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X-Ray Diffractometer: User Guide
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Author(s):
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N. Lawler & A. Armstrong
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Reviewer(s):
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H. Barnes, K. Bronk
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Supervisor approval:
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D.J. Houpt (Supervisor of Analytical Systems)
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Origination date:
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2006 Demob
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Current Version:
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V378P | V372 | December 2017 I Reviewed X375 I March 2018
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Previous Versions:
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V1.3 10/5/16, V1.2 | 1/3/14 (IODP-II), V1.1 | 5/28/13
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Domain:
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Chemistry
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System:
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X-Ray Diffraction
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Keywords:
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clay mineralogy
Table of Contents
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Introduction
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Manual Information
In This Manual
Introduction
Theory of Operation
References
Apparatus, Reagents, and Materials
Instrument Hardware
Instrument Software
Apparatus Preparation
Sample Preparation
References
Running Samples in the D4
Scanning Samples
Processing Sample Results
Cleaning Sample Holders
Quality Assurance/Quality Control
Health, Safety, and Environment
Maintenance and Troubleshooting
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The X-Ray Laboratory onboard the R/V JOIDES Resolution performs diffraction analyses of minerals and rock powders.
The laboratory uses a Bruker AXS D4 Endeavor XRD. Associated software, DIFFRACplus and TOPAS, allow for powder diffraction analysis of minerals, including peak-matching and mineral and chemical compound identification. The XRD lab provides the scientist with a quick and reliable tool for mineral identification; particularly useful for identifying fine-grained minerals or mixtures of alteration minerals. In addition, XRD can be used to determine mineral proportion.
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The instruments in the lab need to be turned on in this order: (1) HASKRIS and (2) D4. The HASKRIS cools the water supplied to the D4 to prevent the X-ray tube from overheating. Turning the D4 on prematurely will damage the X-ray tube.
Figure 1. HASKRIS Control Panel. (A) Actual temperature. (B) Set temperature. (C) On/Off switch. (D) Flow meter
Procedure
- Flip the "On" switch (Figure 1C) to the HASKRIS and the water in the tank will begin to cool. The water temperature needs to reach 55°F (Figure 1A).
- Flip the ON switch (Figure 2A) on the side of the machine.
- The solid green "Low Voltage Ready" light (Figure 2F) turns on.
- You will hear several beeps and the "System Activity" light (Figure 2D) will start flashing green.
- Press the "High Voltage Enable" button (Figure 2B).
- The "System Activity" light turns green.
- An orange "High Voltage Ready" (Figure 2E) light will turn on.
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).
Figure 3. D4 top control lights.
5. Turn the “Generator Power” key to the right for a few seconds and look at the lights on top of the D4 (Figure 4)
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.
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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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- Cut open the sealed sample bags and fold the top edge over to keep the bag open.
- Take the top of the bell off of the dryer and arrange samples in the bell, making sure no sample bags are pinched closed.
- Close the vacuum valves slowly so that you do not cause a large rush of air to blow the samples around. Figure 5A shows the configuration to dry samples and Figure 5B shows the configuration for loading and unloading samples.
- Set the freeze dryer to resemble the settings shown in Figure 6 and flip the "On" switch located on the right side of the machine.
- Press the "Auto Refrigeration" button (Figure 6A) and then the vacuum button (Figure 6B). The temperature will start to drop and the vacuum pump will turn on.
- When the temperature drops to –40°C, the vacuum is created in the bell and the pressure drops.
- Expect the temperature to be between –42° and –52°C and the pressure to be ~0.350 mBar.
- The indicator lights (Figure F6D) show how the cooling and pressure reduction are progressing. When all indicator are lights are on the freeze dryer is at its peak performance.
- If there is an error the red "Alarm" light will turn on. Press the "Menu" button (Figure F6C) to view it and clear it
- After samples are dry, slowly open the valves to let out the vacuum in the bell. Remove the samples from the bell and store them inside the desiccator until they are ready to be ground to prevent reabsorption of moisture.
Figure 6. Freeze dryer control panel.
Grinding Solid Samples
There are three primary ways to grind samples:
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Mortar and pestle is the most common method. Below, each method is outlined.
Mortar and Pestle
Choose the appropriate mortar and pestle size (large or small) and place it on the counter. Obtain a glass slide, a sample holder, and a scoopula. Clean all items after each use with isopropyl alcohol and a KimWipe.
Figure 8: Mortar and pestle sample preparation set up.
Pour sample into the mortar and grind the sample with the pestle. When finished, the sample should be the consistency of talc powder. Test the sample by taking a pinch and rubbing it on your skin. If the sample feels gritty, it needs to be ground more. If the texture is good and the sample looks homogenous, you can pack the sample into a sample holder to be placed in the D4.
Mixer mill
There are two mixer mills located in X-Ray Prep. Both mills operate very similarly but do have slight differences. The 8000 is featured on the top and the 8000M on the bottom.
Figure 9: 8000M mixer mill. (A) Safety latch (B) Minute timer (C) Seconds timer (D) Start button (E) Pause/Stop button (F) Timer countdown LCD display.
Figure 10: 8000 mixer mill. An older simplified version of the 8000M. Featured are the safety latch, timer dial, and start/stop button in the middle of the dial.
The main difference between the two mixer mills is the timer. The 8000M timer uses 2 buttons to adjust the minutes (Figure 9B) and seconds (Figure 9C), 2 separate buttons to start (Figure 9D) and manually stop (Figure 9E), and counts down time on the LCD display (Figure 9F). To operate the 8000 mixer mill, turn the knob to the desired time and press the "Start" button in the middle. That button will also stop the mixer mill. The dial does not move automatically, so if it is turned to 5 minutes it will stay there. The dial does not need be set back to 0 to work.
Grinding Vessels
There are three types of grinding vessels available: alumina ceramic, tungsten carbide, and hardened steel (Figure 11). Tungsten carbide and steel vessels are better for more robust grinding, and alumina ceramic is better for minimizing contamination. Check with the Science Party to see which vessel type is preferred.
Figure 11: Three types of mixer mill grinding vessels.
Each grinding vessel has its own components. Parts should not be shared amongst the different types of vessels. Combining pieces made of different materials can cause severe damage to the pieces involved.
Below are the components for each type of vessel. The steel (Figure 12) and tungsten carbide (Figure 13) both have a vessel body with attached lid and one separate lid that is screwed on. Cross-threading is very easy with these containers, so be very careful when screwing on the lid. Also note that the steel container has an O-ring, whereas the tungsten carbide does not. The alumina ceramic vessel (Figure 14) is assembled differently than the other two vessels: two cork rings are placed inside each lid, and the lids slip onto either side of the vessel body.
Figure 12: Steel vessel components. (A) Lid (B) Container (C) Steel Grinding Ball (D) O-Ring
Figure 13: Tungsten carbide vessel. (A) Vessel container (B) Lid (C) Tungsten carbide grinding ball
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. 
Figure 15: Inside the 8000M mixer mill. Highlighted is the sample holder clamp that holds the grinding vessels, the primary lock, and the secondary lock.
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.
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This method will leave a small gap in the well of no powder. For this packing method it is ok and the material should be tightly packed in.
Back-Load samples
Back-loading samples is a preparation method to reduce mineral orientation. This method may be desirable for quantitative XRD
Figure 16. Back-loading 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 16). There are also two loading pieces. One piece helps funnel the powder in and the other taps down the powder into a flat surface.
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- 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 17). Now the powder will fall on a smooth flat surface that will be easy to flip over.
Figure 17. Ring upside down on glass. Funnel piece next to unit.
3. Take the funneling piece and put It inside the ring (Figure 18).
Figure 18. Funnel inside ring.
4. Load powder into the ring. Try to load the powder evenly across the well.
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The dismembrator setup is shown on the left in Figure 19. 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 19 (above): The dismembrator set up. Included is the soundproof box and the Probe with power source.
Figure 20: 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 20. Flip the "ON" Switch (Figure 20A). The settings are already set to our needs. To run as is, press the "Start" button (Figure 20B). If you need to change a setting, see the "Set" button (Figure 20D) and the "Mode" button (Figure 20C). 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 21). 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 21: 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.
Additional Clay Treatments before Scanning
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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 22) 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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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
First initialize the Sample Changer by clicking on Init SC (Figure 23A). The checkmarks (Figure 23B) 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 23C). On the Jobs screen, click on "Create Jobs".
Figure 24: 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 24 will pop up. Fill in the Position, Sample ID, Parameter File, and Raw File columns.
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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 25)
Figure 25. File Exchange Desktop Icon
The initial window (Figure 26) 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. 
Figure 26: 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
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 26C) and select "UXD". Then double click on the DATA folder (Figure 26D) and direct files to the "IN" Folder.
Move to the left side of the screen and select your input files. The file type (Figure 26A) should already be set to "Raw". Click on the DATA folder (Figure 26B) and go to the "IN" folder. Here you will see all your samples. Select all the samples and then click the "Convert" button (Figure 26E) 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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Go to the DATA > IN folder where all the sample files are currently stored. Double click on the RAW file and it will open in the Eva software.
Figure 27. Print Icon
- Click on the Printer icon at the top of the software outlined in red in Figure 27. A Print Preview window will open up. On the top bar, click the icon for "Export as a PNG" outlined in red in Figure 28. This opens the File Save window. Save with the same name as the RAW file. If the names do not match exactly, the files will not upload. Then close the windows and repeat the process for the next sample.
Figure 28: 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):
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- Open scan (remember the QAQC parameter file Corundum QAQC continuous 20 to 130.dql ran without the anti-air scatter screen).
- Subtract the background (Figure 29).
Figure 29: EVA diffractogram.
The arrow points to the Background Subtract tool.
3 .Strip Kα2 and Append (Figure 30).
Figure 30: EVA diffractogram with the background subtracted. (1) Dropdown Menu to Append Scan
(2) Strip Kα2 Tool
4. In the "Data Tree" panel there are two scans: Background Subtracted Scan and Kα2 Subtracted Scan (Figure 31). 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 31: 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 below in Figure 32. Click on either scan so that it is highlighted (Figure 32-1). Then click "Create Area" (Figure 32-2). A New window will pop up where you can enter the left angle and right angle(Figure 32-3, 32-4)
Figure 32: 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
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 33). 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 33: 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 34). Do the same for the Kα2 appended scan. This creates another tab on top with the Area data in column format.
Figure 34: Data Tree panel Scan Area list.
8. Open the QAQC corundum standard Equipment Verification 3.3.xls Excel spreadsheet.
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- 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)
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
10. The spreadsheet has the calculations already embedded.
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Open the Configuration Program on the desktop.
In the left side panel navigate to Motorized Drives > 2Theta. In this window go to Zero Reference - Home of the Axis. Enter the corrected ZI value from the excel spreadsheet into the 'Zero' space.
Select 'File' > 'Save and Download' or click on the red CNF arrow.
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'. The new configuration will take a moment to download to the Diffractometer.
Now that the scan is complete put the Anti Air Scatter Screen back on. Move the y drive to the 360 position and open the front door. Line up the Screen with the screw holes. There is a small divet and you will feel the Screen settle into place when positioned correctly. Then carefully put on the screws. When the Screen is back in place close the door and put the cover back on the base.
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If X-rays have not been turned on in longer than 24 hours you must turn on tube conditioning to avoid damaging the X-ray tube. In D4 Tools select "X-RAY" under the Instrument tree, then Utilities -> X-Ray Utilities -> Tube Conditioning ON/OFF (Figure 37)
Figure 37: 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 38).
Figure 38: Tube Conditioning On Indicator
After about a minute the kV will start to increase in increments from 20kV to 55kV. The whole program takes about one hour and when kV returns to 20 the program is complete. Note the operational status on the maintenance spreadsheet posted in the lab. To do this click on Manual Control (small head icon) and type GS11. The resulting number is the status number.
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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 39).
Figure 39. 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 40). 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 40: First page of parameter file setup.
The second page declares the detector and PSD electronic window (Figure 41). These settings are PSD: VANTEC-1 and 3. Do not deviate from these values. Click "OK" and continue to Scan Settings.
Figure 41: Detector declaration.
Scan Settings includes Scan Type and Sample Rotation (Figure 42). 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 42: Scan Settings parameter window.
Scan Parameters includes the scanned angle range, angle step size, number of steps, time per step, and delay time (Figure 43). 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° 2theta) there is a very sharp peak. This is caused by beam overspill onto the sample holder.
Figure 43: Scan Parameters window.
Generator Settings contains the X-Ray Tube Configuration and Generator Configuration (Figure 44). 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 44: Generator Settings window.
The Beam Optics settings lists the Divergence Slit and AntiScattering Slit (Figure 45). 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 45: Beam Optics window.
Save the file under a new name to the path Local Disk C: > DIFFDAT1 > DIFFDAT1_old computer pre March 2013. 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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There is no way to set up multiple runs with this method. Please note a sample can also be loaded in the 'Adjust' tab by entering 'Man' in the Sample Position box and then selecting the 'Load' button.