Hi Carlos,
My previous exposure to MD for EXAFS was as part of a collaboration here:
J. Synchrotron Rad. (2013). 20, 555–566
There, to get estimates of energy shift and amplitude (So^2), a
simplified model was used
to fit the experimental data. In your case, that could be done by
performing a FEFF
calculation for an atom best representing the average.
The FEFF calculation won't include deviations in Eo or So^2 or even
temperature effects by default. DEBYE, s02 (or HOLE or EDGE), and
CORRECTIONS cards
could be used in generating the FEFF chi.dat.
If your MD simulation gives you N, R and sig^2
for each shell (and each atom) you wish to include in your comparison, then
you can implement the Eo-shift and amplitude values from the simplified
fit in each shell
of a simulation (using the FEFFNNNN.dat files) up to whatever shell you
have the energy to try
to include in the simulation...I would suggest starting with the first shell
and include the second once you get a good agreement with the first.
There may still be deviations in peak position between experiment and
calculation.
That can be considered by examination of a known standard.
You should consider the same k-space ranges for experiment and theory
when comparing
your own results...comparison itself would be done in R-space,
particularly if only using
a few shells.
For comparison with the results of others, it would depend on
available data
ranges and quality as to how to proceed. e.g. If I analyse 3 to 18 A-1
and want to compare to
someone else who analysed 3 to 10 A-1 due to their data limits, then I
should also
look at my results over their range to give a fair comparison. If the
reverse situation is present,
then the comparison is only within the limits of available data.
regards,
Robert
On 11/5/2015 10:31 AM, Carlos Triana Estupinan wrote:
Hello
ROBERT
Thanks for your kind answer
I have an amorphous structure with 216 atoms, 72 of them are absorbing
atoms. So, I did FEFF calculation for each of those absorber to get
individual EXAFS, and then I dis an average of them to get an averaged
EXAFS (total EXAFS).
I don't want to refine a structural model, but I want to compare the
experimental EXAFS data with the averaged EXAFS I got for my model.
My question is, if I get the EXAFS just from FEFF calculation (chi(k)
or xmu.dat), then I can import it to artemis, and compare with the
experimental (but without do any fiting), just to compare EXAFSs. From
FEFF I can obtain chi(k), u, u0, and X as a function of energy. Which
of those (chi(k), u, u0, and X) should I compare with the experimental
data.
Also, if I compare mi experimental EXAFS with other EXAFS spectra
already published in papers, should be the EXAFS the same or it
depends on the range for the fourier transform.
regards.
2015-11-05 18:50 GMT+01:00 Robert Gordon <ragor...@alumni.sfu.ca
<mailto:ragor...@alumni.sfu.ca>>:
Hi Carlos,
Please clarify somethings for me regarding your inquiry.
You have a structural model and you have data.
You calculated a FEFF simulation of your structural model.
You did not use the FEFFNNNN.dat files to try to fit the model to
your data,
but instead just did a comparison of the simulated chi(k), presumably
with just some default settings in FEFF.inp in addition to your
structural model.
Is that correct?
Generally, it is the fit to the data that gives one feedback on
the validity
of the structural model (GIGO rules apply).
If you have a model, then you have a model coordination number and
can use
a program (e.g. Artemis) to refine amplitude, distance,
mean-square-relative displacement
and energy shift. Do you need explanations of what these
parameters represent?
So, to address what you were wondering, I believe the answer is
yes...you need to actually
do a fit, and the goal isn't to get the obtained spectrum to look
like your simulation.
Data is sacred. The goal is find a model that best reproduces the
data (within a confidence
level governed by the goodness of fit).
regards,
Robert
On 11/5/2015 7:06 AM, Carlos Triana Estupinan wrote:
Dear
Bruce
I am doing calculation of EXFAS for a amorphous structure created
by molecular dynamics. I am using FEFE to obtain chi(k) and the
file xmu, however, when comparing with experimental data with the
calculated EXFAS I have the following problems.
1) The Fourier transform of the EXAFS calculated by FEFF has the
same shape that the experiment spectra, however it is higher in
amplitude.
2) The calculated EXFAS by FEFF has the same oscillation in
K-space, but it does not match the oscillation in K (both of them
are shifted to each other).
I am wondering if I need to do an extra correction to the
calculated EXAFS by FEFF in order to match the K-space and the
amplitude in R-sapace. Shall I change the energy shift or the
Edge step to match the experimental spectra. I so, how can I am
sure about the obtained spectra really correspond to my molecular
dynamics simulation.
Thanks for your help.
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