Training and maintenance videos can be found on the XRD technician computer, Desktop/XRD_ICP Prep Documents/Bruker TRAINING VIDEOS
Table of Contents
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The X-Ray Laboratory onboard the R/V JOIDES Resolution (Foc's'le deck) performs diffraction analyses of minerals and rock powders. The laboratory uses a Bruker AXS D4 Endeavor XRD (a.k.a. Bruker or D4) and a PANalytical Aeris XRD (a.k.a. Aeris) diffractometers (Figure 1).
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Figure 1. A. Bruker D4 Endeavor XRD. B. PANalytical Aeris XRD in the X-Ray lab
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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 (Figure 2):
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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
Figure 2. Bragg's law
References - Further reading
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.
Books are available in the X-Ray lab upon request.
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This section presents instrumental characteristics of the Bruker AXS D4 Endeavor X-ray diffractometer (XRD) in the X-Ray lab. For the Aeris, see the Aeris Advanced User Guide.
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- Goniometer
- X-ray source (sealed vacuum tube with line focus): on the JR, a Siemens ceramic X-ray tube KFL Cu-2K, 2.2 kW, 60 kV, 0.4mm x 12mm is used
- Tube housing (ceramic body that protects the tube and shields from X-rays)
- Mount
- Sample holders
- Vantec-1 detector
- Optics
- Slit systems
- Haskris water chiller for the X-ray tube
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 (Figure 3).
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During the measurement of the characteristic diffraction pattern of a polycrystalline sample, the sample rotates with a constant angular velocity around the goniometer center (θ circle). Simultaneously to this θ rotation the detector rotates at double angular velocity around the goniometer center (2θ circle) and sample, respectively. The 2θ rotation is perpendicular to the measurement plane as well and concentric to the θ circle. In other words, the diffraction angle 2θ where the detector is positioned is the angle between the primary beam direction and the diffracted beam direction.
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.
Component | Specification |
Measuring circle diameter | 401 mm |
Operating mode | Vertical, θ/2θ |
Max angular range | –8° < 2θ < 170° |
Smallest step width | 0.0087° |
Reproducibility of θ/2θ angle | ±0.0002° |
Absolute accuracy (θ/2θ) | <±0.005° |
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.
Component | Specification |
Active area | 50 mm x 16 mm; 1600 pixels |
Max 2θ range covered | 12° at 435 mm diameter; 11° at 500 mm |
Usable wavelength | Cr–Kα to Mo–Kα |
Max local count rate | 400,000 cps |
Spatial resolution | <50 µm; >1600 channels |
Gas fill | 3.04 bar Xe-CO2; no external supply needed |
Power rating | 120 W |
Ambient temperature | 41°–104°F (5°–40°C) |
Operating temperature | 57°–93°F (14°–34°C) |
Relative humidity | Maximum 80 %, non condensing |
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
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.
Amount of Powdered Sample | Sample Holder |
Large: 2.0 mm depth | Steel |
Medium: 1.8 mm depth | Steel |
Small:1.0 mm depth | Steel with quartz or zero-background Si spacer |
Smallest (vein/vesicles, scrapings) | Slurry (see Sample Slurry/Smear Slide Mounting for Small Sample Amounts) |
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DIFFRAC Plus XRD Commander 
is the running software of the Bruker D4 XRD.
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- DIFFRAC.SUITE.EVA, version 3.0 software for evaluation
(a more recent version, version 5.1, is also available
) - DIFFRAC.TOPAS version 4.2.0.1 software
for diffractogram analysis
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The instruments in the lab need to be turned on in this order: (1) HASKRIS water chiller and (2) D4 XRD. The HASKRIS cools the water supplied to the D4 to prevent the X-ray tube from overheating. Turning the D4 on prematurely (i.e., before the water chiller) could damage the X-ray tube.
Procedure for Turning on Instruments
Turning on Haskris and Bruker D4
- Flip the "ON" switch (Figure 4C) to the HASKRIS and the water in the tank will begin to cool. The water temperature needs to reach 69°F (Figure 4A). The Haskris temperature can range between 65°F to 69°F (18-21ºC). Ensure all water valves to/from Haskris are open.
Figure 4. HASKRIS Control Panel. (A) Actual temperature. (B) Set temperature. (C) On/Off switch. (D) Flow meter
- Flip the "ON" switch (Figure 5A) on the side of the Bruker D4 XRD.
- The solid green "Low Voltage Ready" light (Figure 5F) turns on.
- You will hear several beeps and the "System Activity" light (Figure 5D) will start flashing green.
- Press the "High Voltage Enable" button (Figure 5B).
- The "System Activity" light turns green.
- An orange "High Voltage Ready" (Figure 5E) 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 needs to be conditioned. Go to the Maintenance section under Tube Conditioning for instructions and log the date of tube conditioning in the XRD maintenance log in XRD's Lab Notebook on Confluence.
Shutting Down the Bruker D4
The Bruker D4 can be kept on when not in use. However during extended periods such as Tie-ups or if there is not someone to check on the instrument it can be shut down. The Haskris can also remain on, or it can be turned off if no one is able to monitor it. If the Bruker D4 is on, the Haskris must be on as well.
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4. Turn off the main CPU button A as shown in Figure 5.
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NOTE: Sample Preparation for XRD Analyses is in the main Laboratory Manuals, Guides and Resources>XRD confluence page.
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.
Preparing Sample Holders for the D4
There are three ways to load a sample holder: front load, side load, and back load. 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 front loading if preparing samples for semi-quantitative analysis.
Make sure the sample from the sampling table (in the Core lab) is enough material to fill a sample holder - sample size for bulk powder is generally a 1-2 cm QRND (Quarter Round) from the section half. This will produce more than enough material to fill a sample holder. You do not want more than this as it will be wasted.
Front-Load Samples
This technique is commonly used to prepare samples to be measured with the D4.
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The sample 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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Figure 10. Back-loading sample preparation for the D4 sample holders.
Very Small Amount of Material (tooth pick, small crystals, secondary minerals or void filling material)
See XRD Sample Preparation for a small amount of material
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Before beginning measurements, confirm the scan parameters (singles, step and time) with the Science Party. Scientists can use previous Expeditions for examples of ideal scan parameters. Generally the D4 is used to scan from 5 to 70 º2θ.
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Figure 14. Adjusting a motorized drive via D4 Tools. (A) Select the drive to initialize. (B) Initialize button. (C) First Aid button may help with positioning errors or other errors with the window.
Entering Sample information into the XRD Commander
In the XRD Commander, click on the 'Jobs' tab next to the 'Adjust' tab (see Figure 11) . On the 'Jobs' screen, click on the "Create Jobs" icon 
in the toolbar (Figure 15A).
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The other fields will automatically populate, you do not need to fill these in and they should not need to be adjusted. Refer to the D4 Commander User Manual for more info on these fields.
Starting a Scan
When all fields have been filled in, click on the "Start" button on the bottom left corner of the screen (Figure 15H). 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. The program will automatically run the samples sequentially. The measurement is finished when it is displayed 'Finished' in the "Status" column of the 'Jobs' tab. If there is an error while scanning the program will stop and notify the user of the error. You can try restarting the software and/or the D4. A sample handler crash may require an experienced D4 XRD tech or you may need to contact Bruker. With the D4 off you can manually move the Z-drive and the sample swing loader, just be aware that the moveable drives are set up to avoid each other during the sample loading sequence, if you move a drive it may cause a crash on start up.
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When the scans have finished, the results will show up in the "C: > DATA > IN" folder. Two additional file types need to be made by the X-Ray lab technician before uploading the data to the LIMS database. The D4 outputs a .RAW file. The X-ray lab technician additionally has to create a .UXD and .PNG files. In addition to the LIMS upload, it is also helpful to create an "XRD Data" folder for the scientists in DATA (\\NOVARUPTA)(S:> Uservol > File Name) to save copy of the .RAW and .UXD files (or any file the scientist would like to have access to). After all three file types (.RAW, .UXD, and .PNG) 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 Diffrac.Eva software, whereas the .UXD file is a text file that can be read by other programs, particularly by HighScore Plus (available to the scientists via a virtual computer, see HighScore Software Quick Start Guide).
To convert a .RAW file to an .UXD file, click the Diffrac.File Exchange software icon on the desktop (Figure 16).
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The new .UXD files will show up on both sides (window circled in green in Figure 17) and you can close down the program (click on File > Exit).
Printing Scan to PDF or PNG
Go to the DATA > IN folder where all the sample files are currently stored. Double click on a .RAW file and it will open in the Diffrac.Eva software.
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Click on the 'Print Preview' icon 
in the toolbar at the top of the software window. A Print Preview window will open up. On the top toolbar, click the icon for "Export Image" 
. This opens the File Save As window. Save as .PNG with the same name as the .RAW file. If the names do not match exactly, the files will not upload to LIMS. Then close the windows and repeat the process for the next sample.
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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U1565A_1R1_3_4_clay_WDGE11053881.xrdml
U1565A_1R1_3_4_heated_WDGE11053881.xrdml
U1565A_1R1_3_4_glycolated_WDGE11053881.xrdml
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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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The following QA/QC is for the Bruker D4 Endeavor XRD.
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. Be careful not to hit any of the limit switches within the D4 as this will cause error and possible collision of the motorized drives. The screen is only removed when running the corundum standard to allow a larger range of angles without any interference. The anti-air scatter screen should always be on when running samples. (Review the video on Desktop/XRD_ICP Prep Documents/Bruker TRAINING VIDEOS to see this done before proceeding).
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Scanning the NIST 1976 Standard and Verifying QA/QC, homing the axis inside the XRD.
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 X396). 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. Under the "Raw File" tab, set the path to the DATA>IN folder; this scan will not be uploaded to the LIMS database.
Click Start and wait for the scan to finish.
Processing the Scan
- Open scan in EVA (remember the QAQC parameter file Corundum QAQC continuous 20 to 130.dql ran without the anti-air scatter screen).
- Subtract the background (do not append, just simply close background menu) (Figure 19).
- Strip Kα2 and Append (Figure 20).
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If the RED "ZI correction must be applied" shows up (Figure 25C), you will need to enter the corrected Vi into the Config program. This will adjust the home position for the 2Theta drive. If there is no message just save the worksheet under a new name (Expedition) and no more action is needed.
Apply ZI Correction to the XRD
1. Open the Configuration Program on the desktop (Figure 28). Password: DIFFRAC.
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Now that the scan is complete put the Anti Air Scatter Screen back on. Move the y drive to the 350 position and open the front door (instructions above Removing the Anti Air scatter Screen section). 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. Turn the XRay generator back on with the Key on the front of the instrument.
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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.
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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 the icon with the computer and plug. This connects the program to the instrument. Click on the X-RAY generator green button on the status screen, this will show the screen in Figure 31. Or Select "X-RAY" under the Instrument tree. Then select Utilities -> X-Ray Utilities -> Tube Conditioning ON/OFF (Figure 31).
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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 33).
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Save the file under a new name to the path Local Disk C: > DIFFDAT1. 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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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.
Credits
This document originated from Word document XRD_UG_375.doc (see Archived Versions below for a pdf copy) that was written by H. Barnes and K. Bronk; edited by N. Lawler and A. Armstrong. Credits for subsequent changes to this document are given in the page history.
Archived Versions
LMUG-XRDUserGuide-230220-1933-176.pdf
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