- Ifeffit - millenia.cars.aps.anl.gov

NiO-test-athena-project
by mazhar iqbal 17 Jun '16

17 Jun '16

Hello I would appreciate valuable comments on the NiO spectrum processed in athena. I am a new in this area so please comment on any mistake I have made while processing. Best Regards

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Athena crash on Mac when exporting empirical standard
by Chloe Yi-Yi Wu 17 Jun '16

17 Jun '16

Hi all, I'd like to export an empirical standard from Athena to fit EXAFS with Artemis. However, once I clicked on the element for scattering in the pop-up window, Athena was frozen and no .es file was generated. Does anyone know how to fix the problem? Thanks, Chloe -- Yi-Yi (Chloe) Wu Kung Research Group Dept. of Chemical and Biological Engineering Northwestern University Evanston, IL USA

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Sorbed complex in Atoms
by Gnu script 09 Jun '16

09 Jun '16

Dear All, I am relatively new to Ifeffit and Artemis. I am trying to find a way to create four-shell model of an outer-sphere complex in Atoms or some other way readable by Atoms. I have no idea about the geometry, space group but some rough guess of bond-distances. The model to test against the EXAFS data is: Ni is the central atom Ni-O first shell Ni-Ni second shell Ni-Ti third shell Ni-Si fourth shell The model aims to test the adsorption of Ni on the surface of Ti-containing silicate mineral. Could you please help. Thanks.

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Question about fuzzy degeneracy
by Mirko 09 Jun '16

09 Jun '16

Hey, I am quite new to EXAFS and therefore very glad about this mailing list, it helps a lot. My question is about the fuzzy degeneracy mentioned in the paper "Path degeneracy and EXAFS analysis of disordered materials" (Ravel, B. J Synchrotron Radiat. <http://www.ncbi.nlm.nih.gov/pubmed/25343794>2014 Nov;21(Pt 6):1269-74.) I investigate disordered systems like aqueous salt solutions and would like to use the method on my FEFF calculation. However, I obtained my structure for the FEFF calculation from a MD-Simulation and would like to average over several hundreds of FEFF calculations. To handle this amount of data I use LARCH, which doesn’t have the feature to degenerate similarpaths to one. I would like to use the method by myself to degenerate the first coordination shell of my oxygen atoms around the salt. How do you merge the FEFF parameters from each scattering paths after they are grouped together in a bin with the extended pathfinder algorithm (I think, you can’t just make an average of for example the phase shift or the mean free path … right?) Best regards and thanks a lot! Mirko ------------------------------------------------------------------------

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Substantial problems running ATOMS in Demeter 0.9.24
by Jeff Catalano 08 Jun '16

08 Jun '16

The message sequence from this morning prompted me to inquire if anyone can provide help with ATOMS crashing on my own computer. I am running Demeter 0.9.24 on Windows 10 Pro 64. I did a fresh install of Demeter after having removed all older versions of Demeter 0.9, including the Demeter folders in C:\Users\<username>\AppData\Roaming\. My problem is unfortunately simple and something I do not know how to fix: Whenever I hit the "Run Atoms" button, stand-alone atoms crashes. The program simply dies, and no files are written. I am able to enter text, save an atoms.inp file, and reload an atoms.inp file, but "Run Atoms" crashes the program. I have tested this with a simple compound, NaCl, using the attached atoms.inp file. Note that I don't want to work on NaCl, I just used this to test a simple structure. The log file associated with the crash is attached. The log file says Windows 8, but I think this is just hows Windows 10 shows up as that is what I am running, from a clean Windows 10 install. Anyway, when I load this atoms.inp file or enter the same information by hand the program crashes. I was able to load and run this atoms.inp file in the old version of atoms (3.0.1) and produced the attached feff_oldATOMS.inp file. I thus don't think it is a data entry problem. I hope that I have provided enough information. I have no problems running ATHENA, ARTEMIS, or HEPHAESTUS. Given the log file I suspect this is something unique to my computer, but I am stumped as to what it could be as I am running a standard OS with a standard install on Demeter. Thank you, Jeff -- Jeffrey G. Catalano, Associate Professor Department of Earth and Planetary Sciences Washington University 1 Brookings Drive, Campus Box 1169 Saint Louis, MO 63130 USA http://aqgeochem.wustl.edu/

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Re: [Ifeffit] Artemis file opening
by Dien.Li＠srs.gov 06 Jun '16

06 Jun '16

Hi, Bob and Bruce With upgrading the Demeter 9;24, I am able to open files from 9.21. Thanks you all. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520 From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Date: 06/06/2016 03:01 PM Subject: Ifeffit Digest, Vol 160, Issue 8 Sent by: "Ifeffit" <ifeffit-bounces(a)millenia.cars.aps.anl.gov> Send Ifeffit mailing list submissions to ifeffit(a)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(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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 160, Issue 7 (Dien.Li(a)srs.gov) 2. Re: Ifeffit Digest, Vol 160, Issue 7 (Farquhar, Erik) ---------------------------------------------------------------------- Message: 1 Date: Mon, 6 Jun 2016 13:50:42 -0400 From: Dien.Li(a)srs.gov To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Ifeffit Digest, Vol 160, Issue 7 Message-ID: <OF0754ACB2.B29F1774-ON85257FCA.00619402-85257FCA.006206D8(a)srs.gov> Content-Type: text/plain; charset="us-ascii" Hi, Bob and Bruce Thank for your quick response. No, I have not upgrade to 9.24 yet, because if one version Artemis is not able to open another version files, I am worried about that I can not open my all other current files, maybe the newer version is able to open the older version files. By the way, when I clicked the Artemis fitting file from my collaborator, after I saw Artemis picture logo, and several Artemis window flashed, and then gone, so that I failed to open. Thanks for any instruction. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520 From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Date: 06/06/2016 01:06 PM Subject: Ifeffit Digest, Vol 160, Issue 7 Sent by: "Ifeffit" <ifeffit-bounces(a)millenia.cars.aps.anl.gov> Send Ifeffit mailing list submissions to ifeffit(a)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(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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. Questions (Dien.Li(a)srs.gov) 2. Re: Questions (Robert Gordon) 3. Re: Questions (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Mon, 6 Jun 2016 11:50:05 -0400 From: Dien.Li(a)srs.gov To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Questions Message-ID: <OF4DB5BE28.5E4C9E2D-ON85257FCA.0056CE0F-85257FCA.0056FBB2(a)srs.gov> Content-Type: text/plain; charset="us-ascii" Hi, All I am using Demeter Artemis version 9.18, however, I could not open the Artemis file that was generated from Artemis Version 9.21 from my collaborator, anyone can instruct or help? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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Re: [Ifeffit] Ifeffit Digest, Vol 160, Issue 7
by Dien.Li＠srs.gov 06 Jun '16

06 Jun '16

Hi, Bob and Bruce Thank for your quick response. No, I have not upgrade to 9.24 yet, because if one version Artemis is not able to open another version files, I am worried about that I can not open my all other current files, maybe the newer version is able to open the older version files. By the way, when I clicked the Artemis fitting file from my collaborator, after I saw Artemis picture logo, and several Artemis window flashed, and then gone, so that I failed to open. Thanks for any instruction. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520 From: ifeffit-request(a)millenia.cars.aps.anl.gov To: ifeffit(a)millenia.cars.aps.anl.gov Date: 06/06/2016 01:06 PM Subject: Ifeffit Digest, Vol 160, Issue 7 Sent by: "Ifeffit" <ifeffit-bounces(a)millenia.cars.aps.anl.gov> Send Ifeffit mailing list submissions to ifeffit(a)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(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)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. Questions (Dien.Li(a)srs.gov) 2. Re: Questions (Robert Gordon) 3. Re: Questions (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Mon, 6 Jun 2016 11:50:05 -0400 From: Dien.Li(a)srs.gov To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Questions Message-ID: <OF4DB5BE28.5E4C9E2D-ON85257FCA.0056CE0F-85257FCA.0056FBB2(a)srs.gov> Content-Type: text/plain; charset="us-ascii" Hi, All I am using Demeter Artemis version 9.18, however, I could not open the Artemis file that was generated from Artemis Version 9.21 from my collaborator, anyone can instruct or help? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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Questions
by Dien.Li＠srs.gov 06 Jun '16

06 Jun '16

Hi, All I am using Demeter Artemis version 9.18, however, I could not open the Artemis file that was generated from Artemis Version 9.21 from my collaborator, anyone can instruct or help? Thanks. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

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atoms crashes
by Jesús Eduardo Vega Castillo 03 Jun '16

03 Jun '16

Hello everyone, I have manually introduced the crystal structure of La4Fe3O10 into Atoms and generated and .inp file. The structure contains 2 sites of La, 2 sites of Fe and 4 sites of O. When I try to run Atoms from this file it crashes. This is the inp file: ## This Atoms file was generated by Demeter 0.9.24 ## Demeter written by and copyright (c) Bruce Ravel, 2006-2015 title = La4Fe3O10 (LSFC) space = I 4/m m m a = 3.83900 b = 3.83900 c = 27.87050 alpha = 90.00000 beta = 90.00000 gamma = 90.00000 rmax = 5.00000 core = Fe1 # polarization = 0.0 0.0 0.0 shift = 0.00000 0.00000 0.00000 atoms # el. x y z tag La 0.00000 0.00000 0.56860 La1 La 0.00000 0.00000 0.70130 La2 Fe 0.00000 0.00000 0.00000 Fe1 Fe 0.00000 0.00000 0.13840 Fe2 O 0.00000 0.50000 0.13810 O1 O 0.00000 0.00000 0.06980 O2 O 0.00000 0.00000 0.21050 O3 O 0.00000 0.50000 0.00000 O4 Any help would be appreciated. Yours, Jesús

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Re: [Ifeffit] Heavy Scatterer Resonance
by Matt Newville 02 Jun '16

02 Jun '16

Pieter, Please use the ifeffit mailing list for questions about XAFS Analysis. I am CCing this reply to that list. On Thu, Jun 2, 2016 at 2:35 AM, Pieter Tack <Pieter.Tack(a)ugent.be> wrote: > Dear Dr. Newville, > > > During the analyses of some metallic Au EXAFS I noticed the Au-Au single > scatter first shell is characterised by a split peak in the chi(R) > spectrum. I was wondering what caused this, as I would expect a single > scatter path resulting in only one scatter distance and thus one peak in > the chi(R). However, I could not find much on the matter except for a quote > of you stating it is "due to the resonance in the scattering for heavy > scatterers" ( > http://permalink.gmane.org/gmane.science.physics.ifeffit/2352 ) > In short: XAFS chi(R) is *NOT* a pair distribution function, due mostly to the complex electron scattering that alter the amplitude and shift the phase of potoelectron in addition to the simplistic "backscatter from a point source atom". The most obvious effect of this is a ~0.5 Ang shift to lower R from the value you might expect if chi(R) was a pair distribution function. Other effects include broader and asymmetric peaks, and the resonance effect such as you notice for heavy elements (easily noticeable for Z>40 or so, but unmistakable for Z > 60 -- that Z is for the *scattering atom*). At certain energies (or for a narrow range of energies), the photo-electron has very low scattering probability from a heavy element, and the phase jumps dramatically, as if the electron was able to tunnel through or hop over the potential well of the scattering atom. This is usually (and I think properly) called a Ramsauer-Townsend resonance. There are many papers, review articles, and slides from talks available that describe this in more detail. Google "ramsauer townsend effect exafs" for detailed articles. > I don't really understand what this means, which physical process causes > this. Could you perhaps provide me with additional info on this matter or > direct me to some papers that explain this? > > > Thanks in advance! > > Best regards > > Pieter Tack > > > --- > X-Ray Micro-Spectroscopy and Imaging Group > Department of Analytical Chemistry > Ghent University > Krijgslaan 281 S12 > B-9000 Ghent > Belgium > Phone: +32 (0)9 264 4723 > Fax: +32 (0)9 264 49 60 > --Matt

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