[Ifeffit] Problems with fit in pyrite structure with Se substitution

[Matt Newville]

Hi Adriana,

On Tue, Jul 3, 2012 at 3:26 AM, Adriana Matamoros Veloza
<A.MatamorosVeloza at leeds.ac.uk> wrote:
> Hi Bruce,
>
> In both projects the data corresponds to Se edge (no sulphur).  Selenium data was collected on natural pyrite grains.  When Se associates to pyrite, it is normally inferred that Se substituted sulphur within the pyrite structure.  Both elements are chemically very similar. Looking at selenium as the core atom, we want to see if it is possible to get the chemical environment related to pyrite (Se-S, Se-Fe bonds).  In natural environments if substitution of sulphur with selenium occurs the proportion is rather than low (perhaps maximum 1% of the population of sulphur atoms). So, in that case we are expecting to get data that fit to the pyrite structure taking Se as the core atom.  For that reason, the Feff calculations were made with the crystal structure of pyrite with sulphur as the core atom and used Se edge instead.  Is that making any sense?
>

What you should do is create the feff input as you did, selecting S as
the absorbing atom, but then change the absorbing atom from S to Se,
 That is where it says (approximately):

    POTENTIALS
        0   16  S
        1   26  Fe
        2   16  S

you should edit this, replacing the above with

    POTENTIALS
       0   34  Se
       1   26  Fe
       2   16  S

Note that 0 in the first column means 'absorbing atom'.  Potential 2
is for the non-absorbing S atoms, which you probably want to leave
alone,  as the structure you want to model is one absorbing Se atom in
pyrite.

You can also edit the list of atomic coordinates (this is useful if
you want to move atoms around).  In your case, you might want to
change the "tag" for the absorbing atom, from something like

  ATOMS
   0.00000     0.00000     0.00000    0   S1              0.00000

to

  ATOMS
   0.00000     0.00000     0.00000    0   Se1              0.00000

That part is optional.  Changing the POTENTIALS is not.   After these
edits, running Feff will generate scattering paths for Se-Fe, Se-S,
and so on.


--Matt