***** Documentation for

For context sensitive help, press F1 key from the active dialog window in Jade. You can capture an active dialog to the PIP zoom by pressing Ctrl+Shift+I keys. You can capture an active dialog to an image file by pressing Ctrl+Shift+O keys. You can print an active dialog window in Jade by pressing Ctrl+Shift+P keys.

Installing Jade 9
Jade 9 is a 32-bit Windows application that runs on Microsoft Windows OS environments. We recommend a 400 MHz or faster Win-XP PC with minimum 512 MB memory and a 17 inch or larger monitor. A display desktop of 1024x768 pixels or more with true 32-bit colors is also recommended to run Jade. You can run Jade on less capable systems but you will compromise performance. For example, on a smaller screen, there is the disadvantage of not seeing the full layout of its main windows. Minimum hard disk space to install Jade is around 20 MB. If you have access to ICDD PDF, FIZ ICSD, and/or NIST Crystal database, more hard disk space is required to create and store the index files after Jade is installed. Installing the Local Hardware License Key: Among the materials supplied with this program is a hardware license key that activates MDI programs on your PC when it is installed properly. This hardware device is provided by MDI in either one of the following types: A small 25-pin adapter in beige color, which has the label 'MDI-R#####' on it. It must be installed on the parallel printer port between the computer and the printer cable before you can install and run Jade. You should turn off your computer and printer for this operation. If you have other Non-MDI keys already installed, this key can be connected as the last in the chain although you may need to experiment with the placement if the key is not recognized by Jade. This hardware key will not affect the printer port in any way and is transparent to your printing operations. A small USB (Universal Serial Bus) token in purple or black, which has the label 'MDI-U#####' on it. You should not plug this key into the USB port before you run the installation program 'setup.exe' to be described later. Installing Jade 9: Before you install Jade, you should close all running applications if possible. On Win-XP/2000/Vista, you must log on to the administrator account to install Jade 9. Note: this installation will not interfere with earlier versions of Jade. You do not need to remove them in order to install Jade 9 on the same computer, and you can run them together with Jade 9 if desired. If you have previously installed Jade 9 on the same computer, the installer will automatically uninstall it before proceeding with a new installation. Insert the Jade 9 CD into the CD-ROM drive and wait for the installing program to start. If it does not start, you can start it by running the 'setup.exe' in the root folder of the CD. After a brief display of an initialization screen, the following dialog should appear:

If you accept the stated MDI license agreement, the following dialog will appear:

Please fill in the 'User ID' and the 'Institution ID'. The former should be the program licensee and the latter will be used by Jade on all printouts and reports. You can later change both IDs from the system registry and the institution ID on user preferences dialog without reinstalling Jade. Click the 'Install' button to begin the installation process. The installer will first install the Sentinel license key driver, which enables Jade 9 to access the MDI license key. If you have multiple copies of Jade 9 with different license key numbers, make sure that the key number being installed matches that shown on the title bar of the above dialog. You may have to restart the computer in order to load the new license key driver, and the installation will resume if an automatic reboot is initiated by the installer. If you have the USB key described earlier, you can plug it into the USB port when the following message appears and then click the 'Retry' button:

Windows will detect the new USB key and configure it automatically. If the license key is still not recognized by the installer, reboot your computer and start the installation again. Should you encounter any warning messages regarding file copying failure, you can ignore them only if all non-system applications have been shut down before you start the Jade installation. Please call MDI for help if you are not sure what to do. If you check the 'Register Non-MDI Pattern File Types' box, files with the extensions of *.RAW, *.RD, *.SD, *.PD3, and *.CIF will be associated with the 'MDI-Jade', and be opened by Jade 9 when you browse them in the Explorer. Creating a Shortcut Icon on Your Desktop to Run Jade: Although you can start Jade from the 'Start | Programs | MDI Jade 9' menu, it's easier to do so from a Jade shortcut icon on your desktop. If the 'Create a Shortcut to Jade on Desktop' is checked, an 'MDI Jade 9' icon will be placed on your desktop as well as in Windows 'Programs' folder at the end of installation. You can also create such a shortcut by locating the 'Jade9.exe' file with the Explorer under the default folder of 'C:\Program Files\MDI Jade 9', then dragging it from the file list and dropping it to the desktop. The additional advantage with a Jade icon on the desktop is its ability to accept XRD pattern files you may drag & drop on it from other applications (such as the Explorer or the File Finder). See drag & drop data files for more information. You may also create more Jade icons to run Jade in 'stealth mode' with the help of task

macros. See auto processing with task macros for more information. Uninstalling Jade 9: If you need to remove Jade from your PC, you should do so using the 'Add / Remove Programs' utility from the Control Panel, rather than using the Explorer directly to delete Jade's program folder. The uninstaller will not remove the Jade 9 folder from your hard drive since there will be program setting files created after the installation. You can delete the Jade 9 folder altogether from the Explorer yourself if you do not place raw pattern files as well as report files created by Jade in this folder. Installation of Jade 9 under Microsoft Windows Network: If you have a network version of Jade, which enables concurrent access of limited Jade licenses over a network by a greater number of users, you should follow the steps outlined below to install it: Attach the network hardware license key to the printer or USB port of a server PC on the local network. This installation only supports Microsoft Windows local area network with TCP/IP or IPX/SPX network protocols. This PC is the one that will run the Sentinel license server program but not necessarily the Jade program. We recommend a Win-XP/Vista PC to service the MDI license key. This server PC should be located on the same subnet as the clients who will be running Jade 9. Insert the Jade 9 CD and wait for the installer to start. If the 'Key-Server' option is selected on the following dialog, the installer will install the Sentinel license key server as well as the license key driver on this server PC with the MDI license key attached.

With the license server running on the server PC, you can now take the Jade 9 CD and install it on any PC on the same network if the 'NetClient' option is selected on the following dialog. The installer will contact the MDI license server over the local network to obtain the license for this installation. To speed up license access and allocation, you should provide the computer name or IP address of the license server on the installation dialog. If you do, this server name or IP address will be saved in the system registry as 'hkey_local_machine\software\mdi\license\server' . If you later move the license server to another PC, make sure your client's registry is updated accordingly. If you have a large local network, you may have to specify the IP address in order for Jade to find the server before the search is timed out.

If you have difficulty obtaining a license from the server with the correct IP address (error #60), it is most likely blocked by the system Firewall. You should therefore bring up the Firewall program and make sure that 'Sentinel Protection Server' is placed and checked in the exception list of programs. Please note that Jade cannot be installed on a server PC to be run from another PC on the network. In other words, Jade and its dependent files must reside and be registered on individual PC, but Jade can seek out the license key across the network and allocate the license as long as the license server program is running on the network. Nevertheless, you can copy the entire content of the Jade 9 CD to a shared folder so that it can be installed from another PC across the network. Normally an allocated license is released when Jade is closed down. To make a good use of the limited licenses, the license server will terminate an allocated license if Jade is left to idle for more than 15 minutes or crashes. If you re-activate Jade after its license has been revoked (such as by moving the mouse), Jade will try to obtain a new license from the server if a free license is still available. You can monitor

the usage of Jade licenses by entering the IP address of the server PC to the Internet Explore address with port #6002 (e.g. http://192.168.1.110:6002), which is used by the server to broadcast its messages. Tip: rebooting the server clears all allocated licenses. Please contact MDI if you would like to know more about network licensing of Jade.

Licensed Options in Jade 9

Various optional functions (plug-in's) are available for Jade 9 at extra cost, as described below. If certain features are not accessible on your version, this may explain why. Features in Option 'Jade Plus': cell refinement; pattern indexing; d-spacing and Miller indices generator; lattice constant calculator; cell data graphing; crystallite size & strain analysis; residual stress analysis; sort-on-similarity (for customers who do not have the search/match option); 'Deja vu' identification from your own pattern archive; Userfile S/M using line-based method; and 'XRD Simulation' which calculates XRD powder patterns from crystal structures and comes with a feature-rich 3D structure viewer and structure database manager to access FIZ icsd database. Features in Option 'Easy Quant': Profile-based RIR analysis with counting statistics; Brindley particle-absorption and preferred orientation corrections; Amorphous content determination with internal standards; 2/3-D pie & bar charts and presentation reports; Generalized internal standard calibration plot; Generalized external calibration curve; Spiking calibration plot; Procedure file creation and application. Features in Option 'Search/Match' (the 'Identify' menu): Whole pattern phase identification with major, minor, trace, and residual phase S/M; Solid solution and preferred orientation S/M; S/M filters such as PDF subfiles, chemistry and crystallography; Factor analysis of S/M hits with isotypical pattern finder and suppression; ICSD-aware filters with ICDD cross reference (for PDF release of 1998 and later). Features in Option 'WPF Refinement': Whole Pattern Fitting and Rietveld Refinement with structure and/or structureless phase data; All new code, designed with advanced optimization algorithms and totally integrated into Jade with interactive dialogs and graphical displays; Automated refinement setup for precise lattice constant determination; Quantitative analysis with/out internal standard and amorphous content; Structure refinement with intelligent constraints on atomic coordinates; Extensive output with presentation printouts and reports; This option also includes the 'XRD Simulation' features described in the 'Jade Plus' option. Features in Option 'Cluster Analysis': Cluster analysis of raw data patterns to classify similar patterns such as polymorphs and amorphous phases using correlation coefficients and similarity indices calculated both from whole pattern and peak search. Efficient algorithms can process and classify 1000 patterns under ten minutes with results easily viewable in the main zoom window. Similar clustering tools can also be used to classify PDF phases and userfiles of d-I lists for similar or isotypical entries in the databases. Please contact MDI if you need more information regarding the above options.

A Simple Example of Processing an XRD Pattern

In the following example, you will read a demo pattern file into Jade, fit its background and strip K2, find peaks and produce a peak listing report, and, if you have access to ICDD PDF database, overlay a PDF reference pattern and print the PDF card. If you are a new user of Jade, you may find the following exercise helpful in learning the Jade interface and some of its basic functions. Double-click the Jade icon on your desktop to start Jade. Refer to Installing Jade topic if you don't see the icon on your desktop. After a brief display of Jade's splash screen, the main window of Jade should appear. Select the 'File | Patterns...' menu, and the following dialog window should appear, for example:

Jade will automatically list the installed demofile files on the above dialog when initialized. You can find these files in the demofile folder under Jade's program folder if you see a different file list on the above dialog. Double-click the 'demo06.mdi' file and an XRD pattern should appear in the upper 'pattern window' as well as the larger 'zoom window' below. You can now examine this pattern using Jade's zoom & pan tools. For example, suppose you want to select a portion of the pattern in the top window to zoom. You can move the mouse pointer into the top window and, while holding down on the left mouse button, drag the mouse pointer to a new location. A 'rubberband' box will appear, showing the region that will be zoomed and moved into the bottom window when the mouse button is released. Experiment with this simple operation several times. Notice that Jade ties the rubberband box to the bottom of windows so you don't have to start out from the very bottom in dragging, and you can do rubberband zooms in the bottom window as well. By the right lower side of the zoom window are 10 icons arranged vertically. These are the zoom & pan buttons. When you place the mouse pointer over one of them, a yellow text label (called a tooltip) will appear describing briefly what the button will do. 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, and you can speed up or slow down the scrolling by holding down the Ctrl or Shift with these buttons. Jade will beep when you reach the limits of zoom & pan. You are encouraged to experiment with these buttons. If you have a mouse with a scroll wheel between the buttons, you can pan the display in the zoom window by scrolling the mouse wheel. You can also zoom and pan by dragging in the zoom window with the right mouse button. Let's now strip K2 and find the K1 peaks. In order to strip K2, we need to fit the pattern with a background curve. Select the 'Analyze | Fit Background...' menu and the following dialog window will appear:

Click the button and you should see a background curve already fitted through a number of background tie points (BG dots) which have been sampled automatically. You can examine how well the BG dots have been sampled using the zoom & pan tools described earlier. In the above figure, the region from about 30 to 52 degrees of the pattern is zoomed in to show more details. If you are not satisfied with the placement of these BG dots, you can move & erase existing ones or insert new ones manually with the mouse. This can be done by selecting the background editing cursor (i.e., depressing the 'B.E.' button) on edit & cursor toolbar. Notice that a short help label appears automatically in the upper-left corner of zoom window to give you some tips on how to edit the BG dots, and you don't have to close the BG fitting dialog in order to click the editing toolbar. The mouse pointer should now turn into a small crosshair when you move it into the zoom window. You can then click any one of these dots and drag it up or down or left or right. Notice that Jade 'lights up' the dot when the cursor is near it and refits the BG curve as you drag it. You can insert a new BG dot simply by clicking the left mouse button at a desired spot, and erase it by clicking it with the right mouse button. The very first & last BG dots can be moved vertically but not erased. When you are satisfied with the fitted BG curve, click the button on the above dialog, and the K2 components will be stripped from the demo pattern. It should be pointed out that the pattern is altered only from a copy of data in the memory. Jade does not save the altered pattern back to the original file under any circumstance, and it will simply be discarded when you close Jade. But you can always save the modified data into a new pattern file in Jade if desired. Now select the 'Analyze | Find Peaks...' menu, and the following dialog will appear:

Click the button and an automatic peak search will be carried out on the K2 stripped pattern. The located peaks will be listed at the bottom of this dialog, and marked with dotted vertical lines in both windows. Like the BG fitting, you can examine the results of peak search with the zoom & pan tools, and edit the located peaks manually using the peak editing cursor from the cursor toolbar (see the above figure). To move a peak marker, click it and drag it to the left or right. To mark a new peak, click under its apex. Jade will determine the peak background, locate the precise peak top, and compute the peak area. To mark a peak exactly where you want rather than where Jade decides it should be, hold down the Ctrl key while you click the mouse button. To erase a peak marker, click it with the right mouse button. Notice that (1) you can do all the above without closing the peak search dialog, and (2) there are no OK and Cancel buttons to dismiss it. The behavior of this kind of dialog in Jade is called a 'modeless' operation, as indicated by the thumbtack icon on the title bar of the dialog window. The word 'modeless' means that the program is not constrained into a particular mode of operation from which it needs to be released. With experience you should find features such as this in the Jade interface extremely flexible in helping you accomplish more things quickly. See Jade's dialog windows for more information. If you click the button on the peak search dialog, you can display the desired labels or markings on the located peaks in the zoom window:

Notice that when you select a peak on the peak list, Jade displays a short vertical blinker in the zoom window along the baseline of the plot indicating where it comes from. If the selected peak is outside the current zoom window, Jade will pan the window to bring it into view. You can resize this dialog in height to see a longer or shorter list. You can customize the peak listing if you click the button on the report dialog before you print and save the report. You can send the list to clipboard with the button, and paste it into a spreadsheet program such as Excel. You can export the listing to a plain text file for data archival or e-mail to colleagues. You can also print the image of marked peaks in the zoom window by selecting the 'File | Print | Zoom Window Image' menu. Accessing PDF Database and Overlaying a PDF Reference Pattern: This demo pattern consists of three phases: hematite, rutile, and anatase. If you have access to an ICDD PDF database, you can overlay their PDF d-I line list as a set of colored vertical line markers in Jade. These markers appear on the 2 axis at points where XRD peaks are expected to occur and with heights corresponding to the expected peak intensities. This can be accomplished simply by entering the mineral name 'Rutile' for example into the PDF recall box on the main toolbar:

If this is the first time you have done so, the following message & prompt should appear:

If you choose Yes, the following dialog will appear, for example:

This dialog will allow you to create the PDF index files which are classified into a number of PDF subfiles and are required by Jade to access the PDF database in a fast and efficient manner. You can click on the first button to let Jade find the PDF database files on your system, or click on the button to find it yourself if it's located on the network. If you have multiple PDF databases from different years, make sure that you select the latest release from the drop-down list. If you have the subscription-based relational database (RDB) of PDF-2/4, Jade will select and create all available PDF subfiles as shown above with the 'RDB' prefix, and you will not be allowed to unselect any of them. However, if you have the old flat-file PDF-2 database, a longer list of PDF subfiles will be accessible on this dialog for you to select, and you should always select the mineral subfile as one of your choices since it enables you to retrieve common mineral phases by their names. MDI recommends creating index files for Inorganics, Minerals, Organics, and ICSD patterns from your PDF database, and all other subfiles are mostly subsets of the Inorganics. If you have created the index files previously, they will be indicated by their creation dates shown to the right of the subfile name. If you click the button after you have checked the desired subfiles, Jade will start the PDF indexing and allow you to continue exploring other parts of Jade's interface in a time-share mode. The indexing process will take some time to complete, depending upon the speed of your PC and the number of PDF subfiles you choose to create. Once the desired PDF subfiles have been created, you can enter the name 'rutile' again on the main toolbar and see the colored sticks of Rutile's d-I list overlaid in the zoom window, and the PDF overlay toolbar should appear on the main window. You can label the d-I lines in a number of different ways either using the quick annotation toolbar located at the bottom right corner of the main window or from the following PDF overlay list dialog which can be viewed by clicking the button on the PDF overlay toolbar:

If you click the

button on the overlay toolbar, a dialog window showing the PDF data (like the classic JCPDS card) will appear:

You can print this view with the printer button on the same dialog. You can also recall a PDF card by its PDF number and retrieve a group of them by their chemistry information, etc. See PDF access & retrieval for more information. We hope this exercise gives you a taste of Jade's powerful user interface. So far you have seen only 'the tip of the iceberg' with regard to what Jade can do for you. Explore and discover for yourself. You can learn a great deal about Jade by reading the tooltips that appear when you leave the mouse pointer over a screen object such as a tool button. Other parts of this on-line help and the manual will have more comprehensive documentation of the Jade interface and its functions. If you have any difficulty, don't hesitate to contact MDI for technical support. E-mail messages with file attachment are preferred and quickly handled by MDI tech-support sometimes even during non-business hours. Direct the messages to mdi@materialsdata.com. Tip: you can bring up your e-mail program by clicking the e-mail address on Jade's splash screen. If necessary, we can be reached by phone at (925)449-1084 during the business hours of 9 am to 5 pm Pacific time or fax at (925)373-1659. When phoning, please be sure to be at your computer and have the serial number of your license key available to assist us in identifying the same version of Jade that tech-support personnel should use.

Features Introduced in Jade 5

The following summary of new and improved features in Jade 5 will be useful to previous Jade 2/3/4 users, although this is by no means a complete list. 32-bit Windows architecture with supports for long file names and direct access of network drives, folders & files. Support of multiple user and project environments with automatic 'log-on' user identification on Win95/98/NT. Support of multiple monitors with Win98. You can place a dialog window on another monitor by pressing the Alt+arrow-keys. Note: This requires multiple video boards in the PC. Support of ICDD release '98 PDF2 CD with ICSD(FIZ) subfiles and ICDD/ICSD cross-reference. Intelligent filters for duplicate and similar phases are available in search/match. New PDF retrievals using data such as chemical groups, Pearson symbols, subfiles in subfiles, and ICSD numbers. A new option (plug-in) is available for profile-based RIR Quantitative Analysis with counting statistics and presentation reports. You can also

build internal & external standard calibration plots, and perform spiking (standard additions) analyses. Automatic peak painting and integration with least-squares fitted baseline. Quick Annotation Toolbar for labeling peaks and reflection markers. You can easily offset and scale overlays of scan patterns and PDF d-I lists in the zoom window by point and drag. Improved peak search algorithm with 4th-order polynomial and longer filters. You can now customize the columns of peak search report. You can use colors for different phases in the peak id reports. You can also choose different font sizes, print orientation, and margins for most report printouts. Improved search/match algorithm and display with new features such as S/M on the residual peaks, similar pattern finder and suppression, dynamic pattern simulation of positive hits with profiles, and automatic tracking of frequent hits. You can now search your own archive of pattern files for similar patterns (Deja vu S/M) with automatic thumbnails. Improved profile fitting with automatic refinement of all peaks and crystallinity estimates. Crystallite size and strain analysis can be performed from peak broadening with profile fitting and counting statistics. A new option (plug-in) is available for performing surface residual stress analysis from peak shifts in the -scans using automatic profile fitting. High resolution vector images (plots) can be exported via the clipboard and Windows metafiles. The goniometer radius can be specified so Jade can compute and report sample displacement value in millimeters rather than in 2 degrees. Peak intensities can be corrected for detector dead-time. Lattice constants can be calculated from a few located peaks with known Miller indices. You can also include an internal standard peak to calibrate the peak positions in the lattice calculator. It is possible to do a cell refinement using the PDF line list rather than all possible reflections generated from the initial cell. Jade will now compute the Smith-Snyder figure-of-merit for a refined cell. You can plot and least-squares fit unit cell data produced from cell refinement using the built-in cell data graphing dialog. Pattern indexing using a specific space group and constraints of Miller indices is supported. You can also look up similar PDF cells from the indexing dialog. d-I lists can be imported directly from d-I listing files created by other XRD applications. You can drag and drop XRD pattern files and Jade's output files from the Explorer or the File Finder. Jade can now auto-detect pattern file types from different XRD hardware vendors. A new file copying dialog makes it easy to archive analysis files to removable media and/or across the LAN, and for casual users (such as students) to process their data and walk away with results. New status-bar functions for easy recalls of saved work and analysis report files. New dialog view of thumbnail browsing with notepads for easier review and editing of notes. Improved Ascii file import dialog--you can easily point and click to set up an Ascii import filter. Improved generic file browser for binary files with hex view and character substitution. Improved data filtering functions such as spike removal and pattern smoothing with longer filters. Completely redesigned task macro interface with extensive list of macro tasks. You can now create specific analysis setting files for certain tasks and assemble them into a task macro. Among the new macro capabilities are, for example, (a) automate cell refinement of multiple patterns, (b) run Jade in stealth mode for QA and production environments. You can now tell Jade to write detailed processing logs for record keeping and QA purposes. HTML help browsing as well as context sensitive on-line help.

Features Introduced in Jade 6

The following summary of new and improved features in Jade 6 will be useful to previous Jade 5 users although this is by no means a complete list. If you are a Jade 2/3/4 user, refer to What's New in Jade 5 for more new features. You can now calculate (simulate) XRD powder patterns from crystal structures. This is an optional feature (See the licensed options for more information), which is totally integrated into Jade's interface and supports direct-access to FIZ ICSD structure database (ICSD stands for Inorganic Crystal Structure Database). You can perform whole pattern fitting and Rietveld refinement with structure and/or structureless phase data. This is an optional feature (See the licensed options for more information), which is all new code, designed with advanced optimization algorithms and is also totally integrated into Jade's interface. You can now search your own archive of pattern files to find those containing a specific sample or scan id. Look for the 'Find...' button on the read pattern files dialog on how to use this feature. An alternative view of Explorer-Like folder tree listing is also implemented on this dialog for easier access to shared folders on the local area network. You can tell Jade to automatically overlay its related pattern files when a particular pattern file is read. This feature may be handy for those who analyze clay samples. See auto-overlay of related pattern files for more information. Some new pattern file types are added to the list of readable pattern files on read pattern files dialog. This includes a generic x-y column file type to read simple x-y column pattern data. Improvements have been made to existing pattern file readers. You can now show scan parameters in addition to the scan/sample id in the listing of all supported pattern files. New industrial-standard XML support for data input and output, which is a great option for (a) data exchange and archive, (b) generating compound reports and web documents, (c) interfacing to your laboratory information management system (LIMS). New Xplorer utility for browsing all XRD-related and Jade-Created files on your computer and local area network. This utility can also be used to view common image files or load XRD pattern files into Jade for processing. New and improved multi-user support on Win-NT/2000/XP (NTFS) with different access controls for power and casual users. New background fitting function to handle amorphous background removal. You can now strip peaks above the background curve if desired. See background fitting dialog for more. New peak search for pattern overlays and peak comparison report of all pattern overlays. See peak search dialog for more. You can now compare observed patterns by tabulating peak listings from multiple pattern overlays. You can now include plot of pattern traces on most report printouts (see the user preferences dialog for the option). You can now perform triclinic indexing to obtain unit cell data to an unknown pattern. You can also save the indexing results and restore them at a later time without the need of time-consuming re-indexing. You can also start the WPF refinement of an indexed cell from the indexing dialog or from the cell refinement dialog. New tetragonal and hexagonal lattice cursors, new multi-orders cursor for examining layer structures, and improved cubic indexing cursors. See Bravais lattice cursors for more information. d-Scales can now be printed in zoom window. You can use the mouse scroll wheel to pan and zoom in the pattern windows. You can also pan and zoom by right-dragging directly in the zoom window. You can now specify lattice strain as well as crystallite size in pattern simulation from the d-I lists. You can also perform dynamic simulation with changing crystallite size and lattice strain (fast PC strongly recommended). You can now tell Jade not to refine a specific profile parameter in profile initialization. You can also fit peak profiles to all pattern overlays automatically - a great time saver if you need to process a large number of scan data. See profile fitting dialog for more information. Improved PDF access and indexing dialog. You can now create PDF index files from ICDD level-1 as well as level-2 PDF database (MDI previously had to create PDF index files for users of level-1 databases). You can also convert index files (such as userfiles) created by Jade to PDF1 or PDF2 database files. Support for ICDD PDF4-RDB (relational database) using ODBC data source connection. With the exception of index file creation (subfiles are prefixed with 'RDB'), access to PDF4-RDB for boolean retrievals and s/m is identical to PDF2. You can now retrieve PDF data by literature references. Soundex algorithm allows recalls of mis-spelled mineral names. X-Y scatter-plot can be performed on PDF phases for cluster analysis. Multiple windows of PDF cards can now be viewed side by side. Persistent reflection markers can be rendered in zoom window when viewing a list of PDF hits, and I%-threshold can be set to eliminate d-I stick labels of weak reflections. You can now customize the PDF hit list to show or hide certain columns of PDF data, and color hits by PDF categories such as quality marks,

data sources, and crystal symmetries. Access to NIST Crystal Data is again supported. You can create index files to retrieve NIST Crystal Data in Jade just like you can with ICDD PDF data. New strong line marker dialog for quick overlay and identification of routine phases (such as clay samples). Improved search/match dialog and algorithms for phase identification of unusual powder patterns. Ribbon plot (like the DNA markers) of checked hits is now supported in search/match display window. Hit list can be placed at the left or right side of pattern window. PDF hits can be accessed as secondary list side by side to the S/M hit list. Improved Deja vu search of your pattern archive. See find similar patterns with thumbnail for more information. Program setting files for wavelength data, FWHM and theta calibration curves, Ascii and d-I import filter files are now made global (i.e. shared) to all user id's created in Jade. They are no longer specific to a particular user ID. You can now idealize a noisy and broad scan pattern using the 'focus scan pattern' filter, a data treatment that proves useful in phase identification for such patterns. You can generate a summary report of pattern statistics on zoom window data & display dialog. You can now view XRD plots and dialog graphs with gradient-fill background colors for enhanced presentation. You can now reverse display order of 3D pattern overlays with a single checkbox. You can now have 'water mark' with your own id information or institution logo on printouts of plots and reports. See print setup dialog for more information. You can now launch other routine applications and browse your favorite web sites directly from customizable drop-down menus in Jade. See interface to other programs topic for more information. Important files to be deleted in Jade will now go to the Windows Recycle Bin so that they can be recovered if you later change your mind. You can place the overlay toolbar in between the pattern the zoom windows, and dock the editing toolbox on it. You can have 'marginless' windows to maximize the view areas of patterns on small laptop screens. You can also dock the zoom & pan toolbar at the left side of the zoom window if you need more vertical space for the color palette. You can list pattern files and all output files from the active data folders in the main window for easy access. You can list peak reports and PDF hits from retrievals and search/match in the top window for quick access. You can load a pattern in another instance of Jade if you hold down the Shift key while selecting a file from the MRU list or double-clicking a file on a list of pattern files. This makes it easy to view and process multiple patterns from the same folder. The number of instances of Jade you can run depends on the free system resources on a Win-95/98/Me PC.

Features Introduced in Jade 7

The main new feature in Jade 7 is the integrated 3D viewer to visualize crystal structures. This is a brand-new 3D viewer written from scratch by MDI. It is completely built into the XRD simulation dialog and does not rely on any external 3D graphics library (such as OpenGL or Java) to run. This 3D viewer now comes with the Jade Plus package since the XRD simulation has been bundled into the licensed options of Jade Plus. Among its notable features are: True 3D ball and stick rendering of crystal structures with true colors, specular lighting, depth-shading, z-buffer hidden surface removals and antialiasing for smoothed images. Viewing options include wire-frame, outline, polyhedra, space-filling, stereo pair, anaglyph view, parallel and perspective projections, multiple view ports and windows. Real time rotation and zooming of large 3D views (up to thousands of atoms, bonds and polyhedra). You can delete atoms in 3D view by point and click, and select atoms to calculate distances, bond angles, and torsion angles. Visualization of translucent atoms, bonds, polyhedra, unit cell facets. A partial-occupied site, for example, can be visualized by translucent atoms with their opacity tied to the occupancy factor. For cool-looking images, built-in and custom textures can be rendered on atom surfaces, custom background image can be applied, and special effects such hulls, halos and shades can be rendered around the atoms. Visualization of translucent reflection planes, Bragg cones and packing surface of 3D lattices from a list of possible reflections. You can also compare packing surfaces of two different lattices from two crystal structures, and bring them together in 3D by easy-to-use xyz-sliders and inplane rotation tools.

 Instantaneous re-simulation of complete powder diffraction pattern by dragging a symmetry-related atom in 3D view. Unique cavity search and visualization tools such as filling cavities with tiny 'ping-pong' balls, peeling and slicing of a packed 3D volume along any viewing direction. Comparison of two crystal structures in 3D (side by side or superimposed) with manual and automatic alignment of 3D orientations. A similarity index is also computed by Jade to gauge two similar structures. Visualization of random atomic thermal vibrations (as indicated by the isotropic thermal parameters), and auto-tumbling of 3D view by tug. Visualization of small organic molecules and large proteins with special rendering options and tools. High resolution hardcopy printout, image file creation and built-in slide show for any list of crystal structures. Export 3D view to POV-Ray (Persistence of Vision Raytracing program from 'www.povray.org'). Please see 3D Crystal Structure Viewer topic for details. Other new and improved features in Jade 7 are: Support of 9-digit PDF number in PDF4 RDB (e.g. 01-070-0001, the first 2-digits being the database code), creating more rooms for calculated powder patterns without fear of duplicating PDF set numbers. Jade can now read the XML file exported from PDF4 RDB for its d-I list and crystal structure data. Hyper-link of PDF# and ICSD# for easy cross references in the comment fields of PDF card dialog and XRD simulation dialog. You can now recall PDF by available CAS# in literature references or enter 'CAS=#' in the PDF box of main toolbar. You can now retrieve from all PDF subfiles at once and perform histogram analysis of existing hits. You can also limit the number of possible elements per hit in the chemistry search. Improved annotation toolbar for persistent display of reflection markers in the zoom window (see the new button for ease of pattern simulation). Phase listing in Jade's main window for quick and easy d-I overlay of routine PDF and customer phases. Thumbnail listing and file listing in Jade's main window for quick and easy access to data and reports. Customizable x,y-axis captions for XRD pattern printout, and background image can be included with XRD pattern. You can now embed greek & math symbols, subscripts and superscripts in printing sample id, plot captions, phase legends and custom-text with user-definable prefix characters. Jade automatically prints chemical formulas with stoichiometric subscripts. See the Misc tab of print setup dialog for more information. Jade will now show and print the greek symbols in PDF database, Miller indices with bars over (hkl), and space group symbols with bars and screw axes. Support table-printing of tab-delimited columns on XRD pattern plots. You can send a table of numbers (such as a profile fitting report) to clipboard and paste them directly into the print preview. You can also create these tables in Excel or Wordpad and paste them into Jade's notepad. Jade turns on table-printing automatically if tabs are detected in the notepad (note: your table may not appear correctly in the notepad). Support 'unlimited' undo and redo functions via the 1st button on the main toolbar. By default, important changes made in the analysis after loading a new pattern are automatically saved by Jade for sake of undo. You can disable this auto-save of undo-redo on the Misc tab of user preferences dialog. You can now perform pattern deconvolution with improved instrument profile calibration for better estimate of crystallite size and strain. New wavelet denoising filter to smooth data in addition to the classic Savitzky-Golay filters. Improved S/M engine on residual peaks and S/M display with alternative ribbon plot and adjacent PDF entries. The S/M display is now a modeless dialog, allowing for simultaneous access to all other dialogs that are accessible from the main window. Improved peak search dialog by combining search and report dialogs into a more efficient one. Improved profile fitting with display of K-alpha2 profiles and customizable columns in profile report. Improved structure database manager, which now allows for retrievals from all databases at once and trimming of existing hits using crystallographic Boolean filters. Improved WPF refinement dialog with summary of refined phases and quantitative report for batch processing. You can now impose shiftlimits on lattice constants and profile broadening in refinement, and observe the shifts of atoms in the 3D structure viewer as they are being refined, and compare the before/after structure models in the Rietveld refinement. You can now unify FWHM curves for multi-phase modeling or refine crystallite size and strain directly with instrument FWHM curve. You can now refine the K1/2 intensity ratio of X-ray source and a new surface-roughness parameter (SR on the Global tab).

 Le Bail extraction of reflection intensities in WPF refinement for ab-initio structure solver and Fourier synthesis. A number of symbols are now supported for plotting individual data points for primary pattern and overlays. Shadow and outline printing of pattern traces has been implemented for 2-pixel and 3-pixel line width. Framing of prints can now be omitted when y-axis is not shown for offset overlays. Positive and negative areas in difference plot can now be painted in different colors and you can also just paint the areas above the current background curve. You can now display pattern overlays in a separate window above the main zoom window, and save/restore background curve from the 'Analyze' menu or the 'BC' item on the status bar. It's now easier to compare a list of files one overlay at a time (see the new button on the overlay toolbar). Support for fractional counts of intensity data, which eliminates the 'staircase' effect from integer roundoff when CPS data of long count time are displayed. Enhanced X-Y column file reader now supports for normalization using monitoring counts (3rd column data). Improved Ascii file import reader for easier setup and automatic data point count per line. Jade can now read XRD patterns of up to one million data points per scan range with a minimum stepsize of 0.0001 degrees. Enhanced file listing with alternate coloring on sorted names and dates, and viewing of recent dates in chronological terms such as today, this week, or last week. You can now use calendar to find recent files. Updated wavelengths of standard anodes (G. Holer, etc, 1997, Physical Review A, V56, 6) and support for two different synchrotron wavelengths. You can now impose limited access to Jade functions on casual users of Jade on Win-XP/Vista. You can now tie d-I overlay colors to PDF numbers (i.e. assign fixed colors to routinely used phases). Multiple instances of file and XML browsers and menu listing of all minimized/hidden modeless dialogs. Multiple gaps can now be embedded along the z-axis (depth) in 3D view of pattern overlays. You can now decrement or increment most parameters in Jade by scrolling the mouse wheel beside the buttons.

You can now zoom and pan with editing cursors as long as you click and drag above the pattern trace in the zoom window or simply by holding down the Alt key. New quick peak marking feature by clicking the '0 peaks' status item and intensity cursor toggle by right-click at the 'I=#' box ('P=#' indicates data point of the pattern rather than cursor location). You can also mark peaks by pressing the 'M' or 'N' key while the zoom window has the keyboard focus. See zoom window display for the complete list of keyboard shortcuts. Auto-processing with task macros now utilizes the pattern overlays to analyze a list of pattern files (i.e. Jade automatically runs the macro through the current overlay list). You must remove the overlays if they are not intended for running the macro. If you run Jade in macro mode from the command line, you can suppress processing the overlays with the command switch "/o". You can now tell Jade to automatically look for new files in a data folder and process them using the active task macro. You can now switch between tab and tile layouts on the XRD simulation and WPF refinement dialogs - why not put those megapixels of your new LCD monitor to work! Enhanced interface, on Win-XP only, with fade-in/out dialogs and translucent view of modeless dialogs when deactivated. This feature can be turned off from the Display tab of user preferences dialog. You can now turn on auto-pan and EKG-like feature for smooth scroll of display with a single mouse click or key-press. A number of shortcut keys are implemented for display when the zoom window has the keyboard focus (press ? key for the list). Intelligent pan of pattern is now implemented with scroll-wheel, which automatically snaps to the next or previous peaks. If you are a Jade 3/4/5 user, please refer to What's New in Jade 6 for more new features. We have addressed issues in previous releases of Jade that have been brought to our attention by our users. For a program as complex and integrated as Jade, it is expected that an adventurous user may encounter some features and routes that do not perform in an expected manner. We greatly appreciate your report of any problem (no matter how trivial) in all releases of Jade. May the adventurous spirits be with you - happy exploring and discovering!

Features Introduced in Jade 8

The main feature introduced in Jade 8 is 'Phase Screening by Whole Pattern Fitting (WPF)', which will identify and quantify phases with a single mouse click. You can perform this function from four different places in Jade 8: Use the button on the PDF overlay toolbar: if you have a list of PDF overlays of identified phases in the zoom window, left-click at this button launches the WPF on them, and right-click at this button to access WPF options and setup dialog.

 Use the button on the S/M setup dialog: this launches the search/match followed by WPF refinement to screen the hit list. Parameters of this procedure are accessible on the Advanced tab of this setup dialog. Iterations between S/M and WPF will be carried out automatically to identify and quantify all significant phases in the pattern. Use the button on quick S/M toolbar in the S/M display window: this button allows for quick WPF refinement of phases compiled by yourself in the S/M. Right-click at this button brings up a list of WPF options such as entering RIR values for certain phases in the mix. Use the button on the Phase tab of WPF refinement dialog: here you have full control over how to perform WPF refinement in phase screening from crystal structure database. Brute force screening of every phases in a database can be performed, but S/M tools and chemistry filters are available to speed up phase screening. Other new and improved features in Jade 8 are listed below: Keyless operation: you can now enable 'keyless operation' in Jade from the 'Help | Run Programs | Keyless Operation' menu. This would allow you to run Jade for two weeks without the MDI license key attached to the pc. This is for the sake of users who travel or run Jade on a laptop with limited USB ports. Under the MDI license agreement, you are not allowed to use the same license key on another pc to run MDI software. This keyless operation is automatically canceled when the same license key is re-attached to the pc. Note: this operation is not available (a) with the network license, (b) for non-primary users of Jade, and (c) for older license keys. Previewing pattern files in zoom window when you click in the main file list, in recent file list, and in the file list of read pattern file dialog. See the new 'PV' check above the pattern window. Jade will change the display range to accommodate the previewed pattern (auto-intensity scaling is used) and dim the primary pattern if it's being displayed in full range in the zoom window. If you zoom in the primary pattern, autoscaling in full range and dimming will not be applied. You can remove the preview from the zoom window either by clicking at the same file in the list again or by doing something in the zoom window. Identify possible phases using the K2 cursor simply by clicking a peak in the zoom window. Jade will search the active PDF subfile specified either on the S/M setup dialog or on PDF retrieval dialog (if you don't have the S/M option) for phases having a strong reflection (not necessarily the 100% line) near the peak being clicked at. This is very much like a single peak search/match, and thus is effective mostly on low angle peaks. Automatic phase identification (Auto-S/M) if you let jade idle for more than 2 seconds after loading a new pattern file. See the new 'ID' check above the pattern window. If you have the S/M option, you can specify the PDF subfile for this action on the S/M setup dialog; otherwise, Jade will search any userfile or the included 'mdi-500' or 'mdi-mnd' subfile designated by you on the userfile manager dialog or the PDF retrieval dialog. New wavelength cursor on edit & cursor toolbar, which allows for derivation of new diffraction patterns from the primary pattern or the active pattern overlay in various radiation wavelengths simply by dragging it in the zoom window. Tip: you can drag without holding the Ctrl key down if you click anywhere below the profile of derived pattern. New rendering options of pattern display in zoom window and in print preview by pressing one of four keys: E, F, J, K while the window has the keyboard focus (press ? for full list of all shortcut keys). The E, F keys fade pattern trace colors from bottom up to another color that can be specified on the color setting dialog. The J, K keys can be used to color diffraction peaks associated with PDF d-I overlays (i.e. phase coloring), which may better be viewed by selecting the opaque view of primary pattern in the zoom window. These renderings are pixel graphics of snapshots and non-persistent in nature. You can copy them to clipboard by pressing the Ctrl+C keys and save them image files if desired. In print preview window, Jade only prints a pixel image of screen resolution if any one of these pixel graphics is shown. Improved and faster pattern indexing function by incorporating Ito method for monoclinic and triclinic indexing with automatic determination of zero offset in the scan pattern. More automated and extensive output with XML file format: you can now tell Jade to create an XML pattern file automatically upon reading a non-XML pattern file (see the 'XML' checkbox above the pattern window), and use it for subsequent analyses. You can now save the WPF refinement controls with structure data in an XML file, making it possible to encapsulate pattern data and all analyses in a single XML file. If you start out with an XML pattern file or create one in Jade, all subsequent analysis output will now be directed to this file automatically. Enhanced PDF access with instant hit counts on chemistry, stoichiometry, unit cell and miscellaneous data retrieval dialogs. PDF color recall has been subsumed into the chemistry dialog. You can now view a list of phases and add them to the overlay list directly on these dialogs as well. Display Greek characters in PDF phase names in the list view of hit list: see the Display option of 'Use Arial-Greek to List PDF Data' on the user preferences dialog, which tells Jade to use a special arial-font to render embedded Greek characters in PDF database. Note: this feature is automatic on versions of Jade (such as Japanese and Chinese) which use Unicode or double-byte character sets. Improved background editing and restoration function: you can now click above the pattern background to insert tie points and Jade would place them on the background using 5-point averages. You can therefore fit a decent background curve simply by clicking at spots between peaks. You can also use the scroll wheel to change sampling of background dots. When you remove (purge) the background, Jade automatically saves the background curve by creating an *.bc file, and restores it for all future operations that involve and/or require the background curve. Left/right-click at the 'BC' item on the status bar now turns on background editing and pops up a short menu of fitting options.

 Convert unconventional orthorhombic cells to standard settings for comparison of crystal structures. Support up to 9 different user wavelengths with L1, L2, ..., L9 entries on the radiation dropdown list. Support CIF format for exporting pattern data (see Ascii import & export dialog for the option). View a list of phases in a PDF subfile on the S/M setup dialog before you start a S/M session. Support square-root and Log10 intensity scalings in 3D view of pattern overlays. You can now render 2D contour map of 3D overlays, for example,

Support full cover of zoom window in the main display (double-click in zoom window with the Ctrl key). You can now print d() values together with 2 angles in x-axis or print a secondary d() scale on top of the plots (see the Annotation tab of print setup dialog for the options). You can now derive XRF% (elemental composition) from quantitative wt% values in WPF and Easy-Quant analysis, and from PDF d-I overlay list dialog. You can now close most modeless dialogs (such as PDF card view, report and file browser) by clicking the same button/icon which brought them up in the first place, and thus reduce the amount of mouse movement. You can now have slanting labels on peaks and reflections beside the horizontal & vertical (see the new angle parameter on the Misc tab of user preferences dialog. You can also set slanting angles by right-click the button on the quick annotation toolbar. You can also display these labels in opaque font/print (right-click the button), which makes for easier reading. You can now customize the buttons on the main toolbar (right-click the new refresh button) and lock down all toolbars:

You can now render background stripes (i.e. colored-bands) in most listviews. See the Display tab of user preferences dialog for the options. An example of this display is given below:

 You can now zoom and pan display beyond the scan range (to the 0-180 degree limits but default to 120 degs) by holding down the Shift key with the buttons on the zoom & pan toolbar or by right-dragging in the zoom window. This display option can be turned on/off on the user preferences dialog. When it's on, Jade will pause at the left & right ends of scan pattern before you can continue beyond with right-dragging or scroll wheel. You can set the range limit on the Misc tab of user preferences dialog. You can now paint the differences between two scan patterns (i.e. primary pattern and active overlay, not their difference pattern). See zoom window display topic for the option and an example. Jade 8 is now Win-OS Vista compatible. Because Vista uses virtual folders for file creations when an application is run under normal privilege, Jade must be 'Run as administrator' (right-click the shortcut icon for this option) in order for you to create PDF and CSD index files in the program diretory that are accessible to other logon users. New utility tool of periodic table with elemental properties, accessible from the button on the PDF chemistry recall dialog.

If you are a Jade 6 user, please refer to what's new in Jade 7 for more new features. May the adventurous spirits be with you - happy exploring and discovering!

Features Introduced in Jade 9

The main new features introduced in Jade 9 are: Cluster analysis to classify similar raw patterns such as polymorphs and amorphous phases using correlation and similarity indices calculated both from whole pattern and peak search. Efficient algorithms can process and classify 1000 patterns under ten minutes with results easily viewable in the main zoom window. The analysis can also identify unique data set and outliers quickly among batches of samples in highthroughput experiments. Similar clustering tools can also be used to classify PDF phases and userfiles of d-I lists for similar or isotypical entries in the databases. This is a licensed option in Jade 9 and accessible from the button in the main window or from the 'Analyze | Cluster Analysis...' main menu for raw pattern analysis. Similar icons and menus are implemented on PDF retrieval dialog and Structure Database manager for phase clustering analysis.

Spherical Harmonics Functions (SHF) for preferred orientation correction in WPF refinement in addition to the March function. Fully

automated SHF fitting with symmetry constraints of SHF orders and coefficients, which can handle multiple orientation poles without the need of specifying their (hkl)'s. You can also visualize the shape plot (see examples below) of fitted SHF with (hkl) labels (i.e. distribution of oriented crystallites) with a single mouse click. This function makes easier and more effective phase screening of oriented samples in whole pattern fitting and in search/match.

Determination of amorphous content in WPF refinement without an internal standard for glassy samples (SiO2). This is accomplished by a nominal RIR or density value for the amorphous material calibrated from a known standard. You can tie profile broadening of a minor phase to that of a major phase in WPF refinement when the minor phase overlaps substantially with the major phase. Multiple ties can be made to the same major phase and this constraint stabilizes and improves the refinement of multiple phase mixture when the pattern has numerous peaks that are not well resolved. Calculate XRF concentration as elemental wt% or oxide% from quantitative phase results, and stoichiometries of common oxides are customizable in XRF report. This option is available on WPF refinement dialog, PDF Overlay List dialog, and Easy Quant dialog. Support ICDD WebPDF-4+ database using the same types of PDF index files and interface dialogs as those for the locally-installed RDBPDF4+. While it takes longer to create the index files from this database, all PDF retrievals and search/match functions in Jade afterwards are carried out in the same efficient manners as using the local RDB-PDF4+. When browsing the full content of a phase (i.e. PDF Card view), Jade will cache the data fetched from the web in order to speed up subsequent access to the same phases. You can browse, display and overlay experimental patterns (PD3 data set) that are included in the latest PDF-4+ database. Please look for the 'PD3 Patterns...' item of the main menu 'PDF' and for the 'PD3 Phases...' item of the miscellaneous menu on PDF retrieval dialog, for example,

Improved Search/Match functions (such as identifying patterns with one dominant peak) and more robust WPF refinement dialogs and performances.

Highlights of Interface Enhancements in Jade 9: The phase list on the right side of main window will now list all PDF subfiles and userfiles that have less than 10,000 phases. Thumbnail browsing of pattern files directly in the main zoom window by left/right-clicking the icon above the file lists:

Display scan (sample) id's in the main file list as an option as shown below:

d-I Ribbon browsing of a phase list in the main zoom window: right-click in the phase list for this menu option (see the image below). Tiling of 3D crystal structures from a phase list in the main zoom window: right-click in the phase list for this menu option (see the image below).

Wheel scrolling of file and phase list in the zoom window: this allows you to change the selection (i.e. highlighted item) in a list simply by wheel-scrolling in the zoom window in order to browse the patterns or to view its d-I list markers.

 A new viewing feature of d-I overlays to dim segments of scan trace that are not overlapping with the d-I markers, for example,

Fade-in & out display of d-I markers (i.e. transition display) in the zoom window and automatic tooltip of phase info (see the Display tab of user preferences dialog). You can plot difference pattern in ESD scale, i.e. the differences are scaled (normalized) to the square-roots of individual observed data points, much like an error-bar plot. This display option has the advantage of statistical relevance to the R-value calculated in WPF refinement. See the Display tab of user preferences dialog for this option, which is also accessible on the WPF refinement dialog. You can display the thresholds (i.e. two horizontal lines) at 3 ESDs by clicking the little square at the right end of the center line in the difference plot. You can display threshold ribbon (lightly fill-band) if you click the square while holding the Shift key down. You can alter the scaling of ESD plot by left/right-clicking the square while holding the Ctrl key down. Improved PDF-RDB indexing speed (by a factor of 3) and you can also stop and resume a lengthy indexing run. Enhanced PDF retrieval with instant display of hit lists of phase data on PDF boolean dialogs (such as the Chemistry lookup). If you are a Jade 7 or 8 user, please refer to what's new in Jade 8 for more new features that were introduced in Jade 8.0 and 8.5. May the adventurous spirits be with you - happy exploring and discovering!