TOPAS-Academic TutorialTOF calibration / refinement of CeO2
CeO2 data are used in this example from ISIS
HRPD and comprises a sharp pattern TA-Tutorials\data\tof\sh1.xy1 and a
broad patterns TA-Tutorials\data\br1.xy1 which form part of the size-strain
round robin conducted by the IUCr CPD 1 (Balzar, 2001). Section 3.2.2
of the TA Users Manual also discusses this data.
In this tutorial the sharp pattern will
be fitted first in order to obtain instrument constants. These constants
will then be used to fit to the broad pattern with the instrument constants
fixed in order to determine specimen broadening.
Note that there are now better functions available for describing the
instrumental peak shape of HRPD than the exponentials used here, but
these probably don't have signficant impact for the tutorial as the
sample contribution from CeO2 dominates. See the Topas wiki (search
"tof" and you should find a file "time_of_flight_tof_isis_instrument_standard_files").
A Pawley refinement will be performed on
the sharp pattern as structural data is not sought; peak shapes are
important here.
Click on the jEdit toolbar icon Open the jEdit XInsert treeview item "TOPAS-Academic,
INP format/TOF Refinement".
Work your way down the treeview clicking
on the items x_calculation_step, weighting, TOF_LAM, TOF_x_axis_calibration,
TOF_Exponential and a Chubychev background. Note, there's no need to
include neutron_data and the TOF scaling of D_spacing^4 as we are doing
a Pawley refinement.
The jEdit screen should now look like:
Notice the # character in the TOF_x_axis_calibration
macro. Typically the User finds these constants from the instrument
local contacts and it would be a matter of entering the right ones.
In this case however we are going to determine the constants starting
from an approximate t1 of 1548018, thus change the line to look like
the following:
TOF_x_axis_calibration(t0, 0, t1, 1548018, t2, 0)
Notice the removal of the characters !
and thus we will be refining on the three parameters t0, t1 and t2.
Open the XInsert node called "Phase level-
hkl_Is". Here we will insert the Pawley phase. Position the cursor on
the bkg line and Click on hkl_Is, Cubic, and space_group. Clicking on
space_group inserts the keyword space_group plus a $ siign. Change the
dollar sign to the space group "Fm-3m". Change the Cubic line to correspond
the known CeO2 lattice parameter which wont be refined, it should look
like:
Cubic(5.4103)
Go to the "TOF Refinement/Phase level"
and click on TOF_PV; this represents part of the instrument function.
Its a PseudoVoigt with a FWHM that varies in X-axis as a function of
D_spacing. It may be useful at this stage to view the TOF_PV macro in
the file TOPAS.INC. Load it into jEdit from the XInsert node of "TOPAS-Academic,
INP format/Help/Standard macros - Topas.inc" and search for TOF_PV by
pressing Alt-s or use the jEdit menu option "Search/Find".
The jEdit screen should now look like:
Press Alt-b to go back to the sh1.inp file.
Now we will do a preliminary refinement
on sh1.inp.
Click on the icon
You will notice that the fit is poor with
a background that looks wrong. Looking at the pattern we notice that
some of the observed data at low and high tof space is oscillating considerably.
Go to the XInsert node of "TOF Refinement"
and insert a start_X of 800000 and a finish_X of 5000000. This will
remove the low and high parts of the pattern which is causing the poor
background fit.
This brings up the important point that
"Refinement" typically comprise a series of refinements each including
small modifications to the INP flie leading to progressively better
fits.
Save the INP file with the new start_X/finish_X
keywords by pressing Alt-w or use the jEdit menu option File/Save or
simply click on the icon Alt-Tab to TA and refine again and save
the parameter values by answering Yes to the prompt.
The fit should be good with an Rwp of 8.8%.
Increase the number of background Chubychev coefficients to 6 by adding
three zeros '0' to the end of the bkg line and then refine again; the
Rwp should refine to around 8.67%.
Zoom into a region of the scan and the
fit should look something like:
Alt-Tab back to jEdit and the INP file
should look like:
This completes fitting to the sharp data
and determining the instrument constants found in the TOF_x_axis_calibration
line, the TOF_Exponential line and the TOF_PV line.
Even though it is fast to work down the
treeview and insert required items; it is even more expeditious to use
the sh1.inp file as a template and to modify it to accomodate a new
data set.
Save the sh1.inp file as br1.inp and change
the xdd line to include the data br1.xye.
Remove the refine unique '@' characters
from the TOF_Exponential lines and the TOF_PV line. Stop refining on
the t0, t1 and t2 parameters by prepending the character ! to the parameters
names in the TOF_x_axis_calibration line, ie.
TOF_x_axis_calibration(!t0,-403.55857, !t1, 1545934.99243, !t2,-218.54623)
Place an @ sign in the Cubic line to refine
on the cubic lattice parameter, ie.
Cubic(@ 5.4103)
Click on the icon The fit is poor as seen below and clearly
the peaks of br1.xye are much broader than the calculated pattern. We
will now include some specimen broadening.
Place the curcor somewhere after the hkl_Is
keyword and click on the XInsert items of TOF_CS_G and TOF_CS_L which
are found under "TOF Refinement/Phase level".
Save, Alt-Tab to TA and perform a refinement;
you should notice a very good fit with an Rwp of 4.86%.
|
[Modified 06-May-2020 by John S.O. Evans. Pages checked for Google Chrome.]