Exp397P/T X-Ray Technical Report

Exp 397P - Tie up, Cape Town, SA, 7 Aug - 10 Sep, 2022 - Jessica Riekenberg

Exp 397T - Transit, Cape Town, SA to Lisbon, Portugal, 10 Sep - 11 Oct, 2022 - Bridgette Cervera

Summary

Expedition 397P consisted primarily of the Bruker service visit and the 'Kick the Tires, Light the Fires' (KTLF) procedures surrounding the upgrade of all instrument host and workstation computers, including testing all data generating systems using play samples, uploading and downloading data. For X-Ray, this meant the XRDs, pXRF, and LOI data. Early during the tie-up period, a Bruker service technician came to service the D4 Endeavor XRD as it would randomly shut off. This service visit was successful in repairing the D4, with the diagnosis being a failing power supply in the computer rack. The X-ray tube was also replaced at this time, as well as general preventative maintenance. Further testing of all the various instruments and machines in X-ray was successful, with the exception of the Bruker Tracer5 pXRF, which is currently inoperable and probably needs a new onboard PC.

Expedition 397T

Sample Totals

For KTLF, only play core and test samples created or made up under Project 999, site U9397 were analyze on the XRDs and for LOI. These were used to test that data could be generated by the instruments with the new instrument host computers, that the data could be successfully uploaded and download without alteration or error. This was successfully accomplished. All raw data generated was uploaded to \IODP_Share\Exp397P KTLF.

Instrument Updates

Aeris

The Aeris has been running and analyzing without issue since early in the tie-up.

When the instrument host computer was replaced, the connection was reestablished with scans automatically being sent to C:\XRD Data\IN. These files were uploaded and downloaded without issue.

Daily runs include either a corundum or silicon standard. A standardized naming convention was established for these two standards: Corundum YYYYMMDD and Si Std YYYYMMDD. This format will make it easier to sort the files and identify which standard and when it was analyzed. At least one of these should be analyzed at the beginning and end of each shift while at sea (if samples have not been analyzed), as this is when we tend to see errors if the instrument is not run daily.

Bruker D4

The service visit from 15-17 August was successful in repairing the D4 Endeavor. Tinus Schutte (Bruker technician), was able to diagnose the problem as a failing power supply in the CPU rack. While a new power supply was being sent from Johannesburg, Tinus replaced the X-ray tube and performed general preventative maintenance and checks of the instrument. The beam was aligned to within satisfactory tolerances and Tinus said everything else was in very good order. Replacing the CPU power supply was very straightforward with no issues encountered. During this service visit, the D4 was unbolted and rotated in order to access the right panel. Before the D4 was secured again, a vacuum was used to remove any build up of dust inside the lower instrument panels. The fans under the CPU rack and the X-ray generator were inspected and found to be relatively clean with very little dust. After the service visit, the sample handler table was also cleaned with vacuuming and a damp cloth.

PC Mover was used to transfer the Bruker folders and files from the old computer to the new XRDIH. During this process, however, approximately 30-40 files were missed. This resulted in the D4 being unable to analyze samples entered into the 'Jobs' tab of XRD Commander as the sample would be loaded, then immediately unloaded an error displayed (Fig. 1). Once the files were restored, this issue was resolved.

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Figure 1. Error encountered in XRD Commander 'Results'.

Among the missing files was also the installation files and executable for XRD Wizard. However, once these files were replaced, XRD Wizard could still not run as there was 'Missing side-by-side configurations'. With MCS Thomas's assistance, it was discovered that the XRD Wizard application needs Microsoft Visual C++ Runtime installed on the computer to run. Once this was installed, the program opened and operated with no issue. 

Bruker Tracer5

The Tracer5 worked well during initial testing of play samples for KTLF. While learning to operate the device, multiple measurements were made and the various methods of data processing were investigated. While testing, however, it was discovered that there was quite a bit of data saved on device in it's internal memory, in the main 'Data' folder and in the 'Archive' data folder. As the capacity of the device is only 512MB (about 2500 readings), it was running quite slow when trying to access these folders. We also discovered that several folders of measurements were saved in multiple places on the device. The data was copied from Bruker → Data, Bruker → Archive → Data, and the USB to the desktop of the laptop. However, while deleting data from the device, an unexpected execution error popped up. The menus were navigated to 'Log off' and the device was powered off. Upon attempting to restart the device, the laptop indicated the 'USB was not recognized' with further explanation that the device was malfunctioning. The power light illuminates green and you can hear it initializing inside, but the screen remains black and the interface program will not start up. Several attempts to restart and disconnect/reconnect to the laptop were attempted with no different results. Inquiry with Rick from US Analytical and the South African hand held XRF contact indicate that the onboard computer has been corrupted or is faulty, potentially due to the amount of data that was on the device. The current plan is to prepare the device to be shipped to the Bruker Nano office in Germany from Lisbon after the ship arrives. Ideally, the device will be fixed and returned to the ship at Tarragona in time for Exp 398.

As part of the user guide for this device, data should be transferred off the device every few weeks during an expedition to prevent reaching the maximum internal memory, which the device gives no warning is happening. This should be incorporated into an established method for saving and exporting the data that does not save data files in multiple places on the device and actively transfers them off in a consistent manner.

A new tool was printed by C. Furman to aid in disassembling the new pXRF sample cups. These sample cups are similar sized to the previous, but have a more streamlined profile making them more challenging to get apart. Also, the sample cups do not fit in any of the previous tools. Although they are similar sized, the caps and rings are not interchangeable between the 2 smaller sample cup types. This disassembler (Fig. 2, A and B), dislodges the cap from the sample cup body while also dislodging the ring in a single push down of the plunger (Fig. 2, C-F). 

A) B) C) D) E) F)

Figure 2. pXRF sample cup disassembler. A) Base and plunger, B) Plunger in base, C) Sample cup cap down into the base, D) Plunger fit into sample cup in base, E) Plunger stroked fully down, F) Disassembled sample cup.

To address the inability of the current pXRF laptop used with the Tracer to connect wirelessly to the network, MCS Thomas prepared a ship laptop to be used with the Bruker pXRF going forward. This new laptop can connect to the network wirelessly and access the OES and Uservol without the use of a blue ethernet cable. All relevant software was uploaded to the laptop, but this laptop has not been utilized as the Tracer 5i is inoperable and the connection with the device cannot be set up further. The Bruker Instrument Tools application is accessible without an administrative password.

Dismembrator

The dismembrator worked fine on several samples for KTLF. The instructions indicate that the 'Continuous' mode (Fig. 3, Box) must be selected, however, this mode can only be stopped manually by pushing the 'Start/Stop'. If the 'Time (min/sec)' mode is selected (Fig. 3, Arrow), then the probe will shut off automatically after approximately 1.5 minutes. This was added to the 'XRD Sample Preparations Clay Separations' manual.

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Figure 3. Dismembrator power supply.

Muffle Oven

The muffle oven worked as expected during KTLF. All of the saved programs were determined and posted on the oven door for reference. The programs are as follows:

• Program 1: Ramp up to 900°C at 3°C/min and hold for 1 hour. Then ramp up to 1025°C at 3°C/min and hold for 4 hours.

• Program 2: Ramp up to 950°C at 3°C/min and hold for 4 hours.

• Program 3: Ramp up to 550°C at 3°C/min and hold for 1 hour.

• Program 4: Ramp up to 900°C at 3°C/min and hold for 1 hour. Then ramp up to 1025°C at 3°C/min, no hold.

These were added to the 'ICP Sample Preparation' manual.

Mixer Mill

The mixer mill was serviced by ET Garrick. The mounting was tightened and new rubber was added to the springs, as well as light maintenance of appropriate motor areas was performed. The mill now runs more quietly and vibrates much less. It worked fine when testing sample material for KTLF.

Software Updates

All software for instruments should be backed up on the TAS server (TAS\dml\software\labsystems\XRD Software). This folder was updated with the latest software for the Aeris, HighScore Plus, Bruker (DIFFRAC.Plus), Bruker Tracer pXRF, and the Databases phase identification (mineral databases). 

DIFFRAC.Eva

For the 5 computers with DIFFRAC.Eva, some were able to open Eva without further action after PC Mover was used, however, some were not able to find their license. The licenses are located on a dongle that is in the back of each of these computers. For the computers that could not verify their license, it was necessary to reinstall the CodeMeter program that interacts with/verifies the license on the dongle. Once reinstalled, the network server access must be enabled. Instructions for this process are saved with a copy of the software files on the TAS server. It was also necessary to recompile the PDF2 mineral database for use in the 'Search/Match' feature of Eva and enable it via Eva's 'Settings' icon in the 'Database' tab. Instructions for this process are also saved on the TAS server.

HighScore Plus

HighScore Plus was reinstalled fresh on the new XRDIH from files sent from Malvern Panalytical. A license activation was used in this process with at least 1 activation remaining for this license. XRDMP Creator and DataViewer, both requiring no activation, were also installed. Further, to be able to utilize the ICDD PDF-4/Axiom mineral database for scientists performing the 'Peak Search & Match' function, a new registration code was applied for from ICDD. Once this was received, the database was activated and enabled within HighScore Plus. Instructions and additional documentation for this process are saved with a copy of the software files on the TAS server. A hard copy of the registration.txt file and the received text indicating the new registration key are stored in the envelope with the 'XRD Computer' PDF-4/Axiom dongle. This database will expire in September 2022 and is in the process of being renewed.

Mettler Toledo (Balance Master 5000)

While testing the balances with LOI measurements for KTLF, it was discovered that when sample material was added to the crucible, the weight decreased instead of increasing. The problem was revealed to be that, upon fresh installation after the XRDBL computer was replaced, the COM ports in the 'Configuration' section of the software defaults to selecting 'COM1' for the first COM and then 'COM2' for the second COM. These should actually be switched so that the proper weight is referenced when measure sample material; 'COM2' should be listed as the first COM and 'COM1' should be listed as the second COM. Further, the software must be closed and reopened for this setting configuration to be implemented.

MUT

When attempting to upload test data from the Aeris XRD, MUT was not recognizing .jpg file names that contained text within the sample name. Example: U9397_12X1_33_35_clay_CYL11711231.jpg. This text is important for samples that we analyze, treat (such as heat or glycolation), then reanalyze. After notifying a developer, this problem was resolved. For Aeris XRD data, MUT is looking for paired .xrdml and .jpg files for each text ID. For Bruker D4 XRD data, MUT is looking for three files with matching text ID: .raw, .uxd, and .png. 

Spreadsheet Uploader

When uploading test data, the results were showing up in LORE not as expected. After discussion with a developer, it was clarified that when using the LOI spreadsheet upload template, the 'Replicate' column should be left empty. If left empty, this value will default to zero, which is desirable, and each sample measurement will be represented properly. If true replicate data for one sample (not redoing the sample) is being uploaded, then the replicate numbering in the 'Replicate' column should begin at '0', then '1', then '2', etc. If number begins at '1', an extra line will be created in LORE that does not contain sample data. Further, do not upload measurements more than once (duplicate data) as each upload session is considered a unique event and there is no check that the measurements are identical. This was updated in the 'ICP Sample Preparation' manual.

Lab Updates

Alumina Ceramic Crucibles

As use of the alumina ceramic crucibles was highlighted last expedition, this information was added to the 'ICP Preparation' manual in the 'LOI' section. These crucibles should be used when carbonate-rich or sediment samples are analyzed for LOI. Carbonate-rich and sediment samples usually react with the quartz crucible, which contaminates the sample. Therefore, it is desirable to have an alternate material crucible available if this occurs and the sample can be re-ignited (if enough sample material remains). It may be prudent to advise scientists of this occurrence so that they can forewarn if a sample they have chosen is carbonate-rich and the unnecessary waste of quartz crucibles can be avoided. To prepare for their use, a cleaning method was formulated and added to the instructions for cleaning crucibles in the 'ICP Sample Preparation' manual. The crucible cleaning procedure now reads as follows:

 'Cleaning the Quartz or Alumina Ceramic Crucibles:

1. Wash the crucibles with DI water and a small piece of a scouring pad (no soap).

2. Rinse several times with DI water.

3. Place crucibles in a 10% HNO₃ bath for 12 hr. If in urgent need, the quartz crucibles can be soaked a minimum of 2 hours, but extra flux blanks will need to be made and added to batches that use these crucibles.

4. Rinse the quartz crucibles 3 times with DI water after the acid bath. For the ceramic crucibles, rinse 3 times with DI and then soak them in a large beaker of DI water for 4-6 hours to dilute the acid absorbed by the crucibles.

5. Dry the either type of crucibles in the oven at a maximum temperature of 60°C. For the ceramic crucibles, heat them to 800°C in the muffle furnace for 2 hours and allow to cool to room temperature before removing.'

pXRF Supplies

All of the pXRF supplies stored in the Upper Tween Storage (UTS) area have been relocated to the X-ray lab. This includes XR5111 (Sample cups), XR5112 (Film, polypropylene circles), XR5113 (Filter paper, 2.4cm circles), and XR5114 (Film, Ultralene rolls). These items now appear on the FXL check-out sheet and are located on the high shelf. Item XR5115 (Polystuffing) has been inactivated as we now use the 2.4cm round foam spacers to fill the space behind the sample material in the sample cups.

Freight

Received

• 6 small rubber pads for SPEX Shatterbox (XR0189)

• 5 diamond grinding discs 220 grit (XR5072)

Off-going

• Bruker Tracer5 pXRF device for repair (from Lisbon).

Ordered

To receive

See the XRD Laboratory Notebook for current comments and further detail on all XRD/XRF lab equipment at the close of the expedition.