TOPAS-Academic Tutorial
Simple Rietveld refinement of Laboratory
X-ray data of Rutile
TiO2 data were recorded on the durham
d5000 with fixed slits and it is appropriate to refine a height
correction. As you have a cif file for the material it can be read
in directly. In cases where you don't have a .cif file you'd click
through the items in the "Structure - no cif" folder.
If you'd like to see the structure in 3D click on "view_structure".
Then save the file and run it in TA.
Perform the following steps:
Start jEdit.
Click on the toolbar icon
. Select from the browser the file TA-Tutorials\data\rutile\d5_05005.raw.
After selecting the data file an input file for running topas with
the same name but extension .inp is created in the same directory.
The jEdit screen should now look something
like the following:
Now we need to insert some keywords
into the INP flie corresponding to things like anode used, instrument
details and structural details.
Open the XInsert node called "TOPAS_Durham"
then open the node called "Simple Lab Rietveld". The jEdit screen
should look like the following:
Click on node called "File Header".
This inserts some default keywords like r_wp etc...
The jEdit screen should now look like
the following:
Position the cursor on the line with
the xdd keyword.
Click on node called "Background".
This inserts the keyword bkg which defines the coefficents of a
Chubychev polynomial.
The jEdit screen should now look like
the following:
Thus using jEdit to create INP file
involves working ones way down the XInsret treeview and inserting
items as required.
Perform the following to complete the
setting up of the Rutile INP file.
Open the XInsert node "Instrument/Corrections"
and click on "Durham_d5000".
Click on "Refine zero point".
Click on "Refine sample height". N.B.
zero point and height are highly correlated so you would normally
refine one or the other.
Open the "Structure - cif" node and
click on "Read a CIF file". Browse to TA-Tutorials\data\rutile\rutile.cif
and select it. The jEdit screen should now look like the following:
Now we are ready to do a preliminary
refinement on the data set.
Click on the icon
to start TA. Note, once TA is started it is not necessary to start
it again.
Click on the icon
which sends the name of the present INP file to a text file in the
main TA directory called LAUNCH_FILE.TXT. This simply instructs
TA to operate on this INP file.
Alt-Tab to TA and press the Fit Window
icon ;
this starts the refinement.
After refinement the TA screen should
look like the following:
TA automatically loaded the observed
pattern (blue) and then shows the calculated pattern in red after
each refinement iteration.
Alt-Tab back to jEdit. jEdit will
automatically load the modifed INP file with refined parameter values
updated and in red. The jEdit screen should look like the following:
This CIF file did not include any temperature
factors (typically they do); thus add them manually by appending
to the end of each site line "beq @ 1".
Save the INP file by pressing Alt-w
(if INP keystrokes are implemented) or File/Save or click on the
icon .
Alt-Tab back to TA and run the refinement
again; the Rwp should drop by around 0.9% with the beq values refining.
Place the jEdit cursor somewhere after
the "str" keyword and click on "view_structure". Save and run the
refinement again. Now you should see the structure displayed in
an OpenGL window.
To instruct TA to calculate errors
for the refined parameters; uncomment out the "do_errors" line at
the top of the INP file; ie. remove the line comment character of
'.
Save the INP file by pressing Alt-w
or click on the icon .
Alt-Tab to TA and run the refinement.
Alt-Tab to jEdit and the INP file should
now look like the following:
Appended to refined parameter values (red
numbers) is an underscore followed by a number; these numbers are
the errors.
Also, the keyword C_matrix_normalized is
appended to the bottom of the INP file (if it does not already exist).
Following the C_matrix_normalized keyword is the normalized correlation
matrix.
This completes the tutorial.
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