From TA insert peaks using the menu option
"View/Search peaks". Inspect the inserted peaks and add/remove peaks
such that their positions looks reasonable.
Expand the TA treeview to the "Peaks
Phase" and click on the column heading called "Position". Press
the right mouse button on the yellow colored column and execute
"Copy all/selection". This copies the peak positions to the clip
board. The TA screen should look like the following:
Paste the peak positions into jEdit.
Open the XInsert node "TOPAS-Academic,
INP format/Scan file level". Click on "Emission profile" and insert
the CuKa5 emission profile.
Open the XInsret node "Background"
and click on "Chubychev".
Open the XInsret node "Instrument"
and click on "Diffractometer Radius", "Slit_Width", "Divergence"
and "Full_Axial_Model"; enter appropriate instrument values.
Open the XInsret node "Miscellaneous"
and click on "start_X" and "finish_X" and enter the appropriate
values.
Open the XInsret node "Phase level
- xo_Is" and click on "xo_Is", "CS_L", "CS_G", "Strain_L" and "Strain_G".
Enclose the peak psitions within braces
in the text "load xo I { }".
The jEdit screen should now look like
the following:
Note, the User should typically know
the instrument conditions corresponding to things like receiving
slit width, axial divergence parameters, divergence, emission profile
etc...
A zero error was not included as the
peaks are free to move independently. A Lorentz Polarization factor
was also not included as the peak intensities are not sought.
Also note that an xo_Is phase is used
to fit the peaks and that the jEdit column cursor is used to insert
the columns of '@' and the intensities of '1'.
It may be useful at this stage to step
through the jEdit column copying/cursor feature. If the INP keystrokes
have been installed then to create a column cursor:
Press Ctrl-KeyPad_Plus; the jEdit
status line should show an 'R' indicating that rectangular mode
is on.
Hold down the Shift key and arrow
down, you should see a column cursor.
Type the character @ and you should
see a column of '@' charatcers. Type another character and see what
happens.
To cut a column press Ctrl-KeyPad_Plus,
hold down the Shift key and use the arrow keys to select the desired
rectangle. Press Shift-Del to cut the column. Move to where you
would like the column pasted and press Shift-Ins.
To turn off rectangular mode then
press Ctrl-KeyPad_Minus. Note, column copying/pasting works excellent
in jEdit and it would be worthwhile to spend a minute or two becomming
familiar with it. Under the XInsert node "TOPAS-Academic, INP format
/ Help" is "keyboard basics" which is useful to view.
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 intructs TA to operate
on this INP file.
Alt-Tab to TA and refine. The fit
to the peaks should look like the following:
It is important to view the fit carefully
and to make sure that peaks have not wandered off their approximate
positions during the fit. The displayed vertical peak lines assists
in this process. Note that the DEMO version of TA does not display
the peak lines.
Indexing
We will now use the refined peak positions
in an indexing run.
Save the pbso4.inp file to a file
named indexing.inp. We will modify this file to perform indexing.
Delete everything from the INP file
except for the peak positions and intensities.
Open the XInsert node called "Indexing"
and work down the tree such that the INP file looks like the following:
Click on the icon
. Alt-Tab to TA and refine.
The indexing run produces a file with
the same name as the INP file but with an NDX extension and in the
same directory as the INP file. Load this file, INDEXING.NDX, into
jEdit. The first part should look like the following:
Here we see that the correct lattice parameters
have been determined. Note that the space group for PbSO4 is Pbnm.
The solution with the highest FOM is Pna21. Pna21 however has the
same lines as Pbnm as far as powder data is concerned; see Table 12.6
of the Technical Reference. Thus the correct space group grouping
was determined.
The solutions contained in indexing.ndx
can be viewed graphically using TA.
First load indexing.inp into TA using the TA menu
option "File/Import INP file".
Copy the whole contents of the
indexing.ndx file to the clipboard from jEdit. Alt-Tab to TA.
Click on the Solutions Tab of the indexing range and execute
the option "Paste INP to Node/Selections". Click on one of the indexing solutions and the TA screen should
now look like:
Note that high FOM values are observed
for volumes that are multiples of the true solution of 319.
Note also that the loading of indexing.inp into TA would not be possible when
keywords that are not understood by the GUI are used. In such cases then an indexing range
can be manually created using the option "Create Indexing Range" found by clicking on the "Global" treeview item of TA.
Once the indexing range is created then the 2Th/Intensity peak values can be copied from jEdit and pasted into the
"Data" tab of TA. A window for displaying the indexing peak positions can be created using the TA menu
option "Window/New Scan Window". Thus graphical display of indexing solutions can always be easily displayed.
This completes peak fitting and indexing.