[Ifeffit] Sorbed complex in Atoms

Gnu script iam.gnu.py at gmail.com
Thu Jun 9 11:12:36 CDT 2016


Hi Bruce,
Thanks for your reply. I am familiar with outer-sphere complexation and how
it works but I am much less familiar with Artemis and how such question can
be approached. In the past we used Excurve and DL-Excurve where you can
simply name the backscatter with initial estimates of N and R but without
any need for STRUCTURE. Now, having moved away from these tools into
Demeter and Artemis I am trying to learn rather than asking people to do
work for me!

So, what I have done so far was to replace Ti in the Atoms file by Ni but
it is not clear to me what I need to change in order to test outer-sphere
vs inner-sphere complexes of Ni.


space = P b c n
a     =   8.71280    b    =   5.23270    c     =  14.48700
alpha =  90.00000    beta =  90.00000    gamma =  90.00000
rmax  =   7.84905    core  = Ti
# polarization = 0.0  0.0  0.0
shift =     0.00000    0.00000    0.00000
atoms
# el.     x           y           z        tag
  Na     0.06430     0.64500     0.15370   Na
  Ti     0.15130     0.13220     0.33090   Ti
  Si     0.34210     0.29610     0.52670   Si
  O      0.00000     0.00600     0.25000   O1
  O      0.18170     0.44070     0.27580   O2
  O      0.33360     0.29670     0.41520   O3
  O      0.00890     0.24280     0.42800   O4
  O      0.23570     0.05980     0.56700   O5


Thanks,
 G








On Thu, Jun 9, 2016 at 3:58 PM, Bruce Ravel <bravel at bnl.gov> wrote:

>
> This is an very vague and open-ended question.
>
> Have you read any of the very extensive literature applying EXAFS to
> outer-sphere complexation?  Have you tried anything ... anything at all ...
> to solve your problem?
>
> If you ask specific questions, you will get good answers.  If you ask
> folks on the list to do your work for you, that won't go so well.
>
> B
>
>
>
> On 06/09/2016 10:25 AM, Gnu script wrote:
>
>> Dear All,
>>
>> I am relatively new to Ifeffit and Artemis. I am trying to find a way to
>> create four-shell model of an outer-sphere complex in Atoms or some
>> other way readable by Atoms. I have no idea about the geometry, space
>> group but some rough guess of bond-distances. The model to test against
>> the EXAFS data is:
>> Ni is the central atom
>> Ni-O first shell
>> Ni-Ni second shell
>> Ni-Ti third shell
>> Ni-Si fourth shell
>>
>> The model aims to test the adsorption of Ni on the surface of
>> Ti-containing silicate mineral.
>>
>> Could you please help.
>>
>> Thanks.
>>
>>
>>
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>>
>
> --
>  Bruce Ravel  ------------------------------------ bravel at 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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