Re: [Ifeffit] question about sigma2 and atomic distance

[Robert Gordon]

I imagine they could, yes. Motivation to do so is another question entirely.

Considering myself more of an experienced amateur, and a fan of the
Socratic Method, let me ask you a few questions:

What do you currently understand about the relationship between two atoms
in a material and the mean square relative displacement
(i.e. sigma^2) associated with the distance between them?
What does it mean to have a mean-square-displacement? ..and then a
mean-square-relative displacement?
How would correlated, anti-correlated and uncorrelated relative motion
affect the msrd?

Now extend this thinking to an ensemble of atoms.
What might you expect to be the source of a msrd in a perfect crystal at
finite temperature?
What additional contribution may result from imperfections?








On Wed, Jun 7, 2017 at 7:12 PM, Shaofeng Wang 
wrote:

> Dear everyone,
>
> Could experts explain the relationship between sigma2 and atomic distance
> of same two atoms?
>
>
> Best regards,
>
> Shaofeng
>
> --
> Shaofeng Wang, Ph.D of Geochemistry
> Environmental Molecular Science Group
> Institute of Applied Ecology, Chinese Academy of Sciences
> Shenyang, 110016, China
> wangshaof...@iae.ac.cn
> www.iae.cas.cn
>
>
> *From:* Shaofeng Wang 
> *Sent:* Friday, June 02, 2017 4:32 PM
> *To:* XAFS Analysis using Ifeffit 
> *Subject:* [Ifeffit] a question about S02
>
> Hi everyone,
>
> I am fitting a standard material scorodite. The fitting results are pretty
> good, but the S02 is around 1.2 when the k range = 4-13.5. Is this result
> reasonable? Please see the attached files.
>
>
>
> Best regards,
>
> Shaofeng
>
> --
> Shaofeng Wang, Ph.D of Geochemistry
> Environmental Molecular Science Group
> Institute of Applied Ecology, Chinese Academy of Sciences
> Shenyang, 110016, China
> wangshaof...@iae.ac.cn
> www.iae.cas.cn
>
> --
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Re: [Ifeffit] Error using Atoms

[Robert Gordon]

Hi Adam,

I opened the cif file you provided and Artemis/Atoms immediately gave the
atoms.inp file attached.
Running Atoms gave the feff.inpI don't see a problem.

Could you provide more detail on how you achieved this erroneous result?
i.e. step by step...
e.g. I opened Artemis v0.9.25
I clicked 'add' under Feff calculations
I selected Rh.cif and clicked open
et voila! Much humble praise to Bruce...

-R.



On Thu, Jun 8, 2017 at 5:50 AM, Clark, Adam  wrote:

> Dear Mailing List
>
>
> I have encountered an issue when using the version of Atoms within
> Artemis for the calculation of the scattering paths on metallic FCC
> systems. Attached are both the cif file and the generated feff.inp file
> from using Atoms from within Artemis. Here the problem that occurs is the
> generation of two short atoms at distances of 1.91 Å before the first shell
> atoms at distances of 2.70 Å for metallic Rh.
>
>  ATOMS  * this list contains 69 atoms
>  *   x  y  z ipot tag   distance
> 0.00.00.0  0  Rh1   0.0
> 1.654110.955000.0  1  Rh1.1 1.91000
>-1.65411   -0.955000.0  1  Rh1.1 1.91000
>-1.654110.955001.91000  1  Rh1.2 2.70115
> 0.01.910001.91000  1  Rh1.2 2.70115
> 1.65411   -0.955001.91000  1  Rh1.2 2.70115
> 0.0   -1.910001.91000  1  Rh1.2 2.70115
>-1.654110.95500   -1.91000  1  Rh1.2 2.70115
> 0.01.91000   -1.91000  1  Rh1.2 2.70115
> 1.65411   -0.95500   -1.91000  1  Rh1.2 2.70115
> 0.0   -1.91000   -1.91000  1  Rh1.2 2.70115
>
>
> Using the same input CIF file within WebAtoms does not produce these short
> distances.
>
>
> Adam Clark
>
>
> PhD Student
>
>
>
> Industrial Doctorate Centre in Molecular Modelling and Materials Science,
>
> Department of Chemistry,
>
> University College London
>
>
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atoms.inp
Description: Binary data


feff.inp
Description: Binary data
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[Ifeffit] Error using Atoms

[Clark, Adam]

Dear Mailing List


I have encountered an issue when using the version of Atoms within Artemis for 
the calculation of the scattering paths on metallic FCC systems. Attached are 
both the cif file and the generated feff.inp file from using Atoms from within 
Artemis. Here the problem that occurs is the generation of two short atoms at 
distances of 1.91 Å before the first shell atoms at distances of 2.70 Å for 
metallic Rh.

 ATOMS  * this list contains 69 atoms
 *   x  y  z ipot tag   distance
0.00.00.0  0  Rh1   0.0
1.654110.955000.0  1  Rh1.1 1.91000
   -1.65411   -0.955000.0  1  Rh1.1 1.91000
   -1.654110.955001.91000  1  Rh1.2 2.70115
0.01.910001.91000  1  Rh1.2 2.70115
1.65411   -0.955001.91000  1  Rh1.2 2.70115
0.0   -1.910001.91000  1  Rh1.2 2.70115
   -1.654110.95500   -1.91000  1  Rh1.2 2.70115
0.01.91000   -1.91000  1  Rh1.2 2.70115
1.65411   -0.95500   -1.91000  1  Rh1.2 2.70115
0.0   -1.91000   -1.91000  1  Rh1.2 2.70115



Using the same input CIF file within WebAtoms does not produce these short 
distances.


Adam Clark


PhD Student



Industrial Doctorate Centre in Molecular Modelling and Materials Science,

Department of Chemistry,

University College London



feff.inp
Description: feff.inp


Rh.cif
Description: Rh.cif
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