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Figure 3. Schematic drawing of the beam path of the Bragg Brentano geometry in the Bruker (from the D4 Endeavor User Manual).
The X-Ray radiation generated by the electron beam in the anode material (i.e., Cu for our instrument) of the X-ray tube hits the sample in the goniometer center and is diffracted by the crystalline properties of the sample (Figure 3). The diffracted radiation is detected by an X-ray sensitive detector and gives qualitative and quantitative results according to the properties of the sample (i.e., chemical composition and physical properties like crystallinity).
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When the scans have finished, the results will show up in the "C: > DATA > IN" folder. Two additional file types need to be made by you the X-Ray lab technician before uploading the data to the LIMS database. The D4 outputs a .RAW file and we . The X-ray lab technician additionally has to create a .UXD and .PNG file files. In addition to the LIMS upload, it is also helpful to create an "XRD Data" folder for the scientists in DATA (\\NOVARUPTA)(S:> Uservol > File Name) to save copy of the .RAW and .UXD files (or any file the scientist would like to have access to). After all three file types (.RAW, .UXD, and .PNG) have been made, they can be uploaded to the LIMS database through MUT.
Converting a .RAW File to an .UXD File
The .RAW file is only readable by the Diffrac.Eva software, whereas the .UXD file is a text file that can be read by other programs.
Click the , particularly by HighScore Plus (available to the scientists via a virtual computer, see HighScore Software Quick Start Guide).
To convert a .RAW file to an .UXD file, click the Diffrac.File Exchange software icon on the desktop (Figure 3016).
Figure 3016. File Exchange Desktop Icon
The initial window (Figure 3117) will open. The left half of the screen is the file input where you select the files you want to convert. The right half of the screen is where you select the new converted file type and where the files should go.
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Figure 30: 17. First window in File Exchange. (A) Input Output File Type dropdown menu, (B) Input Output DATA folder, (C) Output Input File Type dropdown menu, (D) Output Input DATA folder, (E) Convert button
First, direct where the new files should be saved and select the converted file type. On For that, on the right side, click on the file type dropdown menu (Figure 30C17A) and select ".UXD". Then double click on the "DATA" folder (Figure 30D17B) and direct files to the "IN" Folder.
Move Next, move to the left side of the screen and select your input files. Select the file type "None" (Figure 30A17C) "Raw". Click on the "DATA" folder (Figure 30B17D) and go to the "IN" folder. Here you will see all your samples. Select all the samples and then click the "Convert" button (Figure 30E17E) on the bottom right of the screen.
The new .UXD files will show up on both sides (window circled in green in Figure 17) and you can close down the program (click on File > Exit).
Printing Scan to PDF or PNG
Go to the DATA > IN folder where all the sample files are currently stored. Double click on the a .RAW file and it will open in the Diffrac.Eva software.
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Click on the
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'Print Preview' icon 
in the toolbar at the top of the software
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window. A Print Preview window will open up. On the top
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toolbar, click the icon for "Export
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Image" 
. This opens the File Save As window. Save as .PNG with the same name as the .RAW file. If the names do not match exactly, the files will not upload to LIMS. Then close the windows and repeat the process for the next sample.
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Uploading Files to LIMS
The XRD
Figure 32: Export Image as PNG Icon
Uploading Files to LIMS
The XRD files are uploaded using the MegaUploadaTron 5000 program
. Three files are needed for each scan (.RAW, .UXD, and .PNG):
- Open the uploader
. Make sure the correct Expedition is selected or else your data will not upload properly. Samples that have all three of the necessary files (.RAW, .UXD and .PNG) will have green check marks next to them. A purple question mark indicates that one or more file types is missing for a sample or something else is not quite right. Make sure the name of the file is the same for each. If you have issues uploaded contact one of the software application developers onboard. " Check all the files you wish to upload and then click "Upload." Green and orange arrows will pop up next to the samples while MUT is uploading them. When finished uploading, the samples move out of the uploader and from the "IN" folder to the "Archive" folder on C:\DATA. Any problematic samples will either remain in the uploader with a question mark or move to the "Error" folder, again you may need to notify a programmer to help remediate uploading issues. - Check that the files moved into the archive directory and uploaded into the LIMS database.
If you are running clay samples you will end up with multiple runs that have the same sample info. To make sure we can differentiate this in the database you must add extra text before the TextID so that it looks like these examples. Do this step when entering the sample name in the Bruker software so that it gets included in the metadata of the file. MUT will recognize the files written this way as long as there is matching file names. However, only one .jpg file is allowed per TextID, so a .jpg of the combined pre- and post- heated scans was uploaded.
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The following QA/QC is for the Bruker D4 Endeavor XRD.
At the beginning of each expedition, use the NIST 1976 corundum standard to check instrument alignment and detector intensities. Use the Excel instrument verification spreadsheet saved in C:\Documents and Settings\daq\Desktop\XRDdocs\Standard QAQC file name QAQC Corundum std Equipment Verification 3.3.xls. This Excel spreadsheet also has imbedded instructions explaining how to analyze the scan in EVA.
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Before running the NIST standard, carefully remove the anti-air scatter screen. Be careful not to hit any of the limit switches within he XRD the D4 as this will cause error and possible collision of the motorized drives. The screen is only removed when running the corundum standard to allow a larger range of angles without any interference. The anti-air scatter screen should always be on when running samples. (Review the video on on Desktop/XRD_ICP Prep Documents/Bruker TRAINING VIDEOS to see this done before proceeding).
- Make sure the Xray X-ray generator is off (Key on front is in off position and Red 'Xray X-ray is On' lights are off).
- With two people, carefully remove the cover over the sample staging area, making sure not to hit any wires. The cover is not fastened to the base and will lift off directly.
- Open D4 Tools and click "Online Status".
- Click the computer icon to connect with the configuration files in the instrument.
- Click "Positioning Drives" and "Sample Changer Y" direction.
- Click "Go", enter "360", and hit "Enter". The sample changer will move in the Y-direction to position 360. This allows you to open the front door to the XRD and gain access to the anti-air scatter screen.
- Open the front door with a socket wrench (tools specific for the XRD are on the XRD Sample Area). Loosen the two bolts on the door and slide the bolts to their opposite side. Carefully let down the door.
- Remove the anti-air scatter screen (Figure 3318). Using an Allen wrench, unscrew the four screws holding up the anti-air scatter screen. These screws are very tiny and easy to drop inside the D4. Be very careful while unscrewing them. The screws are the main support for the screen, so hold onto the screen while removing the screws or else it can fall.
- When the screws are removed, take off the screen without hitting the theta drives. If the theta drive is knocked, the instrument may signal a hard limit switch error.
- Close the front door and use the socket wrench to slide the bolts back to their original position and tighten. Go back to the software and move the Y-drive back to Position 1. (Enter "1", "Go", and press "Enter".)
Figure 3318. Anti-air scatter screen in place inside the instrument (top image) and after being removed (btm image).
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Run the scan as you would for a sample. With D4 Tools closed, open XRD Commander. Initialize the drives and click on the "Create Jobs" tab. Enter the sample position. The corundum standard does not have a text ID, so name it with an informative convention (e.g., Corundum NIST 1976 X396). Make the sure the name matches the name entered in the "Raw File" column. The parameter file, Corundum QAQC continuous 20 to 130.dql, is found at Local Disk C: >DIFFDAT1. Under the "Raw File" tab, set the path to the DATA>IN folder; this scan will not be uploaded to the LIMS database.
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- Open scan in EVA (remember the QAQC parameter file Corundum QAQC continuous 20 to 130.dql ran without the anti-air scatter screen).
- Subtract the background (do not append, just simply close background menu) (Figure 3419).
- 3 .Strip Kα2 and Append (Figure 3520).
Figure 34: 19. EVA diffractogram.
The arrow points to the Background Subtract tool.
Figure 35: 20. EVA diffractogram with the background subtracted. (1) Dropdown Menu to Append Scan
(2) Strip Kα2 Tool
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4. In the "Data Tree" panel there are two scans: Background Subtracted Scan and Kα2 Subtracted Scan (Figure 3621). For both of these scans, you will "Create Area" and "Append Area" for four angle ranges. This will insert area information as a subtree entry under that scan.
Figure 36: 21. Diffractogram with two scans in Data Tree panel. Top arrow points to the Background Subtracted scan. The bottom arrow points to the Kα2 scan
5. Select the area around each peak as shown in Figure 3722. Click on either scan so that it is highlighted (Figure 3722-1). Then click "Create Area" (Figure 37–222–2). A New window will pop up where you can enter the left angle and right angle (Figure 37–322–3, 3422-4).
Figure 37: 22. Create Area for Scan Angles. (1) Arrow points to scan name (2) Create Area tool (3) Left Angle entry field (4) Right Angle entry field
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6. After you enter in both angles click again on the left angle. This populates the rest of the fields. When all fields are populated, you can click on "Append Area" (Figure 3823). Do this for each of the following angle ranges for both scans:
- 25.576°2θ (24.7°–26.2°2θ)
- 35.149°2θ (34.0°–36.2°2θ)
- 88.993°2θ (88.1°–89.7°2θ)
- 126.8–129.0 (angle range is not necessary but recommended).
Figure 38: 23. Create Area Window A. Append this Area button.
7. Right-click on the "Area List #" subheader for background-subtracted scan and select "Create and Area Column View" (Figure 3424). Do the same for the Kα2 appended scan. This creates another tab on top with the Area data in column format.
Figure 39: 24. Data Tree panel Scan Area list.
8. Open the QAQC corundum standard Equipment Verification 3.3.xls Excel spreadsheet. QAQC Corundum std Equipment Verification X384.xls on on the XRD computer . (Figure 40.25)
Figure 40: 25. QAQC Verification Spreadsheet. Zeroing the goniometer.
9. Instructions provided by the vender can be found via the Instruction cell in the QAQC sheet. Enter your name and date and select "Vantec-1" for the detector (Figure 40A25A). Enter the following values into the appropriate columns:
- For 2Theta Obs, use the Chord. Mid values from the Kα2 appended scan areas (Figure 41–126–1)
- For I Obs, use Net Area from the background subtracted scan areas (Figure 42–127-3)
- For FWHM, use the FWHM from the Kα2 appended scan areas (Figure 41–126–1)
Figure 41: 26. Kα2 subtracted Scan Area column view. (1) Chord Mid value (2) FWHM value
Figure 42: 27. Background Subtracted scan area column view. (3) Net Area value
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11. Enter the XRD's Current Zi into the QAQC verification spreadsheet (Figure 40B25B). The current Vi value is found in the Configuration program on the desktop (icon Figure 4328). Open Config program, Password is: DIFFRAC. Click Motorized Drives > 2 Theta. Use the value under Zero Reference - Home of the Axis (Figure 4429).
If the RED "ZI correction must be applied" shows up (Figure 40C25C), you will need to enter the corrected Vi into the Config program. This will adjust will adjust the home position for the 2Theta drive. If there is no message just save the worksheet under a new name (Expedition) and no more action is needed.
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1. Open the Configuration Program on the desktop (Figure 4328). Password: DIFFRAC.
Figure 4328. Configuration program icon
2. In the left side panel navigate to Motorized Drives > 2Theta (Figure 4429). In this window go to Zero Reference - Home of the Axis. Enter the corrected ZI value from the excel spreadsheet into the 'Zero' space (Figure 4429).
Figure 4429. Configuration 2Theta page
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DO NOT CHECK THE BOX FOR THE PSD CONTROLLER. Downloading the config file to the PSD Controller corrupts the Controller. For more information see the Troubleshooting section. Always backup the config.file on the server. With ONLY the 'Save Configuration' and 'Download Configuration to Diffractometer' boxes checked select 'OK' (Figure 4530). The new configuration will take a moment to download to the Diffractometer.
Figure 4530. Save and Download Configuration page. Correct settings to save
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The "Emergency Stop" button located on the front of the D4 Endeavor, when pressed, stops all control electronics, high-voltage generator, and all components connected to the three mains sockets on the mains distribution unit. The X-ray source is turned off and all moving drives will stop immediately. Use only in an emergency.
Chemical Hazards
Ethylene Glycol
Ethylene glycol is toxic and should not be ingested. It is also harmful if inhaled or absorbed through the skin and eyes. Proper personal protective equipment should be used when handling this compound.
Borax
This chemical largely consists of potassium sulfate and is not expected to be a health hazard.
Nitric Acid, Concentrated, or 10%–15% for the Water Bath
Concentrated nitric acid (50%–70% HNO3~ v/v) is highly dangerous. It can cause severe tissue damage on contact, is highly toxic, and the fumes present similar risks of poisoning and chemical burns. When mixed with water, nitric acid liberates large quantities of heat, so appropriate care should be used when diluting this compound. This compound is also a strong oxidizing agent, so nitric acid waste should not be mixed with any organic materials. Note that the nitric acid used in the water bath is still dangerous and should be treated with the appropriate care.
Hydrochloric Acid, Concentrated, or 2 M for Carbonate Dissolution
Concentrated hydrochloric acid (~12M) is highly dangerous. It can cause severe tissue damage on contact, is highly toxic, and the fumes present similar risks of poisoning and chemical burns. When mixed with water, hydrochloric acid liberates large quantities of heat, so appropriate care should be used when diluting this compound. Note that the 2 M hydrochloric acid used in the carbonate dissolution procedure is still dangerous and should be treated with the appropriate care.
Acetic Acid, Glacial, or 10% for Carbonate Dissolution
Glacial acetic acid (~100%) is highly dangerous. It can cause severe tissue damage on contact. When mixed with water, glacial acetic acid liberates a lot of heat, so appropriate care should be used when diluting this compound. When diluted to ~10% concentration, it is very similar to white vinegar, so while it is still acidic and could cause tissue damage, it is not as hazardousray source is turned off and all moving drives will stop immediately. Use only in an emergency.
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If X-rays have not been turned on in longer than 24 hours (is this correct? I thought it was >120 hrs) you must turn on tube conditioning to avoid damaging the X-ray tube. In D4 Tools select the icon with the computer and plug. THis This connects the program to the instrument. Click on the XRay X-RAY generator green button on the status screen, this will show the screen in Figure 4631. Or Select "X-RAY" under the Instrument tree. Then select Utilities -> X-Ray Utilities -> Tube Conditioning ON/OFF (Figure46Figure 31).
Figure 46: 31. D4 Tools X-ray subtree window. (A) X-ray subtree button (B) Utilities command (C) Standing kV and mA
Only click on tube conditioning on/off once. In the bottom right corner of the screen you should see a message 'Tube Conditioning On' (Figure 3732).
Figure 47: 32. Tube Conditioning On Indicator
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First turn off the D4 in the opposite order that you turned it on: Turn the key to off, turn off the mains power, disengage high voltage, and turn off the power switch The Haskris chiller must remain running for at least one hour after turning off everything else to properly cool down the xX-ray tube. The D4 can be off while leaving the chill water on, but if the HASKRIS is off the D4 must be off.
Cleaning the Diffraction System
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A parameter file tells the D4 the conditions that a sample will run under. This is a DQL file made with the XRD Wizard program. The parameter file includes scan settings, scan parameters, generator settings, and beam optics. Some of these settings are constant because they are hardware features of our D4.
To start, double-click the XRD Wizard icon on the Desktop (Figure 4833).
Figure 4833. XRD Wizard Desktop Icon
An empty gray screen will open. There options on the top bar to either open a preexisting file or open a completely blank sheet. It is better to open and edit an old file and save it under a new name. Many settings are fixed, and editing a file reduces the chance of entering in a wrong value.
After a file (new or old) is opened, this first screen will open (Figure 4934). Change the "Operator" to your name and click "OK" at the bottom of the page. You can click "Update" to get the current date and time.
Figure 49: 34. First page of parameter file setup.
The second page declares the detector and PSD electronic window (Figure 5035). These settings are PSD: VANTEC-1 and 3. Do not deviate from these values. Click "OK" and continue to Scan Settings.
Figure 50: 35. Detector declaration.
Scan Scan Settings includes Scan Type and Sample Rotation (Figure 5136). Scan Type should stay set to "Locked Coupled". This is a hardware setting indicating that the theta and 2theta positions move together. Under Sample Rotation, the Spinner can be set on or off. This spinner spins the sample while being scanned. This is typically on because it captures all potential angles of the sample giving a complete image of the material. Rotation Speed is set to 30 rpm and .5 rps (you only have to enter in one of these fields). Click "OK" and continue to scan parameters.
Figure 51: 36. Scan Settings parameter window.
Scan Parameters includes the scanned angle range, angle step size, number of steps, time per step, and delay time (Figure 5237). Adjust the angle range depending on the material and scientific objectives. For example, if looking for clays, set a low angle (3°–30°). The step size determines how much the goniometer will move before recording more data. The number of steps will adjust itself based the step size and angle range. Time/Step controls how long each step is measured. The Delay Time will add in an amount of time to wait before scanning the next sample. The machine does have limits on these settings and if something is entered outside of its range it will alert you. Click "OK" and move onto Generator Settings. At low angles (2–4°2theta2–4°2θ) there is a very sharp peak. This is caused by beam overspill onto the sample holder and into the detector.
Figure 52: 37. Scan Parameters window.
Generator Settings contains the X-Ray Tube Configuration and Generator Configuration (Figure 5338). The X-Ray Tube values are constant. You can adjust the kV and mA in the Generator Settings. The voltage is typically between 30 and 40 kV and the current is 40 mA. Lowering these values too far can reduce peak intensity. Click "OK" and continue to the Beam Optics window.
Figure 53: 38. Generator Settings window.
The Beam Optics settings lists the Divergence Slit and AntiScattering Slit (Figure 5439). Both of these are constant values based on our hardware setup. The Divergence Slit should be set to .300°. Click "OK" and you will have finished all the settings and will loop back to the first window.
Figure 54: 39. Beam Optics window.
Save the file under a new name to the path Local Disk C: > DIFFDAT1. You can print this file by clicking the "Report" tab at the top the subtree window and then clicking the print icon. Occasionally scientists will ask for a printout of the settings to put in their reports.
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