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 mailto:aderson.mir@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

_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

-- Bruce Ravel ------------------------------------ bravel@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