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Click on the Jobs tab (Figure 23C). On the Jobs screen, click on "Create Jobs". 
Figure 24: Create Jobs window. (A) Sample position In D4 sample magazine (B) Sample ID (C) Parameter file (D) Open Directory button (E) Raw file (F) Start button
The window shown in Figure 20 24 will pop up. Fill in the Position, Sample ID, Parameter File, and Raw File columns.
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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.
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The RAW file is only readable by the Eva software, whereas the UXD file is a text file that can be read by other programs.
Click the File Exchange software icon on the desktop. (Figure Figure 25)
Figure 22: First window in File Exchange. (A) Input File Type dropdown menu (B) Input DATA folder (C) Output File Type dropdown menu (D) Output DATA folder (E) Convert button Figure 25. File Exchange Desktop Icon
The initial window (Figure 2226) will open. The left half of the screen is the file input where you select the files you want to convert. The right half of the screen is where you select the new converted file type and where the files should go.
Figure 26: First window in File Exchange. (A) Input File Type dropdown menu (B) Input DATA folder (C) Output File Type dropdown menu (D) Output DATA folder (E) Convert button
First, direct the where new files should be saved and select the converted file type. On the right side, click on the file type dropdown menu (Figure 22C26C) and select "UXD". Then double click on the DATA folder (Figure 22D26D) and direct files to the "IN" Folder.
Move to the left side of the screen and select your input files. The file type (Figure 22A26A) should already be set to "Raw". Click on the DATA folder (Figure 22B26B) and go to the "IN" folder. Here you will see all your samples. Select all the samples and then click the "Convert" button (Figure 22E26E) on the bottom right of the screen.
The new UXD files will show up on both sides and you can close down the program.
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Go to the DATA > IN folder where all the sample files are currently stored. Double click on the RAW file and it will open in the Eva software.
Figure
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27. Print Icon
- in EVA Click on the Printer icon at the top of the software outlined in red in Figure 2327. A Print Preview window will open up. On the top bar, click the icon for "Export as a PNG" outlined in red in Figure 2428. This opens the File Save window. Save with the same name as the RAW file. If the names do not match exactly, the files will not upload. Then close the windows and repeat the process for the next sample.
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Figure
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28: Export Image as PNG
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Icon
Uploading Files to LIMS
The XRD files are uploaded using the MegaUploadaTron 5000 program. Three files are needed for each scan (RAW, UXD., and PNG):
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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.
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- Open scan (remember the QAQC parameter file Corundum QAQC continuous 20 to 130.dql ran without the anti-air scatter screen).
- Subtract the background (Figure 2529).
Figure 2529: EVA diffractogram.
The arrow points to the Background Subtract tool.
3 .Strip Kα2 and Append (Figure
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30).
Figure 2630: EVA diffractogram with the background subtracted.
(1) Dropdown Menu to Append Scan
(2) Strip Kα2 Tool 
Tool
4. In the "Data Tree" panel there are two scans: Background Subtracted Scan and Kα2 Subtracted Scan (Figure 31). For both of these scans, you will "Create Area" and "Append Area" for four angle ranges. This will insert area information as a subtree entry under that scan.
Figure 2731: Diffractogram with two scans in Data Tree panel. Top arrow points to the Background Subtracted scan. The bottom arrow points to the Kα2 scan 
scan
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5. Select the area around each peak as shown below in Figure
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32. Click on either scan so that it is highlighted (Figure
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32-1). Then click "Create Area" (Figure
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32-2). A New window will pop up where you can enter the left angle and right angle(Figure
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32-3,
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32-4)
Figure 2832: Create Area for Scan Angles. (1) Arrow points to scan name (2) Create Area tool (3) Left Angle entry field (4) Right Angle entry field
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6. After you enter in both angles click again on the left angle. This populates the rest of the fields. When all fields are populated, you can click on "Append Area" (Figure
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33). Do this for each of the following angle ranges for both scans:
- 25.576°2θ (24.7°–26.2°2θ)
- 35.149°2θ (34.0°–36.2°2θ)
- Figure 29: Create Area window
(A) Append this Area button8888.993°2θ (88.1°–89.7°2θ) - 126.8–129.0 (angle range is not necessary but recommended)
Figure 33: Create Area Window A. Append this Area button.
7. Right-click on the "Area List #" subheader for background-subtracted scan and select "Create and Area Column View" (Figure 34). Do the same for the Kα2 appended scan. This creates another tab on top with the Area data in column format.
Figure 3034: Data Tree panel Scan Area list. 
8. Open the QAQC corundum standard Equipment Verification 3.3.xls Excel spreadsheet.
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9. Enter your name and date and select "Vantec-1" for the detector.8. Enter the following values into the spreadsheet
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Figure 31: Kα2 subtracted Scan Area column view. (1) Chord Mid value (2) FWHM value
Figure 32: Background Subtracted scan area column view. (3) Net Area value 
(Figure 35, Figure 36):
- For 2θ Obs, use the Chord. Mid values from the Kα2 appended scan areas (Figure 31-1)
- For I Obs, use Net Area from the background subtracted scan areas (Figure 32-1)
- For FWHM, use the FWHM from the Kα2 appended scan areas (Figure 31-1)
Figure 31: Kα
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2 subtracted Scan Area column view. (1) Chord Mid value (2) FWHM value
Figure 32: Background Subtracted scan area column view. (3) Net Area value
10. The spreadsheet has the calculations already embedded. Remove background (subtract background).
If you get the RED "ZI correction must be applied" message, you need to open the configuration program Motor Drives > 2θ > Zero Refer. Enter the current ZI value in the excel spreadsheet – the Corrected ZI value is what you need to update/change the configurations ZI value to. Save and Download. DO NOT CHECK THE BOX FOR THE PSD CONTROLLER. Downloading the config file to the PSD Controller corrupts the Controller. For more information see the Troubleshooting section. Always backup the config.file on the server.
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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Maintenance
Tube Conditioning
Figure 33: D4 Tools X-ray subtree window.
(A) X-ray subtree button
(B) Utilities command
(C) Standing kV and mA 
If X- 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 33)
Figure 34: Tube Conditioning On IndicatorOnly ON/OFF (Figure 37)
Figure 37: D4 Tools X-ray subtree window. (A) X-ray subtree button (B) Utilities command (C) Standing kV and mA
Only click on tube conditioning on/off once. In the bottom right corner of the screen you should see a message 'Tube Conditioning On' (Figure 3438).
Figure 38: Tube Conditioning On Indicator
After about a minute the kV will start to increase in increments from 20kV to 55kV. The whole program takes about one hour and when kV returns to 20 the program is complete. Note the operational status on the maintenance spreadsheet posted in the lab. To do this click on Manual Control (small head icon) and type GS11. The resulting number is the status number.
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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). 
Figure 39. XRD Wizard Desktop Icon
An empty gray screen will open. There options on the top bar to either open a preexisting file or open a completely blank sheet. It is better to open and edit an old file and save it under a new name. Many settings are fixed, and editing a file reduces the chance of entering in a wrong value.
After a file (new or old) is opened, this first screen will open (Figure 3440). Change the "Operator" to your name and click "OK" at the bottom of the page. You can click "Update" to get the current date and time.
Figure 3440: First page of parameter file setup.
The
The second page declares the detector and PSD electronic window (Figure 3541). These settings are PSD: VANTEC-1 and 3. Do not deviate from these values. Click "OK" and continue to Scan Settings.
Figure 3541: Detector declaration. 
Scan
Scan Settings includes Scan Type and Sample Rotation (Figure 42). Scan Type should stay set to "Locked Coupled". This is a hardware setting indicating that the theta and 2theta positions move together. Under Sample Rotation, the Spinner can be set on or off. This spinner spins the sample while being scanned. This is typically on because it captures all potential angles of the sample giving a complete image of the material. Rotation Speed is set to 30 rpm and .5 rps (you only have to enter in one of these fields). Click "OK" and continue to scan parameters.
Figure 3642: Scan Settings parameter window.
Figure 37:
Scan Parameters window.Scan Parameters includes the scanned angle range, angle step size, number of steps, time per step, and delay time (Figure 3743). Adjust the angle range depending on the material and scientific objectives. For example, if looking for clays, set a low angle (3° – 30°). The step size determines how much the goniometer will move before recording more data. The number of steps will adjust itself based the step size and angle range. Time/Step controls how long each step is measured. The Delay Time will add in an amount of time to wait before scanning the next sample. The machine does have limits on these settings and if something is entered outside of its range it will alert you. Click "OK" and move onto Generator Settings. At low angles (2-4° 2theta) there is a very sharp peak. This is caused by beam overspill onto the sample holder.
Figure 43: Scan Parameters window.
Generator Settings contains the X-Ray Tube Configuration and Generator Configuration (Figure 3844). The X-Ray Tube values are constant. You can adjust the kV and mA in the Generator Settings. The voltage is typically between 30 and 40 kV and the current is 40 mA. Lowering these values too far can reduce peak intensity. Click "OK" and continue to the Beam Optics window.
Figure 3844: Generator Settings window.
The Beam Optics settings lists the Divergence Slit and AntiScattering Slit (Figure 3945). Both of these are constant values based on our hardware setup. The Divergence Slit should be set to .300°. Click "OK" and you will have finished all the settings and will loop back to the first window.
Figure 3945: Beam Optics window. 
Save the file under a new name to the path Local Disk C: > DIFFDAT1 > DIFFDAT1_old computer pre March 2013. You can print this file by clicking the "Report" tab at the top the subtree window and then clicking the print icon. Occasionally scientists will ask for a printout of the settings to put in their reports.
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