[Ifeffit] Question about using a proper model

[pushkar shejwalkar]

Dear Matt,
          Thank you very much for your reply. Yes it generates list of XYZ
cordinates. I am wondering if its ok to use such information. The reason is
that while converting the XYZ file into .inp file, the format is different
and hence I am simply typing the coordinates into it, however I am not sure
as to should I change nleg values, Rmax values and other mphase mfeff
values and all. Is it same for all the program? just changing the
coordinates is enough?
About lower E0 value, I read in Shelly's paper that mostly ppl do not
report E0 value and if they and if it is >10 then there may be problem with
modelling or so. one of the method to reduce such chances of high E0 is by
properly aligning spectra in athena. She mention in this a method to use
first artemis for getting first shell fitting using E0=0 and then coming
back to the athena and using this file as reference. But I am not sure how
to open artemis file in athena because if I open .fpj file in athena it
doesnt recognise and says that the format is not readable if you continue
then athena shutdown. In artemis I cannot save file as .prj. is there a way
around? OR IT IS JUST THAT I AM DOING IT ALL WRONG?
Thank you very much for your help.
Pushkar

On Mon, Oct 27, 2014 at 11:12 PM, Matt Newville <newville at cars.uchicago.edu>
wrote:

> On Mon, Oct 27, 2014 at 1:14 AM, pushkar shejwalkar
> <pshejwalkar2004 at gmail.com> wrote:
> > Dear All,
> >             I am new to XAFS data analysis and have very limited
> knowledge
> > about using modelling structures for XAS analysis. I am not sure as to if
> > this question is directly related to Demter or XAFS analysis as such but
> its
> > a part of it for sure.
> >      Question number one
> >  I am trying to analyze the sample I recently collected at SPring-8
> > facility. The structure I am hoping to be formed during the reaction is
> more
> > of a organometallic complex at silica interface. In order to establish
> the
> > structure I was told that there are two methods I could use.
> > 1) Use a counter part compound which is exact/looks like the structure I
> am
> > hoping (so basically known compound) and then do traditional comparison
> > method to establish the structure.
> >       UNFORTUNATELY I cannot synthesize such compound in lab nor such
> > material is available in literature ( including crystal structure).
> > 2) is to use the model.
> > right now for modelling such structure I am using Spartan program (again
> I
> > have not used it earlier in my graduate work) So I want to know as to
> how to
> > generate the models in order to get the correct crystal parameters?
> (atoms
> > positions?) Is spartan good enough to do job? is there any other method
> for
> > doing such fitting?
>
> Sorry, I'm not familiar with Spartan -- it can probably generate a
> list of atomic X, Y, Z, atomic_number coordinates.... is that correct?
>  If so, converting that into a feff.inp input file is not too hard,
> but if you haven't done that before, I'd suggest starting by running
> Atoms on a crystal structure with roughly comparable composition and
> the same central atom, and then it can be modified from there.
>
> >     Question number two
> > In order to get lower E0 values after the fitting, I read that there is a
> > method to use in which delE value can be set to 0 intentionally and then
> > recalibrating the spectra in athena again in order to accurately
> calibrate
> > the E0. I read paper by Shelly kelly and Bruce Ravel. Also I have seen
> the
> > steps in one of shelly kellys PDF formatted lecture, although I am still
> not
> > sure about the exacts steps to take in order to do such calibration.
> Could
> > someone explain me the steps in details (especially taking artemis files
> to
> > athena and then using it as STD spectra for calibration purposes, I am
> > confused about that)
>
> Why is it important to you to get a lower value for E0?
>
> --Matt
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-- 
Best Regards,
Pushkar Shejwalkar.
Post-doctoral -Researcher,JSPS Fellow
Hokkaido University,
Sapporo,
Japan
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