Table of Content

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Introduction

This guide is a quick introduction to the DIFFRAC.TOPAS software and how to use the program for profile fitting and Reitveld Refinements. For detailed information and an in-depth guide refer to DIFFRAC.TOPAS User Guide & Technical Reference available in hard copy in the XRD lab or online in Cumulus.
DIFFRAC.TOPAS is not a phase identification software. If you do not know the minerals present, first identify the phases using DIFFRAC.EVA and then use DIFFRAC.TOPAS to quantify those minerals.

Part 1: Opening a Diffractogram in DIFFRAC.TOPAS

Select the DIFFRAC.TOPAS icon on the desktop to open the software (Figure 1).

Figure 1. DIFFRAC.TOPAS icon

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The main screen has the following areas (Figure 2):

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When a scan is loaded in it appears in the Parameter Window as the title of the scan (Figure 3). 'Global' is always present.

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In DIFFRAC.TOPAS a scan is referred to as a 'Range'. Multiple scans can be loaded and refined simultaneously.

Part 2: Identify Peaks

Peaks can be defined either automatically or manually inserted.

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1. On the Toolbar select the 'automatically insert peak' icon (Figure 4)

Figure 4. Automatic-ally insert peak icon

2. A 'Peak Search' window will appear (Figure 5). Here adjust the peak width, noise threshold, and K-Alpha 2 removal. Each vertical line is a detected peak and the scan updates as the parameters change, increasing or decreasing the amount of detected peaks. When satisfied with the peak selection select 'Add Peaks'.

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3. The peaks now appear in the Parameter window within the range (scan) under 'Peaks Phase' (Figure 6). To delete any peaks right-click on the peak and select 'delete nearest peak'.

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1.  Select the magnifying glass icon located on the toolbar (Figure 7).

Figure 7. Peak details icon

2. The 'Peak Details' window pops up (Figure 8).  The Peak Details window controls the displayed peak label information. The left column has 5 different fit models: 'FP', Fundamental Parameters, is the only model that uses instrument parameters; the other models are purely mathematical fits assuming nothing about the instrument. The middle column changes what information is displayed: peak position, area, crystal size, and strain. The right column determines how the information is displayed, ie a numerical value, a fixed or refined text label, measurement error. Set the peak details parameters.

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3. With the mouse click on the center of each peak you want to identify directly in the scan window. The peak details window can be pulled up again to change the peak values.

Part 3: Set Refinement Parameters

Refinement parameters are set in the 'Parameter Window' and changed in the data grid. In the Parameter Window there are two parameter definitons: Global and Range. Global parameters apply to all scans in the parameter window. Range parameters will only apply to that specific scan.
To select a parameter, check the box in the 'Use' column in the parameter row (Figure 9). A parameter can then either be fixed or refined. Switch between 'fix' and 'refine' under the 'Code' column. Click inside the box next to your parameter. Select the drop down menu and choose between 'fix' or 'refine'. Note that a fixed parameter remains black and a refined parameter turns red. A fixed parameter can also be denoted with a '!' and a refined parameter with an '@'

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1. Right click on 'Instrument' and select 'Load Instrument Details'.
2. Navigate to Local Disk C > TOPAS 4-2 > Instrument details > D4EndeavourParameters.par
3. Select the file and click 'open'

Part 4: Run Refinement

When the parameters are set run the refinement.

1. Go to the Toolbar inside the 'Refinement window and select the 'play' button (Figure 10). In the window you will see a graph showing the refinement converge on a solution.
   
   

   Figure 10. Play button

2. Figure 10. Play button  When the refinement finishes a window pops up asking to accept or deny the refinement (Figure 11). It is recommended to first examine the calculated curve.
   

   

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3. Examine the measured scan versus the calculated scan. The blue line is the measured values and red line is the calculated result. Ideally the red line lies over the blue line with the peak position in the middle (Figure 12).

Figure 12. Example of calculated curve over measured curve

4. If the calculated line looks good select 'Yes' in the window to accept the refinement. If the calculated line does not look good select 'No' to reject the refinement and then go back to the parameter window and tweak the parameters. When a refinement is rejected the calculated curve will remain there until another refinement is run.

Part 5: Find Area Under Curve

1. In the parameter window go to your scan tree and select 'Peaks Phase' (Figure 13).

Figure 13. Peaks Phase Grid

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3. These values can be copied and pasted into a personal spreadsheet.

Part 6: Weight Percent Analysis

A structure file contains crystallite size and indice values for minerals. Add structure files of each mineral present for TOPAS to calculate the weight percentage and/or the crystallite size. If evaluating multiple scans and using the same minerals to quantify each this can be done in 'Global' tree. If doing one scan or using different minerals for each scan, add structures scan by scan.

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1.  Right click on the desired scan and select 'Load STR(s)' (Figure 14)

Figure 14. Load STR(s) pathway 

2. Select the minerals from the pop up window (Figure 15). You can search through the mineral groups or start typing in the mineral and it will appear in the bar.

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1.  In the Parameter Window select 'Global'. Then in the display window hit 'ctrl' and select your scans, highlighting them as seen below in Figure 16.

Figure 16. Add STR files to multiple scans at once 

2. Back in the Parameter Window, right click on 'Global' and select 'Load STR(s) for Selected Files' (Figure 17).

Figure 17. The 'Global' pathway to Load STR(s) 

3. Select the minerals from the pop up window (Figure 18). You can search through the mineral groups or start typing in the mineral and it will appear in the bar

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4. Now when the scan is expanded in the parameter window a mineral structure is included at the bottom (Figure 19).

Figure 19. Structures present in parameter window under range tree

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1. Go to the parameter window and look at all the scans loaded in.
2. The colored box next to the scan indicates that a scan is active. Clicking on the box alternates it between 'active' and 'inactive'. In Figure 20 there are two active scans, quartz is blue and Illite is black. In Figure 21 the white box next to Illite illustrates that this scan is now inactive.
   
   

   Figure 20. Two Active Scans

   
   
   

   Figure 21. One Active Scan and one inactive scan

3. One scan can be run at a time so click on the colored boxes next to all but one scan. After this there should only be one scan seen on the graph.
4. Go to the refinement window and select 'Play'.
5. The message will appear stating the refinement converged and asking to accept or deny the refinement. Check the data before selecting an answer.
6. In the upper right corner, the weight percent of each mineral appears. Check the areas by following instructions listed in Part 5.

Part 7: Save and Export Image

Save a File

1. Select 'File' on the Menu Bar and go to 'Save project As…' (Figure 22)
   
   

   Figure 22. Save Project Pathway

   
   2.  Navigate to a place on the desktop on server and save the file.

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1.  Select the printer icon on the toolbar (Figure 23)

Figure 23. Printer Icon

2.  This brings up the 'Chart Options' Box. Select 'Print / Print Setup' (Figure 24)

Figure 24. Print Setup Window

3. Select the dropdown drop-down menu to select a printer. Choose 'Microsoft XPS Document Writer' to get a digital image of the graph (Figure 25). Then select 'Print'.

Figure 25. Print Window with Printer drop-down highlighted

Credits

This document originated from Word document DIFFRAC.TOPAS QSG V372.doc, written by N. Lawler. Credits for subsequent changes to this document are given in the page history.

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