[Ifeffit] Is it possible to use ATOMS to solve this problem?

Bruce Ravel bravel at bnl.gov
Tue Nov 5 10:44:00 CST 2013



Possibly helpful:

https://speakerdeck.com/bruceravel/modeling-non-crystalline-samples

Particularly this page:

https://speakerdeck.com/bruceravel/modeling-non-crystalline-samples?slide=11

B

On 11/05/2013 10:46 AM, Matt Newville wrote:
> Hi Aderson,
>
>
> On Tue, Nov 5, 2013 at 8:16 AM, Áderson Miranda <aderson.mir at gmail.com
> <mailto:aderson.mir at gmail.com>> wrote:
>
>     Dear Prof. Newville,
>
>     I am a PhD. student from Brazil and I am trying to use ATOMS to a
>     solve a particular problem in my thesis. I would like to generate a
>     big cubic unitary cell  with a S2O3 molecule surrounded by six water
>     molecules in the center of cell and to put heliums atoms in their
>     six vertices.
>
>     I have all the atoms positions optimized to my problem, except by
>     the helium atoms, that I want to place in a enough distance to have
>     only one molecule of S2O3 surrounded by water in the simulation of
>     EXAFS. I tried to insert the data in atoms and generate an input for
>     the  simulation of EXAFS. I was not successful in my try, so is it
>     possible to construct this kind of cell and simulating the "EXAFS"
>     for this specific problem?
>
>     Sincerely,
>
>     Áderson Miranda
>
> Yes, it should be possible to do this.  It would be most helpful to see
> what you've tried and what worked and what did not.    It's not obvious
> to me that helium will give a noticeable contribution to the EXAFS, but
> it's worth being able to calculate.
>
> I am using the Ifeffit mailing list to respond to this mail, as many
> people reading this have extensive experience constructing such
> molecular coordinates.
>
> --Matt
>
>
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-- 
  Bruce Ravel  ------------------------------------ bravel at bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
  Building 535A
  Upton NY, 11973

  Homepage:    http://xafs.org/BruceRavel
  Software:    https://github.com/bruceravel



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