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Vendor’s service manual is located on Confluence in the XRD Lab Notebook AERIS and on XRD Desktop>Aeris>Aeris Diffractometer References.  Also on the orange Panalytical USB.  Backup PDF’s of the service manual are in IODP Share> IODP Technical Manual

Introduction

The X-ray Laboratory onboard the R/V JOIDES Resolution performs diffraction analyses of minerals, clays, and rock powders.

The X-ray laboratory uses the benchtop Malvern Panalytical AERIS Research Edition XRD. Associated software, HighScore Plus allows for powder diffraction analysis of minerals, including peak matching, mineral, and chemical compound identification. The X-ray Laboratory provides the scientist with a quick and reliable tool for mineral identification. In addition, XRD data can be used to determine mineral proportion. 

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.

Instrument Apparatus and Hardware

• Benchtop Malvern Panalytical AERIS Research Edition X-ray Diffractometer (XRD)
• Goniometer

  • The goniometer is the core of the diffractometer. The goniometer radius is 145 mm. The minimum step size for the angle of incidence (ρ) and the scattering angle (2θ) is 0.001°.

• X-ray Source, Copper (Cu)
  • The X-ray tube is made of ceramic. The anode is at a maximum of 40 kV above ground potential and is cooled with a glycol mixture of 25% glycol and 75% water.

  • The window of the X-ray tube is made of beryllium and is 300 µm thick.

• PIXcel1D-Medipix3 dectector
  • Soller slits
  • Beta filter
  • Divergence slits
  • Beam mask
  • Beam knife
  • Si standard
  • Corundum standard
• Sample Holders

Safety

When properly operated within the specifications, the radiation level at a distance of 10 cm from the outside surf ace of the instrument is less than 1 µSv/h.

The cover has a door lock to prevent accidents. As a safety measure, you cannot open the shutter of the X-ray tube if the cover is not correctly closed and locked. Other safety precautions are that you cannot open the cover when the shutter is open, when a goniometer arm moves, or when the instrument initializes.

You can open the lid while the X-ray warning lights are on.  The shutter of the tube remains closed which makes it safe to do so.  The instrument will not allow you to run a sample or open the shutter while the lid is open (Figure 1).

Figure 1. Aeris touchscreen safety information. The closed circle icon on the screen indicates when the shutter is closed and it is safe to open the lid.

The "X-RAYS ON" lights on the top corners of the instrument and 2 more on the inside of the cover give a visual warning when high tension is applied to the X-ray tube. The "X-RAYS ON" lamps are 'fail safe' lamps and they are part of the safety circuit. The result is that if one of the lamps fails, no high tension can be applied to the instrument.

When you turn the HT key switch clockwise, the HT generator goes on. If the instrument is energized and the safety loops are closed, the HT generator is automatically set to 40 kV, 15 mA or 40 kV, 7.5 mA.

When the HT generator is in the ON condition, the indicators are as follows:

• The kV and mA indicators on the touchscreen show the settings (see Figure 1)
• The four X-RAYS ON lamps on the corners of the instrument are on.

When you turn the HT key switch counter-clockwise, the HT generator goes off.

The HT key switch is also used to reset the Xsafe system. If the HT key is removed from the instrument and an unsafe condition is sensed, you cannot switch the high tension on again.

NOTE: The HT key can be removed and kept in a safe place.

Aeris Start Up

The main power switch is on the rear lower right-hand side of the instrument (Figure 2A). This can generally be left on. The unit is plugged into the UPS power box and that should remain on at all times. The vendor recommends we leave the entire instrument and X-ray key switch on all the time. If restarting is necessary to clear an error, there is no need to toggle the key switch. Obviously, this should be done for dry dock, or when it’s totally necessary, we can shut everything down. BUT, it’s not good to be turned off and on often.

Figure 2. Turning on the Aeris XRD. A) Power switch in the back right of the instruments. B) Push the green Power button on the right of the screen to power on the screen. Turn HT keyswitch clockwise to start the X-ray generator (the key is vertical when it is ON). 

1. Make sure at least one sample holder spot is empty before turning on (to allow the sample changer to zero itself).
2. Turn the Aeris front computer on by pressing the power button on the right side of the screen (Figure 2B). Let it initialize. Sample changer arm should move and initialize.
3. Screen will prompt you to turn the key-switch, turn it clockwise and the "X-RAYS ON" yellow lights around the instrument will light up. The Aeris screen goes to sleep when not in use, just move the mouse or touch the screen.
4. To turn off the instrument, press the power button on the side of the screen (Figure 2B), and then toggle the key-switch counter-clockwise.

Sample Preparation and Holders

Aeris sample holders cannot be interchanged with the Bruker sample holders. The size is slightly different and they are magnetic which lets the machine to know there is a sample in the slot.

Bulk Powder Backloading

Most common method is backloading. The sample holder is in two parts, the top ring (B) and the base (C) which the top ring clips into and is loaded using the sample table (A) which is the small device with a center platform and three round buttons around it (Figure 3).

Follow the steps below along with the figures below to pack and assemble the backloaded sample holders (Figure 4).

1) Place the top ring upside down on the sample prep table and clip it in by pressing the button on the side. Take care not to scratch the center platform.
2) Mound the powder up slightly in a conical shape.
3) With a blade or glass slide make chopping motions on the powder to help spread it out evenly.  Press it down with the cylindrical press.
4) Scrape off the excess with a blade or glass slide.
5) Brush away excess powder so that the outer ring is clean for attaching the sample holder base.
6) Press and clip the sample holder base into the top ring. It should snap in cleanly and easily.
7) Turn the entire sample prep table upside down, resting the sample holder base on the countertop, and press the release button on the side to release the completed sample holder. Sample surface should be flat and flush with the edge of the holder.  With the brush or kimwipe, clean any powder off the ring surface because that comes in contact with the sample spinner.

Tips:

If the powder sticks to the sample table when you flip it upside down to release, try it again with a piece of weighing paper placed on top of the platform and then clip the top ring in. If you don’t have enough power to fill the sample holder, after pressing down with the cylindrical press add one of the cardboard spacers so that the cardboard spacer is flush with the ring top and then clip in the holder base (Figure 5). Also note that if there is too much sample the back of the holder will not attach.

Figure 3. Backloading sample holder (view from the top). A) Sample preparation table, B) Top ring, C) Base which the top ring clips into.

Figure 4. Sample preparation for Aeris backloading sample holders.

Figure 5. If there is not enough sample powder to fill the holder (A), use a cardboard spacer (B) to fill area

Cleaning and Disassembling Sample Holders

When the measurement is finished, first check the scan to make sure the counts and other parameters are satisfactory. If the scan is acceptable, pour the sample back into the sample bag. Next, remove the top ring. The ring is magnetically connected and should pop off by hand very easily (Figure 6A). Disassemble the rest of the sample holder (Figure 6B). In Figure 6 a cardboard spacer was used. To clean the sample holder, rinse each piece with DI water and then with isopropyl alcohol with kim wipes.  Isopropyl alcohol should remove the marker (Sharpie) label on the front of the sample holder. Once clean and dry, store the sample holder back in the box or use it to make next sample.

Figure 6. Disassembling the sample holder.

Small Sample Amount and Slurry/Smears

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 silicone disk inserts or Aluminum spacers. Although not useful for semi-quantitative analysis, this method is useful for rapidly determining mineralogy.

1. Place a small amount of sample powder in the center of a silicone 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.

Use the sample rings, clip, aluminum spacer, and zero background silicon disks (Figure 7).  Do not scratch the mirrored silicon disks, always use an aluminum spacer so the clip does not scratch the surface.  A tiny amount of powder can be mixed with alcohol to make a slurry and then smeared in the center of the silicon disk.

Figure 7. Sample ring, clip, zero background disk and aluminum spacer.

Turn the ring upside down and place the silicon disk in the indentation.  Use the flat side or the side with the shallow well for your sample (amount of sample will determine if you use the flat or well), depending on how much you have.  Put the aluminum spacer on the silicon disk, then press the clip in and turn it to secure both in place. 

If doing heating steps (clay analyses) remove the disc with sample and place on tray to go in the oven. DO NOT heat the sample holders they will deform and will no longer be of use.

 Don’t heat the holders! Only silicon disks can be heated!

Ceramic disc: Ceramic disc are specifically for clay separations. The ceramic is porous and preferentially orientates the clay crystals. We currently have not developed an in-house sample preparation method for using the ceramic disc.  Creating our standard slurry and drying them in the desiccator should be ok. Another method is to dry using a vacuum system, which has not been developed on board. 

Creating/Editing A New Measurement Program

With Aeris XRDMP creator (Figure 8) you can open previous expeditions scan parameters or set up a new parameter file (Figure 9). This is where the scan range and step time is set. Name your file with the expedition number for future reference. If starting off with one of the Panalytical predefined programs located in C: > Panalytical > XRDMP Creator > Panalytical Predefined Programs > Aeris and listed below in the section "Importing a measurement program to the Aeris XRD", remember to only use the files marked Cu Mineral (copper X-ray source which is what we have). The Co indicates a cobalt source that our Aeris XRD does not have.

Figure 8. Aeris XRDMP Creator (measurement parameter set up) icon

Figure 9. Home Screen: Measurement Program selection window to create or open a measurement program

Scan Parameters Setup

Scan Parameters include the range of scan angles and step time. Vendor supplied scan parameters for Bulk and Clay analyses are listed below in the section "Importing a measurement program to the Aeris XRD".

Discuss with your scientist the scan parameters (scan angle range and step time) they wish to use for the samples (Figure 10). Direct the scientist to previous expeditions to obtain scan parameters or review previous expedition's files on the XRD PC for examples. The scientists can also decide if they wish a single scan or repeated scans for a sample. Save the measurement program with a name including the expedition number and selected parameters. For instance, in Figure 10 below, the measurement program is named "X391 5-100deg 1/4 div 21 min" to describe a measurement program used during Expedition 391, with a scan angle range between 5 and 100° 2θ, a divergence slit of 1/4°, for an estimated time of 21 minutes per sample.

Figure 10. XRDMP Creator. Edit or create new scan parameter files: A. Setting scan angle range and step time, B. Single or Repeated scans (note that the estimated time is per sample), C. Save button, D. Home button

Hardware Setup

The Excel file Aeris Setup Guide (Aeris Setup Guide.xlsx ) helps the user choose the best hardware setup for your scan parameters (Figure 11). Hardware is generally only changed when your scan angles change. For example scanning at angles less than 5° 2θ you will need to lower the knife (a.k.a. anti air scatter screen on the Bruker). You will scan at lower angles for clay identification, so switching from bulk sediment analyses (angle range of 5 to 100° 2θ) to clay analyses (angle range of 2 to 30° 2θ) will require a hardware change. Use the Aeris Setup Guide to determine the best hardware set up.

That being said, if you did not change the hardware, you would not damage the instrument, and the diffractograms may be ok, but they could be better if you follow the suggestions for hardware from the setup guide. Start in the first Excel tab, "Slit Guide" and enter the desired information such as start and end angles, the diameter of the sample holder and the sheet will provide suggestions for recommended hardware options. The other values provided in the Excel sheet are not something we need to change or take into account for our XRD scanning onboard. 

Figure 11. Aeris Setup Guide for hardware. The scan angles will determine the beam knife height and other hardware such as divergent slit. 

Changing Hardware 

Adjusting the hardware will allow for optimum results. Use the Aeris Setup Guide.xlsx to obtain the best setup for the scan parameters as discussed above in "Hardware Setup".

If you change the hardware, please remind to update the hardware settings in XRDMP Creator as well (Figure 12).

Figure 12. Changing hardware settings in XRDMP Creator: A. Divergence slit, B. Beam mask, C. Spinner speed, D. Save button

To access the internal drives and hardware:

On the Aeris touchscreen, press the 'Menu' button on the top left corner and press the Advanced mode option (Figure 13). A password is needed to go to the Advanced Mode (Figure 14).

Password is: panalytical

Figure 13. To go to the Advanced Mode. Press 'Menu" (A) then (B). Note that the lock indicates protected access by password.

Figure 14. Entering password to go to the advanced mode

In the Advanced Mode, select 'Manual Control', and then 'Unlock Cover' (Figure 15).  Then lift the cover slowly until it stops on the ceiling. Use canned air to dust off any parts before inserting, the divergence slits tend to get dust in them. 

Figure 15. Unlock cover to access the hardware

Beta Filter

Typically a beta filter is not needed on the source (tube) side. Two filters are supplied: a Ni and Cu filter (Figure 16). Ni filter may be used to run the Si standard blank for a system check. If you do need to insert or remove this beta filter it should slide in an out completely freely without resistance and proper placement is sliding all the way in. The writing will be facing the beam knife. 

Figure 16. A. Ni and Cu Beta filters, B. Writing (circled in blue in A) facing the beam knife 

Divergence Slit

You may need to change the divergent slit to run a low angle scan (Figure 17). For instance, a 1/4° slit is typically used for bulk samples, and a 1/16° for clay speciation. There is writing on both slides of the slit, but when looking at it from the side of the beam knife the writing will be right side up. Slide it in until the first small click. It is possible to push it further and feel another click but that is too far and should be backed out. 

Figure 17.  A. Set of divergence slits, B. the writing " 1/2º " appears upside down and this is correct. 

Beam Mask

Beam mask may need to be changed if the diameter of the exposed sample is different in different sample holders (Figure 18). For classical measurement with backloaded samples, a beam mask of 20 mm is usually used. The writing should be facing the beam knife (Figure 18B). It should feel tight when inserting or removing, you need to put your finger in the opening to pull it out.  When inserting it should slide all the way down, no clicks or anything but you won't be able to push it too far. The picture on Figure 18C is what it looks like fully inserted.  

Figure 18. A. Beam masks, B. Inserting beam mask, C. Fully inserted beam mask with diameter information facing the beam knife.

Beam Knife

Beam knife reduces air scatter and noise in the detector, it may need to be changed for low angle scans or system checks. Knife goes in the position you can read. 

Figure 19. Beam knife

Beta Filter (detector side)

This Ni filter should never need to be removed except when doing a Factory Acceptance Test or instructed to do so by PANalytical service techs for troubleshooting.  When sliding in and out it should slide freely.  When inserting you will feel a click in the middle and continue to push all the way in.

Image AddedFigure 20. A. Ni beta filter for the detector. B. NEVER remove from the detector unless necessary.

Importing A Measurement Program to the Aeris XRD

1. Open Navigate to C:/ PANalytical/XRDMP Creator/ to open an existing file on the XRD computer to edit or rename by clicking OPEN and navigate to C:/ PANalytical/XRDMP Creator/, or . OR open the XRDMP creator software and open and a previous parameter file. See 'Creating/Editing A New Measurement Program' and Figure 10 above. Make any needed edits to the start and end angles and click 'Save As and rename ' (Figure 10). Rename for the current expedition.
2. Save the creator parameter file onto a USB drive. The USB can then be inserted into the side of the Aeris screentouchscreen (see Figure 2B).
3. Click on the Menu button and select 'Advanced Mode'. The password is panalytical
4. Click on Menu again and select 'Data Management. Then click Import Programs.' (Figure 21, arrow A). Select the 'Import Programs' tab (Figure 21)
   
5. Source should auto populate as the USB drive (Figure 21, arrow B). Select the measurement program (arrow C), and then click Import Program.Remove the USB drive and click 'Import Programs' (arrow D)
   
6. Click Menu to return to Measurement screen.

Figure 21. Importing a program from a USB drive to the Aeris XRD. 

PANalytical recommended measurement programs

PANalytical recommended measurement program settings are as follows

. This is from a document named AERIS_Suggested_Config.docx, from the factory/ installation. Please update your parameters as necessary.

Based on

this document, for bulk samples the scan rate is 40 sec/step (

leading to a 17-min scan from 5 to

90º 2θ) and you might use a scan rate as slow as 200 sec/step for really challenging samples (or repeat the scan at 40 sec/step five times and sum the results)

.

Bulk Samples Scan Parameters

• Start angle: 5 deg 2theta5º 2θ
• End angle: 90 deg 2theta90º 2θ
• Step Size: 0.0108664 deg 2theta0108664º 2θ
• Time per step: 40 sec/step (longer as needed)
• Incident (Tube) Side
• Beta Filter: None
• Soller Slits: 0.04 rad
• Divergence Slit: ¼ deg
• Beam Mask: 20mm
• Sample Stage
• Beam Knife: Beam Knife high
• Spinner speed: 1 rps
• Diffracted (Detector) Side
• Anti-Scatter Slit: AS Slit 9mm
• Soller slits: 0.04 rad
• Beta Filter: Large beta filter Nickel
• Detector
• Type: PIXcel1D-Medipix3 detector
• Mode: Scanning line detector (1D)
• Active Length: 5.542 deg 2theta542º 2θ
• PHD levels: Use defaults

Clay Speciation Scan Parameters

• Start angle: 2 deg 2theta2º 2θ
• End angle: 30 deg 2theta30º 2θ
• Step Size: 0.0108664 deg 2theta0108664º 2θ
• Time per step: 40 sec/step (longer as needed)
• Incident (Tube) Side
• Beta Filter: None
• Soller Slits: 0.04 rad
• Divergence Slit: 1/16 deg
• Beam Mask: 20mm
• Sample Stage
• Beam Knife: Beam Knife low
• Spinner speed: 1 rps or NONE (if peaks seem broad because sample is wobbling)
• Diffracted (Detector) Side
• Anti-Scatter Slit: AS Slit 9mm
• Soller slits: 0.04 rad
• Beta Filter: Large beta filter Nickel
• Detector
• Type: PIXcel1D-Medipix3 detector
• Mode: Scanning line detector (1D)
• Active Length: 5.542 deg 2theta 542º 2θ for fast (8 min) or 0.978 deg 978º 2θ for slow (35 min) with better background
• PHD levels: Use defaults

Very Low Angle Data Scan Parameters (clays) (Note: the Bruker instrument should not be used to scan at angles <

5º 2θ)

• Start angle: 1 to 0.5 deg 2theta5º 2θ
• End angle: 30 deg 2theta30º 2θ
• Step Size: 0.0108664 deg 2theta0108664º 2θ
• Time per step: 40 sec/step (longer as needed)
• Incident (Tube) Side
• Beta Filter: None
• Soller Slits: 0.04 rad
• Divergence Slit: 1/32 deg
• Beam Mask: 20mm
• Sample Stage
• Beam Knife: Beam Knife low
• Spinner speed: NONE (if peaks seem broad because sample is wobbling)
• Diffracted (Detector) Side
• Anti-Scatter Slit: AS Slit 9mm
• Soller slits: 0.04 rad
• Beta Filter: Large beta filter Nickel
• Detector
• Type: PIXcel1D-Medipix3 detector
• Mode: Scanning line detector (1D)
• Active Length: 0.5 to 0.109 deg 2theta 109º 2θ (make the active length slightly smaller than ½ the start angle)
• PHD levels: Use defaults

Scanning A Sample in Aeris XRD 

1. Place sample into one of the six slots on the sample changer. Be careful not to touch the center arm that comes in and out of the shutter door.
2. Click on the MENU button in the top left of the screen and go to Measurement.
3. The 6 circles along the top of the screen correspond to the six sample slots.  Click on an active one to get started. (You can't click on one that is empty). (Figure 12).
4. Select the appropriate measurement program in the dropdown.
5. Use the barcode scanner (on the right side of the Aeris) to scan the sample ID label into the sample ID field, or type it in with the keyboard. The file name will auto populate. Add any comments as necessary such as clay separation, heated, standard, test. 
6. NOTE: If you are running clay samples you will end up with multiple runs that have the same sample info if you do not add extra info in the sample name.  To make sure you can differentiate this in the database you must add extra text before the TextID so that it looks like the examples below.  Do this step on the Aeris touch screen so that it gets included in the metadata of the file.  MUT will recognize the files written this way as long as there is a .xrdml and .jpeg with matching file names.  There is a character limit on the Aeris so you may shorten the extra text to something like heat, or glyc. U1565A_1R1_3_4_clay_WDGE11053881.xrdml, U1565A_1R1_3_4_heated_WDGE11053881.xrdml, U1565A_1R1_3_4_glycolated_WDGE11053881.xrdml
7. Click Start and the program will run right away. The screen changes to a live view of the scan in progress (Figure 13). If the sample is not in the sample changer you will not be able to click Start.
8. While the instrument is running the first sample, click on another circle where there is a sample and add the sample information and you can click "Add to Queue". 
9. When the sample has finished running, click on Next Measurement and you can add the next sample.

• Once a sample is added to the Queue you cannot cancel it.  If you decide there is a mistake and you don't want to run a sample that has already been added to the queue, simply remove the sample from the sample changer. When the instrument gets to the empty slot it will show a warning that no sample is present and skip to the next sample.  Then you can place a sample back in the slot, click on the corresponding circle, and enter the new information.
• You cannot enter any sample information into a slot that doesn't have a sample holder placed in it.  The sensor must sense a sample holder and then you will be able to add information and add it to the queue.

Uploading Data (confirm the correct files and update the info below)

Viewing and Analyzing Scans

• Run the corundum standard at the beginning, middle, and end of every expedition and compare to the original file in XRD Data > QAQC. 
• Open the scans on top of each other in HighScore and they should line up exactly on top of each other.  Over time the peak intensities may reduce slightly and that is normal.  PANalytical service technicians advise that when to replace the x-ray tube is at our discretion if we feel the intensities are too low. 
• If the scans do not line up you must figure out how much to correct the x-axis offset in HighScore and that must be done to any data files that might be affected. 
• Email PANalytical service team that the x-offset must be corrected and they will be able to remote in to the instrument to make those corrections.  See Laboratory Notebook for /wiki/spaces/LN/pages/7338165984.

Maintenance 

• Use a 6mm allen key to remove both the vent plug and fill plug.
• Use the gooseneck refilling bottle to slowly add DI water into the fill plug up to the high mark. Do not overfill. Aeris does not need a lot of water (Figure 19).
• Replace the fill plug and vent plug. Replace the side panel.
• Aeris needs water added in the middle and end of each expedition when being used regularly.

Network setup

Troubleshooting

• Check the wires to make sure they are secure.
• The data will not export to the computer if the network is down. See the MCS if there is a network issue.
• After the instrument is turned off and back on, the file transfer does not work and needs to be reconnected.
• To be able to transfer files you will need to go to "Advanced Mode" password is "panalytical"
• Once in "Advanced Mode" go to file, menu, and minimize screen
• In the bottom right hand corner you will see a red "x". Click on this icon and it will open up the file. You will see "XRD Data"
• Double click "XRD Data" file, it will open and reconnect itself.
• The files will be able to be transferred again.
• If the issue persists see the MCS.