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X-Ray Diffractometer: User Guide

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Manual Information

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In This Manual

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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Introduction

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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Theory of Operation

A mineral is a three-dimensional structure that forms a crystal lattice. When a focused X-ray beam is directed onto the crystal structure of a mineral, part of the beam is diffracted. X-rays are diffracted differently depending on the atomic composition and arrangement within the crystal lattice. Each mineral has a unique fingerprint that is determined based on a characteristic set of d-spacings (space between adjacent planes of atoms in the crystal lattice). This is a fundamental characteristic of minerals that allow mineral identification through X-ray diffraction. X-rays are generated in a vacuum tube and directed to a powdered sample, when the X-rays hit the powdered sample, they are diffracted onto a detector. The X-ray detector then converts the signal to a count rate. The angle between the X-ray tube, sample, and detector are varied during measurement to produce an X-ray scan . Using the angle between the X-ray tube, sample, and detector (2θ, which can be measured) and the wavelength of a generated X-ray beam (λ, which is known based on the material generating the X-rays), the scientist can determine the d-spacings by using Bragg's law:
nλ = 2dsinθ
n = order of the diffracted beam
λ = wavelength of the incident X-ray beam
d = distance between adjacent planes of atoms (d-spacings)
θ = angle of incidence of the X-ray beam
The d-spacings generated by an X-ray scan provide the unique fingerprint of the mineral or minerals present in the sample.

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References

Cullity, B.D., 1978. Elements of X-Ray Diffraction, Second Edition. Addison-Wesley Publishing Company, Inc., Massachusetts.
Bish, D.L., and Post, J.E. (Editors), 1989. Reviews in Mineralogy Volume 20, Modern Powder Diffraction. The Mineralogical Society of America, Washington, D.C.

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Apparatus, Reagents, and Materials

Laboratory Apparatus

• Haskris water chiller for X-ray tube
• Cahn Model 29 or 31 microbalance
• Mettler-Toledo XS204 dual-balance system
• Powdering equipment:
• Agate mortar and pestle
• Mixer mill
• Shatterbox
• X-Press
• Glass bottles
• Sonic dismembrator
• Glass rod
• Glass beakers
• Pasteur pipette/eye dropper
• Centrifuge and centrifuge tubes
• Desiccator
• Labconco Freeze Dryer

Reagents

• Ethylene glycol (clay glycolation)
• 2 M HCl: 16.4% v/v (carbonate dissolution)
• Glacial acetic acid, 10% v/v solution (carbonate dissolution)
• Distilled (reagent) water (DI)
• 1% w/v Borax solution

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Instrument Hardware

• Bruker AXS D4 Endeavor X-ray diffractometer (XRD)
• Goniometer
• X-ray source (sealed vacuum tube with line focus)
• Tube housing (ceramic body that protects the tube and shields from X-rays)
• Mount
• Sample holder
• Vantec-1 detector
• Optics
• Slit systems

X-Ray Diffractometer

The Bruker AXS D4 Endeavor XRD can analyze powder, liquid, and solid samples in a variety of sample holders. The sequence of the beam path is X-ray source > primary X-ray optics > sample > secondary X-ray optics > detector.

Goniometer

The goniometer has 2 circles: the theta (θ) circle, which sets the sample position, and the 2θ circle, which moves the detector. The position of the X-ray tube remains fixed. The goniometer center is defined by the concentric circle axes.

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Sample Holders

Sample holders for powdered XRD samples are steel or steel with a silicon or quartz spacer. The selection of a sample holder depends on the volume of sample to be analyzed.

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Detector

The VANTEC-1 detector features the fastest simultaneous recording of XRD patterns within a wide 2θ angular range. For powders, measurement time is reduced by a factor of up to 100 in comparison to other detectors.

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Detector Optics

• Detector window slits
• Debye slits
• Kβ filter: suppresses characteristic Kβ radiation
• Antiscatter slits: reduce primary air scatter, which influences diffraction background patterns
• Soller slits: reduce primary and secondary air scatter
• Window opening scales

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Instrument Software

• DIFFRAC.SUITE.EVA, version 3.0 software for evaluation
• DIFFRAC.TOPAS version 4.2.0.1 software for diffractogram analysis

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Apparatus Preparation

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.

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Figure 1. HASKRIS Control Panel. (A) Actual temperature. (B) Set temperature. (C) On/Off switch. (D) Flow meter

Procedure

1. 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).
2. Flip the ON switch (Figure 2A) on the side of the machine.
   1. The solid green "Low Voltage Ready" light (Figure 2F) turns on.
   2. You will hear several beeps and the "System Activity" light (Figure 2D) will start flashing green.
3. Press the "High Voltage Enable" button (Figure 2B).
   1. The "System Activity" light turns green.
   2. An orange "High Voltage Ready" (Figure 2E) light will turn on.

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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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Sample Preparation

Sample preparations are split into two main categories:
A. Bulk powder samples
B. Clay separations
Before running samples, go over the methods with scientists and check for any special sample requests.

Bulk powder samples

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.

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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 6. Freeze dryer control panel. 

Grinding Solid Samples

There are three primary ways to grind samples:

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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

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

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The 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.

Side-Load Samples

Side-loading samples is a preparation method to reduce mineral orientation. This method may be desirable for quantitative XRD

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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

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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

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 inserts. Although not useful for semiquantitative 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 dessicator to dry before running in the XRD.

Clay Separations

Clay Separations focus on separating the clay size fraction, <2um, from the rest of the material. In order to get only that size fraction we prepare the sample in a different way. Do not freeze dry samples waiting for clay separations. If the samples have already been dried the treatments will still work but using fresh, wet samples is easier. Below are outlined various treatments and methods we do on board.

Removing Carbonates before Clay Separation

It may be necessary to dissolve the carbonates in the sediment to better identify the clay minerals. The goal is to remove as much carbonate as possible to isolate the material contained within the carbonate for analysis. There are two standard methods for removing carbonate aboard the JOIDES Resolution: hydrochloric acid (HCl) and acetic acid. Ask the Science party which method they prefer. If there is no preference, use acetic acid.

Acetic Acid Treatment

This is the recommended treatment for carbonate removal. The process is slightly more involved than the HCl procedure, but far less damage is done to the mineral structure. The following steps are from Kitty Milliken (UT-Austin).

1. Place ~2 cm³ of undried sample into a 50 mL centrifuge tube. This should approximately fill the bottom cone of the tube. Then add 25 mL of a 10% acetic acid solution. Mix well and let sit until the reaction ceases; this may take a few minutes or up to an hour. The samples can sit in the acid overnight with no harm. You may need to stir the sample and break it up with a spatula a few times.
2. Periodically shake the sample until the reaction has stopped (i.e., no more bubbles).
3. In the Chemistry Laboratory, spin the sample in the centrifuge for 15 minutes at 1500 rpm
4. Decant the acetic acid solution into the sink while running water down the drain to flush the acid through the pipes.
5. Add 25 mL of DI (nanopure) water to the centrifuge tube and centrifuge again for 15 minutes at 1500 rpm.
6. Decant the water.
7. Repeat the "wash cycle" (Steps 4 and 5). The water wash should be done at least twice to flush out all of the acetic acid. When the sample stops smelling strongly of vinegar, you can move on to separating clay.

Hydrochloric Acid Treatment

HCl is the simplest method for removing carbonate from sediment but does have severe drawbacks. Strong acids damage the mineral structure, especially within trioactahedral minerals. Before proceeding, be aware that this treatment may affect clay crystallinity.

1. Place undried sample on a glass slide or quartz disk.
2. Using a Pasteur pipette, slowly drop 2M HCl on the sample until bubbling/fizzing stops.
3. Desiccate and transfer sample to sample holder for analysis.

Separating Clay

There are various methods for separating clay from coarser material involving a series of centrifuging or gravity settling. Those listed below are methods used on-board.
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.

Suspending Material

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.

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1. Add ~25 mL of a 1% borax solution into the centrifuge tube. Borax prevents the sample from flocculating. Too much Borax however will increase flocculation. 
2. Put the tube into the bottom clamp inside the dismembrator case. When satisfied with the positioning, press the "Start" button on the probe power supply (Figure 17B). If the material does not appear to be circulating throughout the whole tube or the tube is heating up, adjust the probe position and start the dismembration over.
3. Let samples settle overnight (~12 hours). The next morning, the material should be separated out with the clear liquid filling most of the tube and sediment filling the bottom cone.

"Quick and Dirty" Clay Separation Method: Not for Semi-quantitative Analysis

1. In centrifuge tube, mix a small amount of bulk sample (~5 mL; fresh, not dried) with 1% borax solution. Use an ultrasonic bath or dismembrator, if necessary.
2. Centrifuge the borax solution/sample mix at 1000 rpm for 5 minutes to remove the >2 µm size fraction.
3. Decant the borax solution (containing suspended clays) into a new centrifuge tube and spin it at 1500 rpm for 15 minutes to remove the remaining <2 µm clay size fraction.
4. Decant the borax solution and wash the clay residue with distilled water.
5. Spin-down again at 1500 rpm for 15 minutes. Repeat Steps 4 and 5 as necessary to remove the borax.

Preparing the Mount

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

Treating with Ethylene Glycol

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:

1. Vapor
2. Quick

 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.

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Before placing samples in the D4, wipe all sides of the sample holder with a Kim Wipe to remove any ethylene glycol. Ethylene glycol is sticky and can damage the grabber arm and sample spinner.

Quick Treatment

1. Using a glass rod or eye dropper, apply a drop of ethylene glycol directly to the surface of the sample mount.
2. Samples are ready to be analyzed as soon as the glycol is uniformly absorbed on the sample mount. Excess ethylene glycol may be gently mopped up with a Kim Wipe.

Heating Samples

Several clays have intensity peaks at very similar angles making it difficult to distinguish one clay from another. Heating clays is a way to work around this. We can run a sample through the D4, heat the sample in the muffle furnace, run again, and then compare the scans. For example, kaolinite and chlorite have overlapping peaks, making it hard to differentiate one from another. Heat morphs kaolinite, and it develops an amorphous signal, essentially removing its presence in the scan and leaving only the chlorite signal. The amount of kaolinite and chlorite can be determined by comparing these scans.

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1. When the muffle furnace has finished its program and is cooling down, wait until the temperature reaches between 100° and 200°C before removing the sample. The sample can be placed in the desiccator until it reaches room temperature. Once it has completely cooled down it can be run in the D4.

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References

Jackson, M.L., 1956. Soil Chemical- Analysis Advanced Course by Hsueh-Wen Yeh, Hawaii Institute of Geophysics, 1980.
Moore, D.M., and Reynolds, R.C., Jr., 1989. X-ray Diffraction and the Identification and Analysis of Clay Minerals: New York (Oxford University Press).

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Running Samples in the D4

Running a regular XRD sample requires the following steps:

1. Scan the samples on the XRD.
2. Convert the raw sample results to an UXD file.
3. Export the raw scan to a PDF or PNG file.
4. Upload the raw UXD and PDF/PNG files to the LIMS database.

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Scanning Samples

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.

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The other fields will automatically populate. These should not need to be adjusted. Only change the other settings if you know what to do and refer to the D4 Commander User Manual.

Starting a Scan

When all fields have been filled in for all samples, click on the "Start" button on the bottom left corner of the screen (Figure 24F). 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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Processing Sample Results

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 25)

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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.

Printing Scan to PDF or PNG

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.

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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):

1. Open the uploader. Make sure the correct Expedition is selected or else your data will not upload properly. Samples that have all the necessary files 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. Investigate further. "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. Any problematic samples will either remain in the uploader with a question mark or move to the "Error" folder.
2. Check that the files moved into the archive directory and uploaded into the LIMS database.

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Cleaning Sample Holders

After the scan results are uploaded, clean the scanned sample holders.
Tap out the powder from the holder and, transfer it back into the sample bag or vial. Clean out the holders with isopropyl alcohol and a Kim Wipe.

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Quality Assurance/Quality Control

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.

Removing the Anti-Air Scatter Screen

Before running the NIST standard, carefully remove the anti-air scatter screen. Failure to do this may result in a collision of the drives. The screen is only removed when running the corundum standard to check and adjust system alignment. The anti-air scatter screen should always be on when running samples.

1. 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.
2. Open D4 Tools and click "Online Status".
3. Click the computer icon to connect with the configuration files in the instrument.
4. Click "Positioning Drives" and "Sample Changer Y" direction.
5. 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 and remove the anti-air scatter screen.
6. Open the front door with a socket wrench. Loosen the two bolts on the door and slide the bolts to their opposite side. Carefully let down the door.
7. Remove the anti-air scatter screen. 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.
8. 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.
9. 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".)

Scanning the NIST 1976 Standard and Verifing QA/QC

Running the Scan

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 X342). 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>DIFFDAT1_old computer pre March 2013. Under the "Raw File" tab, set the path to the DATA>IN folder; this scan will not be uploaded to the LIMS database.

Click Startand wait for the scan to finish.

Processing the Scan

1. Open scan (remember the QAQC parameter file Corundum QAQC continuous 20 to 130.dql ran without the anti-air scatter screen).
2. Subtract the background (Figure 29).

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If the RED "ZI correction must be applied" shows up, you will need to open the Configuration and adjust the home position for the 2Theta drive. If there is no message just save the worksheet under a new name and no more action is needed. 

Apply ZI Coorection

Open the Configuration Program on the desktop.

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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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Health, Safety, and Environment

The D4 Endeavor has several safety issues that should be reviewed. Please see the Bruker Manual D4 Endeavor XRay Diffractometer – Introductory User Manual for the list of precautions.

Warnings

Danger: Radiation

The diffraction system has a strong X-ray source, and the direct source beam is very intense. Exposure to radiation for even a fraction of a second can cause severe burns. Longer exposure can cause severe or even lethal injury.
Emitted radiation is minimized by shielding and safety equipment to be <2.5 µSv/h during operation. The enclosure of the diffraction system serves as protection against the scattered radiation produced during the measurement. Ensure the enclosure is configured correctly as follows:

• The goniometer must be fixed in the interior of the radiation protection enclosure.
• The X-ray tube mount must be attached to the goniometer.
• The primary optics must be mounted.
• The radiation protection enclosure must be installed completely.

Danger: High-Voltage

Voltages up to 50 kV are generated, but they are not accessible from the outside of the system. High voltages exist in the high-voltage generator, the X-ray tube, and the high-voltage cable.

Caution: Electrical Shock

When equipment is connected to the mains supply, some terminals of the mains distribution unit may be live. Switch off the external mains supply before opening the side panel; it is not sufficient to simply turn the "Power Off" button.
To prevent electrical shock, turn off the D4 main power supply before:

• Touching components on the main distribution board
• Inserting/removing fuses
• Exchanging the fluorescent tube or USB hub
• Connecting/disconnecting electrical devices to the AC outlets
• Installing or removing an internal or external cooling unit
• Connecting or disconnecting an external water valve

Caution: Moving Mechanical Components

The cover of the sample magazine can be opened at any time during measurement. When the cover is open, sample handler drives stop and stay frozen until the cover is closed again; however, active measurements being made inside the X-ray enclosure will continue.
If the S604 key switch is activated, sample handler drives will not stop when the magazine cover is open and the drives inside the radiation enclosure will continue to run even if the front or rear panel is removed. Do not touch any moving components when the key switch is activated.

Danger: Injury

Goniometer components move quickly during operation. If parts of the radiation enclosure are removed, the goniometer may be accessible during operation.
When opening or closing the sample magazine, hold the cover with your hand until the final open or close position is reached. Do not release the magazine cover in an intermediate position.

Danger: Beryllium

Do not touch the front window of the X-ray detector or the X-ray tube, as they contain beryllium. Beryllium is potentially hazardous if ingested, inhaled, or absorbed through the skin.

Warning: Batteries

Disposal of batteries from electronic boards must comply with safety regulations.

Emergency Stop

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% HNO}3~ 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 hazardous.

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Maintenance and Troubleshooting

Maintenance

Tube Conditioning

 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)

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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.

Turning off the D4 and HASKRIS

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 x-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

To clean the interior of the enclosure and exterior of the detector components, use dry cleaning utensils only. Do not use water or aggressive cleaning agents.
Air flow is critical to maintaining proper operation of the detector electronics. Do not place anything on the controllers that may restrict air flow. Regular cleaning includes removal of air flow restrictions, including dust.

Changing HASKRIS Tank

Regularly check the filter in the HASKRIS tank. If there is a lot of debris it may be necessary to drain the tank and refill with DI water only. The filter can be sprayed off in a sink taking care not to puncture the screening. If the water flow rate to the system begins to drop close to 4 L/minute it may mean there is a clog in the quick disconnect points behind the back panel or the sprayer head in the X-ray tube housing needs to be cleaned.

Checking QAQC Files

Compare the QAQC corundum scan with past results. X-Ray Tubes deteriorate. When the intensity of the Corundum scan is approximately half of what it was at the date of installation it is time to replace the tube. Check the scans for Tungsten lines, if any appear it is time to replace the X-Ray tube even if the intensity is still acceptable.

Making a Parameter File

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).

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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.

Checking Quality of a Scan

A peak should have have a minimum of 5 data points above the halfway up a peak. During an active scan in XRD Commander go to the main 'Adjust' tab and right click in the measurement window. Select 'dots'. The scan changes from a continuous line to the individual data points. Zoom in on a few peaks and count how many dots are above the halfway point on a scan. It is fine to have more than 5 points but less than 5 means the peak shape is not well resolved. If less than five suggest to scientist a longer measuring time.

Troubleshooting

For specific errors or instructions on adjusting or realigning components on the D4 please refer to the D4 hardware maintenance binders in the XRD lab.

Display data on computer screen has flatlined or is nonexistent

Ensure the detector type VANTEC-1 PSD is selected in the "Details" tab of the COMMANDER program.
Ensure the detector setting matches the factory setting and the setting in the Config program. Set the detector to factory settings using the "Set Detector" button.

Angular accuracy peak position data is greater than +0.01° of expected value.

Run the NIST 1976 standard (see Quality Assurance/Quality Control) and import the values into the instrument verification spreadsheet. Perform a Zi correction if needed. Calibration of the VANTEC-1 detector may be required. See the detector manual.

Poor instrument resolution (FWHM > 0.065° of the 104 reflection of NIST 1976)

Repeat alignment of the 2 DOF mount for the VANTEC-1 detector.

Scan outside software limits

Using fixed scan mode, the start to stop range is determined by the configuration and cannot exceed the geometry angle set in Config (max = 12°).

Appendix A: Running Samples in Manual Mode

At some point it may be necessary to run samples in manual mode, for example the automatic sample grabber is not working. Manually loading samples does require the user to load in samples one by one, making a more labor intensive process.
To run the D4 on manual mode:

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