Dear All,
Just to be sure on two of the Q&As:
Le 07/11/2024 à 05:03, Matthew Rowles a écrit :
Great questions!
> Is it worthy to use the parameter known as "Sample Thickness",
associated with the Absorption Correction in TOPAS?
Generally, no. You only need to worry about it if the penetration
depth of your incident beam is larger than the thickness (t) of the
specimen. If that is the case, then "Sample Thickness" and "Scale
Intensity" is necessary to correct for the change in peak shape due to
the finite depth, and the change in diffracting volume.
- Seems from your answer Matthew, that diffracting volume changes (Vd)
through the scan in BB geometry gives rise to some peak shape variations
(I assume here that "shape" includes "width"). I agree that the
diffracting volume changes with theta, and with the sample thickness,
but these two effects should not contribute the same on the peak shape:
-- For a given sample thickness, the diffracting volume varies with
Theta, but to me the main contribution to the peak shape is due to the
irradiated surface (beam track on the sample surface). Since deeper dVd
will be more absorbed than the ones closer to the surface. You can
picture this measuring a 2Theta scan at fixed incident angle, up to
2Theta=90°, the peak width increases notably with 2Theta because of this.
-- For the same theta on the diffraction diagram, varying the sample
thickness will probably not modify this much the shape of the peaks, but
intensities. For the same reasons on dVd. For instance, if measuring 2
samples with a 100 nm and 200 nm thickness respectively, the peak shape
variation will probably not be visible using lab instruments, while the
intensities will differ significantly.
- I do not like much the term "penetration depth" (p), since the depth
reached by x-rays is always infinite. For instance, if as usual p is
defined as 1/mu (mu = absorption coefficient of the sample, the one we
never fully know exactly), using a Theta-2Theta scan in BB on a
t=infinity sample, the measured diffracted intensity is larger than the
one coming from p only. And, on a thin specimen, both absorption and Vd
are varying during the scans, each of them bringing a contribution to
the intensity. On the contrary, for t=infinite specimen, they compensate
each-other and their contribution is the same on the diffracted
intensity throughout the diagram (but the intensity does not come from
the same irradiated volume). I was then wondering if Topas was simply
corrected from volume variations or also including the absorption
variations in the case of "thin enough" samples ?
> Is the negative intensity in the difference curve...
It is showing that there is some mismatch between your model and the
data. The intensities could be off because the peaks positions are
wrong, the peak-shape is wrong, the atomic displacement parameters are
wrong (don't refine these from normal QPA data), the LP factor
correction is wrong, the site occupancies are wrong, the atomic
scattering factors are wrong. Could also be that you have forgotten to
refine a parameter that you should be.
What about preferred orientations ? Anisotropic crystallite shapes and
microstrains ? Improperly defined film thickness can give rise to
variations of the ADPs also.
My 2€cts !
Daniel
On Wed, 6 Nov 2024 at 19:12, Łukasz Kruszewski
<lkruszew...@twarda.pan.pl> wrote:
Dear Rietvelders,
after some years of being a happy user of TOPAS & Rietveld method
(after
working-out a good approach, thanks to a great help from users of
this
mailing list for which I am really thanful, and having it checked by
attendance in Reynolds Cup) I was recently confronted with few
questions
I couldn't answer. I thus have a kind request of a help here:
- does the Absorption correction also influences microabsorption?
This
question arose due to somewhat lowered expected wt.% of pyrite (19
instead of 25), FeS2, even though all the used parameters
(Absorption,
CrySize, Strain - for all the sample components) were checked and
proven
to give value > error, i.e., being physically meaningful for the
refinement model. I was wondering how this supposed non-precision for
pyrite could be addressed...
- Is it worthy to use the parameter known as "Sample Thickness",
associated with the Absorption Correction in TOPAS? I was taught in a
5-day course of TOPAS that it's not a good idea, especially with the
Bragg-Brentano geometry, but I'm not sure...
- Is there any difference, to be expected, in the calculated unit
cell
parameters, between approximating a phase using (1) a chemically pure
STRUCTURE model (i.e., taken directly from a database / CIF file),
and
(2) a STRUCTURE with Occupancy information updated with the known
content of impurities? I always thought that it shouldn't matter,
as the
software simply "iteratively" compares the sample' reflections
with the
structural information contained in STRUCTURE models (?). I have
compared these two situations, and option "2" actually gave me worse
fit. I thus wondered: does it really matter that much which model
(approximation) of the structure - chemically pure or with added
impurity info - is used? For most substances, the reflection
positions
vary even for different standards found in databases like PDF or
COD...
- Is the negative intensity in the difference curve only informing
us of
underestimation of the content of a particular phase, suggesting to
replace the Structure model used with another one?
We have been working using few computers with, supposedly the very
same
version of the software. However, even though we've been using
exactly
the same Structure models, results were varying depending on the
computer stand used. I was wondering if this could have to do with
some
errors in the JAVA script, or maybe a non-identical installation
conditions, or something about the Windows system?
I would be thankful for any tips.
Best regards,
--
Łukasz Kruszewski, Ph.D., Associate Professor
Polish Academy of Sciences
Institute of Geological Sciences
Twarda 51/55 str.
00-818 Warsaw
Poland
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