[Ifeffit] Ifeffit Digest, Vol 172, Issue 4
Clark, Adam
adam.clark.14 at ucl.ac.uk
Fri Jun 9 07:54:16 CDT 2017
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
________________________________
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Subject: Ifeffit Digest, Vol 172, Issue 4
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Today's Topics:
1. Re: Error using Atoms (Robert Gordon)
2. Re: question about sigma2 and atomic distance (Robert Gordon)
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Message: 1
Date: Thu, 8 Jun 2017 15:33:55 -0700
From: Robert Gordon <ragordon at alumni.sfu.ca>
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Error using Atoms
Message-ID:
<CA+FiM0FCdZ5NdupthJLzWrynk2xbXFYE81s5hPVHQrWedqPZow at 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 at 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
>
>
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Message: 2
Date: Thu, 8 Jun 2017 15:59:05 -0700
From: Robert Gordon <ragordon at alumni.sfu.ca>
To: Shaofeng Wang <wangshaofeng at iae.ac.cn>, XAFS Analysis using
Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] question about sigma2 and atomic distance
Message-ID:
<CA+FiM0H6w4Gy5Eu0oQkJom_D_quBv5dv8oSGcTKngKfrYxbGkQ at 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 at 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 at iae.ac.cn
> www.iae.cas.cn<http://www.iae.cas.cn>
>
>
> *From:* Shaofeng Wang <wangshaofeng at iae.ac.cn>
> *Sent:* Friday, June 02, 2017 4:32 PM
> *To:* XAFS Analysis using Ifeffit <ifeffit at 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 at iae.ac.cn
> www.iae.cas.cn<http://www.iae.cas.cn>
>
> ------------------------------
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