Dear Robert


Attached I have given the different feff.inp files generated from using Artemis and from WebAtoms (named accordingly) along with images showing the input screens using default parameters.


The difference comes in the atoms list generated. Using artemis two short atoms are produced at 1.91 A which are not present when I use WebAtoms. Interestingly I have now discovered this does not happen with every artemis project. I have attached a project where I am getting the erroneous feff.inp file generation. To replicate the error it is possible to add another feff calculation into this artemis project with the attached cif. 


The attached project is an example where this error occurs but I have not been able thus far to make a new project that repeats this error.


Adam

From: Ifeffit <ifeffit-bounces@millenia.cars.aps.anl.gov> on behalf of ifeffit-request@millenia.cars.aps.anl.gov <ifeffit-request@millenia.cars.aps.anl.gov>
Sent: 08 June 2017 23:59:09
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Ifeffit Digest, Vol 172, Issue 4
 
Send Ifeffit mailing list submissions to
        ifeffit@millenia.cars.aps.anl.gov

To subscribe or unsubscribe via the World Wide Web, visit
        http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
or, via email, send a message with subject or body 'help' to
        ifeffit-request@millenia.cars.aps.anl.gov

You can reach the person managing the list at
        ifeffit-owner@millenia.cars.aps.anl.gov

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Ifeffit digest..."


Today's Topics:

   1. Re: Error using Atoms (Robert Gordon)
   2. Re: question about sigma2 and atomic distance (Robert Gordon)


----------------------------------------------------------------------

Message: 1
Date: Thu, 8 Jun 2017 15:33:55 -0700
From: Robert Gordon <ragordon@alumni.sfu.ca>
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Error using Atoms
Message-ID:
        <CA+FiM0FCdZ5NdupthJLzWrynk2xbXFYE81s5hPVHQrWedqPZow@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Adam,

I opened the cif file you provided and Artemis/Atoms immediately gave the
atoms.inp file attached.
Running Atoms gave the feff.inp....I 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 <adam.clark.14@ucl.ac.uk> 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 ? before the first shell
> atoms at distances of 2.70 ? for metallic Rh.
>
>  ATOMS                  * this list contains 69 atoms
>  *   x          y          z     ipot tag           distance
>     0.00000    0.00000    0.00000  0  Rh1           0.00000
>     1.65411    0.95500    0.00000  1  Rh1.1         1.91000
>    -1.65411   -0.95500    0.00000  1  Rh1.1         1.91000
>    -1.65411    0.95500    1.91000  1  Rh1.2         2.70115
>     0.00000    1.91000    1.91000  1  Rh1.2         2.70115
>     1.65411   -0.95500    1.91000  1  Rh1.2         2.70115
>     0.00000   -1.91000    1.91000  1  Rh1.2         2.70115
>    -1.65411    0.95500   -1.91000  1  Rh1.2         2.70115
>     0.00000    1.91000   -1.91000  1  Rh1.2         2.70115
>     1.65411   -0.95500   -1.91000  1  Rh1.2         2.70115
>     0.00000   -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
>
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20170608/c6d4a5fc/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: atoms.inp
Type: application/octet-stream
Size: 651 bytes
Desc: not available
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20170608/c6d4a5fc/attachment-0002.obj>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: feff.inp
Type: application/octet-stream
Size: 4478 bytes
Desc: not available
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20170608/c6d4a5fc/attachment-0003.obj>

------------------------------

Message: 2
Date: Thu, 8 Jun 2017 15:59:05 -0700
From: Robert Gordon <ragordon@alumni.sfu.ca>
To: Shaofeng Wang <wangshaofeng@iae.ac.cn>, XAFS Analysis using
        Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] question about sigma2 and atomic distance
Message-ID:
        <CA+FiM0H6w4Gy5Eu0oQkJom_D_quBv5dv8oSGcTKngKfrYxbGkQ@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

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 <wangshaofeng@iae.ac.cn>
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
> wangshaofeng@iae.ac.cn
> www.iae.cas.cn
>
>
> *From:* Shaofeng Wang <wangshaofeng@iae.ac.cn>
> *Sent:* Friday, June 02, 2017 4:32 PM
> *To:* XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
> *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
> wangshaofeng@iae.ac.cn
> www.iae.cas.cn
>
> ------------------------------
> _______________________________________________
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20170608/3f1597f6/attachment.html>

------------------------------

Subject: Digest Footer

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


------------------------------

End of Ifeffit Digest, Vol 172, Issue 4
***************************************