Re: [Ifeffit] Ifeffit Digest, Vol 172, Issue 6

Dear Robert Thanks, following the linked discussions I am also now able to repeat the problem though first running a feff calculation on the Rh2O3 structure and second on the Rh structure. Having now downloaded the pre release version this does indeed fix this problem. Adam ________________________________ From: Ifeffit on behalf of ifeffit-request@millenia.cars.aps.anl.gov Sent: 09 June 2017 14:16:20 To: ifeffit@millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 172, Issue 6 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: Ifeffit Digest, Vol 172, Issue 4 (Robert Gordon) ---------------------------------------------------------------------- Message: 1 Date: Fri, 9 Jun 2017 06:16:15 -0700 From: Robert Gordon To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Ifeffit Digest, Vol 172, Issue 4 Message-ID: Content-Type: text/plain; charset="utf-8" Hi Adam, I think the problem you are seeing is related to one observed back in April. The Rh2O3 crystal you also have in your project has trigonal symmetry, and trigonal symmetry in 0.9.25 tends to override all others. This was discussed in this thread: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2017-April/009083.html Bruce made a pre-release of 0.9.26 available at the time that fixed this problem: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2017-April/009084.html The pre_2 release of 0.9.26 is also available on the main Demeter page: https://bruceravel.github.io/demeter/ -R. On Fri, Jun 9, 2017 at 5:54 AM, Clark, Adam wrote:

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 on behalf of 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 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Error using Atoms Message-ID: 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 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