Re: [Ifeffit] Athena open data project but not shown the curve

[Robert Gordon]

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 FEFF.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 >:


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 FEFF.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 

Re: [Ifeffit] Athena open data project but not shown the curve

[Bruce Ravel]

On 10/28/2015 08:44 PM, 百度知道用户 wrote:

Hi all,
I processed a series of data using IFEFFIT Athena, and saved it as a
project. Later, when I opened the project in IFEFFIT Athena, the plot
window did not show the curve. I tried to open the project in Demeter
Athena, but  popuped "Can't call method "datatype" on an undefined
value". The data curve was also not shown. I want to know what happened
to this? Are the data damaged? I am very thankful if this problem can be
solved.


It is hard to address a problem like this without an actionable bug 
report.  See http://bruceravel.github.io/demeter/pods/bugs.pod.html


B

--
 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Building 535A
 Upton NY, 11973

 Homepage:http://bruceravel.github.io/home/
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
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