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Figure 2. Side control panel on D4. (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. This enables the mains power and activates the sample handler (see Figure 3).
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Figure 4. D4 Front control panel.
6. When the “Alarm” light turns off and the “Ready” light turns on, release the key back into its middle position. 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 now needs to be conditioned. Go to the Maintenance section under Tube Conditioning for instructions.
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Solid samples are prepared for X-ray diffraction by grinding, which depending on the sample matrix, the size of the sample, and/or quantity of prepared material needed can be accomplished by several different methods.
Sample Matrix | Use... |
Soft clay | Agate mortar and pestle |
Hard solids | Mixer mill |
Hard solids in bulk quantities | Shatterbox |
Hard sample too large to fit in the shatterbox | X-Press |
Drying Samples
Freeze-dry sample(s) for at least 12 hours before grinding. If the samples still feel cold when removed from the dryer, the samples still have moisture in them and need to dry longer.
The freeze dryer is comprised of a sample "bell" chamber and a Labconco freeze-dryer. On the bell are two valves, as shown in Figure 5. Each valve has an "Open" and "Closed" position. The top valve controls the vacuum inside of the bell, and the bottom valve controls the air flow between the cooling coil and bell. A valve parallel with the tube is open and allows air flow; a valve perpendicular with the tube is closed. In Figure 5, configuration A (closed) will hold a vacuum, but configuration B (open) will not.
Figure 5. (A) Freeze dryer bell valves in closed position. (B) Freeze dryer bell valves in open position.
To freeze-dry samples,
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Figure 14: Alumina ceramic vessel components. (A) 2 cork rings (B) Vessel body (C) Alumina ceramic grinding ball (D) 2 lids
Label the vessel with a small printed label of the sample it holds. After the sample is ground, transfer that label to an 8 or 16 mL snap cap bottle that will hold the powder.
Loading the Grinding Vessel into the Mill
Put your sample inside the vessel. The material should be approximately the size of a pea to prevent any jamming and to ensure all pieces are ground up. Place 1 to 2 grinding balls inside the container. Tungsten carbide and steel vessels can take up to 2 balls. The alumina ceramic vessel is more brittle and 1 ball is recommended. Finish assembling the grinding vessel and open the lid to the mixer mill. 
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Hold the grinding vessel between the sample holder clamps (Figure 15), flush against one side. Still holding the vessel, start turning the primary lock. The holder will begin to clamp down on the sample. When the vessel is secured, you can remove your hand and continue tightening the primary lock until the sample is firmly gripped. Then tighten the secondary lock until it feels firm. Check the vessel to make sure the lids are resting flat on the clamps. If the vessel is ajar inside the clamp, when the motor starts the vessel can start grinding away at itself or fly loose into the machine.
Starting the Mill
Set the timer to the desired grinding time. The time will vary depending on sample material. Start with a conservative time, 2 to 3 minutes, check the material, and add more time if the sample still feels gritty. Harder rocks can go up to 10 minutes or beyond to grind down to the right sample consistency.
When the mill finishes grinding, remove the vessel the same way as it was put into the clamp: hold the vessel firmly against one clamp while unscrewing the primary lock. Keep the vessel straight and hold it firmly. If one of the lids starts to crack open, sample material will spill into the machine. If this happens, clean up the powder with a damp towel. Any leftover powder can get into the motor and damage it.
Transferring Powder
Collect a metal tray, weigh paper (large or small), 8 or 16 mL clear snap cap bottles, a scoopula, Kim Wipes, and isopropyl alcohol. Clean all materials with isopropyl alcohol. Place a piece of weigh paper on the metal tray. Pour the sample material from the grinding vessel onto the weigh paper. Use the scoopula to scrape the sides and lids of the vessel to remove extra material. Transfer the sample from the weigh paper into the glass vial. Label the vial with a small printed label and label the cap with a permanent marker.
Cleaning the Vessels
Clean the grinding vessels with a toothbrush and DI water. In some cases the vials are still dirty or have sample stains on them. If so, take a small amount, approximately 5 mL, of silica sand and grind it in the mixer mill for ~3 minutes. Then pour out the sand and clean the vessel with DI water and a toothbrush or Greenie Meanie. Lay out cleaned vessel parts on a Kim Towel and dry with a Kim Wipe. The cork rings take a longer to dry, so collect fresh, dry rings before grinding the next sample.
Then can now pack the samples.
Shatterbox
Shatterbox vessels are not commonly used for powder XRD samples. Please refer to the ICP Prep User Guide for instructions for using the shatterbox.
Preparing Sample Holders for the D4
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Back-loading samples is a preparation method to reduce mineral orientation. This method may be desirable for quantitative XRD
Figure 4016. Back-loading smaple sample holder pieces. A. Sample Ring B. Back piece C. Funneling piece D. Tapper
There are 10 back-loading holders. The holder has an empty ring and backing piece that snaps in from behind (Figure 4016). There are also two loading pieces. One piece helps funnel the powder in and the other taps down the powder into a flat surface.
- Take a front-loading holder and put a clean glass slide over it.
Take the ring, flip it upside down and put it on the slide (Figure 4117). Now the powder will fall on a smooth flat surface that will be easy to flip over.
Figure 4117. Ring upside down on glass. Funnel piece next to unit.
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3. Take the funneling piece and put It inside the ring (Figure
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18).
Figure 18. 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 to 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
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There are various methods for separating clay from coarser material. Those listed below are methods used onboard.
If you removed carbonates first, start here after your water washes are finished and the water has been decanted. If you did not remove carbonates, take approximately 5 mL of sample material and put into a centrifuge tube.
Get the sonic dismembrator case and probe power source. Using the dismembrator is a very effective way to fully and randomly suspend the material. Suspended material can then separate out according to size, with the largest grain size on the bottom and the very small clay size fraction on top.
The dismembrator setup is shown on the left in Figure 1619. The power source is connected to the probe. The probe fits into the case through a hole in the top. Put the probe into the top clamp and the sample tube into the bottom clamp. Adjust the positions so the probe goes into the tube. The probe should be about half-way into the sample material without touching the sides of the tube. The probe releases a lot of energy, and if it is touches the sides it will heat up the tube and the sample. 
Figure 1619 (above): The dismembrator set up. Included is the soundproof box and the Probe with power source.
Figure 1720: Dismembrator power source control Panel.
(A) On/Off switch (B) Start button (C) Set button (D) Mode button
The probe power source is shown on the left in Figure 1720. Flip the "ON" Switch (Figure 17A20A). The settings are already set to our needs. To run as is, press the "Start" button (Figure 17B20B). If you need to change a setting, see the "Set" button (Figure 17D20D) and the "Mode" button (Figure 17C20C). From these two panels, you have access to the power, time, and displayed units. For more information, reference the Manufacturer Manual located in the side pocket of the dismembrator case.
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Clay mounts are put onto a zero-background silicon disk that fits into a 2 mm steel sample holder (Figure 1821). Only put the disks into sample holders that have a hole drilled in the bottom. The hole allows the disks to be taken out, otherwise they are stuck inside the holder. The disk should sit flush with the sample holder.. Some of the disks are at different depths, so a quartz insert disk can also be put in the bottom of a sample holder with the silicon disk on top.
Figure 1821: Steel sample holder with silicon disk 
1. Remove the <2 µm size fraction by collecting the uppermost 1 cm of solution with an eye dropper. If necessary resuspend flocculated clay particles using the dismembrator and add more borax solution.
2. If material is still very suspended, try centrifuging the samples for 4 minutes at 750 rpm. In this instance, the >2 µm size fraction will be the only fraction suspended in the liquid and all the larger grains will be packed in the bottom. Take the suspended material with an eyedropper and put it on the quartz disk.
3. Make an oriented clay mount by placing 2–3 drops (enough to cover the disk) of clay suspension directly onto the silicon disk. If the material is not spreading evenly, add a drop or two of 70% isopropanol and spread the material around with a small glass rod. Once spread, let the sample dry in the desiccator. The clay particles orient themselves as the solution dries on the disc.
Once the sample is dry, you are ready to run it through the D4. If there are additional treatments requested, continue to the sections below.
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The following techniques are modified from the U.S. Geological Survey Open-File Report 01-041, A Laboratory Manual for X-Ray Powder Diffraction. Ethylene glycol can be used to expand swelling clays (e.g., smectites, montmorillonite, nontronite, and beidellite), some mixed-layer clays, and vermiculite as an aid to mineral identification. There are two ethylene glycol treatment methods:
- Vapor
- Quick
Vapor Vapor Treatment
The advantage of the vapor treatment is less disturbance of the sample and less amorphous scattering of X-rays by excess liquid than in the Quick method.
Figure 22: Glycolator
- Find the "glycolator" container (Figure 1922) stored in the ICP preparation sink cupboard.
- Pour ethylene glycol to a depth of ~1 cm in the bottom of the container.
- Take off the lid and place the samples on the rack inside the glycolator.
- Place glycolator in an oven (60°–70°C) overnight (~12 hours).
- Figure 19: Glycolator.Keep samples in the glycolator until ready to run through the D4. Glycolation only lasts for 4 hours after the samples are removed from the glycol atmosphere.
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Before beginning this procedure, discuss the desired scan parameters with the Science Party. If you need to make a parameter file, please reference Making a Parameter File under Maintenance and Troubleshooting. Figure 20
Open the XRD Commander program using the icon on the toolbar. Figure 23 is the initial window.
Figure 23: XRD Commander main window.
(A) Initialize Sample Changer button
(B) Initialize Driver Request checkmarks
(C) Jobs tab 
Open the XRD Commander program using the icon on the toolbar. Figure 20 is the initial window.
First initialize the Sample Changer by clicking on Init SC (Figure 20A23A). The checkmarks (Figure 20B23B) indicate the drives that will be initialized. Check the "Div. Slit" box before initializing; the program typically remembers the Theta, 2Theta, and Phi drives. Successfully initialized drives will turn blue. If one or more stay red, you can try restarting the program and reinitializing. If that does not work, close XRD Commander and open D4 Tools. D4 Tools and XRD Commander cannot be open at the same time. Go to the drives that will not initialize and click the "Adjust" button. Then close D4 Tools and reopen XRD Commander. The "Adjust" command can also initialize the drives. The diffractometer's sample-changer drives will adjust inside the instrument. If you hear a crash or the program gives an error, see the procedure for readjusting the sample handler in the Bruker manual. This is a lengthy process.
Click on the Jobs tab (Figure 20C23C). On the Jobs screen, click on "Create Jobs". 
Figure 24 JobsFigure 21: Create Jobs window. (A) Sample position In D4 sample magazine (B) Sample ID (C) Parameter file (D) Open Directory button (E) Raw file (F) Start button "
The window shown in Figure 20 will pop up. Fill in the Position, Sample ID, Parameter File, and Raw File columns.
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When all fields have been filled in for all samples, click on the "Start" button on the bottom left corner of the screen (Figure 21F24F). The program will hesitate for a moment and then load the first sample into the measurement position and a second sample into the sample changer.
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When the scans have finished, the results will show up in the "DATA > IN" folder. Two additional file types will be made before uploading the data to the LIMS database. The D4 outputs a RAW file and we create a UXD and PNG file. In addition to the LIMS upload, it is also helpful to create an XRD Data folder for the scientists in DATA (\\NOVARUPTA)(S
> Uservol > 1Lab_C_Sedimentology_Petrology) that has a copy of the RAW files. After all three file types 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 Eva software, whereas the UXD file is a text file that can be read by other programs.
Click the File Exchange software icon on the desktop. (Figure
Figure 22: First window in File Exchange. (A) Input File Type dropdown menu (B) Input DATA folder (C) Output File Type dropdown menu (D) Output DATA folder (E) Convert button button
The initial window (Figure 22) 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.
First, direct the where new files should be saved and select the converted file type. On the right side, click on the file type dropdown menu (Figure 22C) and select "UXD". Then double click on the DATA folder (Figure 22D) and direct files to the "IN" Folder.
Move to the left side of the screen and select your input files. The file type (Figure 22A) should already be set to "Raw". Click on the DATA folder (Figure 22B) and go to the "IN" folder. Here you will see all your samples. Select all the samples and then click the "Convert" button (Figure 22E) on the bottom right of the screen.
The new UXD files will show up on both sides and you can close down the program.
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Figure 26: EVA diffractogram with the background subtracted.
(1) Dropdown Menu to Append Scan
(2) Strip Kα2 Tool 
- In the "Data Tree" panel there are two scans: Background Subtracted Scan and Kα2 Subtracted Scan. 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.
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Figure 31: Kα2 subtracted Scan Area column view. (1) Chord Mid value (2) FWHM value
Figure 32: Background Subtracted scan area column view. (3) Net Area value 
- For 2θ Obs, use the Chord. Mid values from the Kα2 appended scan areas (Figure 31-1)
- For I Obs, use Net Area from the background subtracted scan areas (Figure 32-1)
- For FWHM, use the FWHM from the Kα2 appended scan areas (Figure 31-1)
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