade
brings up the Print Setup window instead.

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The 2nd button saves the current work to a file (*.SAV) which includes most of the current program
settings as well as all the existing overlays. Notice that the 'SAV' item on the main status bar will light
up upon saving the work, which you can restore simply by clicking the 'SAV' item. A list of available
*.SAV files is accessible from the 'File | Load' menu. Jade can also save the current work for you
automatically upon closing. See the File Output topic for more information regarding the *.SAV file. If
you right-click this button, the 'File | Save' menu will appear for saving various data items that may be
present in the zoom window. Refer to the File Output topic for more information about saving data from
Jade.

Buttons to Process & Analyze Data:

The 1st button carries out the automatic peak search and marks the found peaks in the zoom window.
If you right-click this button, Jade brings up the Peak Search dialog for setting the search parameters as
well as the options of labeling peaks. See the Edit & Cursor Toolbar for how to edit peaks manually,
and the Peak List Report for viewing and printing the peak listing.
The 2nd button applies the active filter to the current data (the active filter is the last item selected
under the 'Filters' menu and by default is pattern smoothing). If you right-click this button, the Pattern
Smoothing dialog will appear together with the smoothed pattern being overlaid in the zoom window.
See the Data Filtering topic for more information on the available filters in Jade.
The 3rd button swaps the display pattern between the 'raw' and the derived data. Jade maintains a
copy of 'raw' and derived data after certain analyses such as background removal, data filtering,
calibration, and simulation. The 'raw' data is the data just before the analysis is carried out. Therefore
it may not be the original raw data after two consecutive steps of analysis. The current pattern will
always be used for subsequent analysis. You may consider this swap button to be a single-level undo in
some situations. You can always restore the original raw data by reloading the file from the most
recently used (MRU) file list, which is conveniently located above the pattern window.
The 4th button shows or hides the difference pattern between the 'raw' and the derived patterns. This
button is activated only when the derived pattern is visible. By default, the difference is I(raw) -
I(derived), but you can invert it to I(derived) - I(raw) if you right-click this button. You can save the
difference pattern from the 'File | Save' menu and Jade will reset negative data points to zeros in
converting the difference pattern to the primary pattern.
The 5th button carries out three possible tasks in this order: (1) applies external theta calibration to the
current pattern if a pre-built calibration curve is available, or (2) builds the calibration curve using the
current PDF overlays, if present, as reference standards or the designated standard on the calibration
dialog, or (3) brings up the calibration dialog if you right-click it. See Theta Calibration dialog for more
information.
The 6th button carries out profile fitting to the peaks in the zoom window using the current profile
parameters. If you hold down the Ctrl key and left-click this button, Jade profile-fits all peaks in the
pattern one by one or cluster by cluster for overlapping peaks. If you right-click this button, Jade brings
up the Profile Fitting dialog. See the Edit & Cursor Toolbar for how to insert and adjust initial profiles
manually.

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Buttons to Identify Phases & Access PDF Database:

The 1st button fits a line or curve through an array of automatically sampled tie points on the pattern
background, or removes the background using the fitted line or curve if clicked once more. Tip: The
search/match (S/M) button will remove the background automatically if the line or curve is present. If
you hold down the Ctrl key and left-click this button, Jade strips the K2 peaks without removing the
background. If you right-click the BG button, Jade brings up the Background Fitting dialog. See the
Edit & Cursor Toolbar for how to edit the BG tie points manually.
The 2nd button carries out phase identification on the data in the zoom window using the current S/M
parameters. If the background level is significant in the pattern, Jade will prompt you to remove it. If
you right-click this button, Jade brings up the Pattern Search/Match dialog.
The 3rd button brings up the PDF Retrieval dialog if the PDF index files have been established;
otherwise Jade brings up the PDF Setup dialog so that you can establish them. The input box next to
this button allows you to add PDF overlays to the zoom window as a set of colored d-I lines if you have
access to the PDF database and have created the PDF index files. You can recall a PDF reference
'standard' (also called a PDF card) by entering its PDF number (such as 46-1045) or a mineral name
(such as Quartz) into this input box and then pressing the Enter key. When entering a PDF number,
Jade recognizes 461045 or 46 1045 or 46,1045 or 46_1045 or 46/1045 or 46.1045 all as 46-1045. If
you enter a number such as 12345, Jade takes it as 12-345.
If you enter a partial mineral name, Jade will recall all minerals whose names contain the partial name.
If you enter a chemical name or formula, Jade will search the PDF database for phases containing the
name or formula you typed. This search tends to be slow but you can always perform fast Boolean
chemistry retrievals from the PDF Retrievals by Chemistry dialog. In any case, Jade overlays the
matches in the zoom window if there are less than 17 hits; otherwise Jade brings up the PDF Retrieval
dialog to list them for selection. Notice that the PDF Overlay Toolbar appears upon overlaying PDF d-I
lines.
You can also enter a filename with the extension of PLF or PDF in the PDF input box. A PLF file can
contain a list of PDF cards that you retrieve and save on the PDF Retrieval dialog. A PDF file can
contain a list of d-I files (*.DSP) as well as the PDF cards that you overlay and save in the zoom
window. If you find that you routinely overlay a certain set of PDF cards, these PLF or PDF files can
come in handy. You can find the existing PLF files by clicking the 'PDF' label before the input box, and
restore a PDF file simply by clicking the 'PDF' item on the status bar.
Jade remembers the last 99 entries you typed in the input box. When you select an entry from this
input list, Jade overlays it in the zoom window automatically. You can hold down the Ctrl key to prevent
this auto-loading if you want to edit the selection.
Tip 1: You can leave out the file extension in the input if you prefix the filename with a period (i.e., dot).
Tip 2: You can bring up the PDF Retrieval by Chemistry dialog if you right-click this CD button.
Tip 3: You can recall an ICSD phase by entering 'ICSD=#' or 'FIZ=#" in the PDF input box, where # is
the ICSD/FIZ number.

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Active Radiation Anode: See Change Radiation Wavelength.

To avoid popping up message boxes that require you to dismiss them, Jade uses the Message &
Progress Indicator area quite often to show what it's up to or has done. You should check this area if
you are wondering about the results of your last action or the appearance of an hour-glass indicating a
time-consuming process. Jade brings up the on-line help if you click in this area. Tip: You can cancel
most of the lengthy processes in Jade by pressing the ESC key.

Task Macro for Auto-Processing:

If you left-click the Macro button when there is an active task macro, Jade executes the macro on the
current pattern. Otherwise the left-click (or a right-click) brings up the Setup Macros dialog. If you have
assembled more than one task macro, you can choose one of them to be active from the macro list
box. To process multiple pattern files using the active macro, you need to bring up the Read Pattern
Files or Thumbnail Browsing dialog, select the files to process, and then click the Macro button on the
dialog window.

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Zoom & Pan Toolbar

This toolbar is activated after one or more patterns have been read into Jade. Its placement is fixed.
The following diagram gives the names of its tool buttons:

Some of these buttons have a unique behavior: they generate continuous actions like the scroll bar
while being depressed; both mouse buttons are used with the right button reversing the action of the left
button. The speed of zoom & pan depends on the complexity of display as well as on the power of your
PC. On a fast PC, you can speed up or slow down the scrolling on the Display tab of the User
Preferences dialog. Jade will beep when you reach the limits of zoom & pan. You are encouraged to
experiment with these buttons.
Zero Offset 2T(0) Button: While holding the Ctrl key down, you can shift the raw pattern to the left or
right by adjusting the overall zero offset of the scan, an operation that's best performed when you have
a reference standard overlaid in the zoom window. The amount of zero offset in 2 is displayed on the
2T(0) box next to the scan ID. If you do not hold down the Ctrl key, clicking the button will reset the
offset to zero. You can also shift the zero using the left/right arrow keys if you hold down the Shift key
while the zoom window has the keyboard focus, and enter a precise offset value in the 2T(0) input box.
You can keep the zero offset for reading a new pattern if you check the 2T(0) box. Jade will consider
the offset value in peak reports as well as search/match, but will reset it to zero for tasks such as theta
calibration, cell refinement, and pattern indexing. In those cases, angular calibration with internal
standards should be used to obtain precise peak locations.
Reflection Marker Height Adjustment Button: If you perform a task such as theta calibration or cell
refinement, a set of reference reflection markers will be displayed in the zoom window. These markers
are not considered as the regular PDF overlays, which have their own set of scaling tools. You can use
this button to adjust the heights of these markers. If you hold the Ctrl key down, clicking this button will
reset the markers to the default heights.
Derived Pattern Vertical Offset Button: If you perform a task such as pattern smoothing and theta
calibration, Jade overlays the derived pattern in the zoom window. This button allows you to offset the
derived pattern up or down so you may have a better view to examine before accepting it for
subsequent analysis. To eliminate the offset, hold down the Ctrl key while you click the button.
Auto Scale and Vertical Offset Button: This button toggles the vertical scale of the zoom window
between the maximum peaks in the zoom window and the whole pattern. You may find it handy in
operations such as search/match focus in which Jade implicitly renormalizes the peak intensities in the
zoom window in order to identify minor and trace phases.
If you hold down the Shift key with this button, you can offset the baseline of the primary pattern for
purposes such as a display of 'mirror' comparison with an overlay that has been flipped upside down (by
entering a negative scaling factor for the overlay on the Scan Overlay List dialog). An example of this
display is given below:

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Vertical offset of the primary pattern could also be desirable for viewing PDF d-I lines when the pattern
has a high background level. You can reset the vertical offset to zero if you hold down the Ctrl key.
Vertical Zoom Button: This button zooms the pattern in or out vertically. You can slow it down by
holding down the Ctrl key, or speed it up by holding down the Shift key with the button. Tip: You can
press the up/down-arrow keys for vertical zoom.
Horizontal Zoom Button: This button zooms the pattern in or out horizontally. Like the vertical zoom
button, you can slow it down or speed it up by holding down the Ctrl or Shift key with the button. You
can use the left/right arrow keys for horizontal zoom if you hold down the Ctrl key.
Horizontal Pan Button: This button pans the zoom window left or right. Hold down the Ctrl key if you
desire a slower pan. You can pan by the whole zoom window at once if you hold down the Shift key.
Tip: You can press the left/right arrow keys to pan it to the left or right.
There are other fast ways to zoom & pan:
Drag out a rubber-band box in the zoom or pattern window any way you like. Tip: It's easier to drag
from top down rather than from bottom up, or drag to the left if you want to zoom to the starting
angle. You can also release or tie the rubber-band box to the bottom of the y-axis on the Display tab
of the User Preferences dialog, and reverse this behavior in dragging by holding down the Ctrl
key---i.e., if the rubber-band box is tied down, holding down the Ctrl key will untie it, and vice versa.
When the rubber-band box is tied down, Jade auto-scales the display to the maximum peak in the
range if you zoom and pan in the pattern window.
Double-click almost anywhere in the zoom or pattern window (such as on top of a peak).
Use the Home & End, Page-Up & Page-Down, and arrow keys when the zoom window has the
keyboard focus.
With the Shift key down, left- or right-click anywhere in the zoom or pattern window for instant vertical
zoom.
You can initiate auto-scrolling by pressing the space bar when the zoom window has the keyboard
focus, and stop it by pressing the space bar again.
Focusing zoom window is a flexible and effective way for Jade to carry out certain tasks in which only a
limited range of your data may be required or desired. These tasks include search/match, plot printing,
and statistics and data output, among others.
Full Range & Zoom Window Display Button: This button flips the zoom window between the full
range display and the last few zooms if any (otherwise it simply refreshes the screen). If you right-click

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it, Jade brings up the Zoom Window Display dialog, on which you can specify, for example, the exact
range of display for purposes such as comparable prints and painting peaks.
Tip: You can pan the display in the zoom window by dragging the zoom-box highlight in the pattern
window left and right, and toggle auto-scaling to the maximum peak by holding down the Ctrl key while
you drag.

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Data Cursors & Editing (Edit & Cursor Toolbar)

This toolbar implements a variety of manual editing functions and data cursors. These buttons apply to
the mouse pointer working in the zoom window. They are mutually exclusive--you click one of them
and it stays depressed to indicate its active state and the mouse pointer changes into a crosshair cursor
while in the zoom window.

Cursor Off/Zoom: This is the default state, in which you can drag out a rubber-band box to zoom or
right-click for a quick menu in the zoom window. If you click this button once more, you can bring up
the docking menu to align the toolbar to the top and bottom pattern windows. You can minimize the
toolbar with this button if you hold down the Ctrl key.
Magnifying Cursor: Activated only if there are more than 500 data points in the zoom window. This
cursor lets you magnify any region of the pattern onto a pop-up window by moving the mouse pointer
with a framing rectangle in the zoom window. You can move and resize the pop-up window if desired.
You can also resize the framing rectangle by left/right-click in the zoom window while holding down the
Ctrl or Shift key. If you simply left-click in the zoom window, Jade zooms to the framed image. If you
right-click in the zoom window, Jade starts the auto-scrolling by sliding the framing rectangle left/right.
You can speed up or slow down the scrolling by pressing the up/down arrow key repeatedly.
Peak Edit Cursor: With this cursor, you can insert, move, and erase peak markers in the zoom window
using the following operations of mouse and keyboard:
To mark a peak, left-click under it. Jade does a centroid fit in the vicinity to locate its apex. Hold
down the Ctrl key to prevent the centroid fit and mark it on the exact location of the crosshair.
To move a peak marker, left-click it to pick it up and drag it away. You can also move a marker using
the keyboard arrow keys after it has been selected. A newly inserted marker is always selected for
the keyboard operations.
To erase a peak marker, right-click it. You can also erase a marker using the Delete key after it has
been selected.
See Peak Search dialog for how to find and label peaks, and Peak Listing dialog for how to review
peaks.
Peak Paint Cursor: With this cursor, you can estimate peak width by moving the mouse, or paint and
integrate one or more peaks by dragging along the baseline. There are other ways to paint peaks and
obtain peak areas. See Paint & Integrate Peaks for more information.
BG Edit Cursor: With this cursor, you can insert, move, and erase the tie points (dots) that control the
shape of the fitted background curve:
To insert a tie point, left-click at the desired spot. You are not allowed to insert points too close to
existing ones.

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Jade 5.0

To move a tie point, left-click to pick it up and drag it up/down. Tip: Jade also drags the adjacent dots
along if you hold down the Ctrl key. You can also move a tie point using the up & down arrow keys of
the keyboard after it has been selected, and hop to adjacent tie points using the left & right arrow
keys. A newly inserted tie point is always selected for the keyboard operations.
To erase a tie point, right-click it. Notice that the first and last tie points can't be removed but can be
dragged up/down. You can also erase a tie point by selecting it and pressing the Delete key from the
keyboard.
You can avoid the need for editing the tie points by adjusting the sampling parameters on the Fit
Background dialog.
If you try to identify weak peaks (less than a few % in peak height) with the Profile-Based S/M, it is
critical that you manually fit the background as precisely as possible, since a slight over- or
under-subtraction of background could dramatically affect the relative peak intensities of the minor or
trace phase(s) you are looking for.
Data Edit Cursor: With this cursor, you can edit the raw data of a pattern graphically. Jade does not
save the altered data back to the pattern file--i.e., only a copy of the raw data is being manipulated
here. The following mouse operations are supported for editing data:
Left-Click: Data point closest to the cursor in x-axis is set to the cursor level.
Right-Click: Data point closest to the cursor in x-axis is restored to the original value.
Left-Drag: Data points in the dragged-out line segment are reset around the line with random
intensities. You can set the randomness parameter (Data Noise Sigma) on the Misc tab of the User
Preferences dialog.
Right-Drag: Data points in the dragged-out line segment are restored to their original values.
Left-Drag with the Ctrl key down: Data points in the dragged-out line segment will be rescaled in
intensity. The scaling factor of intensity is the ratio of the line level to the current background along
the line segment. Therefore it's usually not a constant due to the slope of the line as well as the
fluctuation of background.
Left-Drag with the Shift key down: Drag data points near the cursor--very much like pulling on a
rubber string.
You may find this cursor handy should you have to deal with imperfect patterns which are either merged
or truncated, or which contain electronic spikes or abrupt backgrounds due to failing detector or shutter
or grounding problem.
Profile Fitting Cursor: With this cursor, you can insert and edit initial profiles or remove them
graphically. See the Profile Fitting dialog for the details.
With the above cursors, you can display the coordinate values at the crosshair position on a floating
label if you hold down the Ctrl key and move the crosshair cursor. If you press the Alt key at two
different spots in the zoom window while holding down the Ctrl key, Jade will calculate the 2 values
between the two spots and display it in the message area of the main toolbar. You may find this feature
useful for example in estimating the FWHM value of a peak visually. If you depress the 'Long
Crosshair' button, Jade will display the coordinate label in the Cursor Off/Zoom mode without you
holding down the Ctrl key.
K2 Cursor: When you move the mouse into the zoom window with this cursor, you should be able to
see the K2 and K lines of the active anode. You can also display the tungsten L-lines to check for
filament contamination from an aging anode if you click the same button once more. You may need to
adjust the display range of the zoom window in order to see all the cursor lines. Tip: You can use this
cursor to verify if an adjacent peak is from another phase.
Cubic Indexing Cursor: When you move the mouse pointer into the zoom window with this cursor, a
set of vertical line markers will appear corresponding to the allowed set of Miller indices for the cubic

16
Jade 5.0

Bravais lattices. You can select the desired Bravais lattice for the display by clicking the icon button
once more, which causes the following menu to appear:

The cell constant calculated from the hkl values assigned to the current position of the mouse is
displayed in the message indicator of the main toolbar (see the above diagram). You can change the
hkl assignment by left or right clicks in the zoom window in order to reach larger or smaller cells. You
can visually index a cubic pattern with this cursor. Tip: You can use this cursor to obtain an initial cubic
cell for the Cell Refinement dialog. Refer to the d-I Overlay Toolbar for how to visually index tetragonal
and hexagonal patterns, and to the Pattern Indexing dialog for automatic pattern indexing.
Drag Pattern Overlay Cursor: With this cursor, you can move any of the overlaid scan patterns up or
down by dragging at any point of its colored trace in the zoom window. Jade identifies the dragged
pattern by matching the pixel color, and could therefore fail if there is another pattern overlaid in the
same color. You can get around the problem simply by assigning it a different color. You can scale the
overlay intensity if you hold down the Ctrl key while you drag, and offset its 2T(0) zero (i.e., shift to the
left/right) if you hold down the Shift key. Tips: You can apply uniform offsets to all pattern overlays by
pressing the Ctrl+~ key repeatedly; you can also view them in 3D from the 'View | Overlays in 3D...'
menu.
Drag PDF Overlay Cursor: With this cursor, you can shift and scale PDF overlays by dragging any one
of its colored d-I lines in the zoom window. Like the above cursor, Jade relies on the pixel color to
identify the dragged overlay. You can scale the heights (i.e., I% value) of d-I lines by dragging up or
down. You can offset the d-I lines (i.e., 2T(0) zero value) by dragging left/right if you hold down the
Shift key. You can scale the d-I lines in d-space (i.e., d/d(0) value for solid solution) if you hold down
the Ctrl key instead. See PDF Overlay Toolbar for more information.
Tip: You can bring up a number of dialog windows by right-clicking the cursor buttons on the toolbar.

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Jade 5.0

Overlay Scan Patterns & Scan Overlay Toolbar

This toolbar is accessible only after you overlay scan patterns and it can be placed below the main
toolbar or above the main status bar. You can tell Jade to hide the toolbar when there is no overlay in
the zoom window (see the option on the Display tab of the User Preferences dialog). Notice the
appearance of the overlay color palette alongside the zoom window. You can hide the palette by
right-clicking it.

You can add (i.e., overlay) scan patterns in the zoom window in a number of different ways:
Using the Add button on the Read Pattern Files Dialog or the Thumbnail Browsing Dialog.
Drag & Drop Pattern Files from the Explorer or from the Read Pattern Files Dialog.
Hold down the Ctrl key while selecting a pattern file from (a) the MRU File List, or (b) the 'File | Read'
dialog, or (c) fetching the latest pattern file.
Most pattern processing functions in Jade work with the primary (i.e., the 1st) pattern in the zoom
window. The scan overlays are mostly for pattern comparison. However, you can swap the active
overlay with the primary pattern using the Swap button if desired. The current item in the overlay
listbox indicates the active overlay, which can be manipulated with the toolbar buttons. When you
select another overlay using the blue up-down button, Jade flashes it in the zoom window. Notice that a
color-matching line above the overlay listbox also aids in identifying the active overlay. If you right-click
the Swap button, you can also identify the active overlay by flashing it in the zoom window. Although
you can change the colors of scan overlays from the Scan Overlay List dialog, you can also assign a
new color to the active overlay from the color palette (you need to hold down the Ctrl key if there are
PDF overlays in the zoom window).
When you use the Offset and Scaling buttons, you will get more responsive actions on a slow PC if you
focus the zoom window on a small region of your data. To obtain precise offset and scaling values for
an overlay, use the Scan Overlay List dialog instead. You can reset the offset and scaling values to 0.0
and 1.0 or auto-offset/scaling if you hold down the Ctrl key while clicking these buttons. You can also
offset and scale an overlay by dragging it directly (see the Edit & Cursor Toolbar for how); you can
apply uniform offsets to all overlays by pressing the Ctrl+~ key repeatedly; you can also view them in
3D from the 'View | Overlays in 3D' menu.
The Plus & Minus buttons show or hide the addition and subtraction patterns of the active overlay with
the primary pattern, using the current intensity scaling and angular offset values if present. The minus
(difference) pattern is taken as I(primary) - I(overlay), but you can reverse the difference using the
Swap button. If the active overlay has a different step-size than the primary pattern, an interpolation is
automatically carried out in the addition or subtraction. These patterns are overlaid in the zoom window
and can be saved from the 'File | Save...' menu. You can move the display baseline of an addition or
subtraction pattern by dragging the little square at the end of the baseline up or down.
You can bring up the Scan Overlay List dialog by left-clicking the number button. You can hide all scan
overlays rather than erasing them if you right-click the number button, and bring them back by
right-clicking again. You can also hide all but the active overlay with the 'Hide Others' check box on the
Scan Overlay List dialog.
By default, Jade maintains an independent set of colors to print scan overlays. But you can use the
colors assigned in the zoom window for printouts if you check the 'Same Colors of Overlays on
Printouts' box on the Display tab of the User Preferences dialog.
Merging Scan Overlays:

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Jade 5.0

You can merge scan overlays with the primary pattern from the 'Edit | Merge Segments' menu (if they
are not overlapping in scan ranges), or from the 'Edit | Merge Overlays' menu (if they are). In merging
non-overlapping scan segments, Jade fills the gaps with random counts using linear extrapolation from
the two end points. You can control how much randomness to fill in with the 'Data Noise Sigma'
parameter on the Misc tab of the User Preferences dialog. In merging overlapping scan patterns, you
can choose from three different ways to deal with the intensity data in the overlapping regions: (1) take
the average of overlapping data points, (2) take the maximum point, (3) take the summation (i.e., add
them all up). The resulting scan will inherit the step-size and count time of the primary pattern but will
take on the maximum scan range of all overlays. Note: The current angular offsets and intensity
scalings of the overlays will be applied in merging the scan data.

19
Jade 5.0

Overlay d-I List Data & PDF Overlay Toolbar

This toolbar is accessible only after you overlay d-I list data from the PDF database or from d-I list files
(*.DSP) or from the d-I List Editor. It can be placed below the main toolbar or above the main status
bar. You can tell Jade to hide the toolbar when there is no overlay in the zoom window (see the option
on the Display tab of the User Preferences dialog). Notice the appearance of the overlay color palette
alongside the zoom window. You can scroll the palette to see more colors using the up-down button
located at the bottom of the palette column, and hide the palette by right-clicking it.

You can overlay d-I list data as a set of colored vertical lines in the zoom window in a number of
different ways:
Retrieve the d-I list of a PDF card from the PDF database. This is the easiest way to overlay d-I list
data in Jade. See PDF Setup & PDF Retrieval & Main Toolbar for more information.
Read an existing d-I listing file (*.DSP) from the 'File | Read' menu.
Read a 'foreign' d-I listing file from the 'Edit | d-I List File Import...' menu.
Create a new d-I list from the 'Edit | d-I List Editor' menu, and use the Add button on the editor dialog.
Unlike the scan overlays, Jade shows only the last (active) PDF d-I overlay when you add more than
one in the zoom window. You can change this default behavior with the 'Tack Down All New PDF
Overlays' check box on the Display tab of the User Preferences dialog. Nevertheless, you can show
multiple PDF overlays by using the Tacking button on the toolbar selectively. If you right-click the
Tacking button, all overlays will be tacked or untacked at the same time.
The item in the overlay listbox indicates the active overlay that can be manipulated with the toolbar
buttons. Notice that a color-matching line above the overlay listbox also aids in identifying the active
overlay when multiple overlays are displayed in the zoom window. If you right-click the 'Change Color'
button, you can also identify the active overlay by flashing it in the zoom window. Note: Jade uses only
the visible overlays for most pattern analyses and report printing.
You can assign a new color to the active overlay in three ways: (a) using the 'Change Color' button on
this toolbar, (b) using the color palette alongside the zoom window, (c) using the PDF Overlay List
dialog. You can also set the line width of stick bars with the three line markers on top of the color
palette. Note that Jade uses an independent setting of line width to print d-I lines because printers have
much finer resolutions than the screen. You can find this setting on the Misc tab of the Print Setup
dialog.
The Offset & Scaling buttons enable shifting and scaling of d-I lines (also called lines) relative to the
scan pattern in overall I%, theta (2T(0) & d-space (d/d(0)). You can depress and hold them down for
continuous actions with either mouse button. By default, Jade will automatically scale the d-I lines of a
new PDF overlay in heights to the peak nearest to the 100% line of the d-I list. You can turn off this
auto-scaling feature on the Display tab of the User Preferences dialog, and Jade will scale the d-I lines
to the maximum peak in the scan pattern.
When you shift the lines in d-space, you actually shrink or expand the lattice or unit cell of the phase
isotropically since Jade multiplies the d-spacings of all lines by a single variable defined as d/d(0).
Therefore this button makes it easy for you to examine possible solid solutions in your pattern or to
compare isotypical phases from the PDF database. If you multiply the original cell constants by the
d/d(0) value, the results can be used as the starting parameters for cell refinement. You can reset the
offset and scaling values to 0.0 and 1.0 if you hold down the Ctrl key while clicking these buttons.

20
Jade 5.0

If the active overlay is a tetragonal or hexagonal phase with known cell constants, you can also change
its c/a ratio by holding down the Shift key as you depress the d-scaling button. The lines will be shifted
in real time according to the new c/a ratio displayed in the message area of the main toolbar (e.g.,

). Because the a-axis is kept constant in this operation,

you will notice that lines of Miller indices (hk0) will not move as you alter the c/a ratio.
To illustrate these powerful tools, read the DEMO08.MDI Corundum pattern from Jade's demofile
folder, and overlay the hematite from the PDF database. You can shift the Hematite lines to match the
Corundum pattern without holding down the Shift key (i.e., without altering its c/a ratio). Jade will tell
you the cell constants of Corundum from those of Hematite because Corundum and Hematite both
have similar c/a ratios of about 2.73. Now overlay Calcite, which has a c/a ratio of 3.4, hold down the
Shift key as you depress the d-scaling button so that the ratio reaches about 2.73, and release the Shift
key; then shift the lines in d-space until they match the Corundum pattern--you have just indexed the
Corundum pattern using Calcite data!
The 'Card View Dialog' button will bring up the PDF Card Display of the active overlay. The content of
this dialog depends on the type of PDF overlay and the nature of the PDF database. If you have
access to the ICDD PDF2 CD, the card view will have more complete information.
The 'Number of Overlays' button will bring up the PDF Overlay List dialog for more controls such as line
labeling and list ordering. Jade disables the PDF overlay toolbar when the list dialog appears. You can
hide all PDF overlays rather than erasing them by right-clicking this button, and bring them back by
right-clicking it again.
By default, Jade maintains an independent set of colors to print PDF overlays. But you can use the
colors assigned in the zoom window for printouts if you check the 'Same Colors of Overlays on
Printouts' box on the Display tab of the User Preferences dialog. The advantage of maintaining
independent color settings for overlays is to be able to visualize them in the zoom window with a
non-white background color.
Tip 1: You can offset and scale PDF overlays by dragging them directly (see the Edit & Cursor Toolbar
for how).
Tip 2: You can prevent Jade from removing the current PDF overlays when reading a new pattern file.
See the option on the Display tab of the User Preferences dialog.
Tip 3: You can save and read a set of routine PDF overlays from a file. See the PDF section of the
Main Toolbar description.

21
Jade 5.0

Quick Annotation Toolbar

This annotation toolbar applies to the labeling of located peaks, PDF d-I lines, or reflection markers in
the zoom window. It appears only when you do peak search or overlay PDF d-I lines or display the
reflection markers, and goes away by itself after you erase the peaks, PDF overlays, and the reflection
markers.

If you have both the located peaks and PDF overlays in the zoom window at the same time, Jade
applies the toolbar actions to the PDF overlays by default, but you can apply them to the located peaks
instead if you hold down the Ctrl key while clicking these buttons. You can hide this toolbar with the 'x'
button and bring it back either by right-clicking the same spot on the main window or from the 'View |
Hide Toolbars | Annotation Toolbar' menu.
Notice that you have more control over labeling of peaks from the Peak Search & Labeling dialog, and
labeling of PDF overlays from the PDF Overlay List dialog. You can use the same toolbar to show or
hide the Miller indices on the reflection markers which are generated from analyses such as d-spacing
calculation, cell refinement, and pattern indexing.

22
Jade 5.0

Customize Display Colors

Display colors of screen and printouts are fully customizable in Jade. While color settings of d-I &
pattern overlays are accessible from the PDF Overlay List and the Scan Overlay List dialogs as well as
from the overlay palette alongside the zoom window, you can bring up the following dialog from the
'View | Customize Colors...' menu, or by right-clicking in the right margin of the main window:

When you select the display item to change, the preview area on the dialog indicates the current color
settings of the selected item. You can then assign a new color to it either from the palette on the dialog
or from the Windows color dialog which can be brought up with the Palette button.
The 'Data Points/Dots' item applies when you choose to display dots on individual data points of the
scan pattern (see the Zoom Window Display topic for more information). The 'Derived or Profile' item is
for the overlaid pattern created from analyses such as smoothing, calibration, and pattern simulation.
The 'Reflection Markers' item applies to the display of reference line markers from theta calibration, cell
refinement, or pattern indexing. The 'Crosshair Cursor' and 'Rubber-band Box' items render their colors
in combination with the background color of the zoom window (i.e., XOR color in technical terms),
resulting in colors that are unpredictable if the zoom window has a non-black background color.
Jade can maintain four different color schemes: two of them are program defaults and the other two can
be saved and reloaded from the Setting-1 and Setting-2 buttons. Jade always remembers the current
color settings. Color textures can also be rendered on the background of the main window as well as on
all dialog windows.
Display colors of scan & PDF overlays are automatically assigned with random colors when used for the
first time in Jade. New colors assigned to the overlays will be remembered by Jade for future usage
until you reset to one of the four default color schemes. Jade uses similar dialog schemes and
maintains three independent color settings for printing plots:
Black & White Print: No color setting is required.
Grayscale Print: Good for color printers as well as black & white printers. Jade unifies the color
settings of all scan & PDF overlays on a grayscale print.
Color Print: Good for color printers, and the overlays can have individual colors.
For report printouts such as peak listings and PDF cards, Jade uses the 'Page Foreground' color to print
the body of text. Two more colors can be specified on the Report tab of the User Preferences dialog to
print the report title. Refer to the Print Setup window for more information on setting colors of printouts.

23
Jade 5.0

Tip: You can keep this dialog open while interacting with the main window of Jade.

24
Jade 5.0

Display Axes & Cursors & Scaling

Jade can display XRD pattern using the following types of axes:

You can access this list from the 'View | Change Axes' menu. However, it's easier to change a display
axis by directly double-clicking in the axis area or using the axis button located at the left margin.
For logarithmic axis, Jade will change the minimum scale of display according to the minimum count of
the pattern to reduce blank vertical space below the background. You can prevent Jade from doing so
if you hold down the Ctrl key while selecting the log axis.
Notice that Jade always scales and displays the data linearly in angular space regardless of what type
x-axis you choose. All other types of x-axes are only for reference purposes (i.e., they are not linear in
their own axis space). If you choose a display axis that's invalid for the angular range, it'll just be
ignored (e.g., you cannot show d-spacing if the starting angle is less than or equal to zero). You can tell
what type of x-axis is being displayed from the x-axis label at the bottom status bar. You can specify
the precise display ranges in the zoom window from the Zoom Window Display dialog. Jade accepts
display ranges from -360 to +360 degrees in 2 but will not calculate d-spacing when the mouse cursor
is below 0.001 or above 180 degrees.
You can show or hide the intensity scaling by the zoom window either with the option on the Display tab
of the User Preferences dialog or simply by right-clicking the axis buttons. Jade resets any negative
data points to zero in reading a pattern file and will not allow the y-axis scaling to go below zero. If you
choose logarithmic scaling for the y-axis, the minimum y-axis scale is then set at one count and
zero-count data points will be reset to one.
Energy (keV) and wavelength axes are used for energy-dispersive and wavelength-dispersive data.
You must tell Jade which type of data is being displayed from the Instrument tab of the User Preferences
dialog. For energy-dispersive data, the diffraction angle (D) of the detector is required to map the
reflection d-spacings into energy (keV) = 6.2 / (d * sin(D)) or into wavelength (angstroms) = 2 * d *
sin(D). For wavelength-dispersive data, the diffraction d-spacing (D) of the crystal is required to map
the angles () into energy = 6.2 / (D * sin()) or into wavelength = 2 * D * sin(). The default d-spacing
is 2.013 from the (200) reflection of LiF crystal. Refer to the Ascii File Import dialog for how to import
energy- and wavelength-dispersive data.
Regardless of the types of x & y axes you choose to display the pattern, Jade displays the coordinates
(x, y) of the mouse pointer in the status bar independently. By default, the coordinates are expressed
as 2 & d-spacing vs intensity in counts, but can be altered to show a variety of other coordinates by
clicking the cursor boxes in the status bar. You can also display the coordinates on a pop-up label near

25
Jade 5.0

the mouse pointer (see the Edit & Cursor Toolbar topic for how to do this).
Dotted grid lines can also be displayed in the background of the zoom window on the major tick marks
of the x or y axis. Some printers may not print the dotted lines as you see them on the screen, a known
compatibility issue between some printer drivers and the Windows video drivers.

26
Jade 5.0

Zoom Window Data & Display

Jade utilizes the zoom window data & display for a number of analysis tasks besides printing. The
following 'View | Zoom Window' menu is provided so that you have greater control over some of the
display properties in the zoom window:

You can also bring up this menu by right-clicking in the zoom window while holding down the Ctrl key.
The 'Auto Scale' and 'Full Range' menu items reset the display range in the zoom window and their
functions are readily duplicated on the Zoom & Pan Toolbar. The 'Paint Peaks (Auto/Full)' menu items
paint and integrate peaks in the zoom window. See Paint & Integrate Peaks for more information. The
'Reference Plot' menu item hides or shows the reference plots which are generated in the zoom window
from analyses such as FWHM curve plot, theta calibration, cell refinement, and pattern indexing.
You can also display background grid in the zoom window to simulate strip charts, and put little dots or
circles on individual data points in the scan pattern. Jade won't display these dots when there are more
than 1001 points in the zoom window. You can choose small (1-pixel) or large (2-pixel) dot size on the
Display tab of the User Preferences dialog. An example of a dot view is given below:

The 'Display Range...' menu item brings up the following dialog:

27
Jade 5.0

The precise display ranges can be specified on this dialog if consistent and comparable views or prints
are desired. You may even enter a display range that's wider than the scan range of your data. Jade
accepts display ranges from -360 to +360 degrees but will not calculate d-spacing when the cursor is
below 0.001 or above 180 degrees.
If you check the X and/or Y Locks, the current display range is locked only for reading a new pattern
file. The locks do not prevent you from scrolling the current zoom window. When the range is
unlocked, Jade always displays a new pattern file in its full range. The Reset button on this dialog lets
you toggle the zoom window display between full range and the last few zooms. You can also save and
restore a list of display ranges for purposes such as painting peaks. See Paint & Integrate Peaks for
more information.
You can select the fill styles to view the primary & difference patterns in opaque mode on the above
dialog. If you have the derived pattern (such as the smoothed or simulated pattern), Jade paints it
instead of the primary pattern. You can set the opaque colors independent of the trace colors by
clicking the color rectangles. Refer to the Scan Overlay List dialog for how to set opaque properties of
scan overlays. An example of an opaque view with two pattern overlays is given below:

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Jade 5.0

Note: opaque visualization is limited to <1002 data points per pattern in the zoom window, and to <8002
points on the printout.
Alter or Correct Scan Parameters:
While Jade does its best to read all types of pattern files created by other vendors, there may be
occasions when you need to alter or correct the scan parameters (i.e., starting, ending, and stepping
angles) of the pattern being displayed. In case the parameters were read incorrectly, you should try
other file types first or review the Ascii import filter carefully before altering the parameters from the
above dialog. Jade will maintain the same number of data points in the pattern when you alter the scan
parameters. But you will be prevented from doing so (i.e., the bottom frame of the above dialog will be
hidden) when derived data such as peak listings are present in the zoom window.

29
Jade 5.0

Multiple User and Project Support

Jade is designed to be able to execute and maintain program settings in the concept of a user or project
id. This id could be the same as, or different from, the log-on user name you give to Windows, and it's
up to you to use it as a user id and/or a project id in Jade. While the Windows user environment is
maintained in the system registry, Jade uses a set of files named after a user/project id to save and
load all program settings. These files reside in a folder created after the user/project id under the Jade
folder, and furthermore all output data files from Jade can be sent to this folder. See the option on the
Misc tab of the User Preferences dialog.
A user/project folder in the name of the current log-on user is created automatically when Jade is run
the first time by the log-on user. In other words, Jade will create a user folder automatically for every
log-on user who uses Jade. Therefore you must have full access to Jade's program folder in order to
run Jade on Win NT. If there is no log-on user registered on Win 95/98, the name given in the
installation of Jade is taken instead. In a multi-user laboratory, it is desirable to have more than one
user id so that the program settings of different users can be maintained independently. In a single-user
setup, you may wish to adapt this scheme for different projects or goniometers or batches of samples
that require different sets of pattern processing and analysis parameters. By default, the following
dialog window will appear after you start Jade:

If it does not appear, you can bring it up from the 'File | User or Project' menu. Jade will list all existing
user or project id's which are associated with the current log-on user or installation user. You can add or
remove a user or project id on this dialog. For an id, you can enter up to 61 alpha-numeric characters,
which must also be a valid string for use as a filename. There is no limit imposed by Jade on the
number of user or project id's you can create.
You can switch user/project id to run Jade on the above dialog. You can keep this dialog open in
switching id's if you check on the first box on top of the id list. If you choose not to display the above
dialog on start-up of Jade, Jade will reload the last user/project id automatically next time you run it.
When you remove an id from the list, Jade will list all program setting files to be deleted for you to
review as shown below, and will remove its folder from the hard drive if it's empty.

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Jade 5.0

You can also use the Browse button to view all the files in its folder. You are not allowed to remove a
user id which is being used in Jade or created using the log-on user name or the installation user name.
While Jade always remembers the current program settings, you can create different setting files in the
same user/project folder either from the 'File | Save | Program Settings...' menu or from the the User
Preferences dialog, and restore them from the 'Help | Restore Setting' menu or on the preferences
dialog.

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Jade 5.0

User Preferences Dialog

This dialog window is accessible from the 'Edit | Preferences...' menu. It summarizes a variety of
program options and parameter settings which could affect the analysis results and the interface
appearance. The best way to understand what all these options are for is simply to try them out one by
one. You can always reset them to the program defaults with the Reset button at the bottom of the
dialog. Preferences on the Display tab are described below with the image showing the default settings:

Auto Hide of Overlay Toolbar: If checked, the overlay toolbar will be hidden when all PDF and scan
overlays are removed from the display. You can also hide and show the overlay toolbar from the main
view menu.
Same Colors of Overlays on Printouts: If unchecked, Jade uses independent sets of colors to display
PDF and scan overlays in the zoom window and to plot them on printouts. Since graph printouts are
mostly on white paper, this option is necessary if you prefer the default black background in the zoom
window.
Tack Down All New PDF Overlays: if unchecked, Jade displays only the last PDF overlays when more
than one of them are added to the zoom window. Check this box if you want all them to appear in the
zoom window at the same time. Refer to the PDF Overlay Toolbar for how to tack or untack the
overlays selectively.
Scale New PDF Overlays to Peaks: If checked, Jade will automatically scale the d-I lines of a new
PDF overlay in height to the peak nearest to the 100% line of the d-I list. Otherwise the d-I lines are
scaled to the maximum peak in the scan pattern.
PDF Overlays in Variable-Slit Intensities: Relative I% data from the PDF database are assumed to
be from fixed-slit geometry. If you check this box, Jade will display all PDF overlays in
theta-compensating slit intensities which are calculated using the formula I(v) = I(f) * sin(), where the
theta values are taken from individual line positions of the d-I list. The theta-compensating slit is a
hardware implementation in which the opening of the incident slit is varied in such a way as to maintain
a constant illumination area on the sample by the X-ray beams at different two-theta angles. You can
also convert the scan pattern between variable & fixed-slit intensities. Refer to the Data Filters topic for
more information.
Width of d-I Lines affects only the display in the zoom window. Jade uses an independent setting of
line width to print the d-I lines & peak markers on graph printouts because most printers have much
finer resolution than the screen. You can set the line width for graph printouts on the Misc tab of the

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Print Setup dialog.

Width of Scan Trace affects only the display in the zoom window and is ignored if there are more than
2001 data points in the zoom window. Like the display of d-I lines, you can set the line width for graph
printouts independently on the Misc tab of the print setup dialog. You may need to specify more than a
few pixels to obtain a thick line trace on a high resolution printer, and there is no limit to the number of
data points for thick trace printout.
Size of Data Points affects the display of individual data points in the scan pattern. See the Zoom
Window Display topic for more information on this option.
Size of Circles/Dots affects the display of data points in all calibration curves and regression plots
(such as size & strain fit) as well as the display of background tie points.
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Preferences on the Instrument tab are described below with the image showing the default settings:

You can change the wavelengths of the active radiation anode if necessary. The Wavelength to
Compute d-Spacing is normally set to K1. However, if you don't see any K2 separation in your data
or don't strip the K2 before peak search, you should choose the K-average wavelength instead. By
default, Jade reads the radiation anode in a pattern file if available and uses the corresponding
wavelengths stored in the programs. However, if you specify the US (User Specific) radiation in an
MDI-type pattern file or in an Ascii import file, Jade will read the wavelength value (if any) from the
pattern file. If you check the 'Override Anode in Pattern File' box, the current anode will be kept for
reading new pattern files---i.e., any radiation information in the pattern files will be ignored. You can
also map (convert) data into a new radiation wavelength in order to compare patterns collected with
different anodes. See the Change Radiation Wavelength topic for how to do this.
Default kV & mA settings are used only on graphs & reports if you choose to print the scan settings.
Jade will read these settings from certain types of pattern files if they are available.
Energy & Wavelength Data enable reading and display of energy- and wavelength-dispersive data.
For the energy data, the diffraction angle (D) of the detector is required to map the reflection d-spacings
into energy (keV) = 6.2 / (d * sin(D)) or into wavelength (angstrom) = 2 * d * sin(D). For the latter, the
diffraction d-spacing (D) of the crystal is required to map the angle () into energy = 6.2 / (D * sin()) or
into wavelength = 2 * D * sin(). The default d-spacing is 2.013 for the (200) reflection of LiF crystal.
Refer to Ascii File Import & Display Axis for more information on how to read and display these types of

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Jade 5.0

data.
Detector Dead Time can be specified in micro seconds (ms) to correct pattern intensity for intense
peaks that saturate the X-ray detector / counter. Refer to your detector manual for how to determine
this number, which should be around 100 to 300 micro seconds for a Geiger-Muller counter, and much
shorter (a few micro seconds) for a solid-state detector. Jade uses the following formula for the
correction: I(c) = I(o) / (1 - CPS * T / 1000000), where I(c) is the corrected intensity of a data point, I(o)
is the observed intensity, CPS is the counts per second, and T is the detector dead time in micro
seconds. Jade will not perform the correction if the product of CPS * T / 1000000 is >0.9. See the Data
Filters topic for how to apply the correction. If you check the 'Apply Dead Time Correction upon
Reading Pattern Files' box. Jade will apply the dead time correction to a newly-read pattern file
automatically.
Goniometer Radius can be specified in millimeters for the purpose of sample displacement
correction. Jade will accept radius values in the range of 50 to 10000 millimeters. See the Data Filters
topic for how to correct for sample displacement. If the radius is not specified, Jade will accept and
report the displacement value in degrees of 2T(0). Otherwise, the displacement will be presented in
millimeters, for example, on the Cell Refinement dialog. You can stamp plot printouts with a
goniometer id if you enter it on this dialog tab. See the Annotation tab of Print Setup dialog for the
labeling option.
FWHM Curve is used for Pattern Simulation from the d-I lists and for crystallite size & strain analysis.
It's a 2nd order polynomial of FWHM values as a function of 2 angles. A few of these curves are
supplied for the purpose of pattern simulation when Jade is installed. You can add new curves to this
list and remove unwanted ones. The 'View FWHM Curve' button shows the current FWHM curve for
you to examine:

For crystallite size & strain analysis, the FWHM curve should reflect the instrument broadening of your
data. Refer to the Crystallite Size & Strain Analysis topic for how to make such a curve.
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Preferences on the Report tab are described below with the image showing the default settings:

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Jade 5.0

Normalize Peak Areas to Scan Stepsize: Peak areas can be reported as the sums of raw counts or
the products of counts and scan step-size. The latter option 'normalizes' the data so that the areas are
invariant to a different step-size of scan.
Estimate FWHM in Peak Search or Paint: Jade estimates the FWHM of a peak using the formula
FWHM = SF * Area / Height in peak search and painting, where SF is a constant related to the profile
shape of the peak and is defaulted to 0.85. You may want to try a few different values of SF to obtain
better estimates of FWHM values for your data. You can visually estimate the FWHM value of a peak
with the crosshair cursor, or profile-fit the peak to obtain a more precise number. Just make sure that
you are comparing the FWHM values of the K1 peak.
Estimate Crystallite Size from FWHM Values applies only to peak search & painting. It gives a rather
qualitative estimate of crystallite sizes due to the way FWHM values are obtained, as described above.
See the Crystallite Size & Strain Analysis for how to obtain precise numbers.
Apply 2T(0) and d/d(0) in Peak ID Report: The Peak ID Reports can use or ignore the current theta
offset (2T(0)) and/or d-scaling (d/d(0)) in compiling the peak identification list. Refer to the PDF
Overlay Toolbar for how to shift the d-I lines relative to the located peaks.
Save Reports Automatically upon Printing: If checked, Jade will create a report file in the default
name (i.e., same name as the pattern file but with the default file extension) whenever you print a report
and there isn't an existing file with the same name in the default folder. You can later browse the report
file simply by clicking the three-letter item on the main status bar.
Print Size, Orientation, and Margins apply only to the printouts of text reports. Jade maintains
independent font size & margins for portrait & landscape orientations. The margins could be specified
in inches or centimeters. You may need to set smaller font size and margins or choose the landscape
orientation to print certain reports which contain numerous columns. Jade simply skips printing the
trailing columns should they overflow the width of a page.
You can print the report title in the color specified on this tab. Jade uses the 'Page Foreground' color,
specified on the Display Color Dialog, to print the rest of the report. You can choose to print or omit the
grid lines on most tabulated reports. You can also fine-tune the vertical centering of text between the
grid lines using the 'Offset(pixels)' parameter. Minor offset may be desirable if you choose a different
font to print the reports. The number of hardcopies to print is a printer-dependent option, and is
effective only for the current session. It'll be reset to one after you close Jade to avoid unintended
copies of printouts.

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Jade 5.0

Print Footnote applies to the 'Institution ID, Folder Name & Time Stamp' printed at the bottom of the
page.
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Preferences on the Misc(ellaneous) tab are described below with the image showing the default settings:

Processing Log File: When turned on, Jade writes detailed processing logs for the sake of record
keeping. For all options other than the 'Pattern FileName.LOG', Jade writes the log files to the current
User/Project ID folder using the following naming conventions:
Write 'User/Project-ID.LOG': Jade creates log files using the current user or project id (e.g., 'mdi.log',
'project-x.log', etc.).
Write Daily Processing Log: Jade creates log files named 'yyyy-mm-dd.log', where 'yyyy' is the
current year, 'mm' the current month, and 'dd' the current day.
Write Weekly Processing Log: Jade creates log files named 'yyyy-w#.log', where # is a number from
1 through 52.
Write Monthly Processing Log: Jade creates log files named 'yyyy-mm.log'.
Write Yearly Processing Log: Jade creates log files in the names of 'yyyy.log'.
Write 'Pattern FileName.LOG': Jade creates log files using the current pattern filename (e.g.,
'demo06.log') to wherever the pattern file resides.
You can browse these log files from the 'View | Reports & Files | Browse Log File' menu. Notice that
Jade will jump to the end of the log file so that the latest logs are immediately visible. Please keep in
mind that the browser dialog can display and scroll only 32K of text at a time, but you can use the 'V'
button or press Ctrl+PageUp/Down keys on the dialog to browse the rest of the log file. You can also
clear the log file while you are browsing it.
Auto Load of Pattern File enables auto-loading of the last or the newly-created pattern file on startup
of Jade. Should Jade fail to start due to this auto-load procedure, you can disable the auto-load by
entering the command line switch '/n' to Jade's shortcut icon. Jade also disables the auto-load if it was
not closed down properly.
Prompt before Saving Files: If unchecked, Jade writes new output files with the default names to the
default folder without prompting, and displays the results in the message area on the main toolbar.

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Jade 5.0

Prompt before Erasing Work: If checked, Jade will prompt you to proceed to erase display items such
as overlays, peak listing, and s/m hit list, but will not do the same if you erase items from a list one by
one.
Write Output Files to Data Folder: If checked, Jade writes most output files to wherever the pattern
files come from. If unchecked, they will all be written to the current user/project id folder. See the
Multi-User Support topic for more information.
Save Program Settings upon Exit: If checked, Jade automatically saves the current program settings
upon closing. You can also save program settings while running Jade from the 'File | Save | Program
Settings' menu. However, you can prevent Jade from doing so when the box is checked by selecting
the 'File | Quit' menu to close Jade.
Save Current Work upon Exit: If checked, Jade will save the current work upon exit without
prompting, and restore it automatically on subsequent start-up. You can also save the current work
while running Jade with the Save button on the main toolbar or from the 'File | Save | Current Work as
*.SAV' menu. See the File Output topic for more information on saving work.
Write Associated Files upon *.SAV: See the File Output topic for explanations.
Copy Floppy Files to Project Folder: If checked, Jade will copy the pattern file to the current user or
project folder whenever you read a new one from the floppy disk or across the local network. See the
main toolbar for more information on floppy access.
Crystallite Size Unit applies to all inputs and reports of crystallite sizes (XS). Jade uses the notations
of XS(A) & XS(nm) as column headers in the listing of crystallite size data. Refer to the Crystallite Size
& Strain Analysis for the 'Crystallite Shape Factor' used in the Scherrer formula.
2-Theta Error Window sets the 2 limit in matching d-I lines to peaks. Jade uses this error window
for analyses such as theta calibration, cell refinement, pattern indexing, and peak id reports. Therefore
the same parameter is also accessible from the dialog windows of the aforementioned analyses.
Data Noise Sigma is used in the generation of random noise for tasks such as editing data and
merging scans. Given a calculated intensity I(c), its randomized value I(r) = I(c) + Noise * (0.5 - RN) *
SQRT(I(c)), where RN is a computer-generated random number between 0 and 1.
Default Font for Plotting & Printing: This setting affects all printouts from Jade as well as the display
of some text on the main window. Only true type fonts are supported by Jade due to the need of font
rotation. You can also choose a different font size to display the axis labels on the main window.
Institution ID is taken from the installation by default and can be altered here for the purpose of
stamping the printouts of all plots and reports.
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Using the Save button, you can save the current preferences together with most of the program settings
by giving them a name id, and restore them in the future by selecting the name id from the listbox next
to the Save button. You can reset all preferences to defaults by right-clicking the Reset button.
Left-click resets only what's on the current tab.
Tip 1: You can also save current program settings from the 'File | Save | Program Settings' menu and
restore them from the 'Help | Restore Setting' menu.
Tip 2: You can flip through all dialog tabs in Jade by pressing the Ctrl+Tab keys.

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Jade 5.0

Data Input and Read Pattern Files Dialog

An example of the 'Read Pattern Files' dialog is given below:

This dialog is used for reading the raw data pattern files only. Output data from Jade such as peak
listings or saved work files are accessible from the 'File | Read...' menu as well as from the status bar
on the main window.
In addition to the file types defined by MDI, Jade supports a variety of others from most of the XRD
hardware vendors. You select the file type and the file folder, and Jade reads the files directly. There
is no file conversion involved in reading all the supported types of pattern files. If you are not sure
which file type to use, choose the 'XRD Pattern Files (*.*)' to list all files in the current folder, and
double-click the pattern file, causing Jade to read it first by matching its file extension, and if that fails,
to give you the option to auto-detect its file type.
The 'N' button (below the Close button) will bring up the Windows file-open dialog to access pattern files
stored across the local network. A network drive or folder connected to Jade will be indicated by the
double backslash '\\' on the folder list. If you right-click the 'N' button or the folder list, Jade starts a
copy of Windows Explorer. You may find it easier to browse the network folders from the Explorer than
from the file-open dialog. You can drag pattern files directly from the Explorer into this dialog or into
the zoom window (when this dialog is not opened). See Drag & Drop Data Files for more information.
Jade auto-detects file type when a pattern file is dropped into the main window.
You can read a new pattern file simply by double-clicking it on the file list. Jade clears the existing data
in the zoom window without warning before showing the new pattern. If desired, you can keep the
existing peak listing and PDF overlays for the new pattern (see the options on the Display tab of the
User Preferences dialog). It should be pointed out that the pattern file is closed after it has been read
into Jade since only a copy of its data is needed in Jade's memory. It's not being kept open like a
document file in word processing. You don't need to close the current pattern in order to read another
pattern file. That's why you don't see the phrase 'File Open' in Jade.
You can add (i.e., overlay) pattern files to the display in the zoom window in the following ways:
Select (highlight) one or more files on the list and click the Read or the Add button. You can select
multiple files either by dragging out a rubber-band box in the 'File Name' column area, or by holding
down the Ctrl or Shift key while you point and click.

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Jade 5.0

Drag a pattern file out of this dialog and drop it onto the main window of Jade. Jade allows you to
drag a file only if you click in the 'Scan ID' or 'Size & Date' columns of the file list. Repeat the
dragging operation to add more pattern files.
Hold down the Alt key and double-click a pattern file on the file list. If you do not hold down the Alt
key, you can still keep the dialog open using the check box before the 'CPS' when you double-click on
the file list.
You can stack the overlays in the zoom window by entering an offset value in the text box located
above the file list (see the above diagram). The offset is specified in percentage of the maximum
intensity of the primary pattern. See Scan Overlay Toolbar for more information on pattern overlays.
Jade can read up to 32,001 data points (minimum 2 points) per scan range in most file types. The
'CPS' check tells Jade to read the data as counts per second. It does not affect the data already read.
If it's unchecked, Jade reads and displays the raw counts as stored in the pattern file. Any fractional
counts of data points will be rounded up to the nearest integers if intensity multiplier is not greater than
one on the File Filter dialog.
If you use MDI's DataScan program to collect multi-range data stored in a single file, Jade reads and
displays them all as pattern overlays automatically. You can then swap any overlay into primary display
for pattern processing from the Scan Overlay Toolbar. You can also merge the multiple ranges into a
single pattern from the 'Edit | Merge Segments/Overlays' menu. Jade will also read the multi-range
data in some file types from other vendors. However, only the essential scan information (i.e., scan
range and radiation anode) will be read, while other instrument configuration data, if any, will be ignored.
To facilitate your file lookup, Jade automatically creates a miniature image (called a thumbnail) of the
pattern upon reading a new pattern file. These thumbnails are monochrome bitmaps of about 1K size,
named with the extension 'jip' after the pattern file. If you have multiple pattern files with the same
name but of different types, it's possible that the existing thumbnail may not match the current file type.
You can then right-click the thumbnail to refresh if that's the case. If you left-click the thumbnail, Jade
'enlarges' it to a resizable pop-up window. You can zoom the display in this window the same way you
would in the main zoom window. You can also choose a different background color for the display by
clicking the little black & white image on the status bar. If you prefer, you can also browse and select
pattern files in Tiled Thumbnail View from the 'File | Thumbnail...' menu. If you use Jade's Notepad to
keep notes about the pattern files, you should find it easier to browse and edit your notes on the
Thumbnail Browsing dialog. Jade also utilizes the thumbnails in Finding Similar Pattern Files among
your pattern file collections.
The 'Recent Files and Folders' list on the 'Read Pattern Files' dialog enables quick access to recent
pattern files from different folders without having to look for them again in the drive & folder tree. You
can remove an obsolete entry from this list with the 'X' button next to the list. You can remove all
folders pointing to floppy drive and network connection by right-clicking the 'X' button.
Jade maintains the current list of pattern files in the sorted order in memory for the sake of quick
access. If a pattern file you just transferred into the folder is not shown on the current list, click the
Refresh button to update the list. If you have thousands of pattern files in one folder to browse, you can
speed up the file listing by unchecking the 'Scan ID' box and 'File Date & Size' box above the file list.
You can also use a variety of file filters to list fewer files with the Filter button. Note that the file
extension of a non-MDI file type is changeable on the File Filter dialog should the default extension
differ from that of your pattern files. You can also browse and read a long list of pattern files from the
'File | Read...' menu or using Windows Explorer if you prefer. It's always a good practice to organize
your file folders so that you don't accumulate too many pattern files in one folder.
If the pattern files have a fixed location to store the scan ID, you can change it in the id text box located
above the file list, and save it back to the pattern file by pressing the Enter key. To rename a file, click
its name again on the file list and wait for the edit-box to appear, then enter the new name. Notice that
you are not allowed to alter its extension in renaming a file. You can delete a file from the list if you
press the Delete key after the file is highlighted. Jade does not keep the deleted file in the Windows
Recycle Bin--i.e., the file will be deleted from the disk permanently.

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Jade 5.0

The Macro button will execute the active task macro on the selected pattern files, which will be read for
task processing one after another in the current order of the file list. Refer to the Auto-Processing with
Task Macros topic for more information. The Browse button brings up Jade's File Browser to view, edit,
or print the highlighted file. If you right-click the Browse button, Jade will browse the pattern note file if
it exists; otherwise Jade browses the pattern file in hex view. The Import button brings up the Ascii
Data Import dialog to read 'foreign' pattern files in plain Ascii formats which are not yet supported by
any of the built-in file types.
You can resize this dialog window to see more or fewer files. You can alter the column widths to see
longer or shorter file names and scan IDs by dragging in between the column headers. You can sort the
file list by clicking the column headers. You can reverse the sorting if you click the same column
again. You can swap the columns by dragging the column headers. The Print, Save, and Copy buttons
allow you to print & export the file list, or send the list to the clipboard if desired. Jade utilizes the
column widths in printing the file list so that you have more control over how to fit the columns to the
printed page.
The three-letter items (SAV, PKS, etc.) in the status bar of this dialog indicates the presence of various
output files in their file extensions which have the same name as the highlighted pattern file. You can
read the SAV file into the zoom window or browse the report files by clicking the corresponding items in
the status bar. To read the PKS(peak list), DSP(d-I list), PDF(PDF overlays), PFT(profile fits),
RPT(phase id report) files, you must read the pattern file into the zoom window first, and then click the
same items in the status bar on the main window. You can hide the display of free disk space in the
status bar by clicking it so that you can see more of the three-letter items.
Jade remembers most of the selections on this dialog. The counters on the title bar are the numbers of
patterns read in the current day, the current week, the current month, and the current year. Pattern files
that are read from the MRU file list as well as for the overlays are not counted in these numbers.
Tip 1: You can read a newly-created pattern file directly from the main toolbar of Jade.
Tip 2: You can tell Jade to read a pattern file on start-up automatically. See the option on the Misc tab
of the User Preferences dialog.
Tip 3: You can sort file names as numbers rather than as characters if you hold down the Ctrl key while
clicking the column header.

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List Fewer Files with File Filters

If you have too many pattern files in one folder, you can use the file filters on the following dialog to list
a subset of them, for example:

This dialog is accessible with the 'Filter...' button on the Read Pattern Files dialog. The 'File Size (KB)'
box allows you to list files of certain sizes in kilobytes. You can specify the sizes in three ways: e.g.,
'>10' to list files greater than 10 KB, '<10' to list files less than 10 KB, and '10' or '=10' to list files ~10
KB. When using file name filters, you can specify up to 8 alphanumeric characters for the range. In the
above example (range from Z1 to Z3), Jade only lists pattern files of names 'Z1...', 'Z2...', & 'Z3...'. If
you are looking for a pattern file you know should be present but Jade isn't finding it, you may have
inadvertedly set this filter to exclude it from the file list.
If the pattern files contain intensity data collected in continuous scan mode, the angle value assigned to
a data point with a given chopper angle (i.e., stepping angle) could be the starting, the ending, or the
middle angle of a step, depending upon the particular data collection program in use. For example, if
you collect a continuous scan from 10 to 60 degrees with a chopper angle of 0.02, the angle value
assigned to the first data point could be 10, 10.01, or 10.02 degrees. It's also possible that your data
collection programs may start the scan at 9.99 rather than at 10 degrees. Since Jade does not collect
data, it's up to you to find out and decide. With the 'Half Step Correction to Scan Angle' option, you can
choose to add or subtract a half step-size to the starting and ending angles that are read from the
pattern files.
The 'Angular Multiplier' and 'Intensity Multipliers' are provided in case your data do not come in the
expected units of counts vs 2 degrees. The intensity multiplier could also be used as a simple scaling
factor, for example to correct for instrument drifting effect in data comparison. These multipliers take
effect only for reading new pattern files.
The file extension of a non-MDI file type is changeable. You should always select the correct file type
before you change the file extension. If you are not sure about the extension for a file type, click the
'Default File Extensions' button. Jade identifies a file type from its extension only when you list all file
types or when you drag and drop files from the Explorer. If you are not sure about the file type, you can
let Jade figure it out for you by dropping the pattern file into Jade from the Explorer.

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Jade 5.0

Thumbnail Browsing and Printing

The following dialog window is accessible from the 'File | Thumbnail...' menu:

Thumbnails are miniature monochrome bitmaps of your pattern files. They are automatically created
when you read new pattern files into Jade and they take very little disk space (about 1KB each). Jade
displays available thumbnails for the pattern files which are being listed on the Read Pattern Files
dialog. You can resize the dialog window or left- or right-click the Scroll button if you have more
thumbnails to browse. You can use the arrow keys to navigate through the thumbnails if you hold down
the Ctrl or Shift key. The green dot indicates the current file selection. You can double-click a
thumbnail to read it into the main zoom window. To select more than one thumbnail for overlays or
printing, use the check boxes above the thumbnails. You can 'enlarge' a thumbnail onto a resizable
pop-up window if you hold down the Ctrl key while you left-click it. You can zoom the display in this
window the same way you would in the main zoom window. You can also choose a different
background color for the display by clicking the little black & white image on the status bar.
You can also browse thumbnails together with printable or non-printable notes using the toolbar buttons
on the upper-right corner as illustrated below:

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Jade 5.0

Like the Read Pattern Files dialog, the three-letter items in the status bar of this dialog indicate the
presence of various output files in their file extensions which have the same name as the highlighted
pattern file. You can read the SAV file into the zoom window or browse the report files by clicking the
corresponding items in the status bar. To read the PKS(peak list), DSP(d-I list), PDF(PDF overlays),
PFT(profile fits), RPT(phase id report) files, you must read the pattern file into the zoom window first,
and then click the same items in the status bar on the main window.
The Print button will bring up the following dialog to print thumbnails:

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Jade 5.0

If you do not check any thumbnail, Jade will print them all (on multiple pages if required). You choose
how many rows and columns of thumbnails to print per page and Jade will resize them to fit the page
size (as previewed on the left side) and print them using the current color setting for plot printout. If you
choose more than two columns per page, Jade may not be able to print all the label items you selected
for the thumbnails. If you check the 'Inside Labels' box, Jade will print the label items inside the
thumbnail frames (with narrower vertical space between thumbnails), rather than above the thumbnail
frames (which requires more vertical space between thumbnails). If you check the 'File Notes' box,
Jade will print the current notes, if any, inside individual thumbnails.
Tip 1: Thumbnail printouts could be useful for your notebook and data archival.
Tip 2: Thumbnails are also used by Jade in Finding Similar Pattern Files among your collections.

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Jade 5.0

Import & Export 'Foreign' Ascii Pattern Files

The following dialog window is accessible from the 'Import...' button on the Read Pattern Files dialog:

It enables you to read and write 'foreign' pattern files in plain Ascii format. You tell Jade where to read
or write the file header (scan parameters) and the intensity data in terms of keywords or line numbers in
the pattern files. Your task is to provide the template of the file format, rather than the actual parameter
values to read or write.
The limitations in importing Ascii files are that the data must be in single scan range and the files must
have consistent header keywords or line numbers. If the intensity data are not aligned into fixed
columns, they must have column delimiters. Jade does not export pattern files in other XRD vendors'
binary or multi-range Ascii formats. The dialog and its rules are described below:
Import & Export tabs set the import and export file formats. Notice that you can have different
formats for data import and export. Jade requires a non-blank file extension from 1 to 3 characters.
The angular and intensity multipliers supersede those specified on the File Filter dialog.
Among the nine items Jade cares about in a file header, only those related to the scan range and
step-size are required if the data block lacks an angle () column. If the angle column is included, the
file header can be ignored altogether because Jade can read the scan range & step-size from the
angle column. The X-ray anode item is optional, and Jade recognizes the atomic number as well as
the elemental names for standard anodes. The default anode shown on the main toolbar will be used
if you omit the anode item. You only need to check the header items you care to read.
You cannot mix keywords with line numbers in the file header (i.e., it must be either all keywords or
all line numbers). The 'Char-# & Width' fields specify the starting column and width of an item in
characters. If the items are set in line numbers, the Char-# is the ABSOLUTE position in the line
counting from the left. If the items are set in keywords, the Char-# is the RELATIVE position from the
last character of the keyword. If the line embeds tab character(s), Jade assumes an 8-character tab
alignment. Multiple items can be read from the same line or using the same keyword. A keyword
could have leading spaces, but must not have any leading character in its line.
The beginning of a data block could be either with a keyword or at a line number. If you enter a line
number, it must specify the ABSOLUTE line count if the header items are also read in line numbers;
otherwise it is the RELATIVE line count from the last keyword item in the header. If data points per
line is more than one, the 'Char-# & Width' settings go with the first data point in the line.

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Jade 5.0

If the file header carries the scan range and step-size, you can ignore the angle column if any;
otherwise you need to check the angle column. If you have more than one data point per line as well
as the angle column, Jade will figure out the angular increment per line. If the data points are in
variable angular steps, Jade can interpolate them to fixed-step data by keeping the same number of
data points (auto) or with a new step-size which you type over the 'auto' keyword in the text box.
The 'End-of-Data' marker can be specified if you rely on Jade to count the data points and there is
more info after the data block in the file. On import, Jade reads the file until it reaches either the
End-of-Data marker or the end-of-file or the expected number of data points, whichever comes first.
The 'Column Delimiter' applies not only to the data block but also to the file header if you have more
than one item in one header line. When you use a column delimiter, be aware that any field in both
the header and the data block must be wide enough to include the delimiter. For example, you may
not be able to insert a comma between the anode and wavelength fields if you only reserve 2
characters for the anode and you wish to export wavelength to the same keyword line.
All keywords could embed control character(s) of Ascii values less than 32. For example, if you want to
specify an end-of-file character Ctrl+Z as the End-of-Data marker, you would enter it as ^Z where the ^
character indicates what follows to be a control character. Examples of control characters are ^G for
bell, ^I for tab, ^J for line feed, ^M for carriage return, ^[ for escape. Jade will skip all blank lines in the
data block. Jade will also detect and skip any page-break lines or headers in the data block.
The easiest way to set up an import Ascii reader is to view one of the files with the Browse button on the
above dialog and the following view will appear, for example:

You can then highlight a desired data item in the file with the mouse, bring up the setup menu as shown
above, select the corresponding item, and watch it being set on the dialog behind.
If you import data not in the form of theta vs intensity, Jade will interpolate it to be linear in 2 while
keeping the same number of data points. The wavelength of the current anode is used to map the
energy or 1/d range to the 2 range. For energy-dispersive data, the diffraction angle of the detector
specified on the Instrument tab of the User Preferences dialog is also used in data conversion via the
relation E(keV) = 6.2 / (d * sin()), where theta is the diffraction angle. For wavelength-dispersive data,
the diffraction d-spacing of the crystal can be specified on the same page of the preferences dialog
when you select wavelength display axis in the zoom window. The default d-spacing is 2.013, the (200)
reflection of LiF crystal. The angular multiplier will be applied before conversions are carried out. See
the Display Axes topic for how to display data in energy or wavelength axis.

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Jade 5.0

When you close this dialog, Jade will select the 'Jade Ascii Import Pattern Files' on the Read Pattern
Files dialog. You can now proceed to read the pattern files. To export pattern files in the specified
ASCII format, select the 'File | Save | Primary Pattern as *.txt' menu, where the 'txt' will be replaced by
whatever file extension you specify. At present, Jade only exports pattern files in 2 vs intensity form.
When you have succeeded in reading or writing an Ascii pattern file, you can save the settings to a file
(*.aff) by giving it a descriptive file name. These files will be listed on the same dialog for you to choose
from. Only one Ascii format can be designated at a time for import or export.

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Jade 5.0

MDI Ascii Data File Format

For backward-compatible reasons, the current format of MDI raw pattern files carries minimum
information on the instrument configuration. An example *.MDI pattern file is given below:

11/01/89 DIF RED PAINT PIGMENT MIXTURE

20.0 0.02 4.0 CU 1.54059 78.0 2901 <1st scan range>
272. 295. 281. 286. 315. 307. 338. 295.
285. 288. 325. 306. 280. 306. 265. 292.
270. 267. 279. 308. 293. 287. 264. 283.
317. 272. 264. 279. 303. 306. 292. 258.
......
20.0 0.01 1.0 CU 1.54059 40.0 2001 <2nd scan range>
272. 295. 281. 286. 315. 307. 338. 295.
285. 288. 325. 306. 280. 306. 265. 292.
270. 267. 279. 308. 293. 287. 264. 283.
317. 272. 264. 279. 303. 306. 292. 258.
......

The very first line contains the scan ID starting from the 21st character column (up to 80 characters will
be read by Jade for scan ID). The date and time stamp of data acquisition (columns 1-15) is not used
by Jade; instead the file date & time of the computer will be read for purposes of sorting and
formatting. The three characters (DIF) at columns 17-19 are ignored by Jade presently but are used by
MDI's DataScan program to identify scan/data type.
The 2nd line carries the scan parameters in the order of starting angle, step-size, count time, anode,
wavelength, ending angle, number of data points, and optional range id. Jade does not care about the
column alignment of these items as long as they are separated by a space or spaces. The starting
angle could be larger than the ending angle if the scan data is written backwards, in which case Jade
will flip the data forward in display. If the count time is a negative value, Jade takes it as the scan
speed in degrees per minute for continuous scan data. Jade prints the dwell time of a step scan as
'(sec)' and the speed of a continuous scan as '(d/m)' in the scan setting.
The anode ID is case-insensitive (i.e., CU, Cu, and cu can all be used). The wavelength item must be
present in the line although it is ignored for standard anodes because Jade uses the built-in table of
wavelengths. However, Jade will read it if the anode ID is US (for user-specific wavelength). Jade also
ignores the stated data count and recalculates it from the starting and ending angles and the step-size.
Jade will then read the data block until it reaches the calculated number or the end of file. The data
points could be in integer counts or decimal numbers. Because Jade stores data points in long integers
in memory, the fractional parts will be rounded up if you do not specify the intensity multiplier on the
File Filter dialog.
You can also store multiple ranges of scan data in a single MDI file, and each range can have an
optional ID string at the end of the scan-parameter line as illustrated above. Jade will automatically
read them in as scan overlays (notice that the Scan Overlay Toolbar will appear). The range ID will be
appended to the scan ID for each overlay.

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Jade 5.0

Drag & Drop Data Files from Explorer and within Jade
Jade is capable of accepting pattern files dragged & dropped from other applications running in
Windows. The two most likely sources to drag pattern files from are Windows Explorer and File Finder.
You can drag & drop pattern files into: (a) Jade's main window, (b) Jade's Read Pattern dialog, or (c) the
shortcut icon of Jade on Windows Desktop--causing Jade to start and read the dropped files. You can
create a shortcut icon of Jade on the Desktop simply by dragging one from its program folder or by
dragging its executable file from Explorer's file list. If you set up Jade to auto-load the pattern file on
start-up, it will be superseded by the drag & drop operations.
You can also drag pattern files from the Read Pattern dialog and drop them into the main window of
Jade. You can do so only if you click and drag in the 'Scan ID/Size/Date' columns of the file list.
In addition to the pattern files supported on the Read Pattern dialog, Jade also recognizes the peak
listing (*.PKS), d-I listing (*.DSP), PDF listing (*.PDF), and saved work (*.SAV) files in drag & drop
operations. By default, Jade clears the zoom window when the first pattern file is dropped into it. To
add (overlay) files in the zoom window, hold down the Ctrl key or drop them to the top pattern window.
When you highlight multiple files to drag, the one being pointed at by the mouse cursor (rather than the
top one on the highlighted list) will be the first one to be dropped into Jade. You can drag multiple types
of data files and drop them into Jade at the same time. Jade will auto-detect the file type of a dropped
pattern file if it has the same file extension as those from different hardware vendors. For example,
when you drop a *.RAW file, Jade can tell if it's a Rigaku file, or a Bruker file, etc. since these file types
have the same file extension but different characteristics. If you drop an invalid Ascii file into Jade, it
will be displayed in Jade's File Browser.

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Jade 5.0

Notepad Dialog and Usage

An example of the notepad dialog is shown below. It's accessible from the 'Edit | Notepad...' menu on
Jade's main window as well as from the 'Show Notepad...' menu on the print setup window.

Notepad notes are stored in a companion note file (*.not) to the pattern file, which can also be browsed
from the Read Pattern and Thumbnail dialogs. Jade automatically reads the note file when loading a
pattern file. Non-printable notes are for record keeping, and they could be entered as well from MDI's
DataScan program before data acquisition.
The printable notes can be included in most of the plot and report printouts. Jade will reserve space on
reports according to the contents of the notes and will perform line wrapping automatically. You can
enter up to 10K non-printable notes and 1K printable notes in a note file. You can cut, copy, and paste
between the two text boxes and from/to the clipboard using the Ctrl+X, Ctrl+C, and Ctrl+V keys. You
can resize this dialog to leave more or less space for notes.

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Jade 5.0

Jade's Generic File Browser

Jade provides a generic file browser which can be used to view, edit, or print any Ascii (plain text) or
binary file as well as all the report files created by Jade. You can bring up this browser with the 'Browse'
button on the Read Pattern Files dialog or from the 'View | Reports & Files | Browse Report File...'
menu. An example is shown below:

You can edit an Ascii file if it has less than 32K bytes of text, and Jade will prompt you to save it upon
closing the browser. For a binary file, it will be browsed in the hexadecimal view, for example:

You can't edit the data manually on this view but you can replace some characters in hexadecimal
forms throughout the file if the file size is less than 10 MB even when partial file is being shown. The 'R'
button shows and hides the substitution toolbar. In the above example, every carriage-return (CR)
character (0D in hex) is replaced by a pair of the carriage-return plus line-feed (LF) characters (0D0A in
hex). If you have done any replacement, Jade will prompt you to save the data upon closing. If you
click in the hex view, Jade displays the data values at the byte location in the current file as byte(C),
short(I) & long(L) integers, single(S) & double(D) decimals, for example:

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Jade 5.0

The scroll view can display about 32K text at once. If you have a large file to browse, you can jump to
the end of file with the 'V' button on top of the scroll bar, and press Ctrl+PageUp/Down to read the next
or previous 32K text from the file. For files which do not contain line break characters (CR and/or LF),
you can wrap the text if you choose the 'Line Wrap' option and enter the desired line width in number of
characters. You can also search the entire file for a particular string of Ascii text (space included) with
the 'S' button, and press the F3 key to find the next occurrence.
You can print the file in the current view and Jade will prompt you to proceed if there are more than two
pages of text to print. You can print only the first page of a large file if you hold down the Ctrl key. If
you highlight more than two lines of text, Jade prints only the highlighted text. Jade uses the
fixed-space font supported by the printer to print the text. You can set page orientation and margins on
the Report tab of the User Preferences dialog. You can switch the default printer if you right-click the
Print button. You can cancel a lengthy print job by pressing the Escape key.

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Jade 5.0

Data Filtering Functions

The available data filters in Jade are accessible from the main 'Filters' menu:

The check mark before a menu item indicates the filter last accessed, which is now attached to the filter
button on the main toolbar for quick access in subsequent pattern processing. In general, data filters
that alter the intensity data (such as the Lp & Slit filters) will also be applied to the pattern overlays if
any. Note that Jade does not usually prevent you from applying the same filter again to the current
data. It's up to you to keep track of what you have done to the data.
Smooth Pattern: Jade implements MDI's proprietary variation of the Savitzky-Golay least-squares
filters for pattern smoothing in the angular domain. You can bring up the following dialog from the
above menu or by right-clicking the filter button on the main toolbar:

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Jade 5.0

Jade carries out the smoothing immediately when you alter the parameters on the dialog, then overlays
the smoothed pattern in the zoom window for comparison. You can choose a filter length from 5 to 99
points by dragging the slider left or right. The 'Quartic Filter' (4th-order polynomial) does a better job in
preserving peak shoulders than the 'Parabolic Filter'. Since the dialog window is modeless (as indicated
by the thumbtack icon on its title bar), you can examine the filtering results in the zoom window without
having to close it down. If you left-click the filter button on the main toolbar, Jade performs the
smoothing and replaces the original pattern with the smoothed one automatically without showing the
above dialog.
If you choose the 'Smooth and Preserve Peaks' option, Jade will preserve the sharp peaks in the pattern
when you choose longer filters to smooth the broad peaks and the background. If you choose the
'Smooth Background' option, Jade will smooth only the background regions in the pattern. Those
regions are determined by the 'Peak Threshold' parameter, which you can specify on the dialog, above
the newly fitted background (BG) curve. The default threshold is 3.0 sigmas, and data points above the
threshold are skipped in the smoothing. You can use the BG Editing Cursor to obtain a better fit of the
curve if necessary by adjusting the BG tie points.
You can also display the 1st or 2nd derivative curve of the pattern using the 'Show Derivatives' options
on the above dialog. Since Jade's peak search is based on the 2nd derivatives, you may be curious to
see what the derivative curves look like for different filter types and lengths.
You can offset smoothed pattern up or down for a better view from the Zoom & Pan Toolbar. You can
display the difference pattern between the smoothed and the original using the difference button on the
main toolbar. To accept the smoothed pattern for subsequent analysis, select the 'Analyze | Take New
Pattern' menu, or click the swap button on the main toolbar. You can restore the original pattern by
clicking the same button again.
You can also smooth the pattern in the frequency domain with the FFT (Fast Fourier Transform) filters
described below, or using the 'Replace Data' option on the Profile Fitting dialog after you profile-fit the
peaks.
The FFT Filters enable manipulation of your data in Fourier frequency space for purposes such as data
smoothing. You may find the FFT filter effective in eliminating noises that are periodic in theta or 1/d
space. An example of the transform is given below:

In this example, the signal peak in frequency space corresponds to a periodic noise in the pattern. Jade
uses only the data in the zoom window in FFT analysis. The vertical lines on the graph mark the
truncation of low and high frequency terms. The low frequency marker starts at the left edge of the
graph if you can't see it. The Damping box allows for a Gaussian damping factor (zero or greater) to be
applied to the amplitudes of frequency terms. The Zoom button toggles the graph between full range
and truncated display. The untruncated and/or damped terms are then reverse-transformed to give the
theta-space pattern that's overlaid in the zoom window for comparison and can be accepted for
subsequent data analysis.
The Remove Data Spikes filter (see the 'Filters' menu at the beginning of this topic) takes advantage of
the fact that the electronic spikes are in general one step-size wide in peak detection. Such artifacts

54
Jade 5.0

may be found in patterns obtained from older strip-chart instruments that were converted to digital
acquisition. The problem existed with the original instrument but was masked by large RC constants
that prevented the pen from recording the real data to the plotter. Some spikes may not be detected
due to their multi-step nature. Nevertheless they can be removed manually using the Data Editing
Cursor.
The Sample Displacement correction applies the formula '2 = D x cos()' to the interpolation of data
points in the current pattern, where the variable D is the angular shift in 2 (2T(0)) caused by sample
displacement at the incident beam direction, and is related to the absolute displacement (S) and
goniometer radius (R) in the form of D = 2x57.2958xS/R. You can specify the goniometer radius (R) in
millimeters on the Instrument tab of the User Preferences dialog. If you don't, Jade will accept and
report sample displacement (D) at 2T(0) in degrees. If you do, it will be presented as the S value in
millimeters. If the d-I lines of the active PDF overlay match the peaks in the pattern, Jade automatically
carries out a least-squares fit to compute the displacement and presents the results for comparison.
Otherwise, you must enter the displacement on the input box to be prompted. The corrected pattern
can be accepted the same way as the smoothed pattern. Notice that the displacement correction can
be replaced by an offset of 2 zero when the scan range is not wide.
The Change Scan Stepsize operation allows you to resample data points in a different step-size.
Some resolution of data will be lost inevitably if you resample at a larger step-size. Certain algorithms
in Jade (such as peak search and phase identification) are optimized for step-sizes in the range of 0.02
to 0.05 degree. This operation could render better analysis results for patterns that are collected with a
step-size <0.02 or >0.05 degree. It's usually unnecessary to acquire data with a step-size less than 0.02
degree for most analyses on conventional diffractometers. Better data and analysis results will always
be obtained if you can afford to count for longer times on each step. When you resample data in a
larger step-size, Jade will add up or average adjacent data points to give better statistics. See Jade's
Registry Entries topic for more information on this operation.
The Fixed <-> Variable Slit filters convert pattern intensities between fixed and theta-compensating slit
scans in the relationship I(v) = I(f) * sin(). The maximum counts of data are maintained in the
conversion. Instead of converting the scan pattern, you can overlay PDF d-I lines in variable slit
intensities. See the option on the Display tab of the User Preferences dialog.
The Lp Correction converts pattern intensities to what they should be if the Lorentz and polarization
effects are removed from a powder diffraction pattern. The resultant peak intensities relate more
closely to the structure factors of the reflections.
The Dead Time Correction can be performed, if you have specified the detector dead time on the
Instrument tab of the User Preferences dialog, to correct pattern intensity for the intense peaks which
saturate the X-ray detector/counter. Refer to your detector manual for how to determine the dead time,
which should be around 100 to 300 micro-seconds for a Geiger-Muller counter, and much shorter for a
solid-state detector. Jade uses the following formula for the correction:
I(c) = I(o) / (1 - CPS * T / 1000000)
where I(c) is the corrected intensity of a data point, I(o) is the observed intensity, CPS is the counts per
second, and T is the detector dead time in micro-seconds. Jade will not perform the correction if the
product of CPS * T / 1000000 is >0.9. Jade can perform the correction automatically on a newly-read
pattern if you check the 'Dead Time Correction' box on the Instrument tab of the User Preferences
dialog.
Absorption & Transmission Corrections are provided for processing Debye-Scherrer film data. The
International Tables values for absorption corrections are built in, and linear interpolation of tabulated
values are used within the allowed ranges of absorption coefficients. You are required to enter the
absorption coefficient on the prompted input box.
The Revert & Invert Scan Pattern filters are provided in case you need to view spectrum data in Jade.
Note: 2nd-level filters under the 'Others (FFT, Film...)' item are accessible only with Jade+ package.

55
Jade 5.0

Background and K2 Removal

You can bring up the background fitting dialog from the 'Analyze | Fit Background...' menu or by
right-clicking the BG button on the main toolbar:

In this example, Jade will sample the tie points (also called the BG dots) from the background regions in
the pattern, and then fit a cubic-spline curve through them if more than three tie points are found. You
can choose a linear or a parabolic fit for patterns of even background or narrow scan range. The beauty
of a spline curve is its flexibility to fit complex backgrounds. This flexibility is controlled by two
variables on this dialog: (a) intervals of background point sampling as presented from the 'Dense' to the
'Sparse'; (b) sampling threshold (in Poisson sigmas of counting statistics) to accept the next tie point
after each previous one. A higher threshold can bend the curve to better fit an amorphous hump, for
example. Therefore tie points usually are not equally spaced along the 2 axis. If you choose the linear
or the parabolic fit, Jade will automatically reject outlier tie points beyond the two sigma threshold of the
fitted line or parabolic curve.
When the 'Automatic Threshold' is checked, Jade starts sampling tie points at a threshold of 2.0
sigmas, and will keep raising the threshold until sufficient points have been sampled to fit the line or
curve. This approach could fail if the pattern starts out with a sudden rise or fall in its background. You
can easily adjust for this by (a) truncating the starting segment of data or (b) editing the data graphically
or (c) manually entering a few tie points closely around the trouble spot. See the Edit & Cursor Toolbar
for how to edit the raw data or the tie points to fit a better curve. To truncate data, set the zoom window
to display the desired starting angle and select the 'Edit | Trim Range to Zoom' menu.
The 'Offset of BG Curve from BG Dots' parameter shifts the fitted BG curve down from the tie points for
the sake of BG subtraction. It's specified as a fraction of the sigma value of the maximum counts in the
pattern. If you are removing background for phase identification (S/M), an offset value of 0.1-0.5 sigma
will help in identifying the minor & trace phases in the pattern. However, if you fit the BG curve for
profile fitting of peaks, the offset should be set to zero.
The K2 stripping uses the Rachinger algorithm and can be carried out once the BG curve is fitted. If
the 'Strip K2' box is checked, the stripping will be performed together with removal of the background.
The 'Strip K2' button instead will allow you to strip the K2 without removing the background, whose
presence is essential to determine the peak threshold in automatic peak search. The Rachinger
algorithm may not perform well for patterns with low backgrounds and sharp & skewed peaks. You may
be able to accomplish better K2 removal through profile fitting of peaks, although it's more involved.
See Profile Fitting dialog for more information on this option.
The 'Area above the Background Curve' reports the integral counts and its percentage in the specified 2
 range above the background curve. If you change the display range in the zoom window, you can
update these numbers by clicking the caption.

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Jade 5.0

Like the pattern smoothing dialog, you can interact with the zoom window to review the fitted BG curve
and edit the tie points if necessary while keeping this dialog open. Any change you make on this dialog
will be applied immediately and a new BG curve will appear with a new set of tie points. Therefore it's a
good idea to close this dialog before you start adjusting the tie points manually. When you are satisfied
with the BG curve, you can remove the background with the BG button on the main toolbar. You can
remove only the K2 peaks with the same BG button if you hold down the Ctrl key. It should be pointed
out that you don't have to remove the background at all in order to perform the automatic peak search
or phase identification. See the Peak Search dialog for how Jade can determine the background in
locating peaks.
You can change the colors of the BG dots & curve from the Change Display Colors dialog and choose
different dot sizes on the Display tab of the User Preferences dialog. You can reset the parameters on
the BG dialog by double-clicking the 'Background Function...' caption. While the current parameters of
BG fitting are always remembered by Jade, you can create additional setting files with the Save button,
and restore one of them by selecting it from the setting file list. These setting files will also appear in
the macro task list for automatic pattern processing.

57
Jade 5.0

Peak Search, Labeling & Scaling Dialog

You can bring up the peak search & labeling dialog from the 'Analyze | Find Peaks...' menu or by
right-clicking the 'Find-Peak' button on the main toolbar. An example is shown below:

Jade's peak search algorithm is based on the Savitzky-Golay 2nd derivatives combined with the
counting statistics of intensity data. The important search parameters are described as follows:
Filter Type: The filter length is the number of data points used in the calculation of the 2nd
derivatives from the least-squares fit of a 2nd-order (parabolic) or 4th-order (quartic) moving
polynomial. The quartic filter, due to its flexibility, can better detect peaks that are barely resolved.
The longer the filter, the broader the peaks that can be detected. If the 'Variable Filter Length/Points'
box is checked, Jade automatically adjusts the filter to optimum length according to the average width
of peaks. You can combine search results from different filters if you uncheck the 'Erase Existing
Peak Listing' box.
Peak Threshold (PT): Each potential peak found in the 2nd derivative space must pass the test of
counting statistics in terms of the threshold which is calculated as PT = BG + TS *
SQRT(Peak-Height), where BG is the peak background, and TS is the 'Threshold Sigmas' that can be
set on the above dialog. If you have a background curve currently in the zoom window, Jade will use
it to calculate the peak threshold and you can view the threshold curve with the Threshold button on
the dialog. Otherwise, Jade automatically scans for the left & right BG points of a peak within the
range specified by the 'Range to Find BG' parameter, and calculates the peak background from a
linear fit of the two BG values which are averaged from a number of adjacent data points, as specified
by the 'Points to Average BG' parameter. Therefore peak search should be carried out on the raw
data if the threshold is to be statistically meaningful. Tip: You can strip the K2 peaks without
removing the background from the BG Fitting dialog. Note: the 'Screen out K2 Peaks' check does
not perform the K2 stripping--it only eliminates well-resolved K2 peaks from the final peak listing.
Intensity Cutoff: This parameter sets the post-search threshold in relative intensity (I%) to reject weak
peaks. If you deal with thin film data that has a very dominant peak, you may need to lower the
intensity cutoff in order to find the weak peaks.
Peak Location: The 'Summit' location of a peak is determined using a 5-point centroid fit, the
'Centroid' from an N-point centroid fit for an N-point search filter, and the 'Parabolic' from an N-point
parabolic fit for an N-point search filter.
The FWHM of a peak is estimated as FWHM = SF x Area / Height, where SF is a constant related to
the profile shape of the peak and is defaulted to 0.85. You can alter the SF value if desired from the
Report tab of the User Preferences dialog. The area of a peak is the sum of net intensities of data
points above & within the left & right BG points. See the Profile Fitting and the Crystallite Size & Strain
Analysis topics for how to obtain precise FWHM values. Like the background fitting dialog, you can
interact with the zoom window to review the located peaks and edit them manually if necessary without

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Jade 5.0

closing the search dialog. See the Edit & Cursor Toolbar for how to insert, move, and erase peaks
manually. The characteristics of manually-inserted peaks are determined in the same way as in
automatic peak search.
You can label the located peaks with a variety of numerical items in the zoom window as shown on the
Labeling tab of the dialog:

You can check multiple items to be labeled on a peak. If you check the 'Asterisk' item, Jade won't
display the asterisks until you uncheck all the other items except the line marker. If you uncheck the
line marker, Jade marks the located peaks with short lines of equal height on the 2 axis. You can
lower or raise these markers either by altering the 3rd 'Marker Scaling' parameter on the above dialog
(default is 2% of zoom window height), or by clicking the marker scaling button on the Zoom & Pan
Toolbar. You can make the markers disappear altogether if you set the parameter to zero. The 1st &
2nd 'Marker Scaling' parameters can be used, for example, to print the peak labels on top of scan
overlays.
To display the hkl indices, they must be assigned to the located peaks. This can be accomplished
either automatically by grafting hkl's from the PDF overlays or manually on the Peak Listing Report
dialog, which can be brought up with the 'Report...' button. Multiple PDF overlays can be used in
grafting the hkl indices. The 'Peak ID...' button will bring up the Extended Peak ID Report if there are
matching PDF overlays in the zoom window. You can also bring up the Compact Peak ID Report if you
right-click the 'Peak ID...' button.
While Jade always remembers the current settings of peak search & labeling, you can save them to a
separate setting file for purposes such as performing a particular type of peak search or running task
macros. You can create as many of these files as you like using the Save button, and restore any one
of them from the file listing next to the Save button. These setting files will also appear in the macro
task list for automatic pattern processing.

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Peak Search Report & Peak Listing Dialog

You can bring up the peak listing dialog either from the 'Report...' button on the Peak Search dialog or
from the 'View | Reports & Files | Peak Search Report...' menu. An example is shown below:

This listing can be customized with regard to the data columns and the type of data to show. The
Customize button shows and hides the following menu items:

The Peak/Noise (P/N) ratios are calculated using the formula: P/N = (PK - BG) / (2 * SQRT(PK)), where
PK is the peak height including the background (BG). The maximum P/N ratio on the list is also shown
in the title bar, which can serve as a quality gauge of your pattern if it's calculated from the raw data
rather than from BG-removed data.
The Print button produces the peak search report. The Copy button sends the list to the clipboard. List
items sent to the clipboard by Jade are always delimited by tabs and are ready to be pasted into the
spreadsheet. The Save button brings up the following dialog for you to save the list to a number of
different peak files:

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These peak listing files are described below:

Peaks/Paints File (*.pks): A binary peak listing file that can be read into Jade to restore the search
display.
Peak Search Report File (*.pid): A plain text file that can be browsed, archived, or e-mailed to your
clients.
Jade d-I Listing File (*.dsp): A d-spacing vs I% listing file in the MDI format. See d-I List File Editor
for more information.
AIDS d-I Listing File (*.aid): A d-spacing vs I% listing file in the ICDD AIDS83 format. You can
choose to scale peak intensities to 100% or 999 from the Customize menu shown in the earlier
diagram.
Tip: You can browse an existing PID file simply by clicking the 'PID' item in the main status bar.
Jade links the dialog to the display in the zoom window. When you select an item on the list, Jade
identifies the corresponding peak with a blinking marker in the zoom window, and will pan the zoom
window if necessary to bring the peak into view. You can interact with the zoom window without closing
this dialog. You can use the Peak Editing Cursor to move, erase, or add peaks in the zoom window,
and Jade will update the list on the dialog automatically. You can also use the Erase button on the
dialog to erase an existing peak from the list, and Jade will refresh the display in the zoom window. You
will find it's easier to erase a bunch of peaks from the list with the combination of the Delete & arrow
keys.
For the purpose of peak comparison, you can keep the current peak listing from being erased when
reading a new pattern file. This can be done either by setting the option on the Display tab of the User
Preferences dialog or by hiding the peaks by clicking on the peak-# item on the main status bar. If you
do keep them, the Rescale button on this dialog can be used to rescale the old peak heights to the new
pattern.
The 'Graft hkl' button, activated only if you show the hkl columns, assigns Miller indices to the peaks
from the matching d-I lines of existing PDF overlays. You can also enter the Miller indices for each
peak using the hkl input boxes to the right of the Help button on this dialog. The Trim button will

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remove all unassigned peaks from the list. The assigned Miller indices can be used to label peaks for
printout, and will be exported to the report files as well as to the d-I listing file (*.DSP, *.AID).

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Overlay Scan Patterns & Scan Overlay Toolbar

This toolbar is accessible only after you overlay scan patterns and it can be placed below the main
toolbar or above the main status bar. You can tell Jade to hide the toolbar when there is no overlay in
the zoom window (see the option on the Display tab of the User Preferences dialog). Notice the
appearance of the overlay color palette alongside the zoom window. You can hide the palette by
right-clicking it.

You can add (i.e., overlay) scan patterns in the zoom window in a number of different ways:
Using the Add button on the Read Pattern Files Dialog or the Thumbnail Browsing Dialog.
Drag & Drop Pattern Files from the Explorer or from the Read Pattern Files Dialog.
Hold down the Ctrl key while selecting a pattern file from (a) the MRU File List, or (b) the 'File | Read'
dialog, or (c) fetching the latest pattern file.
Most pattern processing functions in Jade work with the primary (i.e., the 1st) pattern in the zoom
window. The scan overlays are mostly for pattern comparison. However, you can swap the active
overlay with the primary pattern using the Swap button if desired. The current item in the overlay
listbox indicates the active overlay, which can be manipulated with the toolbar buttons. When you
select another overlay using the blue up-down button, Jade flashes it in the zoom window. Notice that a
color-matching line above the overlay listbox also aids in identifying the active overlay. If you right-click
the Swap button, you can also identify the active overlay by flashing it in the zoom window. Although
you can change the colors of scan overlays from the Scan Overlay List dialog, you can also assign a
new color to the active overlay from the color palette (you need to hold down the Ctrl key if there are
PDF overlays in the zoom window).
When you use the Offset and Scaling buttons, you will get more responsive actions on a slow PC if you
focus the zoom window on a small region of your data. To obtain precise offset and scaling values for
an overlay, use the Scan Overlay List dialog instead. You can reset the offset and scaling values to 0.0
and 1.0 or auto-offset/scaling if you hold down the Ctrl key while clicking these buttons. You can also
offset and scale an overlay by dragging it directly (see the Edit & Cursor Toolbar for how); you can
apply uniform offsets to all overlays by pressing the Ctrl+~ key repeatedly; you can also view them in
3D from the 'View | Overlays in 3D' menu.
The Plus & Minus buttons show or hide the addition and subtraction patterns of the active overlay with
the primary pattern, using the current intensity scaling and angular offset values if present. The minus
(difference) pattern is taken as I(primary) - I(overlay), but you can reverse the difference using the
Swap button. If the active overlay has a different step-size than the primary pattern, an interpolation is
automatically carried out in the addition or subtraction. These patterns are overlaid in the zoom window
and can be saved from the 'File | Save...' menu. You can move the display baseline of an addition or
subtraction pattern by dragging the little square at the end of the baseline up or down.
You can bring up the Scan Overlay List dialog by left-clicking the number button. You can hide all scan
overlays rather than erasing them if you right-click the number button, and bring them back by
right-clicking again. You can also hide all but the active overlay with the 'Hide Others' check box on the
Scan Overlay List dialog.
By default, Jade maintains an independent set of colors to print scan overlays. But you can use the
colors assigned in the zoom window for printouts if you check the 'Same Colors of Overlays on
Printouts' box on the Display tab of the User Preferences dialog.
Merging Scan Overlays:

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You can merge scan overlays with the primary pattern from the 'Edit | Merge Segments' menu (if they
are not overlapping in scan ranges), or from the 'Edit | Merge Overlays' menu (if they are). In merging
non-overlapping scan segments, Jade fills the gaps with random counts using linear extrapolation from
the two end points. You can control how much randomness to fill in with the 'Data Noise Sigma'
parameter on the Misc tab of the User Preferences dialog. In merging overlapping scan patterns, you
can choose from three different ways to deal with the intensity data in the overlapping regions: (1) take
the average of overlapping data points, (2) take the maximum point, (3) take the summation (i.e., add
them all up). The resulting scan will inherit the step-size and count time of the primary pattern but will
take on the maximum scan range of all overlays. Note: The current angular offsets and intensity
scalings of the overlays will be applied in merging the scan data.

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Scan Overlay List Dialog

You can bring up the following dialog window from the number button (that shows the # of overlays) on
the Scan Overlay Toolbar or from the 'View | Scan Overlay List' menu:

This dialog complements the overlay toolbar although it duplicates some of the toolbar functions. The
precise values of overlay offsets and intensity scalings can be entered here by clicking the column
headers. To change a Scan ID, click the id text directly and wait momentarily for the edit-box to
appear, then enter the new id text. You can set up identical vertical offsets for all overlays by entering
an I% offset value to the first overlay, or by pressing the Ctrl+~ keys repeatedly on the main window.
You can shuffle the overlay list simply by dragging and dropping the highlighted item on the list so as to
get the desired sequence of overlays on the report or printout.
The Scale button brings up the menu options to scale the overlay intensity to the primary pattern:

These options allow you to match the maximum, the average intensity, or the total counts of two
patterns. The 'Hide Others' check on the dialog hides all but the active overlay from display, making it
easier to see, especially when you assign new color or line/fill style to the active overlay. Line color and
fill color can be set independently for each overlay. Note: Opaque visualization of the primary pattern is
set from the Zoom Window Display dialog, and is limited to <1002 data points in the zoom window and
to <8002 data points on the printout.
Tip: You can also view and print scan overlays in 3D from the 'View | Overlays in 3D' menu.

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Overlay d-I List Data & PDF Overlay Toolbar

This toolbar is accessible only after you overlay d-I list data from the PDF database or from d-I list files
(*.DSP) or from the d-I List Editor. It can be placed below the main toolbar or above the main status
bar. You can tell Jade to hide the toolbar when there is no overlay in the zoom window (see the option
on the Display tab of the User Preferences dialog). Notice the appearance of the overlay color palette
alongside the zoom window. You can scroll the palette to see more colors using the up-down button
located at the bottom of the palette column, and hide the palette by right-clicking it.

You can overlay d-I list data as a set of colored vertical lines in the zoom window in a number of
different ways:
Retrieve the d-I list of a PDF card from the PDF database. This is the easiest way to overlay d-I list
data in Jade. See PDF Setup & PDF Retrieval & Main Toolbar for more information.
Read an existing d-I listing file (*.DSP) from the 'File | Read' menu.
Read a 'foreign' d-I listing file from the 'Edit | d-I List File Import...' menu.
Create a new d-I list from the 'Edit | d-I List Editor' menu, and use the Add button on the editor dialog.
Unlike the scan overlays, Jade shows only the last (active) PDF d-I overlay when you add more than
one in the zoom window. You can change this default behavior with the 'Tack Down All New PDF
Overlays' check box on the Display tab of the User Preferences dialog. Nevertheless, you can show
multiple PDF overlays by using the Tacking button on the toolbar selectively. If you right-click the
Tacking button, all overlays will be tacked or untacked at the same time.
The item in the overlay listbox indicates the active overlay that can be manipulated with the toolbar
buttons. Notice that a color-matching line above the overlay listbox also aids in identifying the active
overlay when multiple overlays are displayed in the zoom window. If you right-click the 'Change Color'
button, you can also identify the active overlay by flashing it in the zoom window. Note: Jade uses only
the visible overlays for most pattern analyses and report printing.
You can assign a new color to the active overlay in three ways: (a) using the 'Change Color' button on
this toolbar, (b) using the color palette alongside the zoom window, (c) using the PDF Overlay List
dialog. You can also set the line width of stick bars with the three line markers on top of the color
palette. Note that Jade uses an independent setting of line width to print d-I lines because printers have
much finer resolutions than the screen. You can find this setting on the Misc tab of the Print Setup
dialog.
The Offset & Scaling buttons enable shifting and scaling of d-I lines (also called lines) relative to the
scan pattern in overall I%, theta (2T(0) & d-space (d/d(0)). You can depress and hold them down for
continuous actions with either mouse button. By default, Jade will automatically scale the d-I lines of a
new PDF overlay in heights to the peak nearest to the 100% line of the d-I list. You can turn off this
auto-scaling feature on the Display tab of the User Preferences dialog, and Jade will scale the d-I lines
to the maximum peak in the scan pattern.
When you shift the lines in d-space, you actually shrink or expand the lattice or unit cell of the phase
isotropically since Jade multiplies the d-spacings of all lines by a single variable defined as d/d(0).
Therefore this button makes it easy for you to examine possible solid solutions in your pattern or to
compare isotypical phases from the PDF database. If you multiply the original cell constants by the
d/d(0) value, the results can be used as the starting parameters for cell refinement. You can reset the
offset and scaling values to 0.0 and 1.0 if you hold down the Ctrl key while clicking these buttons.

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If the active overlay is a tetragonal or hexagonal phase with known cell constants, you can also change
its c/a ratio by holding down the Shift key as you depress the d-scaling button. The lines will be shifted
in real time according to the new c/a ratio displayed in the message area of the main toolbar (e.g.,

). Because the a-axis is kept constant in this operation,

you will notice that lines of Miller indices (hk0) will not move as you alter the c/a ratio.
To illustrate these powerful tools, read the DEMO08.MDI Corundum pattern from Jade's demofile
folder, and overlay the hematite from the PDF database. You can shift the Hematite lines to match the
Corundum pattern without holding down the Shift key (i.e., without altering its c/a ratio). Jade will tell
you the cell constants of Corundum from those of Hematite because Corundum and Hematite both
have similar c/a ratios of about 2.73. Now overlay Calcite, which has a c/a ratio of 3.4, hold down the
Shift key as you depress the d-scaling button so that the ratio reaches about 2.73, and release the Shift
key; then shift the lines in d-space until they match the Corundum pattern--you have just indexed the
Corundum pattern using Calcite data!
The 'Card View Dialog' button will bring up the PDF Card Display of the active overlay. The content of
this dialog depends on the type of PDF overlay and the nature of the PDF database. If you have
access to the ICDD PDF2 CD, the card view will have more complete information.
The 'Number of Overlays' button will bring up the PDF Overlay List dialog for more controls such as line
labeling and list ordering. Jade disables the PDF overlay toolbar when the list dialog appears. You can
hide all PDF overlays rather than erasing them by right-clicking this button, and bring them back by
right-clicking it again.
By default, Jade maintains an independent set of colors to print PDF overlays. But you can use the
colors assigned in the zoom window for printouts if you check the 'Same Colors of Overlays on
Printouts' box on the Display tab of the User Preferences dialog. The advantage of maintaining
independent color settings for overlays is to be able to visualize them in the zoom window with a
non-white background color.
Tip 1: You can offset and scale PDF overlays by dragging them directly (see the Edit & Cursor Toolbar
for how).
Tip 2: You can prevent Jade from removing the current PDF overlays when reading a new pattern file.
See the option on the Display tab of the User Preferences dialog.
Tip 3: You can save and read a set of routine PDF overlays from a file. See the PDF section of the
Main Toolbar description.

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Paint and Integrate Peaks

Although you can obtain XRD peak characteristics such as FWHM and area from automatic peak
search, these are more qualitative estimates than quantitative. In the case of overlapping peaks, they
could well be mischaracterized. However, you can obtain more precise and accurate peak
characteristics with peak painting and profile fitting. There are a number of ways you can paint and
integrate peaks in Jade.
Paint Peaks Manually:
With the painting cursor selected on the Edit & Cursor Toolbar, you can drag out a line starting at a
desired spot along the baseline of a peak or peaks, and release the mouse button when you reach the
point on the baseline where you want to end. Jade will paint the peak(s) within the line segment and
display the results in an info-box as illustrated below:

Obviously it's up to you to decide exactly where the baseline of peak(s) should be as well as the range
to integrate. Notice that you can have both positive and negative areas depending upon where you
draw the baseline. Jade adds up both areas to give more consistent net area. You may choose to
remove the background and/or strip the K2 peaks from the pattern before you paint as long as you use
the resultant areas consistently in your analysis. You can paint as many peaks as you desire, and erase
an existing paint by dragging over it again or by right-clicking in the paint info-box.
The paint info-box can be printed if desired, and you can move it to eliminate overlaps by dragging it
directly with the left mouse button. Its content items can be customized on the Misc tab of the User
Preferences dialog. You can prevent the info-box from appearing altogether if you hold down the Ctrl
key while you paint. The centroid of a painted peak is based on all data points in the painted area. The
FWHM is calculated from the formula FWHM = SF * Area / Height, where SF is a scale factor (default
is 0.85) related to the profile shape of the peak and can be changed from the user preferences dialog.
The crystallite size estimate is thereby valid only for a single well-resolved peak.
With the crosshair under a peak in the zoom window and a display range of less than 20 degrees, while
you hold down the Ctrl key, Jade will compute the peak width from the two intercepting points of the
crosshair cursor and display it in the message indicator on the main toolbar (e.g.,

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) as you move the crosshair up & down. To use the peak width
as the FWHM value, you should remove the background from the pattern first, then position the
crosshair at 50% peak height under its apex. Refer to the Profile Fitting dialog for how to obtain precise
FWHM values, and to the Crystallite Size & Strain Analysis for how Jade estimates the crystallite sizes
from the FWHM values.
Paint Peaks Automatically:
If you are not sure where the baseline of peaks should be and you need consistent and reproducible
results from peak painting, let Jade paint them for you! This is where the concepts of 'Full-Range' and
'Auto-Range' painting come into consideration. In full-range painting, you decide the exact range to
integrate with the zoom window and Jade decides where to draw the baseline. In auto-range painting,
you estimate the range with the zoom window and Jade will decide where painting should start and end
in the zoom window while placing the baseline. In both cases, Jade carries out a linear least-squares fit
of data points in the left & right tail regions of the pattern (by threshold of counting statistics) to
determine the baseline. You can perform either kind of painting three difference ways in Jade after you
have selected the region of peaks to paint in the zoom window:
Using the paint button on the Cursor Toolbar: If you hold down the Ctrl key and click the depressed
paint button once more, Jade performs the 'auto-range' painting as described. If you hold down the
Shift key, the 'full-range' painting is performed and the results should be comparable within the
uncertainty of counting statistics. If peaks are already painted in the zoom window, Jade erases them
instead.
From the 'View | Zoom Window | Paint Peaks (Auto) or (Full)' menus: the same results as above
should be obtained.
Using the 'Paint Peaks' button on the Zoom Window Display Range dialog (see below): auto-range
painting is performed if you hold down the Ctrl key while clicking the button.

To avoid specifying the ranges every time you wish to paint, you can save a list (max 16) on this dialog
and select from the list in later analysis of the same or another pattern. Notice that you can also obtain
some counting statistics of your data in the zoom window from the above dialog, and you can perform
profile fitting to overlapping or individual peaks to acquire statistically valid peak characteristics.
Set Paint Color & Style and View Paint Report:
A list of all painted peaks can be browsed from the 'View | Reports & Files | Peak Paint Report' menu,
as shown below:

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You can use this dialog to change the fill color and style of painted peaks and for subsequent peak
painting. You can do the same without affecting the existing paints from the Color Setting dialog, and
keep the dialog open while you paint. You can therefore paint peaks with different colors and/or fill
styles on the same pattern. You can export the paint results to a plain text file or send them to the
clipboard for programs such as Excel. If you save the painted peaks to a *.PKS file from 'File | Save |
Peaks/Paints' menu, you can restore the painted display in the future simply by clicking the 'PKS' item
on the status bar of the main window.
Tip: You can pop up the 'View | Reports...' menu by right-clicking in the top pattern window.

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PDF Overlay List Dialog

You can bring up the following dialog window from the number button (that shows the # of overlays) on
the PDF Overlay Toolbar or from the 'View | PDF Overlay List' menu:

This dialog complements the overlay toolbar although it duplicates some of the toolbar functions. The
precise values of overlay offsets and intensity scalings can be entered here by clicking the column
headers. To change a Phase ID, click the id text directly and wait momentarily for the edit-box to
appear, then enter the new id. The check before the phase id keeps the overlay in the zoom window
when it's not selected. Jade uses only the checked overlays for certain analyses and on printouts. You
can shuffle the overlay list by dragging and dropping the highlighted item on the list so as to get the
desired sequence of overlays on the report or printout.
The RIR, Wt%, and XS (crystallite size) data are used for Pattern Simulation and RIR Quantitative
Analysis. Jade automatically reads the available RIR values from the PDF database. The crystallite
size option enables different Scherrer broadening to be assigned to individual phases in the simulation,
and it supersedes the overall Scherrer broadening that can be specified on the simulation dialog. You
can choose angstroms (A) or nanometers (nm) for the crystallite size on the Instrument tab of the User
Preferences dialog. The phase content tags are assigned initially by Jade from their I% values, are
used only on the printout, and can be altered by clicking the column header repeatedly.
You can label the d-I lines using the row of check boxes below the buttons. The 'Apply to All' check
allows you to label all overlays with the same items checked for the active overlay. By default, Jade
displays only the mineral names (for PDF minerals) and chemical formula (max 16 characters) for
non-minerals in phase id labeling. However, you can switch mineral labels to chemical formulas by
selecting the 'Chemical Formula' option. The 'Line Color' button shows or hides Jade's color palette for
easy assignment of new line colors. Notice that you can also label the d-I lines from the Quick
Annotation Toolbar.
The Print, Save, and Copy buttons send the list to printer, report file, and clipboard. You can convert
the d-I list of the active overlay into the peak list for analysis functions that utilize the peak list. You can
save the d-I list of the active PDF overlay to a d-I file with the 'DSP File' button.
Tip 1: You can bring up the PDF Card View of the active overlay by double-clicking it on the list, and
you don't have to close the PDF card window in order to view another overlay.
Tip 2: You can prevent Jade from removing the existing overlays when loading a new pattern file. See
the option on the Display tab of the User Preferences dialog.

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Change Radiation Wavelength

The radiation list box on the main toolbar contains the anodes and wavelengths Jade supports. The last
entry on the list is for a user specific (US) monochrome radiation such as the synchrotron data where K
2 is irrelevant. Jade recognizes the radiation anode contained in some of the pattern file types Jade
can read. If the pattern files you work with do not carry the anode specification, the current default
radiation is assumed. However, this default can be changed and even set to override the anode in
pattern files. Refer to the Instrument tab of the User Preferences dialog for more information on
radiation wavelengths.
When you select a new radiation anode from the list box after a pattern file has been read, Jade gives
you the option either to rectify an incorrect anode in the pattern file or to convert the data to the new
radiation wavelength if there is no derived data (such as peak list) in the zoom window:

The latter option makes it possible to compare patterns collected with different wavelengths. If there is
a background curve in the zoom window and the 'Convert K2' box is checked, Jade separates the
original pattern into the K1 and K2 patterns, converts them using the K1 and K2 wavelengths
respectively, and adds the converted patterns to form the new pattern. You should therefore make sure
the background curve is fitted properly for this purpose. If the 'Convert K2' box is unchecked, the
pattern is converted using the K1 wavelength only. Consequently the K2 peaks if present will not be
dispersed correctly in the converted pattern. When a pattern is converted to a shorter wavelength, its
peaks will be sharpened due to the fact of maintaining the same number of data points in the pattern.
This mathematical illusion should not be mistaken for an improved optical resolution on the same
goniometer.
If the data is collected with conventional powder diffractometers or Debye-Scherrer cameras, the Lp
correction would account for changes in relative intensities in the new range of diffraction angles. Jade
uses the following formula to correct for the Lp effect:
I(new) = I(old) * Lp(new) / Lp(old) --- Lp = (1 + cos(2)^2) / (sin()^2 * cos())
where Lp(new) and Lp(old) are calculated for all data points using their new and old theta angles. Jade
maintains a constant number of data points and the same maximum counts when converting the scan
to the new wavelength. The resolution of data may deteriorate due to interpolation, and data could also
be truncated due to wavelength cutoff at the 180 degree limit.

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Data Cursors & Editing (Edit & Cursor Toolbar)

This toolbar implements a variety of manual editing functions and data cursors. These buttons apply to
the mouse pointer working in the zoom window. They are mutually exclusive--you click one of them
and it stays depressed to indicate its active state and the mouse pointer changes into a crosshair cursor
while in the zoom window.

Cursor Off/Zoom: This is the default state, in which you can drag out a rubber-band box to zoom or
right-click for a quick menu in the zoom window. If you click this button once more, you can bring up
the docking menu to align the toolbar to the top and bottom pattern windows. You can minimize the
toolbar with this button if you hold down the Ctrl key.
Magnifying Cursor: Activated only if there are more than 500 data points in the zoom window. This
cursor lets you magnify any region of the pattern onto a pop-up window by moving the mouse pointer
with a framing rectangle in the zoom window. You can move and resize the pop-up window if desired.
You can also resize the framing rectangle by left/right-click in the zoom window while holding down the
Ctrl or Shift key. If you simply left-click in the zoom window, Jade zooms to the framed image. If you
right-click in the zoom window, Jade starts the auto-scrolling by sliding the framing rectangle left/right.
You can speed up or slow down the scrolling by pressing the up/down arrow key repeatedly.
Peak Edit Cursor: With this cursor, you can insert, move, and erase peak markers in the zoom window
using the following operations of mouse and keyboard:
To mark a peak, left-click under it. Jade does a centroid fit in the vicinity to locate its apex. Hold
down the Ctrl key to prevent the centroid fit and mark it on the exact location of the crosshair.
To move a peak marker, left-click it to pick it up and drag it away. You can also move a marker using
the keyboard arrow keys after it has been selected. A newly inserted marker is always selected for
the keyboard operations.
To erase a peak marker, right-click it. You can also erase a marker using the Delete key after it has
been selected.
See Peak Search dialog for how to find and label peaks, and Peak Listing dialog for how to review
peaks.
Peak Paint Cursor: With this cursor, you can estimate peak width by moving the mouse, or paint and
integrate one or more peaks by dragging along the baseline. There are other ways to paint peaks and
obtain peak areas. See Paint & Integrate Peaks for more information.
BG Edit Cursor: With this cursor, you can insert, move, and erase the tie points (dots) that control the
shape of the fitted background curve:
To insert a tie point, left-click at the desired spot. You are not allowed to insert points too close to
existing ones.

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To move a tie point, left-click to pick it up and drag it up/down. Tip: Jade also drags the adjacent dots
along if you hold down the Ctrl key. You can also move a tie point using the up & down arrow keys of
the keyboard after it has been selected, and hop to adjacent tie points using the left & right arrow
keys. A newly inserted tie point is always selected for the keyboard operations.
To erase a tie point, right-click it. Notice that the first and last tie points can't be removed but can be
dragged up/down. You can also erase a tie point by selecting it and pressing the Delete key from the
keyboard.
You can avoid the need for editing the tie points by adjusting the sampling parameters on the Fit
Background dialog.
If you try to identify weak peaks (less than a few % in peak height) with the Profile-Based S/M, it is
critical that you manually fit the background as precisely as possible, since a slight over- or
under-subtraction of background could dramatically affect the relative peak intensities of the minor or
trace phase(s) you are looking for.
Data Edit Cursor: With this cursor, you can edit the raw data of a pattern graphically. Jade does not
save the altered data back to the pattern file--i.e., only a copy of the raw data is being manipulated
here. The following mouse operations are supported for editing data:
Left-Click: Data point closest to the cursor in x-axis is set to the cursor level.
Right-Click: Data point closest to the cursor in x-axis is restored to the original value.
Left-Drag: Data points in the dragged-out line segment are reset around the line with random
intensities. You can set the randomness parameter (Data Noise Sigma) on the Misc tab of the User
Preferences dialog.
Right-Drag: Data points in the dragged-out line segment are restored to their original values.
Left-Drag with the Ctrl key down: Data points in the dragged-out line segment will be rescaled in
intensity. The scaling factor of intensity is the ratio of the line level to the current background along
the line segment. Therefore it's usually not a constant due to the slope of the line as well as the
fluctuation of background.
Left-Drag with the Shift key down: Drag data points near the cursor--very much like pulling on a
rubber string.
You may find this cursor handy should you have to deal with imperfect patterns which are either merged
or truncated, or which contain electronic spikes or abrupt backgrounds due to failing detector or shutter
or grounding problem.
Profile Fitting Cursor: With this cursor, you can insert and edit initial profiles or remove them
graphically. See the Profile Fitting dialog for the details.
With the above cursors, you can display the coordinate values at the crosshair position on a floating
label if you hold down the Ctrl key and move the crosshair cursor. If you press the Alt key at two
different spots in the zoom window while holding down the Ctrl key, Jade will calculate the 2 values
between the two spots and display it in the message area of the main toolbar. You may find this feature
useful for example in estimating the FWHM value of a peak visually. If you depress the 'Long
Crosshair' button, Jade will display the coordinate label in the Cursor Off/Zoom mode without you
holding down the Ctrl key.
K2 Cursor: When you move the mouse into the zoom window with this cursor, you should be able to
see the K2 and K lines of the active anode. You can also display the tungsten L-lines to check for
filament contamination from an aging anode if you click the same button once more. You may need to
adjust the display range of the zoom window in order to see all the cursor lines. Tip: You can use this
cursor to verify if an adjacent peak is from another phase.
Cubic Indexing Cursor: When you move the mouse pointer into the zoom window with this cursor, a
set of vertical line markers will appear corresponding to the allowed set of Miller indices for the cubic

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Bravais lattices. You can select the desired Bravais lattice for the display by clicking the icon button
once more, which causes the following menu to appear:

The cell constant calculated from the hkl values assigned to the current position of the mouse is
displayed in the message indicator of the main toolbar (see the above diagram). You can change the
hkl assignment by left or right clicks in the zoom window in order to reach larger or smaller cells. You
can visually index a cubic pattern with this cursor. Tip: You can use this cursor to obtain an initial cubic
cell for the Cell Refinement dialog. Refer to the d-I Overlay Toolbar for how to visually index tetragonal
and hexagonal patterns, and to the Pattern Indexing dialog for automatic pattern indexing.
Drag Pattern Overlay Cursor: With this cursor, you can move any of the overlaid scan patterns up or
down by dragging at any point of its colored trace in the zoom window. Jade identifies the dragged
pattern by matching the pixel color, and could therefore fail if there is another pattern overlaid in the
same color. You can get around the problem simply by assigning it a different color. You can scale the
overlay intensity if you hold down the Ctrl key while you drag, and offset its 2T(0) zero (i.e., shift to the
left/right) if you hold down the Shift key. Tips: You can apply uniform offsets to all pattern overlays by
pressing the Ctrl+~ key repeatedly; you can also view them in 3D from the 'View | Overlays in 3D...'
menu.
Drag PDF Overlay Cursor: With this cursor, you can shift and scale PDF overlays by dragging any one
of its colored d-I lines in the zoom window. Like the above cursor, Jade relies on the pixel color to
identify the dragged overlay. You can scale the heights (i.e., I% value) of d-I lines by dragging up or
down. You can offset the d-I lines (i.e., 2T(0) zero value) by dragging left/right if you hold down the
Shift key. You can scale the d-I lines in d-space (i.e., d/d(0) value for solid solution) if you hold down
the Ctrl key instead. See PDF Overlay Toolbar for more information.
Tip: You can bring up a number of dialog windows by right-clicking the cursor buttons on the toolbar.

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Jade 5.0

Internal & External Theta Calibration

Theta calibration is a means to correct the scan pattern for significant angular deviation due to
instrumental and experimental imperfections. Standard reference materials (SRMs) are required to
provide the reference peak locations for the calibration. You can bring up the theta calibration dialog
from the 'Analyze | Theta Calibration...' menu or by right-clicking the 'theta calibration' button on the
main toolbar. Two examples of the dialog are given below:

Theta calibration consists of two separate procedures: (a) building the calibration curve, (b) applying the
calibration curve. Step (a) requires the scan pattern to be from one of the SRMs or to contain one or
more of the SRMs, so that references can be made to the correct peak locations. The SRMs listed on
the dialog are read from the 'jade5.srm' file in Jade's program folder. You can browse and edit this file
using a text editor, and remove or add SRMs if desired. If there is a PDF overlay in the zoom window,
Jade will use it as the SRM. In other words, the PDF overlays supersede the built-in SRMs in theta
calibration. If the overlay is not intended for the calibration, remove it before invoking the calibration.
You can also tack multiple PDF overlays as the SRMs in the calibration of a single scan pattern. The
calibration curve is a least-squares fit of 2 values between the reference lines and the located peaks
as a function of 2 angle. You should choose the 'Correction Type' to fit the curve according to the
nature of the angular deviation as well as the scan range of the pattern. For example, you can apply
only the 'Zero Offset' correction if there is only one reference peak in the calibration range. You can
use the ESD value described below as a guide to the appropriate type of correction curve to apply--i.e.,
you should choose the curve that gives a lower ESD value combined with fewer rejected data points.
Jade can use a list of profile-fitted peaks in the calibration if there are no peaks located with the peak
search. If neither exists, Jade does an automatic peak search before building the calibration curve. For
best results, use only relevant and well-resolved peaks belonging to the same SRM. Profile-fitted K1
peaks would be ideal for the calibration because the reference peak locations are calculated from the
d-spacings of reference lines using the K1 wavelength of the radiation. Jade will match the reference
lines to the located peaks within the specified 'Error Window' in degrees of 2. If a sufficient number of
matches are identified, the specified least-squares fit (i.e. correction type) is carried out and the
estimated standard deviation of fit (ESD) is calculated. A rejection test is then performed according to
the 'Outlier Sigma' threshold. If one or more matches are rejected, Jade repeats the fitting and the
outlier testing until no more matches are rejected.
If a sufficient number of matches remain, the results are plotted at the top of the zoom window. The
accepted matches are shown as green dots around the fitted curve, and the rejected ones as red dots.
An example of such a plot is shown below:

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Jade 5.0

The 'Plot Scale(%)' parameter on the calibration dialog sets the height of the calibration plot as a
percentage of the zoom window height. The vertical axis of the plot represents the 2 values and is
scaled to the specified error window. The center line in the plot indicates the zero point of 2, and dots
above the center line therefore have positive 2 values. Similar plots are also used to display the
FWHM Curve and the results of Cell Refinement and Pattern Indexing; they are called the 'Reference
Plot' in Jade. You can choose smaller or bigger dots (circles) in the reference plot from the Display tab
of the User Preferences dialog.
The corrected scan pattern produced by interpolation using the fitted curve is also overlaid in the zoom
window. The results should be examined carefully with the zoom & pan tools. You can do so without
closing the calibration dialog. Any mismatch marked in green dots must be removed by erasing the
offending peak, and Jade will automatically rebuild the calibration curve. If insufficient matches were
found in the calibration, you either selected the wrong SRM or set the 2 error window at too small a
value.
The procedure described above is known as internal theta calibration. The calibration curve can be
saved either with the 'Save Curve' button on the calibration dialog or from the 'File | Save | Theta
Calibration Curve' menu. A saved curve will appear on the External tab of the calibration dialog (see
below); it can be applied subsequently to correct scan patterns acquired from the same goniometer
even though they are from samples not containing the SRM used in the curve.

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Jade 5.0

To accomplish such an external theta calibration, which is valid only if there is no aberrant sample
displacement in data collection, you can select one of the existing calibration curves on the External tab
of the dialog and click the Apply button--the calibrated scan pattern should appear in the zoom window
as with the internal calibration described earlier. To accept the calibrated scan pattern for subsequent
analysis, click the swap button on the main toolbar or select from the 'Analyze | Take New Pattern'
menu. As shown in the above dialog, you can also perform external theta calibration from the main
toolbar or ask Jade to do it automatically upon reading a new pattern file. In the latter case, Jade will
replace the original pattern with the calibrated one (rather than overlay), and indicate the action in the
message area of the main toolbar. See description of the main toolbar for more information.
You can browse the report of internal theta calibration either with the Report button on the calibration
dialog or from the 'View | Reports & Files' menu. An example is shown below:

The 2T(r) is the reference angle of SRM, 2T(o) is the observed angle of a located peak, and the  is
taken as 2T(r) - 2T(o). The 'x' character at the end of a line on the report marks a rejected peak in the
calibration. The Trim button will remove all reference lines that do not match the located peaks within
the specified 2error window. The trimming therefore affects only the report printout, not the calibration
curve. When you select a reference line on the list, Jade identifies it in the zoom window with a vertical
blinker, and will pan the zoom window if necessary to bring the line into view. You can interact with the
zoom window without closing the report dialog. Jade will automatically rebuild the calibration curve and
update the report if you edit the located peaks either on the report dialog or in the zoom window.

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When you save a theta calibration curve, Jade automatically creates a report file (*.srm) in the current
user/project id folder. You can browse this report file with the Report button on the External tab of the
calibration dialog. An example is shown below:

Tip: If your scan pattern has significant 2 error (say >0.1 deg), your chance of identifying the minor or
trace phases in search/match will be greatly improved if you can first calibrate the pattern internally or
externally.

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Jade 5.0

Profile Fitting and Peak Decomposition

While automatic peak search does a fairly good job of characterizing the peaks, profile fitting provides
an improved alternative. It's more elaborate in procedure but produces more precise peak positions,
widths, heights & areas with statistical estimates that are more suited for cell refinement and
quantitative analysis. Since you don't need to characterize all peaks in the pattern for these analyses,
the usual method to fit profiles is to select a region of the pattern containing peaks of interest in the
zoom window, and click the profile button on the main toolbar. Jade will insert profiles for the
peaks in the zoom window and refine them automatically. You can then zoom to another region of the
pattern containing desired peaks and repeat the fitting process. If the pattern does not contain too
many overlapping peaks and too complex a background, you can automate the fitting process by
initiating the 'Fit All Peaks' procedure. This can be done simply by left-clicking the profile button on the
main toolbar while holding down the Ctrl key. Jade will segment the pattern into regions of profile fitting
according to the proximity of peaks, and refine them all one region after another.
In the above fitting automation, a segmented linear background is usually refined together with the peak
profiles. Therefore it's imperative to segment the zoom regions in such a way as to contain relatively
straight left and right backgrounds. If the background level is not required/essential to be refined, then
there is another simple way to fit most of the peaks in the pattern. If you fit a background curve
(preferably a cubic-spline type with no vertical offset, see the Background Fitting dialog) before initiating
the profiles, Jade will use it, by default, as fixed background for the peaks to be refined, thus making it
possible to fit most peaks at once without the need of segmenting the pattern. However, if necessary,
you can still segment the pattern manually to obtain better fits in some regions. If you have numerous
peaks to fit in the pattern, it's faster to fit them segment by segment than all at once.
All these automations of profile fitting are intended for simple XRD patterns. User interventions will be
required with more complex patterns. If you right-click the profile button on the main toolbar or select
the 'Analyze | Fit Peak Profile...' menu, Jade brings up the profile fitting dialog shown below:

Jade will insert initial profiles for peaks in the zoom window if none are present and the display range is
less than 20 degrees. These initial profiles will have the profile attributes currently set on the above
dialog. If the 'Reset Existing Profiles' box is checked, any change made to the profile attributes on the
dialog will affect the existing profiles as well as subsequently inserted profiles. But you can have
profiles with mixed attributes in the refinement if you uncheck the 'Reset Existing Profiles' box. For a
complex pattern with broad and overlapping peaks, it may be necessary and desirable to edit the initial
profiles manually before refining them. This can be done with the profile editor on the Edit & Cursor
Toolbar in the following ways:
To insert a profile, left-click beneath a peak. Jade estimates initial profile height from peak height to
accommodate the K2 if present. You can hold the Ctrl key to insert a profile at the exact location
and height of the crosshair. The initial profile width could be assigned from the FWHM curve or by

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the specified value on the above dialog. If you right-click beneath a peak, Jade assigns the
non-default profile type (pseudo-Voigt in the above dialog) to the new profile. Likewise, if the default
profile type is the pseudo-Voigt, a right-click will generate the Pearson-VII profile. In general, you
should choose the profile type that gives the lowest residual error (R%) after the profiles have been
refined. This R% value is calculated as 100 * sqrt(sum((O - C)^2/O)/sum(O) ) , where O is the
observed intensity, C the calculated intensity, and the sum is over all data points in the refined region.
To alter the FWHM of a profile, drag it up/down while holding down the Ctrl key. If the FWHM is
unified (to be described later), all existing profiles will be altered simultaneously. You can set the
FWHM to a minimum value of three step-sizes of the scan pattern, and to the maximum value of 50
degrees in 2.
To alter the skewness of a profile, drag it left/right while holding down the Ctrl key. If the skewness is
unified, all existing profiles will be altered simultaneously. The same skewness applies to both profile
types and takes on a range of -0.9 to +0.9.
To alter the shape/tail of a profile (i.e., the exponent in a Pearson-VII profile, or the Lorentzian factor
in a pseudo-Voigt profile), drag it up/down while holding down the Shift key. Like the FWHM or the
skewness, the shape variables can be unified and altered simultaneously.
To move a profile, left-click its marker to pick and drag it up/down and left/right. You can also move
a profile using the arrow keys after it has been selected. You can alter its shape using the same arrow
keys if you hold down the Ctrl or Shift key. You can erase it using the Delete key. A newly inserted
profile is always selected by Jade for the keyboard operations.
To erase a profile, right-click its marker. If you hold down the Ctrl key while right-clicking and the
profile has been refined, Jade will subtract the profile intensities from the scan pattern, thus producing
a residual pattern without the subtracted peak or amorphous hump.
You can refine the profiles together with a variable polynomial background (BG) or a fixed BG fitted
with the BG editor. The polynomial BG will be adequate to fit a short segment of pattern. It will be
initialized with automatically sampled BG points if the BG dots are not present. If the region to fit does
not have a well defined left or right BG level, the polynomial BG could be initialized too high--causing a
bad fit. You can solve this problem by entering a few BG dots at the desired spots using the BG editor,
and Jade will initialize the polynomial curve using the existing BG dots when you reinitialize the profiles
or switch the BG option on the profile dialog. If you intend to refine all peaks in a pattern having a
complex background, it may be desirable to fit a BG curve manually before you proceed to refine the
profiles.
When you are satisfied with the initial profiles, you can start a refinement with the Refine button on the
profile dialog or by clicking the profile button on the editing toolbar or on the main toolbar. By default,
Jade only refines the profiles in the current zoom window together with the fitted background. You can
freely zoom around the pattern and refine peaks in any desired grouping and order. When you zoom to
a region that has no inserted/fitted profiles, Jade automatically initializes the background and inserts
profiles if you click the refinement button. One thing to avoid doing is to refine too many profiles at
once. You can interrupt the refinement cycles of profile fitting with the ESC key if needed. It should be
pointed out that profile fitting is a non-linear optimization procedure that requires iterations, and the
results (also called refinement convergence) depend more or less on the initial profile values. This
dependency, expressed as profile correlation, will be strong if the peaks are broad and overlapping.
Should the fitting stop before it converges due to profile correlation, you may carry out more fitting
iterations by clicking the refinement button a few times. You can also manually adjust the current
profiles to better shapes and positions, add or remove some profiles, and start the refinement again. If
necessary, you may constrain the profiles to reduce the number of variables (i.e., degrees of freedom)
in the refinement using the 'Unify Variables' options on the following dialog:

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You can bring up the above dialog either with the 'Report...' button on the profile-fitting dialog or by
selecting the 'View | Reports & Files | Peak Profile Report...' menu. When you unify profile variables
such as FWHMs, all profiles will have the same value with regard to the unified variable, and they will
be refined together as a single variable. Note: the apparent FWHM values upon unification will be the
same only when the skewness variables are unified. You can prevent a profile variable from being
refined by unchecking its refinement box in the 'Variables to Refine' group. You can enter new values
of refinable variables (i.e., 2-Theta, Height, Shape, Skew & FWHM) if you hold down the Ctrl key and
click the desired column header--an input box will appear for you to type in the number.
The refined values of peak position, height, area, and I% are only for the K1 peaks if you include the K
2 in the refinement. Their estimated standard deviations will be shown in the parentheses if the 'Hide
ESD Values' box is not checked. These ESD values are calculated using the counting statistics of the
scan pattern in the profile refinement, and they are sensitive to the convergence of profile refinement.
In other words, you should make sure the refinement has converged properly if you desire statistical
confidence in these numbers. One way to convince yourself of the truth is to reinitialize or reinsert and
refine the same number of profiles a few times, and see if they converge to similar values within their
ESD window. Jade will display a '?' in parentheses if a profile variable has not been refined or its ESD
value is greater than a certain threshold set by Jade.
The I% values are the relative areas normalized to the maximum area on the list. The Area% printed in
the status bar on the above dialog is the percentage normalized to the sums of all areas on the list. If
this area is from an amorphous hump in the pattern, it gives the estimate of percent crystallinity in the
sample, assuming the crystallinity is proportional to the total areas of the diffracted peaks. You can use
the check boxes on the list to designate amorphous peaks and Jade will calculate the percent
crystallinity accordingly. You can also set the FWHM threshold (default is 3 degrees wide) above which
a profile is automatically checked by Jade to be amorphous for the crystallinity estimate. The suffix 'p'
or 'v' in the Shape column indicates a Pearson-VII or pseudo-Voigt profile. See the Crystallite Size &
Strain Analysis for how Jade estimates the crystallite sizes from the refined values of profile widths.
Notice that individual profiles are listed and plotted in the order of insertion so that you have control
over which one is in front if you choose to paint them. Nevertheless you can re-sort the profile list
simply by clicking the desired column header on the profile report dialog. While the display attributes of

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individual profiles can be assigned independently, you can unify profile displays with regard to their fill
styles, fill colors, and line styles. You can also paint profiles belonging to the same phase in the same
color in a multi-phase pattern if you overlay the relevant PDF phases in the zoom window. Jade will list
the current PDF overlays on the profile report dialog as shown below:

If you click the 'Assign Profiles' button, Jade will associate the current profiles with the PDF phases
according to the proximity of d-I lines, and paint the profiles belonging to the same phase in the
designated color in the zoom window. If the 'Color Phases' box is checked, Jade also lists the profiles
in colors as shown on the above dialog. You can subtract the profiles of a phase from the pattern with
the 'Strip One Phase' button, and Jade will remove the profiles from the list as well. You can undo
phase association of profiles either with the 'Release Profiles' button or by deleting the PDF overlays.
Once peaks have been fitted properly, you can make good use of them in analyses such as lattice
constant determination and quantitative calculation in which accurate peak parameters are desired or
required. It should be pointed out that the refined profiles are maintained as a separate list from the
peaks located with automatic peak search in Jade. While analysis tasks such as theta calibration, cell
refinement, and pattern indexing will use the profile list automatically if a peak list does not exist, you
can convert and add profiles to the peak list by selecting the 'Analyze | Add Profiles to Peaks' menu. If
you do, you can choose the profile centroids rather than the fitted summits (i.e., those in the 2 column)
by checking the 'Centroid -> Peak Locations' box on the above dialog. You can also use the refined
profiles to build the FWHM curve and perform crystallite size & strain analysis, which can be done from
the 'FWHM Curve Plot & 'Size & Strain Plot' menus under the main menu 'Analyze' or 'View |
Reports...'. The 'Size & Strain Plot...' button on the above dialog will be activated only if you have the
Jade Plus option.
You can export the refined profile traces together with the raw pattern to a *.DIF file in MDI file format
using the Export button on the profile fitting dialog or from the 'File | Save | Refined Profiles as *.DIF'
menu. Jade will export the individual and overall profiles only if they are checked on the profile fitting
dialog. You can skip the export of background curve if you change the BG option to 'Fixed Background'
on the profile dialog and you have no manual BG curve in the zoom window. Jade will not export the
difference pattern even though it's checked and being displayed. Tip: You can choose to paint the
difference pattern from the Zoom Window Display dialog.
While you can strip K2 peaks with the background removal, using the 'Strip K2' button on the profile
fitting dialog, you can eliminate the K2 peaks in a more precise manner if you include the K2 in the
refined profiles. With the 'Replace Data' button on the profile fitting dialog, you can replace the
observed pattern with the overall refined pattern for purposes such as pattern smoothing. If you do so,
you can introduce random noise in the refined pattern by entering a sigma value in the text box next to
the 'Replace Data' button on the same dialog. While you can remove multiple peaks from the scan
pattern by phase association of the refined profiles described earlier, you can also subtract profiles from

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the pattern one peak at a time with the Erase button while holding down the Ctrl key on the profile report
dialog. An example of profile fitting to a polymer pattern with an amorphous hump is shown below:

When the amorphous hump (cross-hatched area) is removed from the above plot, the residual pattern
will look like the following:

Notice that both the profile fitting and report dialog windows are modeless--i.e., you can keep them
open while interacting with the main window. If you add or remove or modify profiles in the zoom
window using the profile editor, Jade will update the profile report dialog automatically. While Jade
always remembers the current profile fitting parameters, you can save and restore additional setting
files on the profile fitting dialog. These setting files will also appear in the macro task list for automatic

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pattern processing.
Tip 1: You can erase all ill-fitted profiles (i.e., whose with '(?)' in their peak heights) by right-clicking the
Erase button on the profile report dialog.
Tip 2: MDI's whole-pattern fitting program, SHADOW, can fit the whole pattern by refining lattice
constants and profile-shape functions as constrained polynomials, rather than by refining individual line
positions and shapes as done here. Peak convolution with instrument profiles is also possible to
determine crystallite size and strain simultaneously.
Tip 3: You can perform profile fitting one iteration per click if you hold down the Shift key.

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Jade 5.0

Profile Fitting and Peak Decomposition

While automatic peak search does a fairly good job of characterizing the peaks, profile fitting provides
an improved alternative. It's more elaborate in procedure but produces more precise peak positions,
widths, heights & areas with statistical estimates that are more suited for cell refinement and
quantitative analysis. Since you don't need to characterize all peaks in the pattern for these analyses,
the usual method to fit profiles is to select a region of the pattern containing peaks of interest in the
zoom window, and click the profile button on the main toolbar. Jade will insert profiles for the
peaks in the zoom window and refine them automatically. You can then zoom to another region of the
pattern containing desired peaks and repeat the fitting process. If the pattern does not contain too
many overlapping peaks and too complex a background, you can automate the fitting process by
initiating the 'Fit All Peaks' procedure. This can be done simply by left-clicking the profile button on the
main toolbar while holding down the Ctrl key. Jade will segment the pattern into regions of profile fitting
according to the proximity of peaks, and refine them all one region after another.
In the above fitting automation, a segmented linear background is usually refined together with the peak
profiles. Therefore it's imperative to segment the zoom regions in such a way as to contain relatively
straight left and right backgrounds. If the background level is not required/essential to be refined, then
there is another simple way to fit most of the peaks in the pattern. If you fit a background curve
(preferably a cubic-spline type with no vertical offset, see the Background Fitting dialog) before initiating
the profiles, Jade will use it, by default, as fixed background for the peaks to be refined, thus making it
possible to fit most peaks at once without the need of segmenting the pattern. However, if necessary,
you can still segment the pattern manually to obtain better fits in some regions. If you have numerous
peaks to fit in the pattern, it's faster to fit them segment by segment than all at once.
All these automations of profile fitting are intended for simple XRD patterns. User interventions will be
required with more complex patterns. If you right-click the profile button on the main toolbar or select
the 'Analyze | Fit Peak Profile...' menu, Jade brings up the profile fitting dialog shown below:

Jade will insert initial profiles for peaks in the zoom window if none are present and the display range is
less than 20 degrees. These initial profiles will have the profile attributes currently set on the above
dialog. If the 'Reset Existing Profiles' box is checked, any change made to the profile attributes on the
dialog will affect the existing profiles as well as subsequently inserted profiles. But you can have
profiles with mixed attributes in the refinement if you uncheck the 'Reset Existing Profiles' box. For a
complex pattern with broad and overlapping peaks, it may be necessary and desirable to edit the initial
profiles manually before refining them. This can be done with the profile editor on the Edit & Cursor
Toolbar in the following ways:
To insert a profile, left-click beneath a peak. Jade estimates initial profile height from peak height to
accommodate the K2 if present. You can hold the Ctrl key to insert a profile at the exact location
and height of the crosshair. The initial profile width could be assigned from the FWHM curve or by

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Jade 5.0

the specified value on the above dialog. If you right-click beneath a peak, Jade assigns the
non-default profile type (pseudo-Voigt in the above dialog) to the new profile. Likewise, if the default
profile type is the pseudo-Voigt, a right-click will generate the Pearson-VII profile. In general, you
should choose the profile type that gives the lowest residual error (R%) after the profiles have been
refined. This R% value is calculated as 100 * sqrt(sum((O - C)^2/O)/sum(O) ) , where O is the
observed intensity, C the calculated intensity, and the sum is over all data points in the refined region.
To alter the FWHM of a profile, drag it up/down while holding down the Ctrl key. If the FWHM is
unified (to be described later), all existing profiles will be altered simultaneously. You can set the
FWHM to a minimum value of three step-sizes of the scan pattern, and to the maximum value of 50
degrees in 2.
To alter the skewness of a profile, drag it left/right while holding down the Ctrl key. If the skewness is
unified, all existing profiles will be altered simultaneously. The same skewness applies to both profile
types and takes on a range of -0.9 to +0.9.
To alter the shape/tail of a profile (i.e., the exponent in a Pearson-VII profile, or the Lorentzian factor
in a pseudo-Voigt profile), drag it up/down while holding down the Shift key. Like the FWHM or the
skewness, the shape variables can be unified and altered simultaneously.
To move a profile, left-click its marker to pick and drag it up/down and left/right. You can also move
a profile using the arrow keys after it has been selected. You can alter its shape using the same arrow
keys if you hold down the Ctrl or Shift key. You can erase it using the Delete key. A newly inserted
profile is always selected by Jade for the keyboard operations.
To erase a profile, right-click its marker. If you hold down the Ctrl key while right-clicking and the
profile has been refined, Jade will subtract the profile intensities from the scan pattern, thus producing
a residual pattern without the subtracted peak or amorphous hump.
You can refine the profiles together with a variable polynomial background (BG) or a fixed BG fitted
with the BG editor. The polynomial BG will be adequate to fit a short segment of pattern. It will be
initialized with automatically sampled BG points if the BG dots are not present. If the region to fit does
not have a well defined left or right BG level, the polynomial BG could be initialized too high--causing a
bad fit. You can solve this problem by entering a few BG dots at the desired spots using the BG editor,
and Jade will initialize the polynomial curve using the existing BG dots when you reinitialize the profiles
or switch the BG option on the profile dialog. If you intend to refine all peaks in a pattern having a
complex background, it may be desirable to fit a BG curve manually before you proceed to refine the
profiles.
When you are satisfied with the initial profiles, you can start a refinement with the Refine button on the
profile dialog or by clicking the profile button on the editing toolbar or on the main toolbar. By default,
Jade only refines the profiles in the current zoom window together with the fitted background. You can
freely zoom around the pattern and refine peaks in any desired grouping and order. When you zoom to
a region that has no inserted/fitted profiles, Jade automatically initializes the background and inserts
profiles if you click the refinement button. One thing to avoid doing is to refine too many profiles at
once. You can interrupt the refinement cycles of profile fitting with the ESC key if needed. It should be
pointed out that profile fitting is a non-linear optimization procedure that requires iterations, and the
results (also called refinement convergence) depend more or less on the initial profile values. This
dependency, expressed as profile correlation, will be strong if the peaks are broad and overlapping.
Should the fitting stop before it converges due to profile correlation, you may carry out more fitting
iterations by clicking the refinement button a few times. You can also manually adjust the current
profiles to better shapes and positions, add or remove some profiles, and start the refinement again. If
necessary, you may constrain the profiles to reduce the number of variables (i.e., degrees of freedom)
in the refinement using the 'Unify Variables' options on the following dialog:

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You can bring up the above dialog either with the 'Report...' button on the profile-fitting dialog or by
selecting the 'View | Reports & Files | Peak Profile Report...' menu. When you unify profile variables
such as FWHMs, all profiles will have the same value with regard to the unified variable, and they will
be refined together as a single variable. Note: the apparent FWHM values upon unification will be the
same only when the skewness variables are unified. You can prevent a profile variable from being
refined by unchecking its refinement box in the 'Variables to Refine' group. You can enter new values
of refinable variables (i.e., 2-Theta, Height, Shape, Skew & FWHM) if you hold down the Ctrl key and
click the desired column header--an input box will appear for you to type in the number.
The refined values of peak position, height, area, and I% are only for the K1 peaks if you include the K
2 in the refinement. Their estimated standard deviations will be shown in the parentheses if the 'Hide
ESD Values' box is not checked. These ESD values are calculated using the counting statistics of the
scan pattern in the profile refinement, and they are sensitive to the convergence of profile refinement.
In other words, you should make sure the refinement has converged properly if you desire statistical
confidence in these numbers. One way to convince yourself of the truth is to reinitialize or reinsert and
refine the same number of profiles a few times, and see if they converge to similar values within their
ESD window. Jade will display a '?' in parentheses if a profile variable has not been refined or its ESD
value is greater than a certain threshold set by Jade.
The I% values are the relative areas normalized to the maximum area on the list. The Area% printed in
the status bar on the above dialog is the percentage normalized to the sums of all areas on the list. If
this area is from an amorphous hump in the pattern, it gives the estimate of percent crystallinity in the
sample, assuming the crystallinity is proportional to the total areas of the diffracted peaks. You can use
the check boxes on the list to designate amorphous peaks and Jade will calculate the percent
crystallinity accordingly. You can also set the FWHM threshold (default is 3 degrees wide) above which
a profile is automatically checked by Jade to be amorphous for the crystallinity estimate. The suffix 'p'
or 'v' in the Shape column indicates a Pearson-VII or pseudo-Voigt profile. See the Crystallite Size &
Strain Analysis for how Jade estimates the crystallite sizes from the refined values of profile widths.
Notice that individual profiles are listed and plotted in the order of insertion so that you have control
over which one is in front if you choose to paint them. Nevertheless you can re-sort the profile list
simply by clicking the desired column header on the profile report dialog. While the display attributes of

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individual profiles can be assigned independently, you can unify profile displays with regard to their fill
styles, fill colors, and line styles. You can also paint profiles belonging to the same phase in the same
color in a multi-phase pattern if you overlay the relevant PDF phases in the zoom window. Jade will list
the current PDF overlays on the profile report dialog as shown below:

If you click the 'Assign Profiles' button, Jade will associate the current profiles with the PDF phases
according to the proximity of d-I lines, and paint the profiles belonging to the same phase in the
designated color in the zoom window. If the 'Color Phases' box is checked, Jade also lists the profiles
in colors as shown on the above dialog. You can subtract the profiles of a phase from the pattern with
the 'Strip One Phase' button, and Jade will remove the profiles from the list as well. You can undo
phase association of profiles either with the 'Release Profiles' button or by deleting the PDF overlays.
Once peaks have been fitted properly, you can make good use of them in analyses such as lattice
constant determination and quantitative calculation in which accurate peak parameters are desired or
required. It should be pointed out that the refined profiles are maintained as a separate list from the
peaks located with automatic peak search in Jade. While analysis tasks such as theta calibration, cell
refinement, and pattern indexing will use the profile list automatically if a peak list does not exist, you
can convert and add profiles to the peak list by selecting the 'Analyze | Add Profiles to Peaks' menu. If
you do, you can choose the profile centroids rather than the fitted summits (i.e., those in the 2 column)
by checking the 'Centroid -> Peak Locations' box on the above dialog. You can also use the refined
profiles to build the FWHM curve and perform crystallite size & strain analysis, which can be done from
the 'FWHM Curve Plot & 'Size & Strain Plot' menus under the main menu 'Analyze' or 'View |
Reports...'. The 'Size & Strain Plot...' button on the above dialog will be activated only if you have the
Jade Plus option.
You can export the refined profile traces together with the raw pattern to a *.DIF file in MDI file format
using the Export button on the profile fitting dialog or from the 'File | Save | Refined Profiles as *.DIF'
menu. Jade will export the individual and overall profiles only if they are checked on the profile fitting
dialog. You can skip the export of background curve if you change the BG option to 'Fixed Background'
on the profile dialog and you have no manual BG curve in the zoom window. Jade will not export the
difference pattern even though it's checked and being displayed. Tip: You can choose to paint the
difference pattern from the Zoom Window Display dialog.
While you can strip K2 peaks with the background removal, using the 'Strip K2' button on the profile
fitting dialog, you can eliminate the K2 peaks in a more precise manner if you include the K2 in the
refined profiles. With the 'Replace Data' button on the profile fitting dialog, you can replace the
observed pattern with the overall refined pattern for purposes such as pattern smoothing. If you do so,
you can introduce random noise in the refined pattern by entering a sigma value in the text box next to
the 'Replace Data' button on the same dialog. While you can remove multiple peaks from the scan
pattern by phase association of the refined profiles described earlier, you can also subtract profiles from

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the pattern one peak at a time with the Erase button while holding down the Ctrl key on the profile report
dialog. An example of profile fitting to a polymer pattern with an amorphous hump is shown below:

When the amorphous hump (cross-hatched area) is removed from the above plot, the residual pattern
will look like the following:

Notice that both the profile fitting and report dialog windows are modeless--i.e., you can keep them
open while interacting with the main window. If you add or remove or modify profiles in the zoom
window using the profile editor, Jade will update the profile report dialog automatically. While Jade
always remembers the current profile fitting parameters, you can save and restore additional setting
files on the profile fitting dialog. These setting files will also appear in the macro task list for automatic

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pattern processing.
Tip 1: You can erase all ill-fitted profiles (i.e., whose with '(?)' in their peak heights) by right-clicking the
Erase button on the profile report dialog.
Tip 2: MDI's whole-pattern fitting program, SHADOW, can fit the whole pattern by refining lattice
constants and profile-shape functions as constrained polynomials, rather than by refining individual line
positions and shapes as done here. Peak convolution with instrument profiles is also possible to
determine crystallite size and strain simultaneously.
Tip 3: You can perform profile fitting one iteration per click if you hold down the Shift key.

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Jade 5.0

Crystallite Size & Strain Analysis from Peak Broadening

The broadening of a diffraction peak is characterized by its FWHM (Full Width at Half Maximum) value
at a particular 2 angle. Because the apparent FWHM of a peak is a mathematical combination
(convolution) of the specimen broadening FW(S) and the instrumental broadening FW(I), it is necessary
to characterize the goniometer in use to obtain the FW(I) values as a function of 2 angle--i.e., an
FWHM curve. This can be done by acquiring a good scan pattern from a standard reference material
that does not exhibit significant specimen broadening, such as the NIST 640A silicon or LaB6. You then
proceed to determine FWHM values of its significant peaks by profile fitting or automatic peak search.
These FWHM values will represent the instrument broadening FW(I), because the specimen
broadening is negligible.
Since the FWHM values are estimated from peak areas & heights in automatic peak search, they may
not be precise enough to be used to establish the instrumental FWHM curve. For more precise work,
you should always profile-fit peaks to obtain statistically reliable FWHM values for the K1 peaks. Jade
will generate the FWHM curve from profile-fitted FWHM values using their variances as statistical
weights in the least-squares fit. Notice that Jade maintains a separate list for profile-fitted peaks. You
don't need to convert them to the peak search list, a procedure called 'Add Profiles to Peaks' under the
Analyze menu, in order to generate the FWHM curve. Jade uses only the profile list if both lists are
present. If you choose the peak list, you should remove the K2 before the peak search. Refer to the
Profile Fitting dialog for how to fit profiles to peaks, and to the Peak List Report for viewing FWHM
values estimated from automatic peak search.
You can fit and display the FWHM parabolic curve (i.e., FWHM = A + B * 2 + C * 2^2) by selecting
the 'FWHM Curve Plot' item under the main menu 'Analyze' or 'View | Reports...'. Jade will select only
the strong and non-overlapping peaks to fit the FWHM curve, while marking the rejected peaks if any in
red dots in the zoom window. An example is shown below:

If fitted profiles are from multiple phases and there are PDF overlays in the zoom window, Jade will
select only those profiles matching the d-I lines of the active PDF overlay to build the FWHM curve (this
option is similar to theta calibration with an internal standard). You can exclude more peaks from the
fitted curve by removing them from the profile/peak list, and save the curve from the 'File | Save |
FWHM Curve of Peaks' menu. A newly saved FWHM curve will appear on the Instrument tab of the
User Preferences dialog and be selected as the current instrumental FWHM curve for subsequent
analysis of crystallite size & strain. You can view the graphical plot of an FWHM curve on the

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Instrument tab of the user preferences dialog as illustrated below:

If the crystallites (i.e., crystalline domains) in the specimen are free of lattice strain, you can estimate
their average size from the specimen broadening FW(S) of any single peak in the pattern according to
the Scherrer formula:
Crystallite Size = K *  / FW(S) * Cos(),
where theta is the peak position, and K is the shape factor of the average crystallite, which can be set
on the Misc tab of the User Preferences dialog. Jade uses the formula FW(S)^D = FWHM^D - FW(I)^D
to estimate the specimen broadening from the apparent FWHM value of a peak, where FW(I) is
calculated from the current FWHM curve and D is called the deconvolution parameter and can be set
anywhere from 1.0 to 2.0 (default is 2.0) on the 'Size & Strain Plot' dialog to be described below. You
should choose a D value close to 2.0 if the profile shape is more Gaussian than Lorentzian. If you
choose the integral breadth to estimate the crystallite size on the profile report dialog, you should set
the D value close to 1.0.
There are three ways to obtain the FWHM value of a peak in Jade: (a) automatic peak search, (b) peak
painting, and (c) profile fitting. Three estimates of crystallite size from the same peak can thus be
obtained with increasing confidence of precision from (a) to (c). You should choose a well-resolved
peak whenever possible and make sure the FWHM value is from the K1 only. If you wish to verify the
calculations of crystallite sizes done by Jade, you must ensure the FW(S) values are converted to
unitless radians so crystallite sizes assume the units of wavelength.
If there are substantial lattice strains in the specimen, which broadens the peaks as a function of 2
angle differently than for small crystallites, you can estimate the crystallite size & strain simultaneously
using the FWHM values of fitted profiles by clicking the 'Size & Strain Plot...' button on the profile report
dialog or by selecting the 'Size & Strain Plot...' item from the main menu 'Analyze' or 'View | Reports...'.
Jade then carries out a least-squares fit of the FW(S) values to determine the size & strain values using
the following equation:
FW(S) * Cos() = K *  / Size + 4 * Strain * Sin().
Notice that the formula turns into the Scherrer equation when the strain term is zero. An example of the
size & strain plot is shown below:

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If the resulting size or strain value is negative, it could mean either (a) the above formula is invalid for
your specimens, or (b) the FW(S) values of the peaks are not obtained correctly. The latter could be
due to poorly fitted profiles or the use of an invalid FWHM curve or deconvolution parameter (D)
described earlier. If you choose to fit the size only to the FW(S) data, you should see a straight
horizontal line in the above plot. This is also the recommended way to determine the average crystallite
size using multiple peaks. If you choose to fit the strain only, you should see a sloping line passing
through the (0,0) origin. Jade uses automatic scaling in the above plot, but you can force the axes to
start at zero if you check the 'Origin(0,0)' box on the above dialog. The red dots in the above plot
indicate the profiles rejected from the least-squares fit because they are too far away from the fitted
line. You can set this outlier threshold in terms of the ESD values in the parameter box next to the
'Origin(0,0)'. Error bars on individual data points are plotted as  ESD value. You can erase data
points in the plot by right-clicking the dots, and Jade will remove the corresponding profiles from the
zoom window as well as from the profile listing on the profile report dialog. If you left-click a dot, Jade
will identify the profile with a vertical blinker in the zoom window. You can erase the profile in the zoom
window using the profile cursor without closing the dialog window of the size & strain plot, and Jade will
update the plot automatically.
If fitted profiles are from multiple phases, you can choose to fit the size & strain plot to the profiles from
just one phase. This can be done using PDF overlays and the phase association options on the profile
report dialog. In this case, you should see the active phase id (rather than the 'All Unrejected Peaks')
being displayed in the status bar of the above dialog. Jade will automatically fit and display a new size
& strain plot when you switch the active PDF overlay either from the profile report dialog or from the
PDF Overlay Toolbar.
Tip: MDI's whole-pattern fitting program, SHADOW, can determine crystallite size and strain
simultaneously from convoluted profile fitting of instrument and sample broadening.

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Residual Stress Analysis from Peak Shifts

With the Residual Stress option in Jade, you can analyze residual stress in the specimen surfaces from
the shifts of high angle peaks in the so-called -scans, in which the specimen surface is tilted at
different angles (i.e.,  angles) relative to that of the detector. Jade currently can read -scan files in
MDI and RINT-2000 formats. In addition, you can overlay individual scan patterns acquired at different
angles and bring up the dialog of residual stress analysis (shown below) if the pattern overlays have
the same scan range and step-size. You can then enter the angles of individual scans in the '
-Angle' column on the dialog window shown below. To enter the  angle, click in the column and wait
for an input box to appear. This dialog window can be brought up from the 'Options | Calculate Stress...'
menu.

You can determine peak positions either by fitting profile or parabola with the 'Fit One' and 'Fit All'
buttons on the dialog. When the 'Parabolic Fit' box is checked, Jade will fit a N-point parabola to the
peak top, where N is a number you can specify on the dialog. This option should be preferred when the
peak is very broad and does not fall to background in the scan range. When the 'Parabolic Fit' box in
unchecked, Jade uses the profile attributes currently set on the Profile-Fitting Dialog to fit the peaks. If
there is only one peak in the scan range, you can fit all peaks from different angles at once simply by
clicking the 'Fit All' button on the above dialog. When there are multiple peaks in a single -scan, it will
be necessary for you to insert the profiles using the profile cursor before you click the 'Fit All' button.
You can then select which peak to use in the stress calculation on the dialog (see the above diagram).
You can also exclude a fitted peak at a particular -angle from the least-squares fit by unchecking it on
the profile list.
The least-squares fit is carried out in the linear function of %(d-d0)/d0 = A + B * sin()^2, where d0 is
the peak position at =0. For triaxial stress analysis, it may be desirable and necessary to specify the
stress-free d0 value rather than that calculated at =0. You can do so if you check the 'd0' box and
enter the desired number to the text box next to the check box. The fit will include statistical weights of
individual variances of fitted peak positions, and the results will have reliable statistical estimates
derived from the quality of scan data. The error bars on individual data points are plotted as  ESD

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value of %(d-d0)/d0. For biaxial stress analysis, you can force the fitted line to go through zero of the
axes by choosing the Y=B*X option on the above dialog, where B = Stress * (1 + v) / E, v is Poisson's
ratio, and E is Young's modulus of the specimen. Therefore a positive slope of the fitted line in the plot
indicates a tensile stress in the specimen surface while a negative slope indicates a compressive
stress. If the peaks come from very high angles and are very broad, they could be rather skewed due to
the combined effects of Lorentz-polarization and absorption (LPA) of X-ray beams. It may then be
necessary to apply the LPA correction to the profile intensities using the formula:
LPA = (1 + cos(2)^2) * (1 - tan() / tan()) / sin()^2,
before you fit the profiles. With the LPA button on the dialog, you can toggle the profile intensities with
or without the LPA correction, and examine the results in the zoom window as shown below. Jade will
indicate the LPA correction by prefixing an asterisk (*) to the LPA button.

You can print, copy, and save the analysis results on the residual stress dialog. Jade will include the
fitted profiles on the printout if you hold down the Ctrl key while clicking the Print button. You can send
the plot of least-squares fit to the clipboard by left-clicking the Copy button (so you can paste it into an
open report document). You can send the fitted profile list to the clipboard instead if you right-click the
Copy button. When saving the analysis results to a file, you can choose to create either the plot file
(*.wmf) of least-squares fit by left-clicking the Save button, or the plain text report file (*.ksi) if you
right-click the Save button. You can later browse the report file (*.ksi) either from the 'View | Reports &
Files...' menu or simply by clicking the KSI item in the main status bar.
While the current analysis parameters are always remembered by Jade, you can create additional
setting files with the Save button and recall any one of them from the setting file list on the stress
analysis dialog. These setting files will also appear on the macro task list for automatic pattern
processing.
Tip 1: You can offset scans of different angles for better view in the zoom window by selecting the
'Edit | Offset Overlays' menu or by pressing the Ctrl+~ keys repeatedly.
Tip 2: You can show or hide the peak position markers with angle labels in the zoom window using the
check boxes on this dialog.

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Calculating Possible Reflections

You can access the d-spacing calculator in Jade from the 'Options | D-Spacing & hkl...' menu to
calculate all possible reflections of a unit cell with or without the Laue symmetry conditions. Jade uses
its built-in space group table to look up the Laue symmetry for a given cell. If there is an active PDF
overlay in the zoom window, Jade will take its cell parameters and automatically calculate its possible
reflections. An example of the calculator dialog is shown below:

The calculator can list up to 2000 reflections at a time, and display them in the zoom window as a set of
line markers for comparison with the current pattern. The 'Same d-Spacing' check will merge
reflections of the same d-spacing into one. If a low-symmetry and/or large cell overflows the 2000 limit,
you can use the 2-theta range controls to generate reflections region by region. You can change the
color of these reflection markers from the Color Setting dialog and alter their heights from the Zoom &
Pan Toolbar. You can show or hide the Miller indices on top of the reflection markers from the Quick
Annotation Toolbar. You can alter the font size or orientation of these (hkl) labels from the same
toolbar. You can erase these reflection markers from the zoom window by selecting the 'Reference
Plot' from the erase menu. You can copy the reflection list to the clipboard or save it to a d-I listing file
(*.dsp) in which the reflection multiplicities are written into the I% column. If desired, you can overlay
the reflections like the PDF d-I list by clicking the Add button on this dialog.
You can also calculate the cell density (g/cm^3) if you enter the chemical formula and the formula units
(Z) per cell. Jade will take the formula & Z-value from the active PDF overlay if any. The density (D) is
calculated using the following equation:
D (g/cm^3) = W * Z / V / 0.6022169 (W = formula weight, V = cell volume).
In the above example, Jade calculates the cell density using the chemical formula and Z-value of
corundum.

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Calculating Lattice Constants from Peaks

In contrast to the d-Spacing Calculator, you can compute lattice constants from the locations of a few
low-angle peaks with known Miller indices. This is useful for example in obtaining approximate cell
constants for a new phase. You can access the lattice constant calculator in Jade from the 'Options |
Calculate Lattice...' menu. An example of the calculator dialog is shown below:

To avoid entering peak locations (in 2) and Miller indices manually on the above dialog, you can locate
the relevant peaks in the zoom window using either the peak editor or peak search or profile fitting. If
you profile-fit the peaks, Jade will use the ESD values of fitted peak angles to estimate the ESD of
lattice constants. If there is a relevant PDF overlay in the zoom window, Jade will graft (i.e., assign) the
Miller indices from its matching d-I lines to the located peaks when you bring up the above dialog. You
can set the 2 error window used in matching the d-I lines on this dialog. In the example, the PDF
overlay of Faujasite (PDF#39-1380) was used to graft the Miller indices to the first six zeolite peaks in
the 'demo16.mdi' file. If you uncheck the 'Higher-Order Peaks' box, Jade will skip peaks for high-order
Miller indices in the calculation--i.e., the (440) peak in the above example will not be used since there is
a (220) peak on the list. A minimum of one peak is required to calculate the cubic cell, two peaks for
the tetragonal & hexagonal cells, three for the orthorhombic cell, four for the monoclinic cell, and six for
the triclinic cell. These peaks must come from different zone axes in order to solve the matrix of
simultaneous equations. To find a unique set of peaks to solve the unit cell, you can add or remove
peaks in the zoom window without closing the calculator dialog, and Jade will recalculate the unit cell
automatically.
You can provide the d-spacing or 2 angle of an internal standard peak in the current pattern on the
above dialog. If you mark or profile-fit this peak in the zoom window, Jade will apply the angular offset
of this reference peak to the peak positions used in the calculation of lattice constants as illustrated in
the above example. With the Apply button on the calculator dialog, you can recalculate the line
positions of the active PDF overlay using the derived lattice constants combined with the Miller indices
of its d-I list. You should therefore see the d-I lines of the active PDF overlay shifted to match the
current pattern in the zoom window if the Miller indices are grafted correctly.
While the current settings (i.e., Miller indices, cell type, internal standard, etc.) of lattice calculation are
always remembered by Jade, you can create additional setting files for different types of lattice
calculation with the Save button on the calculator dialog. These setting files will be listed on the
calculator dialog as well as on the task macro dialog for automatic pattern processing. When you
subsequently select one of these setting files on the calculator dialog, Jade will locate the same set of
peaks in the current pattern as long as they are within the 2 error window used for grafting the Miller
indices. If a sufficient number of peaks are found, Jade will calculate the lattice constants using the
new peak positions and the designated Miller indices. If you click the Refine button on the calculator

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dialog, Jade will profile-fit the located peaks with a linear background, and update the calculation of
lattice constants. If profile fitting with a linear background does not work for the current pattern, you can
always fit those peaks using the techniques prescribed in the profile fitting dialog. If you launch into the
cell refinement right after the lattice calculation and there is no PDF overlay in the zoom window, you
will see the calculated lattice constants appear on the cell refinement dialog. The advantages of lattice
calculation over cell refinement are (a) an initial cell is not required, (b) a minimum number of peaks are
needed. The disadvantages of lattice calculation are (a) lattice constants are not very accurate when
low-angle peaks are used, (b) ESD values cannot be obtained for the lattice constants.

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Refinement of Lattice Constants (Cell Refinement)

Cell refinement enables precise determination of lattice constants from the current list of peaks.
Therefore a careful determination of peak locations should be carried out before launching into the
refinement. Internal or external theta calibration is recommended before locating the peaks. The K2
stripped pattern should be preferred if you use the automatic peak search to locate peaks. Profile-fitted
peak locations would be ideal. Overlapping peaks and weak peaks should be avoided if possible,
although high angle peaks in theory are more accurate. It should be pointed out that you don't need a
single phase pattern to perform the cell refinement. You can use a multi-phase pattern with internal
standard, for example, so long as you can separate the peaks belonging to the phase you want to
refine. After you have obtained a list of acceptable peaks, you can access the cell refinement dialog
from the 'Options | Cell Refinement...' menu. An example of cell refinement with a corundum pattern is
shown below.

Jade will use the fitted profile list in the refinement if there is no peak search list in the zoom window. If
neither exists, Jade does an automatic peak search before showing the above dialog. If you use the
fitted profiles, Jade will include the ESD values of their peak positions in the least-squares weighting of
cell refinement. If there is a PDF d-I overlay in the zoom window, Jade will take the PDF cell as the
initial cell for the refinement and assign/graft the Miller indices to the located peaks within the specified 2
 error window on the refinement dialog. If a sufficient number of peaks are assigned with the Miller
indices, a set of reflection markers calculated with the initial cell will appear near the located peaks in
the zoom window as shown below:

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Jade 5.0

You can change the color of the reflection markers from the Color Setting dialog and scale their heights
from the Zoom & Pan Toolbar. You can show or hide the (hkl) labels on the markers using the Quick
Annotation Toolbar as shown in the above diagram. If the 'Use PDF Line List' option is selected, the
reflection list will correspond to the d-I list of the active PDF overlay. Otherwise Jade calculates all
possible reflections using the initial cell, and some of these reflections may not be observable in the
scan pattern. You can then remove the PDF overlay to have a cleaner view in the zoom window. You
can also hide the d-I lines of PDF overlays in the zoom window without erasing them by right-clicking
the number button on the PDF Overlay Toolbar. If you do not have PDF access or if the cell
information is absent from the PDF database, you must specify an initial cell on the refinement dialog,
and assign the Miller indices by clicking the Calc button. The Refine button will be activated when the
necessary number of peaks are assigned with the Miller indices. There are multiple ways to obtain the
initial cell for refinement in Jade:
The easiest way is to do a search/match and use a matching PDF phase as the starting cell.
If you have a cubic phase, you can easily index it using the cubic cursor on the Edit & Cursor Toolbar.
If you have a solid solution phase, you can use the solid solution algorithm in S/M to find a similar
phase from the PDF database. You can also use the d-scaling tools on the PDF Overlay Toolbar to
alter the c/a ratios of a hexagonal or tetragonal cell in a manner similar to that for the graphical cubic

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cursor.
If you have the Pattern Indexing option with the Jade Plus package, you can try to index the located
peaks to obtain the starting cell.
If you know the Miller indices of a few peaks at the low angle region, you can use the Lattice Constant
Calculator to obtain the initial cell.
The initial cell must be close enough for grafting the Miller indices to the located peaks. You may be
able to get around a not-so-close cell by opening the 2 error window. However, if you have a large cell
or a low-symmetry cell, you may need to narrow the 2 error window so that unambiguous Miller indices
can be assigned to a peak. Jade will remember the current cell parameters for future refinements.
Every time you click the Refine button, Jade carries out a few cycles of least-squares refinement. For
small and high-symmetry cells, you rarely need to click the Refine button more than once. For large
and low-symmetry cells, Jade will reassign Miller indices from reflections that move closer to the peaks
after each cycle of refinement if the 'Auto-Graft hkl' box is checked. If the box is unchecked, the initial
hkl assignments are kept over refinement cycles. You can manually alter the hkl assignments using the
arrow button on the Reflections tab of this dialog as long as unassigned reflections are available
around the peaks on the reflection list:

The 2T(cal) column in the reflection list is the peak position in 2 calculated from the refined cell without
considering the zero offset or sample displacement; 2T(obs) is the observed peak position as located

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with peak search or profile fitting in the scan pattern. By default, 2T(cor) is taken to be 2T(cal) + Zero
Offset + Displacement for the benifits of least-squares refinement and display of line markers in the
zoom window, and thus Delta-2T = 2T(cor) - 2T(obs). However, you can change 2T(cor) to 2T(obs) -
Zero Offset - Displacement for report printing by clicking the '2T(cor)' column header or the
'|Delta-2T|=#' item on the status of refinement dialog. If you do, the Delta-2T value will be 2T(cal) -
2T(cor), and it will neither affect the refinement results nor the display in the zoom window. If you have
calibrated the peaks with an internal standard, you should not include zero offset or sample
displacement in the cell refinement. If the scan range of the pattern is not wide, you should not refine
both zero offset and sample displacement because they would correlate with each other strongly. If you
have specified the goniometer radius on the Instrument tab of the User Preferences dialog, the
displacement value will be in millimeters rather than in degrees (2
The graphical results of cell refinement are displayed in the zoom window similarly to the theta
calibration (see the earlier diagram). The red dots indicate peaks that are rejected from the refinement
because they are either outside the specified angular range or considered as outliers specified by the
'Outlier Sigma' value on the refinement dialog if the 'Use All Peaks' box is not checked. The outlier
sigma is defined according to the 'ESD of fit' value shown in the status bar of the refinement dialog.
These outlier peaks will be indicated by an 'x' in the '?' column on the reflection list. You can interact
with the main window and review the graphical results of refinement without closing the refinement
dialog. When you select a reflection on the list, Jade identifies it with a short blinker in the zoom
window. You can move or delete a peak in the zoom window using the peak editing cursor, and Jade
will update the reflection list on the refinement dialog automatically. You can also delete a peak from
the reflection list by pressing the Delete key after the peak is selected. You need to click the Refine
button again in order to use the remaining peaks to refine the cell. You can also erase all reflections
that are not associated with the located peaks using the Trim button on the dialog. While the trimming
will not affect the refined lattice constants, it cuts the reflection list down so that you may be able to print
the report on a single page.
If the cell does not converge due to uncertainties of hkl assignment and overlapping peaks, you should
try the following approaches in the described order:
Make sure you have collected the best pattern with the highest resolution (e.g., using finer slits) and
long count time to resolve as many peaks as possible.
Locate all peak positions as precisely as possible. Profile fitting is recommended for overlapping
peaks if they can't be excluded from the refinement. Remember that you don't have to use all
available peaks in cell refinement.
Obtain the initial cell as accurately as possible (see the earlier descriptions). You can decrease the 2
error window so that unique Miller indices can be assigned to the located peaks. If the PDF d-I list is
reliable, you should select the 'Use PDF Line List' rather than the 'All Possible Reflections' option to
reduce the number of reflections to work with. You might also want to uncheck the 'Auto-Graft hkl' so
that you can assign the Miller indices to the located peaks manually.

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Start refinement with the low angle peaks and work your way up with the range controls available on
the refinement dialog.
There are other ways to perform cell refinement without worrying about the overlapping peaks, using
MDI's SHADOW and RIQAS programs, for examples. These alternatives apply the whole-pattern
fitting algorithm to simulate the observed pattern and refine the cell directly without need to locate
individual peaks.
The results of a cell refinement can be gauged by three numbers shown in the status bar of the
refinement dialog: (a) the estimated standard deviation of least-squares fits (ESD of Fit), (b) average 2
 value (|Delta-2Theta|), (c) Smith-Snyder figure-of-merit (F(M)=#(N)), which is calculated using the
following equation:
F(M) = M x M / sum(|2|) / N
where M is the number of refined peaks, N is the number of reflections in the refined region (up to 30
max), and the sum is over the number of refined peaks. If the F(M) is >999 due to very small 2
value, Jade prints F(M) as 999. The ESD values of refined lattice constants, zero offset, and sample
displacement are calculated using the following formula in reciprocal space:
ESD(i)^2 = b(i) x sum(w(j) x d^2 ) / (M - P)
where ESD(i) is the ESD value of a refined (i) parameter in reciprocal space, b(i) is its diagonal element
in the inverted least-squares matrix of cell refinement, w(j) is the reciprocal weight of a refined (j) peak,
d is the reciprocal delta d-spacing, M is the number of refined peaks, and P is the number of refined
parameters. Jade also calculates the density (g/cm^3) of the refined cell if the chemical formula and
the formula units (Z) per cell are specified. The density D is calculated using the following equation:
D (g/cm^3) = W * Z / V / 0.6022169 (W = formula weight, V = cell volume).
In the above example, Jade calculates the cell density using the chemical formula and Z-value of
corundum, which are read automatically from the PDF database.
Tip 1: You can reset the refinement parameters by clicking the 'R' item on the status bar of cell
refinement dialog.
Tip 2: You can graph the refined cell data if you select the 'Options | Graph Cell Data...' menu right after
the refinement.

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Graphing of Unit Cell Data

If you process a large number of similar XRD patterns to determine their cell constants, you may find
this cell data graphing tool useful. You can access the graphing dialog from the 'Options | Graph Cell
Data...' menu. An example is shown below:

Jade will insert the newly refined cell as the first data point in the cell listing if you bring up the graphing
dialog right after the cell refinement. You must provide the x-axis coordinate for this new data point
(whatever it may be). You can do so either by entering it in the input box next to the Save button or by
clicking directly in the '@X(i)' column, causing an input box to appear. In the above example,
temperature is the x-axis coordinate. You can enter the desired label for the x-axis on the following
dialog, which can be brought up by clicking the Setup button on the graphing dialog:

You can choose the items of cell data to graph using the check boxes on the left side of the above

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dialog. If you hold the mouse pointer over a check box, a short description of what it is will appear. The
'R' check will cause the item to be scaled to the y-axis on the right side of the graph. You can therefore
have two independent plots on the same graph with two different y-axes. You can choose to fit a line or
parabolic curve through the data points. If you do, Jade can use the ESD values of refined lattice
constants in the weighting of the least-squares fit. If you choose to display the error bars on individual
data points, you may not see some or all of them since the ESD values are normally very small
compared to the refined cell constants.
You can use auto-scaling for the x and y axes or manually set the starting, ending, and incrementing
values. If you do not lock the scaling values as entered, Jade will rescale the axes when new data
points are added to the graph. To accumulate data points in the graph, you simply click the Save
button on the graphing dialog. You can identify a data point on the graph by left-clicking it
directly--Jade will highlight it in the cell listing. You can exclude a data point such as an outlier from the
graph simply by unchecking it in the cell listing. You can even delete it from the list if you press the
Delete key after it is selected. If you click the 'Dialog Layout' label in the status bar, you can flip the
graphing dialog into the following view:

Tip 1: You can change the partition of the graphing window and the cell listing by dragging the border
between them up/down or left/right.
Tip 2: You can use a task macro to automate cell refinement of multiple similar patterns.

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Unknown Pattern Indexing

To index an XRD powder pattern is to find the most likely unit cell with the highest crystal symmetry that
could account for all the observable peaks in the pattern. Jade's indexing works primarily with a single
phase pattern by assigning possible Miller indices to the low angle peaks using an MDI proprietary
algorithm. Therefore you should take great efforts to obtain a pure phase pattern with the highest
possible resolution and count rates. A pattern collected with synchrotron radiation is ideal. Theta
calibration with an internal standard should be applied for best results. The K1 peak positions should
be obtained by removing K2 or fitting profiles to peaks. Weak peaks at low angle should be resolved
by using long count times, and they should not be included in indexing if you are not sure they belong to
the same phase, or if you suspect they may represent beta contamination or reflections from the sample
holder or noise. After you have located a list of reliable peaks, you can access the indexing dialog from
the 'Options | Pattern Indexing...' menu. An example of indexing a corundum pattern from the
'demo08.mdi' file is shown below:

By default, Jade uses the first nine peaks in indexing. You can use the 'Angle Limit' variable to include
or exclude more peaks, but you should avoid clusters of unresolved peaks. You should also avoid high
angle peaks in indexing because small errors of a trial cell calculated from the low angle peaks can
result in large shifts of calculated lines at high angles. To accommodate possible presence of adjacent
peaks from the same zone axis as well as line uncertainty, a minimum of three peaks are required for
cubic indexing, six for hexagonal and tetragonal indexing, and nine for orthorhombic and monoclinic
indexing.
Jade provides four indexing approaches (i.e., Rapid, Routine, Extensive, and Exhaustive indexing) to
tackle patterns of increasing complexity. Rapid and routine indexing require one of the first two peaks
to be indexed, and works well with less anisotropic cells. You should always try rapid indexing first.
Extensive indexing requires one of the first three peaks to be indexed, and exhaustive indexing requires
one of the first four peaks to be indexed; these work better with more anisotropic cells although they
could take a longer time to complete. You can abort an indexing run by pressing the ESC key.
By default, the hit list of possible cells is sorted on the figure-of-merit (the 'fm' column). The lower the
'fm' (range is 0 to 99), the more likely is the hit. You can set the 'fm-Cutoff' to be less than 99 to limit
the number of possible hits. You can sort the list on the other columns simply by clicking the column
header. The 'fn' column gives the equivalent Smith-Snyder figure-of-merit (see the Cell Refinement
dialog for the equation to calculate the 'fn'). The 'p?' and 'r?' columns show the number of unindexed
peaks and reflections below the specified angle limit. You should be aware that an unindexed peak
(especially a strong one) results in large increases in the calculated 'fm' value. Therefore you may need
to remove some low angle peaks or lower the angle limit for indexing if Jade fails to come up with a
possible cell after an exhaustive indexing.

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Unlike most other indexing programs that provide only the cell constants, Jade's indexing also predicts
the most likely space group for a given cell. Therefore you may see identical cells from several
possible space groups on the hit list. If you click the ? on the space group column, Jade will list the
space groups having the same Laue symmetry and extinction conditions as shown below. These space
groups are indistinguishable from an XRD powder pattern.

If you check only one cell type (symmetry) to index, you can constrain the indexing to a particular space
group as shown below:

You can also assign Miller indices to the first six peaks using the check boxes on the Reflections tab of
the indexing dialog (see below). When you check one of the peaks on the reflection list, an input box
will appear for you to enter the Miller indices. In this case, Jade will limit the possible cells such that the
designated Miller indices are maintained in indexing the remaining peaks.

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When you select a possible cell on the hit list, its calculated reflections are displayed in the zoom
window for graphical evaluation, and tabulated with the assigned Miller indices on the Reflections tab as
shown above. The green dots in the zoom window show the deviations of the calculated reflections
from the located peaks. Any unindexed peaks below the specified angle limit will be indicated as red
dots. You can use the zoom & pan tools to examine the results without closing the indexing dialog.
You can also move, add, or delete peaks, and start another round of indexing simply by clicking the Go
button again. As with the cell refinement interface, you can display the Miller indices on the reflection
markers using the Quick Annotation Toolbar, change the color of reflection markers from the Color
Setting dialog, and scale their heights from the Zoom & Pan Toolbar.
If a possible cell has a crystal symmetry higher than orthorhombic, Jade automatically carries out a
least-squares refinement on the cell parameters. If you desire more control over the refinement
process, click the Refine button on the indexing dialog and the Cell Refinement dialog will appear and
be loaded with the indexed cell. When you close the refinement dialog, Jade will replace the indexed
cell with the refined cell. You can also look up similar cells from the PDF database simply by clicking
the 'PDF...' button on the indexing dialog. If you do, Jade brings up the PDF Retrieval by Unit Cell Data
dialog filled with the relevant retrieval parameters. In the indexing example used earlier, the following
dialog window will appear:

The default range to find similar PDF cells is set at 10% of the indexed cell constants. You can alter
this range if you right-click the 'PDF...' button on the indexing dialog. If you click the OK button in this
case, the following dialog window will appear:

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Notice that the PDF hits are from the mineral subfile. You can select a different PDF subfile to retrieve
from. You can also alter the cell range parameters on the unit cell retrieval dialog to find more or fewer
PDF matches.
Jade will calculate the density of the indexed cell if the chemical formula and the formula units per cell
are specified. The density D is calculated using the following equation:
D (g/cm^3) = W * Z / V / 0.6022169 (W = formula weight, V = cell volume).
You can copy the indexing results in tabulated form to the clipboard or export them to a plain text file
(*.hkl). You can later browse the *.hkl file from the 'View | Reports & Files | Browse Report Files...'
menu.
Tip: You should get to know the capability and limitations of Jade's indexing by testing it on known
patterns.

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Auto-Processing with Task Macros

If you wish to process large numbers of XRD patterns for similar types of analyses or to obtain
reproducible analysis results in a quality assurance procedure, Jade's task macros will come in handy.
Unlike the macros implemented by other Windows applications, which record the activities of mouse
and keyboard for playback, Jade's macro dialog provides a list of pattern processing tasks for you to
select and assemble into a task macro. The individual tasks in the macro can be customized with
regard to its parameter settings to tailor different XRD patterns and outcomes, and the tasks can be
assembled in any desired order of execution. Therefore Jade's task macro is largely non-interactive in
its execution and can be applied to process and analyze multiple pattern files automatically. This
automation thus limits the number of possible tasks that can be assembled into a task macro. In other
words, not everything you can do in Jade can be duplicated in a task macro.
You can access the macro setup dialog from the 'Options | Task Macros...' menu or by right-clicking the
'cassette' button at the end of the main toolbar. An example of a task macro setup is shown below:

To assemble a macro, simply drag a desired task from the left box and drop it in the right box. A
double-click to a task item does the same. Indented task items require the data produced by the
non-indented task above them on the task list. Therefore Jade will automatically select the
non-indented task for the macro if you should select its indented task first. Otherwise you can assemble
tasks in any desired order, and multiple entries of the same task are allowed in the same macro. By
default, Jade appends a new task to the end of the task list in the current macro. But you can insert a
new task anywhere in the list by highlighting the task after which the new task is to be inserted. If you
hold down the Shift key before double-clicking or dropping the new task, Jade will insert it just before
the highlighted task in the current macro. This option makes it possible to add a task to the very
beginning of the existing list without starting all over. You can erase a task in the current macro either
by dragging it from right to left or double-clicking it in the list.
Some tasks are simple and require no parameter to run (e.g., the 'Read Most Recent Data File' task).
Others are more complex and require a set of parameters to define the outcome (e.g., the 'Find All
Peaks' task). For certain tasks, you can create their own setting files on their dialog windows. If you do,
these files will appear in the list of available macro tasks as shown below for the 'Find All Peaks' task.

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If you select tasks with the '[Current Settings]' tag, Jade will use the current values of relevant
parameters to execute the tasks. The outcomes of those tasks can thus be altered at will at run time
from the corresponding task dialogs. In the example of the 'Find All Peaks' task, it means that you can
bring up the Peak Search Dialog and change the search parameters before you run the task macro. For
tasks without their own setting files, a snapshot of the current settings of the relevant parameters will be
recorded in the macro when they are selected. In either case, you should always review the dialogs for
the intended tasks and even perform the tasks manually on a test pattern before creating the macro.
Notice that you can interact with the main window, bring up other task dialogs, or even read a new
pattern file without closing the macro dialog. You can also test the current macro with the Apply button
on the macro dialog before saving it. You can introduce a pause between task executions (see the
earlier diagram) so that you can verify the progress and outcomes more easily. You can also pause
and resume the execution of a task macro by pressing the spacebar.
When you finish assembling a new macro, you can save it with a descriptive macro id. Jade will then
create a macro file in the name of 'user/project-id.m##' in the current user/project folder, where '##' is a
two-digit macro number assigned by Jade from 01 through 99. You will need to know these macro
numbers if you want to specify the macros in MDI's DataScan or to run Jade with the macros in the
'stealth mode' (described later). These macro files are written in plain Ascii text, and they can be
browsed and edited if desired by clicking the 'Edit...' button on the macro dialog. The macro file
corresponding to the above example is browsed below:

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Notice that macro tasks are written in the macro file with 5-digit id numbers followed by their relevant
parameters and comments. Jade identifies the tasks in a macro file according to these 5-digit numbers,
and the comments are written for the sake of readers comprehending the macro file. You can delete,
add, shuffle, or duplicate tasks in the macro file. You can alter the task parameters such as the names
of output files. A name syntax like *.PKS means to create an output file in the same name of the
pattern file being processed but with the file extension 'PKS'. For example, if the pattern file is
'sample1.raw', the output file will be 'sample1.pks', and be placed either in the same folder as the
pattern file or in the current user/project folder depending upon the option specified on the Misc tab of
the User Preferences dialog. If there is an existing file of the same name in the output folder, Jade will
either overwrite it automatically or prompt for a different name (see the 'Overwrite' check on the macro
dialog in the earlier diagram). You can replace the wildcard (asterisk) character with a specific name
and an optional path in the macro file. If you do and the output file is of plain text type, Jade will
append analysis results from multiple pattern files to the specified file in running the macro. This
depository file will be placed in the current user/project folder if it does not include a folder name (i.e, a
directory path). You can also specify a network path-name for the output file if desired. You don't need
to edit the macro file just to specify the depository file. Jade will ask for it during macro creation if you
hold down the Ctrl key when you select a task that creates an output file.
A saved macro will appear in the macro list on the main toolbar as well as on the macro dialog. You
can select a macro in the list to be the active macro in Jade. You can then run it on the current pattern
either by clicking the 'cassette' button on the main toolbar or by clicking the Apply button on the macro
dialog. To apply the active macro to multiple pattern files, you can (a) select the files on the Read
Pattern Files dialog or the Thumbnail Browsing dialog, and then click the Macro button on those dialog
windows; (b) include the tasks of reading pattern files in the macro (these tasks will be described later in
the sub-topic 'Running Jade in Stealth Mode'). You should be aware of the fact that Jade will replace
the current settings of relevant parameters with those recorded in a running macro, and will suppress all
dialog prompts that solicit the OK/Cancel or Yes/No options in the execution of a macro. The OK and
Yes actions are usually taken by Jade in those situations.
Certain tasks in the macro will require additional input to execute. Among these are the 'Overlay PDF
Card' & 'Overlay d-I List Data'. These two provisions make it possible to perform analyses such as to
simulate an XRD pattern from d-I lists and to refine lattice constants with initial PDF cells in the macro.
The 'Overlay d-I List Data' will ask for a PDF overlay list file (*.PDF) containing preset values of RIR
(I/Ic), I%, and/or Wt% for the individual PDF overlays. Certain tasks in Jade can work with a selective

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range in the zoom window as well as the full range of scan pattern. These tasks include printing, profile
fitting, and search/match among others. You can select a smaller range of the pattern to work with in
the macro using the 'Set Display (Zoom) Range' task--Jade will prompt you to enter the desired range.
Characterize Peaks or Ranges with Task Macros:
Besides the 'Find All Peaks' and the 'Profile-Fit All Peaks' tasks, you can characterize selective peaks or
ranges in the macro using the 'Paint Peaks (Auto/Full Range)' or the 'Characterize Peaks/Ranges' task.
For the 'Paint Peaks' task, you must paint the desired peaks first in the zoom window so that Jade will
know the ranges to paint as well as the types of painting (i.e., auto or full range) in the macro. Refer to
the Paint & Integrate Peaks topic for more information on auto or full range painting. The 'Characterize
Peaks/Ranges' task differs from the 'Paint Peaks' task in the following ways: (a) you can select
individual peaks with peak markers or the d-I lines of the active PDF overlay besides the painted
regions, (b) you can profile-fit the marked peaks to obtain more precise peak characteristics, (c) Jade
will display a summary report of all characterized peaks if you run the macro on multiple pattern files. If
there are no marked or painted peaks or PDF overlays in the zoom window when you select the
'Characterize Peaks/Ranges' task, Jade displays the following message:

You can proceed to mark or paint peaks without closing the macro dialog. If you select the same task
again, Jade will bring up the following dialog for you to specify the peak characterization options:

If you choose to paint peaks, the painted 2 ranges are remembered and Jade will determine the
backgrounds at the two ends when running the macro on a new pattern file. If you choose to mark
peaks or overlay d-I lists, Jade will search for the left & right background points around the apex of a
peak and integrate the peak accordingly, unless you check the 'Fixed Range' box on the above dialog,
in which case Jade will integrate exactly plus & minus the fixed range around the apex to be located in
running the macro.
If you check the 'Apply Profile Fitting' box on the above dialog, Jade will profile-fit the marked peaks or
those in the painted regions in running the macro instead of integrating and painting them as described
above. If you mark the ranges with painting, Jade will find peaks and fit profiles range by range. If you
mark individual peaks, Jade will fit profiles according to the clustering of the marked peaks--i.e.,
adjacent peaks that are marked closer than two degrees will be refined together. Jade uses the current
profile attributes on the Profile Fitting Dialog to insert and fit profiles. At the end of macro execution
involving peak characterization on multiple pattern files, a browsing window will appear which tabulates

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the characterization results as illustrated below:

If you check the 'Report to Printer' or 'Report to Clipboard' box on the previous dialog, the results will be
sent to the respective destination automatically.
Automate Cell Refinement with Task Macros:
If you must process large numbers of similar XRD patterns to determine their cell constants, a task
macro could save a lot of time. If cell constants do not vary much among the patterns to be processed,
you can set the initial cell and the 2 error window on the cell refinement dialog such that Jade can graft
the Miller indices successfully to all the patterns. Also keep in mind that Jade always keeps the refined
cell from the last pattern for the cell refinement of subsequent patterns. If this is the case, all you need
to do is refine one of the patterns manually to get the initial cell and select the 'Refine Lattice Constants'
task in the macro. Alternatively you can include 'Overlay PDF Card' as the first task in the macro since
the PDF cell always supersedes the initial cell in the refinement. You can concatenate the refinement
results into a single report file if you specify a depository file name in the 'File Refinement Report
(*.ABC)' task. You can also tabulate the refined cell constants of all patterns if you select the 'Save Cell
Data for Graphing' task for which Jade also writes a plain text file (*.cdg). An example of such a macro
is shown below:

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At the end of running the task macro shown above for multiple pattern files, you can browse the 'Cell
Data.abc' and 'Cell Data.cdg' file from the 'View | Reports & Files | Browse Report File...' menu or with
the 'Browse' button on the macro dialog after you highlight the task containing the file name in the
current macro. You can view the graph of refined cell constants saved in the 'Cell Data.ucd' file from
the 'Options | Graph Cell Data...' menu. See the Cell Data Graphing topic for more information.
If cell constants among the patterns to be processed vary such that a single initial cell won't cover them,
you must include other tasks to determine and provide the initial cell for the individual patterns. You
can do so with any one of the following tasks:
Search/Match with the 'Solid-Solution Range%' parameter set at a desired value. Save and overlay
the first S/M hit in the zoom window with the 'Overlay Hits in Main Window' task in the macro. Jade
will use the 'd/d(0)' ratio found in the S/M to scale the PDF cell of the overlay and then take the scaled
cell as the initial cell in the refinement automatically.
Calculate the initial cell with the 'Calculate Lattice [...]' task. This task will appear only if you have
created a calculation file on the Calculate Lattice Constants dialog. Jade will use the calculated cell
as the initial cell automatically if there is no PDF overlay in the zoom window when the cell refinement
task is invoked.
Index the pattern with the 'Index Pattern for Unit Cell' task. You should try to index one of the
patterns manually before you select this task. Jade will use the first indexed cell as the initial cell in
the refinement automatically if the figure-of-merit of the indexed cell is >20 for the 'fn' and <20 for the
'fm'. See the Pattern Indexing topic for more information.
An example of a task macro using the 'Calculate Lattice [...]' task to obtain the initial cell for refinement
is shown below:

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Running Jade in Stealth Mode with Task Macros:

In a production environment and for QA procedures, it may be desirable to run Jade with a preset task
macro in background or batch mode so that the operator does not need to be confronted with Jade's
graphical user interface. This 'stealth' mode of operation can be accomplished with the command line
switches '/m=# /s' provided to the shortcut icon of Jade as illustrated below:

where '/m=#' specifies the task macro number and '/s' turns on the stealth mode. A number of tasks in
the macro are provided to facilitate pattern file input to the stealth operation:
Read Most Recent Data File: Jade will find and read the latest pattern file from the data folder being
pointed to in Jade, and process it according to the tasks listed in the macro.
Read Pattern Files Dated Today: Jade will read all pattern files dated the day the macro is run from
the data folder being pointed to in Jade, and process them one by one according to the tasks listed in
the macro. This feature could be handy if you have a sample changer and collect data in the same
day.
Read Pattern Files Dated Since Yesterday: Jade will read all pattern files dated since yesterday from
the data folder being pointed to in Jade, and process them one by one according to the tasks listed in
the macro. This feature could be handy if you have a sample changer and collect data overnight.
Read a List of Pattern Files from a Designated Listing File: Jade will read the pattern files listed in the
designated listing file, and process them one by one according to the tasks listed in the macro. In this
listing file, you can specify a data folder preceding each file name that is different from the data folder
being pointed to in Jade. However, these pattern files must be located in the same folder and be of
the same file type.

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Prompt for Pattern File Names: Jade will display a dialog window to solicit names of pattern files from
the operator, and will process every file according to the tasks listed in the macro. The operation ends
when no file name is given.
When you double-click a shortcut icon of Jade equipped with the prescribed command line switches,
Jade will start and run with the main window hidden, find and read the desired pattern files, process
them one by one according to the tasks assembled in the designated macro, and disappear from the
memory quietly. All you see on the screen is a message telling you the task being executed by Jade.
You might want to introduce a pause in the macro so that you can make sure the macro is doing the
tasks in the proper order.
Running Other Programs in Task Macros:
You can tell Jade to run other programs in a task macro by selecting the 'Run Other Program' task (a
process called 'Shell' in Windows). Jade will prompt you to specify the name of the program to run and
the window state in which it's to be run. Beside the program name and its folder path, you can provide
any required arguments (such as a file name) and command line switches in the input. You don't need
to provide the folder path to the program if it can be run from the 'Start | Run' menu at the task bar.
Jade will neither verify the program name until the macro is executed, nor wait for the shelled program
to close or finish before processing the remaining tasks (if any) in the macro. You may find this feature
useful for example if you want to process and analyze the output files created in the macro
automatically with customized applications.
Tip: Jade can also interface with MDI's DataScan to automate data collection and analysis with the task
macros.

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Pattern Simulation from d-I Lists

You can simulate powder diffraction patterns from the d-I lists in Jade by reconstituting peak profiles on
the d-I lines, a procedure not to be mistaken for pattern simulation from crystal structures. The quality
of simulation is therefore determined primarily by the accuracy of d-I values. Jade also assumes the I%
values of a d-I list to be from integrated peak areas and will calculate individual peak heights according
to the FWHM curve and crystallite size given in the simulation. You can access the simulation dialog
from the 'Analyze | Simulate Pattern...' menu. An example is shown below:

Jade uses the d-I lists of the PDF overlays in the zoom window to simulate the pattern. If there is more
than one d-I overlay, only the tacked ones will be used in the simulation. Refer to the PDF Overlay
Toolbar for how to tack d-I overlays. Two types of simulation can be accomplished:
Create a new diffraction pattern. For a multi-phase mixture, Jade will calculate the overall I% values
of individual phases if their RIR (Reference Intensity Ratio) & wt% values are given; otherwise, Jade
will use their current I% values in the simulation. See the PDF Overlay List dialog for how to enter the
desired I%, RIR, and wt% values; an example dialog with 50% rutile, 25% anatase (crystallite
size=250A), 25% hematite is given below:

Jade will clear the current display when you click the Create button on the simulation dialog. The
simulated pattern is not saved to a disk file until you select the 'File | Save | Primary Pattern as...'
menu. You can compare the simulated pattern with the primary pattern if you click the Overlay button
instead of the Create button. You can review the simulated pattern with the zoom & pan tools without
closing the simulation dialog.
Perform a least-squares fit of simulated profiles to the observed intensities with respect to the I%
values of individual PDF overlays. If the RIRs of all PDF overlays are given, Jade will automatically
compute their wt% values from the fitted I% values using Chung's matrix flushing. The simulated
pattern will be overlaid in the zoom window for comparison. You can find the calculated wt% values
on the PDF Overlay List dialog. It should be pointed out that the wt% values thus obtained are
semi-quantitative because profile fitting is not used to obtain the precise areas of individual peaks.

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With the Easy-Quant option, you can obtain more accurate wt% values using profile-fitted peak
areas. See the RIR-Quant Analysis topic for more information.
The profile attributes on the simulation dialog are described below:
The FWHM curve selects the pre-determined instrumental broadening as a function of 2 angle. See
Crystallite Size & Strain Analysis for how to determine your instrument's FWHM curve.
Besides the FWHM curve, you can broaden the peak profiles further by specifying an overall
crystallite size in the simulation. You can also provide crystallite sizes for individual PDF overlays on
the PDF Overlay List dialog. This overall crystallite size applies to the PDF phases whose crystallite
sizes are not given. If you click the 'Estimate Sizes' button on the simulation dialog, Jade will carry
out a peak search and estimate the crystallite sizes of individual phases from the FWHM values of the
peaks located near the 100% lines of the phases, and display the results in a phase listing box on the
simulation dialog as shown below:

You can overwrite the estimated sizes by clicking in the 'XS(A)' column and waiting for the input box
to appear. You can hide the phase listing box by clicking the 'Estimate Sizes' button once more.
Skewness of profiles can be specified in the range of -0.9 to +0.9. It applies to both Pearson VII and
pseudo-Voigt profiles.
You can introduce random noise in the simulated pattern. It is calculated as Noise-Sigmas x
(RND-0.5) x SQRT(I), where RND is a computer-generated random number from 0 to 1, and
Noise-Sigmas is a number you can specify on the simulation dialog.
You can add background to the simulated pattern only if there is a background curve being displayed
in the zoom window.
The amorphous area, if added, will be generated using a Lorentzian profile function.
While the current simulation parameters are always remembered by Jade, you can create additional
setting files with the Save button, and restore one of them by selecting it from the setting file list. These
setting files will also appear in the macro task list for automatic pattern processing.

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PDF Setup & PDF Index Files

One of Jade's powerful features in analyzing XRD powder data is the easy access to the PDF database
and comprehensive retrievals of PDF data. For that to happen, you must have the ICDD license for the
database and create the index files required by Jade for efficient interface to the PDF data. The
database comes in two forms:
Level-2 PDF on CD, which is normally supplied directly by ICDD, contains the unit cell data, literature
references, and comments in addition to the d-I listing and chemistry data of all phases. The index
files required by Jade are not on the CD. They must be created using the tools already built into
Jade. When you obtain an update of the CD in the future, you need to update these index files as
well. You can do it without any further help from MDI provided ICDD does not change the database
format. Most PDF retrievals in Jade are carried out from these index files, and the CD is accessed
only for PDF card browsing and printing. If desired, you can put the CD on a shared resource on the
network and run multiple copies of Jade to access it simultaneously without conflict. Depending on
your use, you may need to obtain network license option from the ICDD. In any case, however, the
index files must reside on the individual PCs.
Level-1 PDF, which is a subset of the level-2 database, carries only the d-I listing and chemistry data
of the phases, and is usually provided on a custom CD created by MDI. If this database is purchased
on the same order as Jade, it will be put on the Jade CD and thus be installed when you install Jade.
You do not need to create the index files because your level-1 PDF data come as sets of index files
provided by MDI. If the database comes on a separate CD, you should transfer all the files on the CD
to the hard disk for speedy access and retrieval. Jade cannot access level-1 PDF data you may
already have from another vendor until it has been remastered by MDI for you.
Creating Index Files to Access Level-2 PDF Database:
You can bring up the dialog to create the PDF index files from the 'PDF | Setup...' menu. An example is
shown below:

Index files are grouped in PDF subfiles such as Inorganics, Organics, and Minerals for efficient retrieval
and S/M. Subfiles other than Inorganics, Organics, and the Deleted Cards are mostly subsets of the
Inorganics. You may not be able to access all the listed subfiles if your PDF CD was created prior to

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1998. If you select the inorganic or the organic subfile, you can also create two additional subfiles
containing only the 'Star Patterns' and the 'Calculated' patterns. Note that you don't have to create all
subfiles at once--i.e., you can create some at a later time if desired. However, you must choose the
mineral subfile if you want to recall mineral phases by mineral names. The ICSD subfiles consist of the
calculated PDF patterns from the ICSD structure database. These patterns have PDF set numbers 70
through 85 at present. Jade does not include ICSD patterns in any other subfile you choose to create.
Jade can maintain multiple index file folders for PDF databases of different sets (i.e., years). Jade will
prompt you to create the index files if they are not found under the specified folder, which is defaulted to
the 'pdf' under Jade. You can use the Browse button to locate the index files that reside in a different
folder. You can create a new folder for the index files by entering the folder name into the folder list
box. You can speed up the creation of the index files as well as their future access significantly if you
put them on a hard drive that has ample free space to reduce file fragmentation. You can also copy the
entire contents of the PDF CD to your hard drive for faster access. Jade will find the database file
'pdf2.dat' automatically if you place it in the root folder or in the folder named as 'pdf2' off the root
folder. Otherwise Jade can search all the local hard drives for all copies of 'pdf2.dat' files if you click
the 'Find...' button on the dialog. You can also use the Browse button to access the database file across
the local network.
Creating the index files is a time-consuming process, and a time estimate will be provided once the
process is under way, for example:

You may abort the process at anytime and use the partial index files in Jade, but you must start over
again in order to carry this to completion. You may work with other functions of Jade during the
indexing. If you hide the above indexing dialog, you can bring it back from the 'PDF | Setup...' menu.
You need to keep Jade running for the indexing to finish.

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PDF Access & Retrievals

One of Jade's powerful features in analyzing XRD powder data is the easy access to the PDF database
and comprehensive retrievals of PDF data. For that to happen, you must have the ICDD license for the
database and create the index files required by Jade for efficient interface to the PDF data. See the
PDF Setup topic for how to create the index files.
Once the desired index files are created, Jade is ready to fulfill most of your PDF retrieval needs. To
recall a PDF phase (also called a PDF card in the classic term) by its PDF number or its mineral name,
simply enter it into the PDF input box on the main toolbar. See the PDF Overlay topic for more
information on overlaying d-I list data in Jade. To retrieve a list of PDF phases using Boolean filters
such as chemistry, select the 'PDF | Chemistry...' menu. Jade will bring up the PDF retrieval dialog to
list the phases when more than 16 hits are retrieved from a Boolean filter, as shown in the diagram
below:

Notice that Boolean retrievals are limited to the active PDF subfile on the subfile list. When recalling by
chemical name or formula, Jade does case-insensitive text matching that is left-justified. But you can
get around the left-justified if you append the text with an asterisk '*' or ellipsis '...'. No space is allowed
for matching the chemical formula. You should use the mineral name box if you intend to recall
minerals because it is much faster. Jade will search the ICDD mineral subfile first for a mineral name,
and if there is no match, will then search the ICSD mineral subfile. You can reverse this order of search
by checking the 'ICSD Minerals' box. You can browse a complete list of mineral names from either
subfile by clicking the 'Minerals' button:

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You can hide the mineral listing by clicking the 'Minerals' button again. Jade supports domestic mineral
names in PDF listings and overlays for non-English-speaking users. This is implemented through the
open listings of mineral names and groups in two plain text files named 'minerals.who' and
'minerals.grp'. These two files will be created together with other PDF index files when you choose the
'Minerals' subfile during PDF Setup. You can edit these files using a text editor like Notepad or
WordPad, and translate as many names as you like as long as you don't alter their PDF numbers. You
can also create additional *.who files with a shorter list of translated mineral names in the same folder,
and browse them in the above list if you right-click the 'Minerals' button--causing Jade to prompt you for
a file name. If you check the 'Local Mineral Names' box, which appears only for non-English versions
of Jade, the translated mineral names will be taken when you double-click on the mineral name list, and
they will be used in PDF overlays and on report printouts. You should make a backup copy of the
translated name files, because they could be accidentally overwritten when you update the PDF index
files.
Once a list of PDF phases is obtained, you can overlay one or more in the zoom window by (a)
double-clicking on the hit list, or (b) clicking the Add button on the dialog, or (c) dragging it out of the list
and dropping it into the zoom window. The PDF Overlay Toolbar will appear together with the d-I lines
in the zoom window. When you highlight a hit on the list, Jade displays the first 32 reflections as a set
of line markers in the zoom window for the sake of phase identification. You can scale these line
markers in height either by entering an I% value in the text box on the dialog (see the earlier diagram)
or using the marker scaling button on the Zoom & Pan Toolbar.
If you routinely deal with a limited number of recurring PDF phases, you can save them to a PDF listing
file (*.PLF) for easy recall. A list of these PLF files is accessible on this dialog (see the earlier
diagram). You can also read a PLF file by entering it into the PDF input box on the main toolbar. See
the Main Toolbar topic for more information on using PDF listing files.
You can sort a list of hits by clicking the desired column header, and reverse the sorting by clicking the

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same column header again. A long list of hits can be trimmed (i.e., shortened) using the Boolean
filters. When the 'Trim List Using Boolean Filters' box is checked, all Boolean dialogs and functions
work on the existing list rather than retrieving new hits from the active subfile. In this case, Jade will
use the Boolean filters to remove hits that do not pass the filters. However, you can remove hits that
pass the filters instead by checking the 'Trim List...' box while holding the Ctrl key down (notice that the
check box will be grayed). If you use the chemical name or formula to trim the list, you can enter a
leading minus character (-) to exclude the hits that match the text you type in the chemical name box;
otherwise Jade removes the mismatched hits from the list. When working with a long list of hits from
Boolean retrievals, you can save time if you check the 'List Partial Hits' box, because all Boolean
filterings can still be performed without listing all the hits. As a matter of fact, Jade automatically turns
on this check box if the list is longer than 2500 hits. Note: When you close this dialog, Jade does not
keep the list if longer than 500 hits. You don't need to close this dialog in order to interact with the main
window.
If you have the search/match option, the S/M button will be activated to allow you to run the current hit
list through the figure-of-merit (FOM) calculations and display the results in the S/M window. If you
have the advanced options (i.e., Jade Plus) but not S/M, the SOS button (Sort-On-Similarity) will be
activated to allow you to sort the current hit list on similarity to the peaks in the current pattern. An
example of this SOS listing is shown below:

The similarity is rated in the same FOM as in S/M. The smaller the FOM value, the more likely the
match, and a value greater than 40 indicates a very unlikely match.
If you desire a printout of the list, you have control over how to fit all the columns on the page by (a)
adjusting the widths of the 'Phase ID' and 'Chemical Formula' columns on the dialog, (b) choosing the
print orientation and font size on the Report tab of the User Preferences dialog. Jade simply skips
printing the trailing columns which overflow the page width.
Tip 1: You can add or erase a number of hits at once if you select them on the list by dragging or by

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holding down the Ctrl or the Shift key.

Tip 2: You can recall a whole set of PDF phases from the active PDF subfile by entering the set number
prefixed or suffixed with an asterisk such as *10 or 10*, or by entering 'set 10', for example, in the
mineral name box.
Tip 3: You can recall an ICSD phase by entering 'ICSD=#' or 'FIZ=#" in the mineral name box, where #
is the ICSD/FIZ number.
Tip 4: Refer to the RIR-Quant analysis topic for information on the 'Calc MDI' and the 'Calc Density'
buttons on this dialog.

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PDF Card Display and Printing

The PDF card view of Rutile data in Jade's format is shown below. It does not resemble the classic
JCPDS 3x5-inch PDF cards, but contains all relevant information:

You can bring up the PDF card view from various places in Jade which display PDF listings. The most
likely place would be from the PDF Overlay Toolbar. The dialog will be modeless if it's brought up from
the overlay toolbar or from the PDF Overlay List dialog, making it possible to browse another PDF card
without having to close the dialog window.
The information on the card depends upon the nature of the PDF overlay--i.e., whether it's from level-2
or level-1 PDF, from a *.DSP file, or from an S/M userfile. The reflection list can be browsed from the
Lines (#) tab of the dialog:

The I(v) is the variable-slit intensity converted from the I(f), which is assumed to be fixed-slit I% from
PDF database; the n^2 is the h^2 + k^2 + l^2 of Miller indices. You can customize the card for printing
in the following aspects:

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Show or hide the 'Line-Graph', which can be plotted on linear or square root scale as shown below:

Change the font size on this dialog (the number in the box to the right of the 'Line-Graph' button, and
the print margins from the User Preferences dialog.
The blue frame on the line graph indicates the scan range of your pattern as compared to the full range
in the reflection list. Jade also simulates profile traces over the line markers on the printout. ICDD uses
the notations of $GA, $GB, ..., $GZ to indicate Greek symbols in the PDF database. Jade translates
and shows the Greek symbols only in the note text, but does not print them at present.
Tip 1: You can browse a level-2 PDF card in its native database format with the More button.
Tip 2: You can resize this dialog window to see more or less information.

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PDF Retrieval by Chemistry

Jade implements the following dialog as an intuitive and flexible way to retrieve PDF data by chemistry:

You can access this dialog from the 'PDF | Chemistry...' menu or by right-clicking the CD button on
Jade's main toolbar. It is also accessible from the 'Chemistry...' button on the PDF Retrieval dialog or
the S/M Setup dialog, and will be shown without the PDF subfile list.
You select elements to set up the desired chemistry filter by point & click. Elements not
selected/depressed are assumed to be excluded by the filter. Possible elements are indicated in blue,
and required elements in green (which can be set with one more click to the possible or a right-click to
the excluded). A maximum of six elements can be required, for which you can also specify the
stoichiometry in the input boxes at the bottom of the dialog. A stoichiometry value of 0.0 indicates that
all stoichiometries are allowed. In the above example, Jade retrieves all aluminum oxides and
hydroxides from the mineral subfile. Tip: you can select all lighter elements below the one being clicked
on if you hold down the Ctrl key.
To avoid setting up the same chemistry filter every time you need it, you can save it to a filter file (*.cff)
and later select it from the filter list. By default, Jade always saves the current filter into the
'user/project-id.cff' file. If the chemistry dialog is brought up to retrieve PDF cards (with the PDF subfile
list shown), Jade overlays the hits in the zoom window upon retrieval if the list is less than 17 hits;
otherwise the list is displayed in the PDF Retrieval dialog for selection.
The same dialog (now labeled 'Filter') is used for chemistry analysis of the existing phases after the S/M
or the Boolean retrievals. In this case, Jade will populate the table with the elements present on the hit
list as illustrated below:

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You can then either trim the list by requiring certain elements or eliminating unwanted ones, or display
the 'Element Affinity' maps among the phases with the newly appeared check box. Jade will 'light up'
the elements that are combined with the one being clicked on. In the above example, Jade shows the
elements (in green) that are combined with the iron (Fe) from an S/M hit list.
Import Chemistry Information from Fluorescent Data Files:
At present, Jade can read the Ascii fluorescent files that are exported by Rigaku X-ray Spectrometer
(RIX) software. You select the file to read with the 'Read Fluorescent Data...' button, and Jade will list
all sample id's in the file for you to choose from, for example:

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If the file contains quantitative analysis data, you can set the concentration threshold in percentage
above which an element will be considered as required by Jade automatically. If you check the
'Fluorescent Data' box on the General tab of the S/M Setup dialog, Jade will use the fluorescent data by
matching the scan id or the filename of the current pattern to one of the sample id's contained in the
current fluorescent file.
Tip: See PDF Retrieval by Stoichiometry for another way of using the PDF chemistry.

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PDF Retrieval by Stoichiometry

Besides PDF Retrieval by Chemistry, you can retrieve PDF data by stoichiometry without regard to
specific elements. You can access the following dialog window either from the 'PDF | Stoichiometry...'
menu or from the 'Stoichiometry...' button on the PDF Retrieval dialog:

The above example retrieves all binary A1B3 mineral phases regardless of specific chemistry.
Fractional stoichiometries in tenth precision (e.g., A1.5B1.0) can also be specified. Wildcard retrieval is
assumed when no number is entered in any of the ABCDE boxes.
The stoichiometry filter can be combined with other available filters for PDF retrievals as well as for
S/M. In the S/M case, you must check the Apply box on the dialog to turn on the filter as shown below:

Tip: You can clear all the ABCDE boxes on the dialog if you double-click the '...Wildcard Search' label.

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PDF Retrieval by Unit Cell Data

If you have level-2 PDF, you can access the following dialog either from the 'PDF | Unit Cell...' menu or
from the 'Unit Cell...' button on the PDF Retrieval or the S/M Setup dialog:

The above example retrieves all mineral phases that have the space group Fd3m (227) and cell
constants in the range of 8.0-8.5 angstroms. All parameters on the dialog are taken as Boolean-AND
conditions in the filter. For space group, you can enter a standard name (case-sensitive) or its number.
For cell constants, a value of zero is taken as wildcard.
You can retrieve PDF data according to the Pearson symbols by combining the parameters of 'Cell
Type', 'Lattice Centering', and 'Number of Atoms' in the unit cell:

The above example retrieves all mineral phases with the Pearson symbols 'tP6'. Jade uses a range of 
0.5 for the number of atoms in matching the Pearson symbols. Therefore in this case, Jade could
retrieve phases with Pearson symbols varied from 'tP5.5' to 'tP6.5'.
Tip 1: You can clear the parameters by double-clicking the frame caption or the individual labels.
Tip 2: You can combine the unit cell filter with other available filters for PDF retrievals as well as for
S/M.

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PDF Retrieval by Data Source, etc.

You can access the following dialog either from the 'PDF | Miscellaneous...' menu or from the 'Misc...'
button on the PDF Retrieval or the S/M Setup dialog:

The above example retrieves all calculated mineral phases that have densities in the range of 2.0-2.5
g/cm^3 and line(s) in the range of 20 to 22 degrees. All parameters on the dialog are taken as
Boolean-AND conditions in the filter. For retrievals by the strongest three lines, Jade considers only
phases that have lines below 85 degrees in Cu space (i.e., d-spacing > 1.14A) and of relative intensities
greater than 10%. The 'PDF Subfile ID' parameter specifies classifications of phases within the active
subfile, and can be used to retrieve, for example, a list of organic minerals from the mineral subfile.
Jade's quality marks of the PDF phases are defined as follows:
Star(+): PDF phases meet the following criteria: their PDF quality marks assigned by ICDD are
Star/Calculated/Indexed, and their space group, cell constants, and density are determined. About
25% of the PDF phases satisfy these criteria.
Doubtful(?): PDF phases meet the following criteria: (a) their PDF quality mark assigned by ICDD is
Doubtful Quality; (b) patterns collected at non-ambient conditions (i.e., low or high temperatures and
high pressures); (c) most elemental phases; (d) phases that have more than 4 elements (hydrogen not
counted), except for minerals and organics; and (e) phases containing non-common chemistry (see
the Chemistry Retrieval dialog for Jade's definition of common chemistry). About half of the PDF
phases are 'doubtful' according to these criteria.
Intermediate: PDF phases which are neither Star(+) nor Doubtful(?).
Tip: You can combine this filter with other available filters for PDF retrievals as well as for search/match.

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PDF Retrieval by Color Keywords

If you have level-2 PDF, you can access the following dialog either from the 'PDF | Color Info...' menu
or from the 'Colors...' button on the PDF Retrieval or the S/M Setup dialog:

The above example retrieves all the blue minerals from the PDF database. Note: Color id is an optional
specification in the database. The color keywords listed on the dialog are not necessarily unique--i.e., a
phase in the database could be given multiple color definitions or color ranges.
Tip: You can combine this filter with other available filters for PDF retrievals as well as for search/match.

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Profile-Based Search/Match for Phase Identification

Jade provides two search/match (S/M) approaches to phase identification: i.e., Profile-Based S/M and
Line-Based S/M. The former utilizes the full scan trace of the diffraction pattern without the need of
explicit peak location. The intrinsic broadening of peak profiles largely takes care of the uncertainty of
line position as well as overlapping peaks. The S/M algorithm works very much like visual comparison
of d-I lines to the scan trace, making profile-based S/M a much more effective approach than line-based
S/M for most identification problems.
In contrast, line-based S/M makes use of only the peaks located with peak search, comparing them to
the first 32 lines of a potential phase in the PDF database. The one advantage line-based S/M has is its
ability to accommodate large angular errors (up to one degree in 2) in the data. But you would be
better off with improved instrument alignment as well as theta calibration if your data routinely contains 2
 errors larger than the profile broadening of peaks. Line-based S/M is the only S/M option accessible if
you have just the userfile S/M, which works with your own database. If you have any PDF database,
both S/M options are accessible.
Profile-based S/M usually requires the removal of pattern background (which is why the BG button is
placed next to the S/M button on the main toolbar). But there are two exceptions: (a) if the pattern has
very low background, and (b) if you change search focus (described below) to painted peaks. Jade can
also remove the background automatically, if it's significant in the pattern, when you start a search. See
the Background Fitting topic for how to remove the background for S/M. In general, you should strip the
K2 together with the background removal so as to reduce accidental hits. Pattern smoothing is
normally not necessary unless you have visual difficulty in discerning peaks. If the pattern contains
substantial 2 error (say >0.1 deg), it should be calibrated using the Theta Calibration tools, which come
with the Jade Plus option. If it was collected with variable slits, convert it to fixed-slit intensities. If it
was scanned with more than one second per step, using total counts always gives better results than
using the CPS data.
Search/Match Focus:
To exploit the convenient graphical tools and the power of the profile-based S/M algorithm, Jade
focuses its search effort on the peaks in the zoom window implicitly, always renormalizing peak
intensities to the maximum scale currently in the zoom window for S/M. This renormalization boosts the
minor phases as if they were major ones in the pattern. Peaks truncated in the zoom window as well as
those outside the zoom window will be paid much less attention and can even be ignored altogether in
evaluating the figure-of-merit (FOM) of hits. In other words, Jade will promote only those PDF phases
that have strong lines matching the peaks in the zoom window. Since low angle peaks are much less
populated by PDF phases, your chance to identify minor and trace phases is greatly improved if you
focus the search on the low angle peaks. With the flexible way you can zoom & pan, this approach
makes it easy to identify a multi-phase pattern. It should be pointed out that any segment of pattern
below 85 degrees of 2 in Cu radiation can thus be focused and searched. You can even focus the
search down to a single peak, which may be necessary to identify orientation samples such as clays.
However, peaks above the 85-degree cutoff are not used by Jade in S/M. If the pattern was acquired
with an anode other than Cu, Jade automatically maps it to Cu space in the search and then displays
the results back in the original radiation space.
Search/Match Setup Dialog:
You can bring up the setup dialog of profile-based S/M either from the 'Identify | Search/Match Setup...'
menu or by right-clicking the S/M button on the main toolbar. The General tab of the dialog is shown
and described below:

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The available 'Subfile(s) to Search' are created from the PDF Setup dialog. The two numbers in
parentheses are the PDF sets and the number of phases in the subfile. Incomplete subfiles are
indicated by an asterisk. Jade will always search the highlighted subfile. To select multiple subfiles in
one S/M session, use the checks that precede their names.
When full scan range is displayed in the zoom window, you can set the 'Search Focus' on Major, Minor,
or Trace Phases. There are no absolute intensity thresholds for finding Major, Minor and Trace
phases. Depending upon the nature of your data, Jade can find minor or even trace phases when the
focus is on the major ones, and vice versa. In general, phases with peak intensity below 15% are
considered as minor ones, and those below 3% as trace phases. You should not focus on the trace
phases if the pattern has high background with low count rates. But if you do, you must fit the
background curve very carefully, since slight misfit of the curve can greatly affect the relative intensities
of weak peaks you are trying to identify. In the worst cases, some trace peaks could be erased entirely
by background removal.
If you zoom into a small region of the pattern as described earlier, Jade locks the search focus in the
zoom window. Since peak intensities in the zoom window are renormalized to 100% in the S/M, you
should scale the strongest peak in the zoom window to almost reach the top of the window. This can be
done easily by clicking the auto-scaling button on the Zoom & Pan Toolbar. Truncated peaks are
allowed in the zoom window and will not be focused on in the search. If you don't intend to restrict your
search to the zoom window, you can unzoom to full pattern before showing this dialog.
If it is necessary to search only a few discrete peaks from different regions of the pattern, you can use
either the peak paint function to select them or the data editing function to wipe out the peaks in the
regions not to be searched. See the Edit & Cursor Toolbar for how to paint peaks or edit data. If you
have painted peaks, Jade locks the search focus onto them. Unpainted regions of the pattern are
treated the same way as those outside the zoom window--i.e., they are not totally ignored unless you
check the 'Ignore Data Outside' box on the Advanced tab of the dialog (see below). Painted peaks
supersede the zoom window in the S/M focus and should be removed if they are not intended for S/M.
When the 'Automatic Matching Lines' box on the General tab is checked, Jade sets the minimum

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number of matching lines required for a possible phase (also called a hit) according to the number of
significant peaks in the search focus. This number usually varies from 1 to 4. Single line S/M is
assumed if the number of peaks is less than 3 or the search focus is less than 5 degrees in 2. When
the box is unchecked, you can set the minimum number of matching lines anywhere from 1 to 32. If
you raise this number in order to find the dominant phase in the pattern, you may get better results by
checking the 'Perform Single Phase S/M' box. If you do, Jade will eliminate PDF phases that do not
match most of the strong peaks in the pattern, and keep the top 9 hits regardless of the FOM cutoff.
Normal FOM scoring in the S/M strongly penalizes the missing peaks of a PDF phase. You may want
to check the 'Preferred Orientation S/M' box if your sample has strong texture of crystallite packing such
that some of its strong lines are weak or absent. If you do, Jade will be more lenient in treating the
badly mismatched and the missing peaks. You can also cut the number of matching lines required to 1
or 2, or focus the search on a single peak in the worst case.
You can apply chemistry constraints before or after the S/M. But you should generally avoid this in the
initial round of S/M. Most of the major and minor phases can be found easily without the chemistry
filter. See PDF Retrieval by Chemistry for how to set up the filter. Note: Jade will turn off the chemistry
filter when no hit is found with it. If you use chemistry often, you can save it into a filter file so that it
can be applied easily from the filter list. Other available filters can be set up and combined if necessary
to further limit the number of possible hits. Jade will append an asterisk to the button label to indicate
the filter being used. See Unit Cell Filter, Color Filter, Stoichiometry Filter, and Miscellaneous Filter for
more information. If you do use the filters, you can tell Jade to promote the phases that pass the filters
over those that don't by checking the 'Promote Hits by %' box. Otherwise, Jade eliminates all phases
that do not pass the filters from the hit list.
The Advanced tab of the S/M setup dialog is shown and described below:

Besides the chemistry filter and the others described earlier, you can further exclude or demote PDF
phases on the hit list according to the 'Quality Marks' defined in Jade. When the 'Use QM Weighting'
box is checked, Jade promotes phases of higher quality marks over those of lower quality marks. You
can also exclude duplicate and/or isotypical phases from the hit list with the two check boxes at the

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bottom of this dialog tab. With the level-2 PDF database, the duplicates are defined by Jade as phases
with the same space group & chemistry and very similar cell constants. You may find this option useful
when you search the ICSD subfiles containing a lot of duplicate phases. With the level-1 PDF database
, phases of the same chemical formula and phase id are considered to be duplicates by Jade. The
isotypical phases are defined by Jade as those whose d-I lines match closely in the theta space. In both
cases, Jade will keep the phase that has a lower figure-of-merit (FOM) in the S/M. You can later
browse the duplicate and/or isotypical phases of any hit easily in the S/M Display Window. If the
'Exclude Metallics from Inorganics' box is checked, Jade excludes metal and alloy phases, defined in
PDF except Silicon and oxides, from the Inorganic and ICSD subfiles in the search.
As described in the S/M focus, Jade promotes only phases that have strong lines matching the peaks in
the searched regions and pays much less attention to peaks out of the search focus. The 100% line of
a PDF phase is also considered out of the search focus if it is located in the truncated region of peaks.
If the '100% Line in S/M Focus' box is checked, Jade will not consider a PDF phase whose 100% line is
out of the search focus. If the 'Ignore Data Outside Focus' box is checked, peaks out of the search
focus are treated as if they are outside the scan range--i.e. they do not contribute to the FOM evaluation
of a hit at all. If the 'S/M for XRD Film Data' box is checked, Jade uses FOM scoring specifically tuned
for film data, which usually has large uncertainties in both intensity and angles.
The parameters in the 'S/M Sensitivities & Thresholds' group are described below:
2-Theta Error Window: The profile nature of S/M tolerates an angular error window up to the
broadening of peaks in the pattern. Therefore Jade can score well without any error window for normal
diffractometer data. This parameter instead tells Jade to shift the PDF phases left & right in step-size
0.06 deg up to the specified values, and Jade will save the optimum offset that gives the minimum
FOM among the multiple matches. The search will slow down a bit with increasing error window but
will give better results if the pattern has large 2 errors or solid-solution phases.
Intensity & 2-Theta Matching: These are heuristic constants from 1 to 10. The higher the number, the
more severe penalty a PDF d-I line suffers from intensity and 2 mismatch; thus fewer PDF phases
would appear on the hit list.
Solid Solution Range (%): If greater than zero, Jade applies a special S/M algorithm in which each
potential PDF phase is scaled in d-space up to the specified range in percentage of [d-d(0)]/d(0),
where d(0) is the original d-value of a PDF line. The scaled d-I lines are then compared to the pattern
and the d/d(0) value is saved if it scores a lower FOM than the original (i.e., d/d(0)=1.0). Notice that
scaling in d-space is equivalent to isotropic compression or expansion of the lattice. Therefore this
option is very effective in finding solid solution and isotypical phases. At the end of the search, a
value >1.0 in the d/d(0) column of the hit list indicates a stretched phase, and <1.0 a compressed
one. In general, you need not search more than 5% of the range in order to find the matches. Refer
to the PDF Overlay Toolbar for more information on how to interpret the d/d(0) value.
Max # of Hits per S/M: For most patterns, Jade is capable of finding the right answers in the top 20
hits of the list. However, if a pattern contains one or more high-symmetry phases such as a spinel,
the list may be populated by similar or isomorphous phases. Increase this number accordingly or
check the 'Exclude Isotypical Phases' box.
Figure-of-Merit Cutoff: Jade's S/M evaluates the FOM of a hit in the range of 0-100. The smaller the
FOM, the more likely the hit, and very likely if it's less than 10. That's why the default threshold to
color a hit is set at 10 for the 'Color Hits of FOM <=' parameter. You can set the threshold to zero if
this visual clue of a likely hit is undesirable. You can choose a different color to display likely hits by
clicking the 'Color Hits of FOM <=' label.

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The 'Alert Low Angle Peak%>' parameter tells Jade to indicate, in the S/M Display Window, the
presence of strong PDF lines from a possible hit below the starting angle of the scan pattern. The
default value of 20 means that if there is a PDF line of I% > 20 from the highlighted hit, indicate the
fact by activating the alert icon (see below) in the S/M display window.


If you click the alert icon, Jade changes the starting angle of S/M display to include the low angle
lines. Since low angle peaks are the most important in phase identification, you should consider
rescanning the sample at a lower angle to confirm the presence of the highlighted hit.
By default, Jade displays the hits, sorted on their FOMs, in the S/M window after a quick search. The
hits are not mutually exclusive--i.e. they are compared to the scan pattern individually, but not to
themselves during the search except when you choose to exclude the duplicate and/or the isotypical
phases. You can tell Jade to perform the mutually-exclusive analysis (called S/M factor analysis) on
the hits automatically after the search by selecting the 'Factor-Analyze Hit List' option in the list box
above the 'XRD Film Data' box on this dialog tab. This factor analysis pits the hits against each other in
a profile-based least-squares matrix. The outcomes are a few unique and most likely phases if the
peaks are not too broad, the current FWHM curve reflects the pattern being analyzed, and you have
removed the background from the pattern. If you select the 'Analyze & Trim Hit List' option, hits
rejected by the factor analysis are removed from the list in the S/M display. Refer to S/M Display
Window for more information on the factor analysis.
The Exclusion tab of the S/M setup dialog is shown and described below. This is an example; you
should see a blank tab if you have not excluded any phases in the S/M.

Besides the 'Exclude Duplicate Phases' option described earlier, Jade can maintain a list of explicitly
excluded phases in the S/M. This provision can also be used to prevent duplicate phases in different
PDF sets from appearing in the hit list. You may find it useful if you are annoyed for example by the

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occurrence of multiple corundum phases. To add a phase to the exclusion list, hold down the Ctrl key
while erasing the phase from the hit list on the S/M Display Window. To remove a phase from the
exclusion list, double-click it here. The Apply check tells Jade to ignore the exclusion list altogether.
The list is stored in a tab-delimited text file named after the current user/project id with the extension of
'tag' (e.g., 'MDI.tag'). You can manually edit this file if desired.
The Hits tab of the S/M setup dialog is shown and described below. This is an example; you should see
a blank tab if you have not used the S/M before.

Jade keeps track of the hit frequencies of phases by their PDF numbers in your S/M. Every time you
check a phase to return from the S/M display window, Jade increments its hit counter. You may find
this history information helpful over time in identifying recurring phases in your laboratory. You can
organize the frequent hit list according to your analysis or sample types by entering a different name for
the listing file on this dialog tab.
You can overlay a phase on this list in the zoom window with the Add button or by double-clicking it.
You can search using only this list with the S/M button on the dialog tab. You can also sort the hit list
according to the hit frequencies in the S/M display window. Like the exclusion list, this history list is
stored in a tab-delimited text file named after the current user/project id with the extension of 'hit' (e.g.,
'MDI.hit'). You can manually edit this file if desired. To delete a phase from this list, press the Delete
key after the phase is highlighted on the dialog tab.
It's good practice to start your search/match with the default settings, which can be assured by
right-clicking the Reset button (left-click resets only the parameters on the current tab). Jade will
indicate the status of non-default settings on a dialog tab by appending an asterisk to the tab caption.
While Jade always remembers the current S/M settings, you can create additional setting files for
different types of search/match with the Save button on this dialog. These S/M settings will also appear
under the main menu 'Identify' for you to select and execute.
Tip: You should familiarize yourself with the S/M capabilities by practicing S/M on known samples.
Refer to S/M Tactics & Examples for recommendations.

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Search/Match Display Window

Jade uses a separate window to display the top hits resulting from a quick search/match. An example
of the display window is shown below with definitions of its interface components:

The display provides you with a set of new tools to evaluate the hits graphically, and to launch another
round of S/M if more phases are to be sought. It is modal and so must be closed in order to return to
Jade's main window. If you check one or more positive hits on the list, Jade will add them to the PDF
overlays in the main window and the Overlay Toolbar will appear. You can return to this display window

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without doing another search, via the 'Identify | Search/Match Display...' or the 'View | S/M List
Window...' menu, since Jade always keeps the last S/M hit list, even after you have read another
pattern file.
By default, S/M hits are sorted on their figures of merit (FOMs), which are evaluated heuristically on a
scale of 0 to 100 for each hit. The smaller the FOM, the more likely the hit, but there is no definitive
threshold of FOM below which a hit is positive. That determination can only be made by you. In
general, however, a hit should be seriously considered if its FOM is less than 10. You can set the FOM
threshold of a hit below which Jade will color it on the list as a visual aid. See the Advanced tab of the
S/M Setup dialog for the FOM threshold.
You can sort the list on another column simply by clicking its column header, and reverse the sorting by
clicking the same header again. You can rearrange the columns by dragging the column headers
left/right if desired; but Jade will neither remember the new column order after you close this display
window, nor use it in the printout of the hit list. You can use the up/down arrow keys to select a hit when
the list has keyboard focus. You can then check or uncheck it with the Spacebar, and erase it with the
Delete key. You can erase all hits below the highlighted one in any sorted order by right-clicking the
Erase button by the list window.
Jade displays the d-I lines of the highlighted hit in the middle window in the same color as that of the
peak markers. You should realize that the line display of a hit is affected by three variables; i.e., its
angular offset '2T(0)', overall intensity scaling 'I%', and d-space scaling 'd/d(0)', whose values have
been determined in S/M to match the d-I list to the peaks. The angular offset '2T(0)' is limited by the 2
error window specified on the Advanced tab of the S/M Setup dialog, and it takes on discrete values in
step-sizes of 0.06 degree. The overall intensity scaling 'I%' is determined from the relative intensity of
the peak that matches the strongest line of the phase. The d-space scaling 'd/d(0)' will be set only if you
have done a solid-solution search. A value of 1.0 indicates no d-space scaling. See the S/M Setup
dialog for more information on solid solution S/M.
With the toggle button on the line annotation toolbar (see below), you can display the d-I lines of a hit
either in their original values from the PDF database (unaltered) or by applying the values of the above
three variables (altered).

You can also adjust these three values manually using the offset and scaling buttons by the list window
(see below), and reset them to 2T(0)=0.0, I%=100, and d/d(0)=1.0, respectively, by holding the Ctrl key
down when you click these buttons. Notice that you can also adjust the 2T(0) of the scan pattern on the
main toolbar besides that of the individual hits.

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You can toggle the line view of two similar phases by holding down the right mouse button on the 2nd
phase. Jade flips the view back to the highlighted phase when you release the button. This operation
can also be performed with the left mouse button if you hold down the Ctrl key. If you check a phase to
be a positive hit on the list, Jade will keep its d-I lines in the middle window when you select another
phase, so that multiple matching phases can be viewed at the same time. A color-coordinated label of
the checked phase will appear in the middle window. You can assign a new color to this label by
clicking it directly or the color palette alongside the display window. If you have PDF overlays added
from earlier rounds of S/M in the main zoom window, you can choose to display their d-I lines in the S/M
window as well using the toggle button on the line annotation toolbar.
When the display range in the middle window is less than 30 degrees, you can also annotate the d-I
lines of checked phases with their names/formulas and I% & Miller indices using the toggle buttons on
the line annotation toolbar. In the earlier diagram (S/M Display Window), Hematite, Rutile, and Anatase
phases have been checked so that their colored labels appear in the middle window. The middle
window behaves very much like the main zoom window with its own set of zoom & pan tools. You can
also double-click or drag in the top window to zoom if you choose the full view to be described below.
While the coordinates of the crosshair cursor are displayed in the status bar, you can pop a floating
label to show the coordinates above the cursor if you left-click in the middle window. You can hide this
coordinate label if you left-click again.
By default, the top window shows the segmented profiles of peaks that match the d-I lines of the
highlighted hit. This display is called the 'Cutout View' of the current hit; it can be toggled to show the
full view of the scan pattern with the toggle button by the top window (see the diagram below). The
regions of the scan pattern that have no PDF lines from the hit are excluded from this cutout view.
Therefore its x-axis, though linear in 2, has gaps between the profile segments. When you select a
new hit on the list, the cutout view changes accordingly and thus gives you a quick grasp of a matching
phase without the need of constant zoom & pan. You can tell where the profile segments come from by
click & drag in the top window--Jade will underline the corresponding regions in the middle pattern
window.

If you choose the full view in the top window, Jade shows the 'Low Angle Line Alert' toolbar (the above
diagram), on which you can enter a new starting angle for the display. This option is intended for
viewing possible PDF lines below the starting angle of the scan pattern (SAS). Therefore Jade will only
accept 2values that are less than the SAS. Jade will activate the 'Alert' button, located next to the
starting angle, if the highlighted hit has strong d-I lines below the SAS. If you click this button, Jade will
change the starting angle of display to include the low angle lines. You can set the I% threshold of d-I
lines for this activation on the Advanced tab of the S/M Setup dialog.
Tip 1: You can change the height partitions of these windows by dragging the borders between them up
or down.
Tip 2: You can hide the top window by right-clicking the view toggle button if you need more screen

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space.

Tip 3: You can align the main toolbar at the bottom of the display window with the button on the main
toolbar.

Tip 4: You can display the y-axis scale by right-clicking the button in the left margin of the display
window.
Tip 5: You can bring up the S/M Setup dialog by right-clicking in the middle window.
Tip 6: You can bring up the Change Display Colors dialog by right-clicking in the top window.
Tip 7: You can browse the pattern file by clicking the file name in the status bar.
Tip 8: You can flip the Quick S/M Toolbar into vertical layout by right-clicking the '<' button.
Simulate an XRD Pattern from the d-I Lists of Checked Hits:

Using the toggle button on the line annotation toolbar (see the earlier diagram), you can simulate
an XRD pattern from the d-I lists of the checked hits. When the toggle button is depressed, Jade
simulates the pattern, using the current 2T(0), d/d(0) & I% values of the checked hits, with the current
profile parameters on the Pattern Simulation dialog (see below), and overlays the simulated pattern in
the middle window for comparison.

You can bring up the above dialog by clicking the dialog button next to the toggle button on the line
annotation toolbar. If you choose to display the d-I lines of existing PDF overlays in the middle window,
Jade includes them in the simulated pattern as well. Therefore it's possible to see a simulated pattern
without any phase checked on the hit list. To simulate an XRD pattern close to the observed, you
should choose the relevant 'FWHM Curve' to begin with. If necessary, you can add Scherrer
broadening to peak profiles from an overall crystallite size for the pattern and/or different sizes for
individual phases on the above dialog. You can enter the crystallite size of a checked phase by clicking
in the 'XS(A)' column and wait for the input box to appear. If you click the 'Estimate Sizes' button, Jade
will carry out a peak search and estimate the crystallite sizes of individual phases from the FWHM
values of the peaks located near the 100% lines of the phases. You can add background to the
simulated pattern only if you choose to display the raw pattern and have fitted a background curve in
the main zoom window. See the Pattern Simulation topic for more information on the simulation
parameters.
You can adjust the 2T(0), d/d(0) & I% values of a checked phase using the offset & scaling buttons by
the list window as described earlier, and Jade will update the simulated pattern automatically with the
shifted d-I lines. You can offset the simulated pattern up or down using the offset button by the middle
window. You can paint the simulated pattern by selecting the desired fill style and color on the Zoom

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Window Display dialog, which can be brought up by right-clicking the 'Full Range' button on the zoom &
pan toolbar. Jade will use the simulated pattern to produce the residual pattern if you choose to display
and search the residual. See the descriptions later in this topic for more information.
Factor Analysis of Search/Match Hits:
Using the 'Factor-Analyze' button on the main toolbar (see diagram below), you can group the hits by
performing a special factor analysis that pits the hits against each other in a profile-based least-squares
matrix. The outcomes are a few unique and most likely phases if the peaks are not too broad, the
current FWHM curve reflects the pattern being analyzed, and you have removed the background from
the pattern. See the S/M Setup dialog for more information on the factor analysis.

The analysis will sort the hits according to their most likely ranks; the unlikely ones will have their I%
values set to <1. Isotypical or similar phases will be identified and designated with alphabetic letters
under the column 'G' (see diagram below). In other words, phases that are assigned the same letter are
either identical or very similar and are thereby referred to as a 'similarity group'. You can sort the list
according to similarity groups, and trim a group down to just one unique phase by selecting it and then
clicking the 'Trim Group' button by the list window. Notice that Jade replaces the designated group
letter in the column with the number of hits in the collapsed group. You can restore the group by
clicking the trim button once more. An example of this analysis is shown below:

List Similar Phases and Cross Reference to Other PDF Subfiles:

You can easily retrieve phases similar to the highlighted hit, but which may have been excluded in the
searched subfile, or from a different subfile (cross-reference), using the 'n' button on the 'Quick S/M
Toolbar' as illustrated below:

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Similar phases can be retrieved in the following categories:

Close/Closer/Closest Match: Phases whose d-I lines closely match those of the highlighted phase.
They are mostly duplicate, isotypical, and solid-solution phases.
Same Chemistry: Phases with the same chemistry and stoichiometry.
Same Elements: Phases with the same elements but possibly different stoichiometries.
Pearson Symbol: Phases with the same Bravais lattice and number of atoms (half) in the unit cell.
Mineral Group: Phases belonging to the same mineral group as classified in the PDF by ICDD.
If similar phases are found in the designated PDF subfile, Jade will bring up the PDF Retrieval dialog to
list them. You can then select one or more of them to add to the S/M hit list. You can also add known
or potential phases to the list using the PDF recall and retrieval tools on the main toolbar. An added
phase will be inserted in the list in the current sorting order with an FOM of 99.9. You can adjust its
2T(0), I%, and d/d(0) values to get a better match visually, and calculate its FOM with the 'FM' button
by the list window if desired. You can save the hit list to a file (*.PLF) and read it later from the file list
that appears on the main toolbar. Jade will clear the existing hit list when you read a PLF file.
You can also add the highlighted PDF phase into a S/M userfile by selecting the 'Add to Userfile...'
menu. See Userfile Manager dialog for more information.
Trim S/M Hit List Using Boolean Filters:
While you can set up and use PDF filters before the S/M, you can also trim the existing hit list using a
variety of Boolean filters after the S/M. You can bring up the filter menu either with the '>' button on the
'Quick S/M Toolbar' or by right-clicking the Chemistry button on the main toolbar:

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Filters above the divider (i.e., 'Chemistry...', 'Stoichiometry...', etc.) will bring up the corresponding
dialogs on which Jade will display the existing data from the current hits. You can then proceed to trim
the list using the relevant functions on the dialogs. For example, if you select the 'Chemistry...' filter,
the following dialog will appear:

Jade will populate the periodic table with the elements present on the current hit list. You can then
either trim the list by requiring certain elements and/or eliminating unwanted ones, or display the
'Element Affinity' maps among the phases with the newly appeared check box, in which case Jade will
'light up' the elements that are combined with the one being clicked on. In the above example, Jade
shows the elements (in green) that are combined with the iron (Fe) from an S/M hit list.
Filters below the divider in the filter menu above (i.e., 'Exclude (?) Phases...', etc.) will trim the list down
upon selection accordingly. If you have created the chemistry filter files (*.cff), they will appear on the
filter menu for you to select and execute. You can restore the original hit list by clicking the 'r' button on
the 'Quick S/M Toolbar' to undo the filters.
Search/Match on Residual Pattern and Residual Peaks:
You can flip the intensity scaling of the display between linear and square-root axes using the axis
button in the upper-left corner or by double-clicking in the left margin of the display window. The
square-root axis is helpful for viewing minor or trace phases without the need of vertical zoom. You can
display and search the residual pattern after the checked phases using the 'crescent moon' button on

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the line annotation toolbar. You should be aware that the residual pattern is produced in a non-precise
manner (brute-force chopping) using the current line offset and I% values since profile fitting is not used
in the subtraction. If you simulate an XRD pattern on the d-I lists of the checked phases, Jade produces
the residual using the simulated pattern rather than the brute-force chopping. The results will obviously
depend on how well you simulate the pattern. Therefore we discourage searching the residual pattern.
You can usually identify the remaining peaks, especially those in the low angle regions, using the zoom
window focus. See S/M Tactics & Examples for more information.
You can calibrate the current pattern in 2 using any highlighted hit as an internal standard simply by
left-clicking the theta calibration button on the main toolbar; right-clicking the same button will bring up
the Theta Calibration dialog. Your chances of identifying the minor and/or trace phases are greatly
improved if you can eliminate significant angular errors in the scan pattern. Notice that you can toggle
the display between the uncalibrated & calibrated patterns or between the original & the
background-removed patterns, using the swap button on the main toolbar. Jade always uses the
current pattern for subsequent search/match in the S/M display window.
You can also ask Jade to list the remaining peaks that are not matched by the d-I lines of the checked
phases. You can do so using the 'p' button on the 'Quick S/M Toolbar' (see below) or the 2nd button
(from the top) by the list window.

The unmatched peaks, if any, will be listed in their 2(I%) values. If you double-click any one of them,
Jade will zoom the middle window to display the unmatched peak and launch the single-peak S/M right
away. In other words, Jade will promote only those phases having strong d-I lines in the neighborhood
of the unmatched peak. You can hide this peak listing by clicking the 'p' button again. However, if you
leave the middle window to display the whole pattern with the peak list visible, you can search all the
remaining peaks at once if you click the 's' button on the 'Quick S/M Toolbar'. This operation can be
repeated with new hits checked or unchecked on the list. You may find it helpful to erase the
unchecked hits in this operation, which can be done easily with the 'x' button if you set the highlight on a
checked hit. You can also right-click the 'x' button to erase all the unchecked hits if the highlighted hit is
unchecked.
You can ask Jade to search the remaining peaks automatically by selecting the 'Search Remaining
Peaks' option on the Advanced tab of S/M setup as shown below:

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This search can only be performed from the main window of Jade. When selected, Jade will consider a
hit positive (i.e, checked) if its FOM is less than the cutoff value for coloring hits, and automatically
search the remaining peaks. If there is no hit with FOM value less than the cutoff, the first hit on the list
is then considered positive. The process will be repeated until all peaks have been identified.

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Search/Match Tactics and Examples

The following steps are recommended to find the major phases:
 Step 1: Select the relevant PDF subfile(s).
Step 2: Start the initial search with the default parameters on the S/M setup dialog (right-click the
Reset button).
Step 3: If no positive hit is found, increase the 2 error window and do another search.
Step 4: If no positive hit is found, do a solid-solution search in the few % range.
Step 5: If no positive hit is found, focus the search on a few of the strong peaks at low angle. If there
is a cluster of peaks, zoom around them and do another search.
Step 6: If no positive hit is found, check the 'Preferred Orientation S/M' box and do another search.
Step 7: If no positive hit is found, check the 'Perform Single Phase S/M' box and do another search.
Should you fail to find a positive hit after the above steps, the possibilities are: (a) you either have very
large 2 error or extreme orientation or extensive solid solution in the data, or (b) you may simply have
the incorrect radiation anode and wavelength, or (c) the phase you are looking for is not in the PDF
subfile(s) being searched.
Additional steps are recommended to find minor and trace phases:
Step 8: Start the initial search with the default parameters on the S/M setup dialog. Run the hit list
through the factor analysis. If no positive hit is found, go to Step 10.
Step 9: Evaluate and tag positive hits. Eliminate untagged hits with the 'x' button on the quick S/M
toolbar. If substantial 2 error (say >0.1 deg) exists when comparing a positive hit with the unknown,
calibrate the data with the theta calibration tool on the toolbar. Then go to Step 11.
Step 10: Start another search with increased 2 error window and/or a solid solution search in the few
% range. If a positive hit is found, go to Step 9; if not, go to Step 11.
Step 11: Look for any unmatched peaks with zoom & pan or in the square-root intensity axis or with
the 'p' button on the quick S/M toolbar. Change the search focus to some of them, especially the low
angle peaks. Make sure that the peaks to be searched are properly scaled in the zoom window before
you click the S/M button on the main toolbar. New hits will be found or promoted due to the focus--go
back to Step 9 to evaluate the new list. You may have to iterate between Steps 9 and 11 for a
complex pattern. As fewer peaks remain, focusing the zoom window on them with chemistry
knowledge becomes imperative. If you are looking for trace phases, make sure that the background
removal is done as precisely as possible, since a slight over/under-subtraction of background could
affect the relative peak intensities of a trace phase dramatically.
You should keep in mind that the little peaks you are trying to identify may not always come from
another phase. They could well belong to the phases already identified, since not all PDF patterns are
well characterized, especially when there are possible variations in chemistry and stoichiometry. They
could also come from contaminations such as beta radiation and sample holder. Tip: you can check
possible satellite beta peaks in the vicinity of very strong peaks using the K-beta cursor. Trying hard to
identify weak peaks above high and noisy background data is likely a waste of effort, especially when
the chemistry information is not available. Your effort will be much more effective if you can obtain the
precise chemistry and collect data with improved counting statistics by spending more time on each
step. You do not need to collect data with a step-size less than 0.02 degree on conventional
diffractometers for most samples. You can use even larger step-sizes on samples with broad peaks.
The following examples illustrate the S/M tactics outlined above. These demo files were installed in the
'demofile' folder under Jade. Complete and correct solutions are not necessarily known for some of the
examples.
Example 1: DEMO14.MDI--Apatite + Corundum

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This example illustrates the advantage of profile-based S/M. The apatite peaks are diffused and
overlapped extensively. With profile-based S/M, explicit peak locations are not required. Simply fit the
default background and launch a default search in the inorganic subfile, and you should see corundum
and a number of apatite phases on top of the hit list.
Example 2: DEMO18.MDI--Corundum + Thenardite (minor) + Diaoyudaoite (trace)
This example illustrates how to focus the S/M with the zoom window. If you do a minor phase search
after you have removed the background, you should identify corundum as the major phase and
thenardite as the minor one. Check both phases and change the y-axis of the S/M display window to
square-root by a double-click at the left margin. You should then be able to see clearly an unmatched
peak below 10 degrees. Zoom around it and do another search--Diaoyudaoite should appear in the top
of the hit list. You can also find Diaoyudaoite if you display the remaining peaks with the 'p' button and
then click the 's' button on the quick S/M toolbar. The remaining peaks at 23.9 and 26.5 degrees are
not identifiable due to lack of knowledge about the sample.
Example 3: DEMO12.MDI--Quartz (55%) + Corundum (20%) + Calcite (20%) + Dolomite (5%)
This example illustrates the effectiveness of S/M factor analysis. First select 'NBS Silicon-2' as the
default FWHM curve on the Instrument tab of the User Preferences dialog. Fit a default background to
the pattern. Reset S/M parameters to defaults (right-click the Reset button). Set the 'Quality Mark
Filter' to exclude (?) phases, and do a minor phase S/M on the inorganic subfile. You should see
Dolomite among the 40 hits in the S/M display window. Now click the 'Factor Analysis' button on the
main toolbar and you should see Dolomite promoted as one of the most-likely hits in the list.
Example 4: DEMO16.MDI--Zeolite Sample with Silicon Standard
This example illustrates the isotypical and solid-solution search. You need to fit the background
manually in this example. Once the background is taken care of, do a default search in the inorganic
subfile and print the hit list. Now clear the list and do a solid-solution search in the 3% range, then
compare the results. The zeolite in this example has a cubic cell smaller than most of the zeolites in
the PDF database, as indicated by the d/d(0) values of less than one. The line positions of the
highlighted zeolite phase have been altered by its d/d(0) value in the S/M display so that they appear to
match the peaks. You can view the unaltered line positions by releasing the scaling button on the main
toolbar.

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Line-Based Search/Match for Phase Identification

Jade provides two search/match (S/M) approaches to phase identification; i.e., Profile-Based S/M and
Line-Based S/M. The former utilizes the full scan trace of the diffraction pattern without the need of
explicit peak location. The intrinsic broadening of profiles largely takes care of the uncertainty of line
position as well as overlapping peaks. The S/M algorithm works very much like visual comparison of
d-I lines to the scan trace, making profile-based S/M a much more effective approach than line-based
S/M for most identification problems.
In contrast, line-based S/M makes use of only the peaks located with peak search, and compares them
to the first 32 lines of a potential phase in the PDF database. The one advantage line-based S/M has is
its ability to accommodate large angular errors (up to one degree in 2) in the pattern. But you would
be better off with improved instrument alignment as well as theta calibration if your data routinely
contains 2 errors larger than the profile broadening of peaks. Line-based S/M is the only S/M option
accessible if you have just the userfile S/M that works with your own database. If you have any PDF
database, both S/M options are accessible.
You can bring up the dialog window of line-based S/M from the 'Identify | Line-Based Search...' menu.
An example of the dialog is shown below:

Line-based S/M does not require removing the pattern background, but it does require marking the
peaks to be searched in the zoom window. If they are not present, Jade will do a peak search before
showing the above dialog. Once a list of hits is obtained from searching a designated PDF subfile, you
can hide the peak markers so that you have a better view of the d-I lines of the highlighted phase in the
zoom window. You can do so without erasing the peak list by clicking the '# Peaks' item in the main
status bar.
Notice that this dialog is modeless and resizable. When you select a hit on the list, Jade displays the
first 32 d-I lines in the zoom window. You can examine the line-peak matching in detail using the zoom
& pan tools without closing down the S/M dialog. You can adjust the heights of the line markers (i.e., I%
value) using the marker scaling button on the Zoom & Pan Toolbar. These line markers will be erased
from the zoom window when you zoom or pan, but you can bring them back simply by clicking the hit on
the list again. When you find a positive hit, you can keep its d-I lines in the zoom window by adding it to
the PDF overlay list. You can do so either by double-clicking it on the list, or by clicking the Add button
on the dialog, or by dragging it out of the list and dropping it into the main window.
By default, the hits are sorted on the S/M figure of merit (FOM), which is evaluated heuristically from 0
to 100 for each hit. The smaller the FOM, the more likely the hit, but there is no definitive threshold of
FOM below which a hit is positive. That determination can only be made by you. In general, however,
a hit is very likely if its FOM is less than 10. You can sort the list on another column simply by clicking
the column header, and reverse the sorting by clicking the header again. You can rearrange the
columns by dragging the column headers left/right. Jade keeps the hit list when you close this dialog or
read another pattern file. You can view the list again either on this dialog or on the PDF Retrieval
dialog.

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You can adjust the search parameters in regard to the 2 error window, the sensitivities to the theta &
intensity matching, minimum number of matching peaks, and the FOM cutoff, using the input boxes on
the S/M dialog above the hit list. You can impose chemistry constraints in the search with the
'Chemistry Filter...' button on the S/M dialog, and filter the existing hits in chemistry by right-clicking the
same button. Refer to PDF Retrieval by Chemistry for how to use the chemistry filter.
Tip: You can browse the PDF card of a hit by right-clicking it on the list, and browse another without
closing the card view dialog.

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Find Similar Pattern Files with Thumbnails - Deja vu S/M

If you process large numbers of samples routinely for phase identification, and have accumulated
numerous XRD patterns over time, there is a good chance that a new pattern to be analyzed is similar
to some previously encountered. Jade provides a special file search or 'Deja vu' search utilizing the
pattern thumbnails that are created automatically by Jade. You should find this search feature very
helpful in locating those similar patterns and capitalizing on previous analysis efforts and reports.
You can access this search dialog from the 'Identify | Find Similar Pattern...' menu, and find pattern files
similar to the one being displayed in the main window, whether it is of single or multiple phases. An
example is shown below:

As mentioned above, Jade utilizes the existing thumbnails to perform this magic, and will create them if
they don't exist for the pattern files in the folder or drive being searched. Your initial search may be
slow due to thumbnail creation but future searches will be fast. You can stop a search session by
pressing the ESC key. If you have used earlier versions or releases of Jade, you should delete all
existing thumbnails (*.jip files) and let the current version of Jade 5 create them anew. This will
improve the results of file search. You can use the 'Find All Files' program in Windows to list all the
existing *.jip files, select them all, and then press the Delete key. You should make sure that these *.jip
files were created only by Jade on your computer.
You can choose from three similarity settings beneath the thumbnail window on this dialog to match
more or fewer files. The 'Search Folder' button will find similar files from the current pattern file folder.
The 'Search Current Drive' button will search all folders on the selected drive for all pattern files of the
current file type. You can search pattern files of a different type by selecting from the file type list on
this dialog. If you archive pattern files onto read-only media like the CDs, you should also save their
thumbnail files and analysis report files. If you don't save them, you won't be able to search the
archived media to find similar pattern files and bring up their analysis reports.
If similar pattern files are found, you can overlay any one of them in the zoom window with the Add
button or by double-clicking it directly on the list. You can also 'enlarge' its thumbnail onto a resizable
pop-up window if you left-click the thumbnail. You can view its file content with the Browse button or by
right-clicking its thumbnail. You can view its note file with the Note button if it exists. You can bring up
its Phase ID Report with the 'Report...' button, and Jade will overlay its PDF phases in the zoom
window. You can examine the overlays with the zoom & pan tools without closing down the dialog
window.
You can also find pattern files with a given range of Peak/Noise (P/N) ratios or containing peaks in the 2
 regions you specify, independent of the pattern shown in the main window. The '3-Peaks' button will
show or hide the peak search panel, which will allow you to enter the peak locations and their relative
intensities. An example of this search is shown below:

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You can enter 1 or 2 or 3 peaks to search at the same time. The above example will find all pattern
files containing peaks with intensities >50% in the 2 range of 2 to 6 degrees. When the '3-Peaks'
panel is shown, the 'Search Folder' and 'Search Current Drive' buttons will find files according to the
specified peak locations; otherwise, these two buttons will do the similarity search as described earlier.
Refer to the Peak Listing Dialog for how the P/N ratios are calculated. For example, you can find
pattern files with their maximum P/N ratios from 10 to 12 by entering 10 in the top P/N box and 12 in
the bottom P/N box here.

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Peak Identification Reports

After you have identified the phases in an XRD pattern, you can tabulate the individual peaks identified
by their matching phases in two different reports: the extended & compact peak id reports. They are
accessible from the 'View | Reports & Files' menu after you have located the peaks in the zoom
window. You don't have to check the phases from the Search/Match Display in order to produce these
reports. All you need is a list of PDF overlays in the zoom window, which can be added using the PDF
overlay tools as well. An example of an extended id report is shown below:

Note: Jade uses only the visible PDF overlays in the reports when you have added more than one. A
visible PDF overlay will have its d-I lines shown in the zoom window, and is controlled by the
'thumbtack' button on the PDF Overlay Toolbar. Jade automatically tacks a PDF overlay when it's
checked and added from the Search/Match Display. You can tell Jade to tack all new PDF overlays on
the Display tab of the User Preferences dialog.
The tabulation on the report depends on the 2 error window within which a PDF d-I line is considered
matching the located peak. If there are two or more PDF lines within the error window, the closest one
is chosen for the association, but you can choose another line from the nearby-line list shown above the
peak list. You can set the value of this error window on the Theta Calibration dialog as well as on the
Misc tab of the User Preferences dialog. Since the apparent positions of PDF lines can be altered by
the theta offset (2T(0)) & d-scaling (d/d(0)) values of PDF overlays, you can tell Jade to use or ignore
these values in the reports on the Report tab of the preferences dialog. If the PDF overlays are added
from the search/match, the 2T(0) & d/d(0) values will be set by Jade. Refer to the PDF Overlay Toolbar
and PDF Overlay List dialog for how to browse and alter these values.
As pointed out above, a peak on the extended id report is associated only with one d-I line from one
matching phase. In a multi-phase pattern, it's possible for a marked peak to be associated with several
d-I lines from different phases due to the overlapping of unresolved peaks as well as the close proximity
of d-I lines. In that case, you may find it useful to tabulate the matching phases in a compact id report
as shown below:

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The two numbers in a phase column are the 2 and I% values of the d-I lines. A maximum of 32
phases can be tabulated on this report, and you can scroll the list to the left to see more columns. On
the printout, however, Jade will print only as many phases as will fit on the page, depending upon the
font size and print orientation. Should you have more matching phases than will fit on a single page,
you can use the check boxes on the PDF Overlay List dialog to select the remaining phases to print on
additional pages.
These report dialogs are modeless and resizable. When you select a peak on the report, Jade marks it
with a short blinker in the zoom window. You can zoom & pan the display to examine the matches in
detail while the dialogs are open. You can also edit the located peaks using the peak editing cursor,
and Jade will update the report automatically. If the 'Color Phases' box is checked on the dialog as
shown above, Jade uses the same colors assigned for the d-I lines in the zoom window to display the
phase items on the reports as well as on their printouts.

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Phase Identification Report

Besides the Peak ID Reports, which identify the individual peaks by their matching phases, you can
produce a summary phase id report in Jade. You can bring up the report dialog from the 'View |
Reports & Files | Phase ID Report...' menu regardless of whether you have carried out the phase
identification. An example of this report is shown below:

For a new report, Jade will add the current PDF overlays to the phase list. If the report has been saved
before, Jade will read the phases in it and overlay them in the zoom window automatically. You can
remove a phase from the list by pressing the Delete key after it's selected or delete it from the overlay
list before bringing up this dialog. You can view the PDF card of a phase by double-clicking it on the
list. If the phases have been quantified from RIR-Quant Analysis, Jade lists their weight% values rather
than the content tags on the dialog. You can change the content tag of a phase by clicking the column
header.
By default, the report is a single-page printout with the sample, client, and analyst information on the
top, the graphic plot of the current pattern in the middle, and the stacked ribbon plots of phases (max.
16) at the bottom of the page. If you uncheck the 'Plot on Report Page', Jade prints the phase listing in
tabulated form on the same page. If you check the 'List Phases on Plot', Jade prints the phase listing
on top of the plot as well as on the ribbon plots. Extra pages of the report can be printed depending
upon the options you check on this dialog.
The report can be saved to a *.RPT file in the same name as the pattern file. Jade will read the existing
report file automatically when you bring up the report dialog in the future. You can also browse the
phase id report by clicking the 'RPT' item in the main status bar.

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Jade's d-I List File Editor

Besides the peak listing reports (*.pid files), you can import and export d-I lists via the plain d-I listing
files (*.dsp), and edit d-I lists with a special editor provided by Jade. See the d-I List File Import dialog if
you want Jade to read d-I listing files created by other XRD applications. You can bring up the d-I list
editor from the 'Edit | d-I List File Editor...' menu. An example is shown below:

If peaks are located in the zoom window, they will be loaded into the editor automatically. Otherwise
you may choose to create a new d-I list from scratch or to edit an existing one on the DSP file list. By
default, Jade lists all the DSP files from the current pattern file folder, but you can choose a different
folder for the DSP files with the Browse button on the dialog.
To enter a number into a cell(field) in the grid, simply click the cell and type in the number (you don't
need to press the Enter key). You can use the arrow keys to select another cell. You can cut, copy,
and paste a line using the Ctrl+X, Ctrl+C, and Ctrl+V keys. To erase multiple lines, select them with
dragging and then click the Erase button. Tip: You can select the entire list by clicking the 'L#' label in
the grid header. A maximum of 200 d-I lines can be edited and saved into a DSP file. You can resize
the dialog window to see more or less data, and drag in between the d-I list and the file list to see more
or fewer files.
If you are editing the d-I list converted from the located peaks of the current pattern, you can graft the
Miller indices to the peaks (thus the d-I list) from the active PDF overlay so that you don't have to enter
them manually on this dialog. See the Peak Listing dialog for how to graft the Miller indices. Refer to
Insert Data to Userfile for how to enter d-I list data into a userfile for S/M if your version of Jade has the
S/M capability. Using the Add button, you can overlay the current d-I list in the zoom window directly
without first saving it to a DSP file.
You can rename a DSP file on the file list by clicking its filename again and waiting for an editing box to
appear. Then type in a new filename and press the Enter key. You can delete a DSP file on the list by
pressing the Delete key after it's been selected. Besides this d-I editor, you can create a DSP file in
Jade from (a) the Peak Listing dialog, (b) the D-Spacing & Miller Indices calculator, (c) the PDF Overlay
Listing dialog.

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Jade's d-I List File Import

You can import d-I list files created by other XRD applications into Jade as d-I overlays using a special
import dialog provided by Jade, which is accessable from the 'Edit | d-I List File Import...' menu. The
example below was set up to read the output listing file written by MDI's Rietveld refinement program
'Riqas'.

The basic idea of the import setup is similar to that used on the Import Ascii Pattern Files dialog--i.e., to
provide the format template in terms of the line numbers or keywords where the phase id and d-I listing
can be found in the files. You don't need to count the line numbers if you can provide unique keywords
in the files for the required items on the above dialog. Unlike the ascii file import, you can mix line
numbers and keywords in this setup. The 'Phase ID' input is optional; Jade will use the file name as
phase id if omitted. In the above example, Jade reads 32 characters for the phase id, starting from the
5th character in the first line of 'riqas.lst' file. The 'List Size' input is optional as well; if it is omitted,
Jade reads the d-I list until (a) the end of file, or (b) the maximum number (i.e., 200 lines), or (c) the
'End-of-List' keyword (if specified) is reached.
The beginning of a d-I list can be indicated by its preceding line and/or column header, if any, as shown
in the above example. The relative intensity (I%) and the Miller indices of a reflection are optional in
the input. If the 'Count Columns for d-I List' box is checked, you can specify the data fields (i.e.,
d-spacing or 2, I% & Miller indices) in their column numbers in the line. Otherwise, you must count the
character number from the beginning of the line for the data fields. If the fields don't align in fixed
columns, the only way to read the d-I list is to count their column numbers. If the list is longer than the
maximum 200 lines, you may enter a cutoff value in the 'Min-I%' box to ignore weak reflections in the
list. If the file contains more than one d-I list, you can tell Jade to read them all as multiple d-I overlays
if you check the 'Multiple Phase Data Sets' box on the dialog.
To avoid typos in the input of a keyword, you can select & copy it to the clipboard when you browse the
file, and paste it into a field on the dialog. Notice that Jade shows the file name to be read on the long
button next to the Browse button. When you are ready with the input setup, you can test-read the file by
left-clicking this button, or browse the file again by right-clicking it. If you succeed in reading the file,
Jade will save the setup for you. But you can always save it to a different file with a descriptive name
you provide. You can use the Add button for subsequent reading of the same listing files.

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Add d-I Data to S/M Userfile

In addition to the available PDF subfiles, you can create and maintain your own userfiles for S/M. Two
types of data can be added to a S/M userfile: (a) subsets of PDF phases of interest to you; (b) non-PDF
data obtained and identified by you. The former can be added directly from the Userfile Manager
dialog. The latter can be added from an existing d-I list file (*.DSP) or from the located peaks of a scan
pattern in the zoom window. In this case, Jade does not care if the d-I or peak list consists of a single
phase or multiple phases.
To add the located peaks in the zoom window, select the 'Identify | Add to Userfile...' menu and the
following dialog window will appear:

If there are no located peaks in the zoom window, Jade does an automatic peak search. Obviously you
want to make sure the peaks are located properly. The pattern should be calibrated in 2 if necessary.
Profile-fitted K1 peaks should be preferred for this purpose. Jade will convert the located peaks to a
suitable d-I list that can be browsed and edited using the 'Edit d-I List...' button on the above dialog. If
you obtained the d-I list from other sources and would like to add it to the userfile, use the d-I List Editor
brought up from the 'Edit | d-I List File Editor...' menu. When you finish editing the d-I list, click the 'Add
to Userfile...' button on the editing dialog, and the above dialog will also appear.
You can provide as much information about the d-I list as you please with this dialog. The more fields
you fill in, the easier for you to retrieve it later from the userfile with the available PDF filters in Jade.
The only required fields are the phase id and the 'PDF#' number. Crystallographic & chemistry
information as well as comments will be most desirable when you later search the userfile or browse its
content. Comments up to 1KB in length can be entered at the bottom of the dialog. If you have refined
the lattice constants with the pattern, Jade will take the refined cell for the new entry. If you haven't but
there is a PDF overlay in the zoom window, Jade will graft the PDF cell and chemical formula. You can
remove the PDF overlay if it's not intended for this purpose. You can also graft the Miller indices to the
d-I list from the PDF overlay (see the Peak Listing Dialog for how to do this).
The 'PDF#' of a userfile entry takes on the same set-pattern format as a PDF card. Jade will assign the
'PDF#' sequentially for new entries. You can use set 0, 90 through 99, and pattern numbers 1 through
1000 in a userfile. Set 0 will be assigned to the default empty userfile named literally as 'userfile', but it
can be changed to a different number from 90 to 99 if desired. However, only one set number is allowed
in one userfile, and this set number cannot be changed after you have added an entry into the userfile.
You can rename this userfile on the Userfile Manager dialog. If you do so, an empty new userfile will
still appear on the userfile list, together with the renamed userfile, and be ready to accept new entries.
If you have more than one userfile to maintain, you can select the active userfile to work with from the
userfile list on the above dialog, and view its entries with the Browse button.

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Once you have created a userfile, it will appear on the subfile list on the PDF Retrieval and S/M Setup
dialogs, and it can be used just like the PDF subfiles. You can retrieve a userfile entry the same way
you retrieve a PDF card. If set 0 is used, a userfile entry can be recalled as, e.g., 00-0001, or 0-1, or
simply 1. You can browse the entries in a userfile from the Userfile Manager dialog and edit an existing
entry if necessary.

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S/M Userfile Manager

This dialog window is accessible from the 'Identify | Userfile Manager...' menu. In the following
example, one non-PDF entry (00-0001, highlighted in the list) has been added to the userfile together
with 60 PDF phases from the spinel mineral groups:

Refer to the Add to Userfile topic for how to add non-PDF entries to a userfile. To add PDF phases to a
userfile, you can enter them one by one on this dialog if you know their PDF numbers (you must press
the Enter key after typing the number). However, it will be much easier if you can retrieve them all from
the PDF Retrieval dialog, which can be brought up with the 'PDF...' button on this dialog. When you
click the 'Userfile...' button on the PDF retrieval dialog, the selected PDF phases will be added to the
current userfile. You can also add PDF phases to a userfile from the S/M Display Window. A
maximum of 1000 entries can be stored in a single userfile. You can create and maintain multiple
userfiles by (a) renaming the 'userfile' subfile to something else and an empty 'userfile' subfile will be
there and ready to accept new entries, or (b) saving the current list to a new userfile in a name you
provide. Warning: you should not use the name 'usertemp' for a userfile because the name is used by
Jade for writing scratch userfiles.
You can erase entries from the list one by one, or select a bunch of them with dragging and then click
the Erase button. You can modify an existing entry with the 'Edit...' button, causing the Add to Userfile
dialog to appear and be filled with the data of the selected entry. After you have made the desired
modifications, you can save it back to the userfile using the 'Update' button that now appears on the
Add to Userfile dialog.
When you select a phase on the list, Jade displays its first 32 d-I lines in the zoom window as a quick
view. You can add the phase to the zoom window as a PDF d-I overlay either by double-clicking it on
the list, or by clicking the Add button, or by dragging it out of the list and dropping it to the zoom
window. You can search the userfile against the current pattern by clicking the S/M button. The S/M
Display Window will appear if any hit is found.
If the current 'userfile' is empty, you can convert userfiles created by earlier versions of Jade with the
Import button on this dialog. Note: Jade does not prevent you from importing a userfile with a set
number already used in another userfile. The following dialog will appear when you click the Import
button:

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You select the right type of userfiles and a file name to import. Jade will create a new 'userfile' to store
the entries. You can then rename the 'userfile' if desired.

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RIR Quantitative Analysis

With Jade's Easy-Quant option and the ICSD subfile available with ICDD 1998 and later releases of the
PDF2 CD, you can perform quantitative analysis on multi-phase patterns easily by means of reference
intensity ratios (i.e., RIR, also called I/Ic in the PDF database). The ~40K patterns calculated from the
crystal structures in the ICSD subfile make it possible to look up the RIR values for most of the common
phases you will likely encounter. Since the calculated RIR values are based on the integrated
intensities of reflections, it is necessary to profile-fit the peaks in the scan pattern to obtain the precise
peak areas for the RIR-quant analysis. This is the approach taken in Jade's Easy-Quant package. The
steps involved are outlined as follows:
You first identify the phases in the scan pattern. If they are identified from the ICDD subfile, you can
find their counterparts in the ICSD subfile using the PDF retrieval tools or the cross-reference tools in
the search/match. For phases with duplicate entries in the ICSD subfile, you should in general pick
the one most closely matching the scan pattern. Overlay the identified ICSD phases in the zoom
window and Jade will read their RIR values from the PDF database.
You then profile-fit at least one peak from each phase in the scan pattern. This peak does not have
to be the 100% peak in the phase. You should select strong and well-separated peaks to fit profiles.
You will have better statistics (i.e., smaller ESD values) in the wt% results if you use more peaks. But
you should avoid unresolved or small peaks as much as possible. This will produce a set of peak
areas to be used in the RIR-quant analysis.
You can now bring up the RIR-quant dialog from the 'Options | Easy Quantitative...' menu. Jade will
associate the fitted peaks with the PDF overlays according to the peak locations, and tabulate the
peak areas on the RIR-quant dialog. An example is shown below:

You should review the agreement between the fitted I% and the reference I(r)% (i.e., PDF I%) values in
the I%-I(r) column for each phase (see the above diagram). If a large difference occurs, you need to
understand why. It could be caused either by a poorly fitted profile on a particular peak, or by preferred
orientation of the sample, or by an inappropriate selection of the PDF phase. Since a minimum of one
peak is required to calculate the wt%, you can remove a mismatched peak from the list by unchecking it
in the master list of fitted profiles. You can also review the fitted profiles in the zoom window without
closing the RIR-quant dialog. If you edit and refit the profiles in the zoom window, Jade will
automatically update the profile listing on the RIR-quant dialog. When you are satisfied with the fitted

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profiles and all the RIR values are present, you can calculate the wt% values simply by clicking the
'Calc Wt%' button on the RIR-Quant dialog. You can now view the results in a pie or bar chart by
clicking the 'Show Graph' button as illustrated below. Notice that the 'Show Graph' button turns into the
'Hide Graph' button after you click it.

The Wt% column in the phase list shows the unnormalized wt% values (i.e., the sum of all wt%
numbers does not necessarily add to 100%), the Wt(n)% column shows the normalized wt%, and the
Vol(n)% shows the normalized volume% calculated from the wt(n)% values and the densities (in the Dx
column) of the phases. If you do not specify one of the phases as the internal standard, the wt% values
will be normalized to 100% like the wt(n)% in the calculation. The #L column shows the number of
lines/peaks used in the calculation from each phase, the I%-I(r)% shows the average difference
between fitted and reference I% values in the phase, and the {Area} & {Height} columns show the sum
of peak areas and heights for each phase. Since profile fitting uses the counting statistics to obtain the
ESD values of fitted peak areas, the ESD values of the wt% results can be derived and are shown in
parenthesis.
Using the controls located above the graph, you can choose to plot the wt(n)% and/or vol(n)% as well,
and switch the chart between pies or bars, 2D and 3D as shown below. Using the arrow buttons ,
you can alter the 3D view with regard to its 3D depth & tilt, drop shadow, and pie-labeling. Experiment
and find out for yourself!

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There are limitations with the RIR-quant analysis: (a) the wt% results are as good (or bad) as the RIR
values, (b) it requires well-separated peaks in the scan pattern and will fail if the phases overlap
severely, (c) variation of phases in crystal chemistry among your specimens and those represented by
the ICSD patterns could alter the apparent RIR values and thus the wt% outcomes, (d) the calculated
RIR values are based on the Cu wavelength and fixed-slit geometry. If you acquire data using non-Cu
radiation, you must convert it to the Cu diffraction space with the Lp correction, so that the relative peak
intensities in the scan pattern agree with those calculated in the ICSD pattern. See the Change
Radiation Wavelength topic for more information. If you acquire data with a theta-compensating
(variable) slit, you must convert it to fixed-slit data before you proceed to fit profiles and bring up the
RIR-quant dialog. See the Data Filtering topic for how to convert between fixed- and variable-slit data.
As mentioned earlier, the wt% values are normalized to 100% in the calculation. However, you can
always introduce an internal standard of known wt% in the pattern. If you do, the calculated wt% values
for the other phases will be scaled to the wt% reference of the internal standard. The Wt(n)% column
will now be the normalized wt% without the internal standard. If the sum of all the wt% values is less
than 100%, the remaining material will be labeled 'Others + Amorphous' as illustrated below:

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In this example, the anatase phase is designated as the internal standard with 15% content. If the sum
of all the wt% numbers is over 100%, it means either (a) the wt% value of the internal standard phase is
too high, or (b) the RIR value of the internal standard phase is too high, or (c) the RIR values of the
other phases are too low.
When you are satisfied with the current calculation, you can save the analysis settings into an analysis
file by clicking the Save button above the phase list. Jade will remember the phases as well as how
their peaks are fitted. When you select one of these analysis files after you have read another pattern
file of similar nature, Jade will overlay the same phases and profiles in the zoom window. If you click
the Refine button on the analysis dialog, Jade will fit the profiles in the same manner of grouping as that
employed in the original analysis. These analysis files will also appear in the macro task list for
automatic pattern processing.
The graph on the RIR-quant dialog can be customized with regard to color (foreground & background),
size, and title using the controls below the pie/bar chart. These controls are intended for you to capture
the screen or copy the graph to the clipboard. You can set the initial size of the vector graph in the
clipboard from the General tab of the Print Setup dialog. You can customize the report printout in the
following aspects: (a) font size, page orientation, and margins are on the Report tab of the User
Preferences dialog, (b) overall size of the pie/bar chart is set with the scaling control on the RIR-quant
dialog, (c) 'Print Graph', 'Print Profiles', and 'Print Lines' checks allow you to include or exclude the
graph, profile listing, and divider lines in the printout.
Preferred Orientation & Brindley (Micro Absorption) Corrections:
Among the assumptions in the RIR-quant calculations are (a) the crystallites in the specimen are
randomly oriented, and (b) the X-ray absorption by the particles of different phases in the mixture are
more or less the same. If the linear absorption coefficients (LAC) among the phases differ greatly and

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the average particle (not crystallite) size of the mixture is above one micron, X-ray absorption by the
particles of different phases could change the relative peak intensities among the phases, while the
preferred orientation of the crystallites alters the I% value of peaks from the same phase. Jade uses
the March function to correct for the orientation effect, and the Brindley absorption table to correct for
the particle absorption effect. The former requires the specification of an orientation vector in terms of
the Miller indices and the orientation coefficient that indicates how much more or less the crystallites of
a phase are oriented along the orientation vector. An orientation coefficient of 1.0 means complete
randomness, >1.0 indicates fewer crystallites are oriented along the specified orientation vector, and
<1.0 indicates more crystallites are oriented along the vetor. If you click the ? button next to the input
box of the orientation coefficient after you have selected the orientation vector, Jade will seek the
optimum coefficient that yields the smallest average I%-I(p) value for the phase. An example is shown
below:

You can enter the orientation vector from the keyboard, or select it from the peak list and click the
'HKL=' label. If necessary and justified, you can alter the I(r)% value of a PDF reflection and its Miller
indices to correct for the discrepancy. In this example, Brucite (Mg(OH)2) is strongly oriented along the
(001) direction, and Jade seeks out the optimum orientation coefficient to be 0.7, which means 30%
more Brucite crystallites are oriented along the (001) direction when compared to the randomly oriented
state.

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The Brindley correction requires only the input of an average particle size, since Jade automatically
computes the LAC (MAC is the mass absorption coefficient) of the phase from its chemical formula and
density. When the Brindley correction is applied, phases with higher LACs will have higher wt% values
because they absorb more radiation than the others.
Estimate of RIR by reference to Maximum Defined Intensity (MDI):
The quality of the ~40K calculated patterns based on ICSD structure database is generally excellent.
Nevertheless, MDI has found some of these patterns to be incorrect. Since the RIR-quant is so highly
dependent on correct RIR values, MDI developed a tool to partially overcome a situation where an RIR
value is unavailable or compromised by an incorrect pattern simulation. Details of this method are
reported by Johnson and Zhou in Advances in X-ray Analysis, vol 42. In simple terms, Jade can
estimate, with the 'Calc MDI' button on this dialog, what the maximum RIR could possibly be without
reference to the actual atomic structural arrangement but only using lattice constants, chemical formula
& formula units, and the PDF d-I list. If this number is used in the RIR-quant analysis, the wt%
calculated by Jade will place a lower bound on the amount present. But if any of the data used in the
calculation are incorrect (i.e., lattice constants, chemical formula & formula units, PDF d-I list), the
method will not be successful. Unfortunately, there are some patterns for which this is the case. It is
therefore important to understand the limitations and to check other references in critical cases.
As an alternative to the RIR estimate and calculation from crystal structures, you can measure the RIR
values of the desired phases experimentally in your own lab. You can do so by preparing a specimen
with known content of the desired phases in their pure forms. This specimen is not limited to a binary
mixture of 50-50 wt% as defined by the I/Ic in the PDF. You then acquire the scan pattern from the
specimen in experimental conditions similar to those used to acquire your routine samples. You can
now go through the same steps outlined earlier: overlay the PDF d-I lists of the phases in the specimen,
select and profile-fit the relevant peaks, and bring up the RIR-quant dialog. Instead of calculating the
wt% from known RIRs as you would normally do, you click the 'Calc RIR' button after you have entered
the wt% values for individual phases in the specimen. These calculated RIR values will be scaled to
1.0 for the first phase on the list, but you can tell Jade to scale them to another phase if you check it as
an internal standard.
The 'Internal Plot' button on the RIR-quant dialog brings up the Internal Standard Calibration Plot dialog;

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the 'External Plot' button brings up the External Standard Calibration Plot dialog; the 'Spiking Plot'
button brings up the Spiking (Standard Additions) Plot dialog. These dialogs rely on the same setup of
phases and profiles on the RIR-quant dialog to do their analyses. If you do not have the Easy-Quant
option in Jade, you can still obtain semi-quantitative wt% numbers using the Pattern Simulation from
the d-I Lists dialog.

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Internal Standard Calibration Plot

With Jade's Easy-Quant option, you can build the generalized calibration plot with an internal standard
to characterize the content of a desired phase in an unknown mixture. The steps involved are outlined
as follows:
Prepare a few samples with known weight% of the internal standard (wt%(s)) and the desired phase
(wt%(?)) added in the mixture. You could have other phases in the mixture--i.e., wt%(s) + wt%(?)
does not have to be 100%. Acquire the scan patterns of the samples in the range covering at least
one strong peak from each phase.
Read one of the scan patterns into Jade and profile-fit at least one strong peak from the standard
phase and the desired phase. You can use multiple peaks from each phase for better statistics. You
also need to fit the peaks from other phases if they overlap with those of the standard phase and the
desired phase. Overlay the PDF d-I lists of the internal standard and the desired phase.
Bring up the RIR-Quant Dialog to review the peak assignment; specify the internal standard phase by
checking the 'Internal Standard' box and enter its weight% content (wt%(s)) as illustrated below:

Click the 'Internal Plot...' button to bring up the 'Internal Standard Calibration Plot' dialog as shown
below. Each scan pattern will contribute one data point on the calibration plot of wt%(s) * I(?) / I(s) vs
wt%(?), where I(?) and I(s) are the sum of all fitted peak areas of the desired phase and the internal
standard, respectively. If the same set of peaks are used across different samples, this plot should be
linear according to the theory of powder diffraction. If the 'Y=A+B*X' box is checked, the fitted line will
not be forced to pass through the origin. Since the wt%(s) is factored into the ordinate, you can have
different wt%(s) values in different samples to build the calibration plot. In this example, however, a
constant 20% of the internal standard (i.e., Corundum phase shown in the title bar of the dialog) is
added to all the samples.

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Enter the weight% of the desired phase (wt%(?)) in this sample on this dialog. You can do so either
with the input box next to the Help button or by clicking directly in the wt%(?) column, which causes
an input box to appear. Upon receiving a valid wt%(?) value, Jade fits a statistically weighted
least-squares line through the accumulated data points in the plot. You can then save the calibration
plot with the new data point by clicking the Save button on the RIR-Quant Dialog. Although a
minimum of one data point is required to create the calibration plot, you will have better statistical
results if you use more data points in the plot. Notice that you can have multiple desired phases in a
single calibration plot with each phase having its own fitted line. In this case, you can select the
desired phase to list its data points from the phase list on the calibration dialog. You can change the
display color of a desired phase by clicking its legend in the calibration plot.
To process another sample for the calibration plot, you should close this dialog and the RIR-quant
dialog, and clear the current display by erasing the PDF overlays of the internal standard and the
desired phase. Bring up the RIR-quant dialog again after reading the new pattern, select the saved
calibration plot by its given name on the RIR-quant dialog, and you should see the PDF overlays of
the internal standard and the desired phase appear in the zoom window together with newly inserted
profiles for the same set of peaks used for the previous samples. Fit the profiles by clicking the
Refine button on the RIR-quant dialog to obtain the new peak areas. Jade will fit the profiles segment
by segment if you have used more than one segment to fit the peaks. You can now bring up the
calibration dialog again to fit the new data point when you are satisfied with the results of profile fitting.
If the wt%(?) is not given for a desired phase but there is an existing plot built from other samples,
Jade computes its wt%(?) value in the current sample if the wt%(s) is specified on the RIR-quant
dialog. This is how you use the calibration plot to analyze the unknown sample as illustrated for the
Quartz phase in this example. It should be pointed out that an interpolated data point in the calibrated
wt% range is statistically more reliable than an extrapolated one from outside the calibrated wt%
range.

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You can exclude an existing data point in the calibration plot by unchecking it in the data listing, or
delete it from the list by pressing the Delete key after it is selected. If you click the 'Dialog Layout' label
in the status bar, you can flip the calibration dialog into the following view:

You can change the partition of the plot window and data listing by dragging the border between them
up/down or left/right. You can print the calibration report with the plot using the Print button on the
dialog. If you hold down the Ctrl key with the Print button, Jade will include the scan pattern with the
fitted profiles in the report printout. You can copy or export the plot or the data listing to the clipboard or
a plain text file (*.int) by left/right-clicking the Copy or the Export button. You can later browse an *.int
file from the 'View | Reports & Files | Browse Report File...' menu.

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External Standard Calibration Plot

With Jade's Easy-Quant option, you can build the generalized calibration plot with an external standard
to characterize the content of a desired phase in an unknown mixture. The steps involved are outlined
as follows:
Prepare a few samples with known content of the desired phase added in the mixture, which should
be similar to the real unknown samples with regard to all the substances in it. This known content
does not have to be in weight% (the default unit). It could be any desired measurement of the phase
content as long as it is a positive number. On the external calibration dialog to be described below,
you can enter the desired label for the x-axis of the calibration plot. Acquire the scan patterns of the
samples in the range covering at least one strong peak from the desired phase.
Read one of the scan patterns into Jade and profile-fit at least one strong peak from the desired
phase. You can use multiple peaks from the desired phase for better statistics. You also need to fit
the peaks from other phases if they overlap with peaks of the desired phase. Overlay the PDF d-I list
of the desired phase.
Bring up the RIR-Quant Dialog to review the peak assignment as illustrated below:


Click the 'External Plot...' button to bring up the 'External Standard Calibration Plot' dialog as shown
below. Each scan pattern will contribute one data point on the calibration plot of the fitted peak areas
vs the phase content. If the same peak(s) is used across different samples, this plot should be very
close to a straight line within a narrow range of the phase content as illustrated below. With wider
range of the phase content, the data points should be fitted with a parabolic curve.

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
Enter the content value of the desired phase in this sample on this dialog. You can do so either with
the input box next to the Help button or by clicking directly in the X(i) column, which causes an input
box to appear. Upon receiving a positive number for the phase content, Jade fits a statistically
weighted least-squares line or parabolic curve through the accumulated data points in the plot. If the
phase content is not in weight%, you can enter the desired content label for the x-axis to the input box
shown in the above dialog. You can then save the calibration plot with the new data point by clicking
the Save button on the RIR-Quant Dialog. Although a minimum of one data point is required to create
the calibration plot, you will have better statistical results if you have more data points in the plot.
Notice that you can have multiple desired phases in a single calibration plot with each phase having
its own fitted line or parabolic curve. In this case, you can select the desired phase to list its data
points from the phase list on the calibration dialog. You can change the display color of a desired
phase by clicking its legend in the calibration plot.
To process another sample for the calibration plot, you should close this dialog and the RIR-quant
dialog, and clear the current display by erasing the PDF overlay of the desired phase. Bring up the
RIR-quant dialog again after reading the new pattern, select the saved calibration plot by its given
name on the RIR-quant dialog, and you should see the PDF overlay of the desired phase appear in
the zoom window together with newly inserted profile(s) for the same peak(s) used for the previous
samples. Fit the profile(s) by clicking the Refine button on the RIR-quant dialog to obtain the new
peak area(s). Jade will fit the profiles segment by segment if you have used more than one segment
to fit the peaks. You can now bring up the calibration dialog again to fit the new data point when you
are satisfied with the results of profile fitting.
If the content is not given for a desired phase but there is an existing plot built from other samples,
Jade computes its content value in the current sample automatically. This is how you use the
calibration plot to analyze the unknown sample as illustrated for the Quartz phase in this example. It

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should be pointed out that an interpolated data point in the calibrated content range is statistically
more reliable than an extrapolated one from outside the calibrated content range.
You can exclude an existing data point in the calibration plot by unchecking it in the data listing, or
delete it from the list by pressing the Delete key after it is selected. If you click the 'Dialog Layout' label
in the status bar, you can flip the calibration dialog into the following view:

You can change the partition of the plot window and data listing by dragging the border between them
up/down or left/right. You can print the calibration report with the plot using the Print button on the
dialog. If you hold down the Ctrl key with the Print button, Jade will include the scan pattern with the
fitted profiles in the report printout. You can copy or export the plot or the data listing to the clipboard or
a plain text file (*.ext) by left/right-clicking the Copy or the Export button. You can later browse an *.ext
file from the 'View | Reports & Files | Browse Report File...' menu.

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Spiking (Standard Additions) Plot

With Jade's Easy-Quant option, you can characterize the content of a desired phase in a mixture in
which the component phases are known but their proportions are unknown, using the spiking method
(also known as the method of standard additions). The steps involved are outlined as follows:
Prepare a few samples by adding a different weight% of the desired phase (wt%(s)) in pure form to
the unknown mixture. This desired phase is also called the spiking phase for the obvious reason and
will be referred to as 'phase(s)' in the following diagrams. Acquire the scan patterns of the spiked
samples and the original (unspiked) sample in the range covering at least one strong peak from the
spiking phase and a 2nd phase in the mixture. This 2nd phase serves as a reference to measure the
change of peak intensity of the spiking phase. You should therefore select a 2nd phase that has
minimum overlapping of its strong peaks with those of the spiking phase. If the amount of spiking
wt%(s) as well as the original wt% is very small, you may perform the spiking analysis without the 2nd
phase for intensity reference.
Read the scan pattern of the unspiked sample into Jade and profile-fit at least one strong peak from
the spiking phase and the 2nd phase respectively. You can use multiple peaks from each phase for
better statistics. You also need to fit the peaks from other phases if they overlap with those of the
spiking phase and the designated 2nd phase if any. Overlay the PDF d-I lists of the spiking phase
and the designated 2nd phase if any.
Bring up the RIR-Quant Dialog to review the peak assignment; specify the spiking phase by checking
the 'Internal Standard' box as illustrated below:


Click the 'Spiking Plot...' button to bring up the 'Spiking (Standard Additions) Plot' dialog as shown
below. Designate the 2nd phase (Calcite in this example) by selecting it from the phase list on this
dialog if there are more PDF overlays in the zoom window. Each scan pattern will contribute one data
point on the spiking plot of I(s) / I(?) vs wt%(s), where I(s) and I(?) are the sum of all fitted peak areas
of the spiking phase and the designated 2nd phase respectively, and wt%(s) is the extra weight% of
the desired phase (i.e., the amount of spiking) in the sample and thus its value must be zero for the
unspiked sample. Jade sets the I(?) to 1 if there is no 2nd phase designated for intensity reference. If
the same set of peaks are used from samples with different amounts of spiking, this plot should be
linear according to the theory of powder diffraction, and the negative intercept of the fitted line at the
x-axis is the weight% of the spiking phase in the unspiked sample (i.e., the original unknown mixture)

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as illustrated below:


Enter the weight% of the spiking phase (wt%(s)) in this sample on this dialog. You can do so either
with the input box next to the Help button or by clicking directly in the wt%(s) column, which causes an
input box to appear. Upon receiving a valid wt%(s) value, Jade fits a statistically weighted
least-squares line through the accumulated data points in the plot. You can then save the spiking plot
with the new data point by clicking the Save button on the RIR-Quant Dialog. Although a minimum of
one data point from the spiked sample is required to create the spiking plot, you will have better
statistical results if you have more data points in the plot.
To process another sample for the spiking plot, you should close this dialog and the RIR-quant dialog,
and clear the current display by erasing all the PDF overlays. Bring up the RIR-quant dialog again
after reading the new pattern, select the saved spiking plot by its given name on the RIR-quant dialog,
and you should see the PDF overlays of the spiking phase and the designated 2nd phase (if any)
appear in the zoom window together with newly inserted profiles for the same set of peaks used for
the previous samples. Fit the profiles by clicking the Refine button on the RIR-quant dialog to obtain
the new peak areas. Jade will fit the profiles segment by segment if you have used more than one
segment to fit the peaks. You can now bring up the spiking dialog again to fit the new data point when
you are satisfied with the results of profile fitting. Jade will calculate and show the weight% of the
spiking phase in the unspiked sample automatically when there is at least one data point from the
spiked sample in the plot.
You can exclude an existing data point in the spiking plot by unchecking it in the data listing, or delete it
from the list by pressing the Delete key after it is selected. If you click the 'Dialog Layout' label in the
status bar, you can flip the spiking dialog into the following view:

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You can change the partition of the plot window and data listing by dragging the border between them
up/down or left/right. You can print the spiking report with the plot using the Print button on the dialog.
If you hold down the Ctrl key with the Print button, Jade will include the scan pattern with the fitted
profiles in the report printout. You can copy or export the plot or the data listing to the clipboard or a
plain text file (*.spk) by left/right-clicking the Copy or the Export button. You can later browse an *.spk
file from the 'View | Reports & Files | Browse Report File...' menu.

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Interface to MDI's DataScan

DataScan for Windows is MDI's automated control and data acquisition system for X-ray
diffractometers. It currently can run diffractometers interfaced with the following types and/or series of
controllers, with or without sample changers:
MDI Databox.
Rigaku D/MAX-B and Miniflex.
Scintag PAD-V & PAD-X.
Philips 1710 & 1800 series.
Siemens/Bruker Daco-MP, D5000, and D5005 series.
Random Technology DFC.
DataScan was designed to run in time-share mode under the Windows OS. It can control multiple
diffractometers of the same or different types through multiple COM ports at the same time on a single
PC. It can also multi-task with data analysis programs such as Jade. Partially acquired data can be
saved to the hard disk periodically and processed by Jade while the scan is in process.
You can establish the dynamic data exchange (DDE) link to DataScan from the 'Options | Link to
DataScan' menu. If DataScan is not running at the time you try the link, Jade will start DataScan only if
it's installed in the same parent folder of Jade. Once linked, Jade will automatically read and display a
new pattern file created by DataScan, and will even process it with a designated task macro. This
automation is particularly useful for data collection with a sample changer, making it possible to do
batch processing of similar samples without user intervention. Refer to DataScan's manual or its
on-line help for how to use the DDE link. Please feel free to contact MDI if you wish to learn more
about the DataScan program and/or are interested in automating your existing diffractometers using
MDI technology.

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Jade 5.0

Jade Program Limitations

The current dimensional limits of data handling in Jade are:
Maximum number of characters in a file name = 64
Maximum number of data points per scan range = 32001
Maximum number of hits from PDF retrieval = 32000
Maximum number of d-I lines in pattern simulation = 2000
Maximum number of PDF overlays = 500
Maximum number of d-I lines per PDF overlay = 200
Maximum number of scan overlays = 500
Maximum number of peaks to list = 500
Maximum number of painted peaks = 200
Maximum number of sampled background tie points = 180
Maximum number of fitted profiles to list = 200
Maximum number of profile variables to refine at a time = 200
Maximum number of S/M hits to list = 500
Maximum number of phases in one S/M userfile = 1000
Maximum number of explicitly excluded phases in S/M = 1000
Maximum number of frequent S/M hits to remember = 1000
Maximum number of phases for RIR-quant analysis = 16
Contact MDI if your requirements exceed these limits.

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Jade 5.0

Jade's Registry Entries

While Jade keeps most program settings under the user/project id folder, a number of obscure program
settings are written to and read from the system registry under the
'HKEY_CURRENT_USER\SOFTWARE\MDI\JADE5' key. The 'Data' entries maintain the number of
pattern files which have been read and processed by the current log-on user since Jade was first
installed on your PC. The 'User' entries maintain the following options:
AutoFind: number of subfolder levels for Jade's recursive search of files on your computer.
Average: whether (1) or not (0) to reuse data points in the averaging of intensities when you resample
pattern in larger step sizes under the 'Filters' menu. For example if you change the step size of a scan
from 0.01 to 0.02 degree, a value of 0 means that Jade will average every two adjacent data points to
produce the 0.02 step scan, and a value of 1 means that Jade will average every three adjacent data
points with the every 3rd data points reused in the averaging.
Last: the last user or project ID used to run Jade if you have created more than one id.
MsgBox: number of seconds before Jade automatically closes the message box when you leave it
alone. If less than 3 seconds, the message box is displayed indefinitely until you close it.
Show: whether (1) or not (0) to display the 'User or Project ID' selection dialog on start-up of Jade.

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Jade 5.0

Troubleshooting Tips
Jade for Windows is a robust but complex program. Much effort has been taken in its design, testing,
and refinement over many years. However, no software program is totally immune to problems. Error
conditions could arise from (a) malfunctions of hardware or the operating system, (b) changes of system
environment such as network disconnection and file relocation, (c) I/O problems due to insufficient
computer resources or erroneous data and parameter settings. The recovery tips recommended below
are for solving problems due to error conditions (b) and (c) in running Jade:
If you have problems in printing, first make sure they are not unique to Jade by test-printing from
other Windows applications. If they are unique to Jade, perform a reset of all print settings from
Jade's print setup dialog. Should the problems persist, exit and restart Windows.
If you have problems in pattern analysis, perform a reset of all analysis parameters from the 'Help |
Reset All...' menu. Should the problems persist, reinitialize Jade from the 'Help | Initialize Jade...'
menu. This will restore Jade to the as-installed state by deleting all setting files associated with the
current user or project id.
If you can't start Jade in Windows, restart Windows or reboot your computer. If you still can't start
Jade, delete all setting files that are specific to the current user or project id from its folder under
Jade's program folder. These files have names like 'your name.ini', 'your name.dat', etc. Should the
problem persist, Jade's dependent DLL files may be corrupted or overwritten by other applications. In
this case you need to reinstall Jade (make sure that you first remove Jade using Windows
'Add/Remove Programs' utility).
If you experience intermittent failure of MDI license key recognition, check to make sure that the key
is firmly connected to the printer or the USB port. Some older printer drivers are known to interfere
with the key when bidirectional printing is enabled.
Contact MDI for help if all else fails. Jade also writes an error log file 'jade5.err' in its program folder for
trappable run-time exceptions. You can browse this file from the 'Help | Browse Error Log...' menu. It
will be very helpful for the tech-support if you can fax or e-mail the file to MDI.

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