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Bruker-associated softwares, EVADIFFRACplus XRD CommanderEVA, DIFFRACplus and TOPAS, allow for powder diffraction analysis of minerals, including peak-matching and mineral and chemical compound identification. XRD scans from the Bruker can also be analyzed using HighScore Plus software (used for the Aeris measurements). The X-Ray lab provides scientists with a quick and reliable tool for mineral identification; particularly useful for identifying bulk mineralogy, clays, fine-grained minerals or mixtures of secondary minerals. In addition, XRD can be used to determine mineral proportion.

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Instrument Software

DIFFRAC Plus XRD Commander is the running software of the Bruker D4 XRD.

D4 Tools Image Added is a "troubleshooting' software for the D4. T

Two other softwares are needed to analyze the diffractograms obtained with the D4.

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The instruments in the lab need to be turned on in this order: (1) HASKRIS water chiller and (2) D4 XRD. The HASKRIS cools the water supplied to the D4 to prevent the X-ray tube from overheating. Turning the D4 on prematurely (i.e., before the water chiller) could damage the X-ray tube.

Procedure for Turning on Instruments

Turning on Haskris and Bruker D4

1. Flip the "OnON" switch (Figure 1C4C) to the HASKRIS and the water in the tank will begin to cool. The water temperature needs to reach 69°F (Figure 1A4A). The Haskris temperature can range between 65°F to 69°F . Ensure (18-21ºC). Ensure all water valves to/from haskris Haskris are open.
   
   

   

   Figure 14. HASKRIS Control Panel. (A) Actual temperature. (B) Set temperature. (C) On/Off switch. (D) Flow meter

2. Flip the "ON" switch (Figure 2A5A) on the side of the machineBruker D4 XRD.
   1. The solid green "Low Voltage Ready" light (Figure 2F5F) turns on.
   2. You will hear several beeps and the "System Activity" light (Figure 2D5D) will start flashing green.
3. Press the "High Voltage Enable" button (Figure 2B5B).
   1. The "System Activity" light turns green.
   2. An orange "High Voltage Ready" (Figure 2E5E) light will turn on.

Figure 25. Side control panel on D4 XRD. (A) Power On/Off. (B) High voltage enable button. (C) Alarm light. (D) System activity flashing light. (E) High voltage ready light. (F) Low voltage ready light.

4.      Go to the front of the machine and press the green circular button (Figure 6). This enables the mains power and activates the sample handler (see Figure 4). 

Figure 36. D4 Front control panel.

5. Turn the “Generator Power” key to the right for a few seconds and look at the lights on top of the D4 (Figure

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7). When the “Alarm” light turns off and the “Ready” light turns on, release the key back into its middle position.

Figure 47. D4 top control lights.

6.   The top of the machine should have a solid orange “Ready” light and a solid green “On” light. 

7.    If this is the first time in 24 or more hours that the D4 has been turned on, the X-ray tube needs to be conditioned. Go to the Maintenance section under Tube Conditioning for instructions and log the date of tube conditioning in the XRD maintenance log in XRD's Lab Notebook on confluenceConfluence.

Shutting Down the Bruker D4  

The Bruker D4 can be kept on when not in use. However during extended periods such as Tie-ups or if there is not someone to check on the instrument it can be shut down. The haskris can The Haskris can also remain on, or it can be turned off if no one is able to monitor it. If the Bruker D4 is on, the Haskris must be on as well.

 1. Turn the X-Ray generator off by turning the key counterclockwise (Figure 6).

 2. Push the Red button (Figure 6).

 3. Turn off the High Voltage button B as shown in Figure 25.

 4. Turn off the main CPU button A as shown in Figure 25.

 

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Sample Preparation

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There are three ways to load a sample holder: front load, side load, and backloadback load. Front and side loading methods uses the same sample holders and back-loading uses unique holders. Front Loading loading is the most common method. Back and side-loading are ideal for reducing preferred orientation and should be used over frontloading front loading if preparing samples for semi-quantitative analysis. 

Make sure the sample from the sampling table (in the Core lab) is enough material to fill a sample holder - sample size for bulk powder is generally a 1-2 cm QRND (Quarter Round) from the section half. This will produce more produce more than enough material to fill a sample holder. You do not want more than this as it will be wasted.

Front-Load Samples

This technique is commonly used to prepare samples to be measured with the D4.

1. Unless the sample material is very small, select the appropriate sample holder (see Sample Slurry/Smear Slide Mounting for Small Sample Amounts).
2. Label the sample holder with a unique identifier to keep the samples organized (e.g., text ID or 14H2 77-78)
3. Place enough powder from the labeled sample bottle to fill an empty sample holder. Gently press the powder flush with the sample holder using a glass slide. Roll the glass slide over the powder to fill any gaps in material and smooth the surface of the powder. The surface of the powder must be smooth. Remove excess powder from the sample holder edges and carefully place the holder in the D4 sample magazine (Figure 8).

Figure 8: Front-loading sample preparation for XRD analysis with the D4

The sample material needs to be flush with the sample holder. The beam is set to focus on the height of the sample holder. If the sample is above or below that focal point, the geometry of the beams do not converge properly, the peak resolution decreases, and the peaks are shifted.

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There are 10 back-loading holders. The holder has an empty ring (Figure 9A) and backing piece (Figure 9B) that snaps in from behind (Figure 19). There are also two loading pieces. One piece helps funnel the powder (Figure 9C) in and the other taps down the powder into a flat surface (Figure 9D).

Figure 199. Back-loading sample holder pieces. A. Sample Ring B. Back piece C. Funneling piece D. Tapper

Figure 10 shows the different steps to prepare back-loading samples.

1. Take a front-loading holder and put a clean glass slide over it.
2. Take the ring, flip it upside down and put it on the slide (Figure 2010). Now the powder will fall on a smooth flat surface that will be easy to flip over. 
   
   

Figure 2010. Ring upside down on glass. Funnel piece next to unit.

3. Take the funneling piece and put It inside the ring (Figure 21).

Figure 21. Funnel inside ring. 

4. Load powder into the ring. Try to load the powder evenly across the well.

5. Take the tapping piece and lightly tap down the powder. The idea behind this method is not applying pressure to the measuring face will reduce mineral orientation. Do not tap the powder too firmly or you may unnecessarily orient the minerals.

6. Remove the funneling piece when the powder surface is flat and smooth.

7. Take the back piece and snap it into the ring. Be wary of air displacement.

8. Hold the sample holder and the glass slide. Flip the whole unit over and set it down.

9. Remove the glass. The powder needs to be flush with the holder. It may take a few tries to get the right amount of powder in.

Very Small Amount of Material (tooth pick, small crystals, secondary minerals or void filling material)

Sample Slurry/Smear Slide Mounting for Small Sample Amounts

The following technique is modified from the U.S. Geological Survey Open-File Report 01-041, A Laboratory Manual for X-Ray Powder Diffraction. For a very small amount of sample material (i.e., end of a tooth pick), samples may be ground to a fine talc-like powder and smeared onto one of the quartz disk or zero background inserts. Although not useful for semi-quantitative analysis, this method is useful for rapidly determining bulk mineralogy.

Preparing Smear Slury/Smear Slide

1. Place a small amount of sample powder in the center of a quartz or single crystal quartz disk.
2. Add 2–3 drops of 70 % isopropyl alcohol or distilled water to the sample. Note: Isopropyl dries faster than water.
3. Spread the sample to a thin layer using a glass rod. The slurry should be spread evenly across the disk. If there is not enough material to cover the entire disk, concentrate the sample in the middle of the disk where the X-rays will contact the sample.
4. Place the sample in the desiccator to dry before running in the XRD.

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Running a regular XRD sample requires the following steps:

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Figure 10. Back-loading sample preparation for the D4 sample holders.

Very Small Amount of Material (tooth pick, small crystals, secondary minerals or void filling material)

See XRD Sample Preparation for a small amount of material

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Scanning Samples with the D4

Before beginning this proceduremeasurements, confirm the scan parameters (singles, step and time) with the Science Party. Scientists can use previous Expeditions for examples of ideal scan parameters. Generally the D4 is used to scan from 5 to 70 x 2Thetaº2θ. If you need to make a parameter file, please reference see Making a Parameter File under Maintenance and Troubleshooting. There are several parameter files from previous expeditions saved in the C:/DIFFDAT folder. Generally a previous expedition file is satisfactory for most expeditions. There are scan variations for Bulk samples versus Clay separations. Those parameter files are labeled accordingly in the DIFFDAT folder. Generally clays are scanned to include much lower angles (<5 deg 2Thetaº2θ).

Open the XRD Commander program using the icon Image Added on the desktop or toolbar. Figure 2611 is the initial window. Be sure you are in the 'Adjust' tab (btm bottom left, 26C Figure 11).

Figure 26: 11. XRD Commander main window. (A) Initialize Sample Changer button, (B) Initialize Driver Request checkmarks, (C) Tabs

First initialize the Sample Changer. The checkmarks (Figure 26B11B) indicate the drives that will be initialized. Check all boxes with values before initializing, click . Click on Init SC to initialize the Sample Changer (Figure 26A11A). The program then 'locates' all the mechanical drives in the D4. It typically remembers the Theta, 2Theta, and Phi drives but the Divergent Divergence Slit sometimes does not initialize. That should not be an issue for scanning samples as our Div. Slit is not mechanical, however if the software won't scan a sample because one or more of the drives did not initialize (successfully initialized drives will turn blue) you can try restarting the program and reinitializing, and/or turning off the D4 and the commander XRD Commander software and restarting the instrument then the commander XRD Commander software and repeating the steps above. If that does not work, close XRD Commander and open D4 Tools Image Added from the desktop. Note D4 Tools and XRD Commander cannot be open at the same time.

D4 Tools allows you to see what is causing an error in the D4 instrument and remediate it. In When D4 Tools open, click "Online Status" , then (Figure 12). In D4 Tools, click the icon Image Added('online refresh ON/OFF') on the left (Figure 27A13A), this connects the D4 Tools software with the D4 instrument and completes a diagnostics diagnostic (identifies any errors). The diagnostic screen (Figure 2713) shows the instrument status. Any red squares square indicates an error. You can investigate the error by clicking on the square. Only trained techs should be trouble shooting troubleshooting errors (errors other than drive initialization) on the D4.

To  To initialize the drive(s) that did not initialize with the commander XRD Commander software click the '+' positioning drivesof 'Positioning Drives' to expand the menu, then click the drive that did not initialize (Figure 28A14A). Click the 'Adjust' buttonImage Added  (Figure 28B14B). Please note that when you initialize the drives you can hear the drives moving inside the D4. If you hear a clank or bang and the instrument stops working, you will have to get a trained D4 tech. There is a in-depth sample changer procedure to correct for misalignment in the Bruker Manual ((in the cupboard in XRD the X-Ray lab) but it should only be preformed by trained techs. Alternatively, you can contact Bruker company and they can advise or remote into the D4 to fix any errors.  Note Note that some errors can be fixed by clicking the Red Cross icon 'First Aid' icon Image Added(Figure 28C14C). The program can identify and fix some errors. Try that icon before contacting Bruker.

Image AddedFigure 12. Opening D4 Tools.

Figure 27: 13. D4 Tools Initial Window. (A) Establishes connection between the software and the D4. (B) Positioning drives select drop down.

Figure 2814. Adjusting a motorized drive via D4 Tools. (A) Select the drive to initialize. (B) Initialize button. (C) First Aid button may help with positioning errors or other errors with the window.

Entering Sample

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information into the XRD Commander

Click In the XRD Commander, click on the 'Jobs' tab (Figure 26C11C). On the 'Jobs' screen, click on the "Create Jobs" . 

Image Removed

icon Image Added in the toolbar (Figure 15A).

Image Added

Figure 15. Create JobsFigure 29: Create Jobs window. (A) 'Create Jobs' icon, (B) Sample position In in the D4 sample magazine, (BC) Sample ID, (CD) Parameter file, (DE) Open Directory button, (EF) Raw file, (FG) Start button

The window shown in Figure 2915 will pop up. Fill in the 'Position', 'Sample ID', 'Parameter File', and 'Raw File' columns.

• Position: This is the position of the sample in the loading magazine in the D4, from A1–A6 to K1–K6.
• Sample ID: Scan in the label for your sample here. The only format that MegaUploadaTron (MUT) will recognize is Site_Core_Top offset_Bottom offset_TextID (e.g., U1481A_32R4_91_92_QRND8021751). The barcode scanner in the XRD Laboratory is programmed to scan in this exact format including underscores. For special treatments such as clay, glycol or heat treated you must include the treatment in the file name. Add the treatment in the following way U1565A_1R1_3_4_clay_WDGE11053881.
• Parameter File: This is a premade DQL file that sets the conditions under which samples will be scanned. Access the file by clicking on the "Open Directory" button (Figure 29D) This directs you to the Control Panel. Follow the path "Local Disk C: > DIFFDAT1. This has a list of all the parameter files from previous expeditions. Select the one that is best suited for your scan parameters.
• Raw File: Sets the location where the results will be saved. Set the location by clicking on the three dots at the end of the cell. Then follow the path "Local Disk C: > DATA > IN". Copy the sample ID into the "Open" line in the window. The sample ID and the name entered into the "IN" Folder must be identical or else the information will not be stored correctly.

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