[Ifeffit] Need your help

[Bruce Ravel]

Hi Jin,

I am CCing my response to the Ifeffit mailing list:
  http://cars9.uchicago.edu/mailman/listinfo/ifeffit/

If you are not already a member of the mailing list, I encourage you
to join.  It is a great place to ask questions and learn about XAFS
and the Ifeffit-based software.


On Sunday 16 September 2007, you wrote:
> Dear Ravel:
>
>      I am just a student of Shanghai Applied Physics Institute, CSA. And I
> meet some problem by using FEFF process.
>
> When I know the coordination number and the coordination distance of known
> structure macular, how to set the atom inp file or feff inp file?

I'm afraid that I am little unsure what you exact question is.  If you
know the coordination number and distance because your material is a
known crystal, then you can just use a CIF file or an atoms.inp file
of the sort described here:
  http://cars9.uchicago.edu/~ravel/software/doc/Atoms/Atoms/node4.html
or available for many materials at this database:
  http://cars9.uchicago.edu/~newville/adb/search.html

If you know coordination and distances because you have structural
information of the sort that you might find in a protein data bank
file or some other molecular format, then you should skip the use of
atoms and simply convert the molecular data to a feff.inp file as
described on page 36 of this talk I recently gave:
   http://cars9.uchicago.edu/~ravel/talks/pimst2.pdf

It is important to remember that Atoms is a tool for converting
crystallographic data into a list of atomic coordinates.  That's all
it does.  If you are doing XAFS on something that is not a crystal,
Atoms is of no use.

> And another question is how get the usefully muffin tin from the XRD data
> in the protein data bank?

Feff computes muffin tins.  In 99% of all situations, you do not need
to modify how Feff does tht nor do you need to specify muffin tin
radii.  Feff's algorithm for determining muffin tin radii given a list
of atomic coordinates is relatively simple, but surprisingly effective
and completely automated.

> I have tried many time as the handbook shows, but I also don't know how to
> do? So I need your help ? Thank you very much

You may find it useful to ask explicit questions on the mailing list
by posting examples of the problem you are having.  For instance, if
you are having trouble running Feff, asking a question about the exact
thing that is confusing and posting an example of the feff.inp file
that is giving you trouble will help the people on the mailing list
help you.

Good luck and I hope this was helpful,
Bruce


> Smiling everyday,
>
> Best wishes,
>
> Jin Chan



-- 
 Bruce Ravel  ---------------------------------------------- bravel at anl.gov

 Molecular Environmental Science Group, Building 203, Room E-165
 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007

 Argonne National Laboratory         phone and voice mail: (1) 630 252 5033
 Argonne IL 60439, USA                                fax: (1) 630 252 9793

 My homepage:    http://cars9.uchicago.edu/~ravel 
 EXAFS software: http://cars9.uchicago.edu/~ravel/software/