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

Cool math expression
by Anatoly Frenkel 19 Jun '20

19 Jun '20

I thought I share a really good idea I found in someone's fit project that was shared with me. Instead of varying deltaR and then doing something like: "after R_final = 2.79 + deltaR" to have Artemis calculate the actual bond length (and then looking for its uncertainty in the list of guess parameters in the log file for the corresponding deltaR variable's uncertainty), it can be written in the Artemis data window as: [image: image.png] where A_Cr is the bond length, and its uncertainty will be written in the same place with the best fit value in the guess parameters list. Probably I am the only one not using this trick, but I still thought it would be good to share. Anatoly

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Exporting fit from ARTEMIS_problem with k-weight
by Manju 19 Jun '20

19 Jun '20

Hello there I got an issue with k-weight of fit whileexporting the fit from ARTEMIS I fitted the data in k2, but it is exporting k3. I saved the fit at k2 weight and when I opened again, it was again set at k3. Is there any way I could choose the k-weight of my choice while exporting? Regards Manju Junior Research Fellow Department of Basic and Applied Sciences Punjabi University, Patiala- 147 002 Punjab, India.

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Ga standards
by Christian Wittee Lopes 18 Jun '20

18 Jun '20

Dear colleagues, Does anyone have the XANES spectra of the different Ga2O3 polymorphs (alfa, beta, gamma) and α-GaOOH? I'm treating some data and I need to rule out the presence of such phases in my samples. Thanks in advance!!! -- *Christian Wittee Lopes* *Postdoctoral Researcher* Institute of Physics, Universidade Federal do Rio Grande do Sul (UFRGS) Phone: +55 54 992430264

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Requested: NiFe2O4 Fe K and Ni K XAS spectra
by Valentijn De Coster 17 Jun '20

17 Jun '20

Dear mailing list, I am looking for Fe K and Ni K edge XAS spectra of NiFe2O4 - if possible, containing both the XANES and EXAFS region. Then again, if energy regions of 7100-7200 eV (Fe K) and 8320-8420 eV (Ni K) are available, this is already sufficient. Spectra obtained at room temperature would be much obliged. This is with the intention of a comparative study for XANES features of an as prepared Ni-Fe catalyst. Thank you in advance. Kind regards, Valentijn

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Re: [Ifeffit] FOLP error in Feff calculation
by Kewei Zhao 26 May '20

26 May '20

Dear Matthew, Thanks for the suggestion. The cluster structure is generated from molecular dynamics trajectories, and I just picked a random one out of 10k+ clusters. The Ca-Cl distance varies between 3-8 A. And not all calculations of Cl-containing clusters return such error. The cluster is not charge-neutral. But using the ION card did not solve the problem. Best, Kewei -- Kewei Zhao Ph.D. Student Myneni Lab Princeton University From: Matthew Marcus<mailto:mamarcus@lbl.gov> Sent: Tuesday, May 26, 2020 5:50 PM To: Kewei Zhao<mailto:keweiz@princeton.edu> Subject: Re: [Ifeffit] FOLP error in Feff calculation Here is your feff.inp, reworked as follows: 1. Subtract the position of Atom 0 (Ca) from all others. 2. Sort on distance from Ca, which is the new column. As you can see, a lot of the distances are way too close to Ca, which is a big atom. That may be part of the problem. Your lone Cl is almost 7A from the Ca. Was that intended? It does seem odd that this only happened when you included that distant atom. Also, I didn't count - is this cluster charge-neutral? Sincerely, Matthew Marcus On 5/26/2020 1:10 PM, Kewei Zhao wrote: > Dear colleagues, > > I'm using Feff to simulate the EXAFS of an aqueous Ca cluster. But I got this error when I tried to include Cl in the structure (potential type 0 is Ca, 1 is O, 2 is H, and 3 is Cl): > > Feff 8.50L > Ca in water > Calculating potentials ... > free atom potential and density for atom type 0 > free atom potential and density for atom type 1 > free atom potential and density for atom type 2 > free atom potential and density for atom type 3 > initial state energy > overlapped potential and density for unique potential 0 > overlapped potential and density for unique potential 1 > overlapped potential and density for unique potential 2 > overlapped potential and density for unique potential 3 > muffin tin radii and interstitial parameters > FOLP for POTENTIAL type 3 is too big. > Reduce overlap using FOLP and rerun > MOVRLP-1 > > If I change the type 3 atom to other elements or move its position, the error is gone. However, I do not want to change the input structure. Including FOLP or AFOLP cards in the input file did not work. Is there anyway to bypass this error? Please find my input file attached. > > Thanks, > Kewei Zhao > > -- > > Kewei Zhao > > Ph.D. Student > > Myneni Lab > > Princeton University > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit >

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FOLP error in Feff calculation
by Kewei Zhao 26 May '20

26 May '20

Dear colleagues, I'm using Feff to simulate the EXAFS of an aqueous Ca cluster. But I got this error when I tried to include Cl in the structure (potential type 0 is Ca, 1 is O, 2 is H, and 3 is Cl): Feff 8.50L Ca in water Calculating potentials ... free atom potential and density for atom type 0 free atom potential and density for atom type 1 free atom potential and density for atom type 2 free atom potential and density for atom type 3 initial state energy overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 overlapped potential and density for unique potential 2 overlapped potential and density for unique potential 3 muffin tin radii and interstitial parameters FOLP for POTENTIAL type 3 is too big. Reduce overlap using FOLP and rerun MOVRLP-1 If I change the type 3 atom to other elements or move its position, the error is gone. However, I do not want to change the input structure. Including FOLP or AFOLP cards in the input file did not work. Is there anyway to bypass this error? Please find my input file attached. Thanks, Kewei Zhao -- Kewei Zhao Ph.D. Student Myneni Lab Princeton University

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Artemis crash upon empirical standard import.
by George Sterbinsky 22 May '20

22 May '20

Hello, I am trying to import an empirical standard (.es file created in Athena) into Artemis. Upon import, Artemis crashes. This occurs with both the latest mac and windows releases (0.9.25 on mac and 0.9.26 on windows). I have attached an Athena project file containing the data used to generate the .es file (Co1-13C-std) and the data to be fit (Co1-57C-toFit). I have also attached the .es file. Following the instructions at https://bruceravel.github.io/demeter/documents/Artemis/extended/empirical.h…, I import Co1-57C-toFit into Artemis and the choose "import an empirical standard" in the data window. When I choose the .es file from the file selection dialog, Artemis crashes. Thank you, George

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FEFF: problem with calculations of La and Eu XANES spectra with UNFREEZEF card
by Павел Засимов 15 May '20

15 May '20

Dear XAFS community, I have got a problem with FEFF9 calculations of La and Eu XANES spectra with UNFREEZEF card (The calculation don't converge, but it runs without any problems if I do not use UNFREEZEF card). This problem does not depend on the chemical form of the element (i.e. it occurs in La2O3, EuPO4, LaTp3, EuTp3, where Tp is trispyrazolylborate) and seems to be element-specific: the same feff.inp files where La/Eu are replaced with Ce or U are processed by FEFF program without the problem. To note, SCF settings were the same as recommended in the FEFF9.6 manual: SCF 3.7 0 30 0.05 10. Logfile (log1_er.dat), as well as an example of an input file (feff_er.inp), are attached to this mail. The fragment of logfile reporting about the error is shown below: Electronic configuration iph il N_el 0 0 1.683 Found bad counts. Occupation number in getorb is 4.000 Will repeat this iteration. 0 1 7.372 0 2 10.521 Found bad counts. Occupation number in getorb is 1.000 Will repeat this iteration. 0 3 0.727 ... 3 3 0.000 Core-valence separation Bad counts found repeatedly - pot will exit now. Did anyone notice anything similar? Thanks for any help, Zasimov Pavel

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Change in fixed baseline after fit in XAS Viewer
by George Sterbinsky 11 May '20

11 May '20

Hello, I have observed changes in fixed parameters while running a pre-edge peak fit in XAS Viewer. I first run a baseline fit. This provides a good match to the data in the baseline fitting region. I would like to subtract the baseline from the data and then numerically integrate the data. In order to export the baseline fit and data, I fix all of the fitting parameters for bline and bpeak and then click "fit model". This generates a baseline and fit that no longer match the data well in the baseline fitting region. Additionally, in the "Fit Results" window, the reported best-fit values of the fixed parameters are slightly different from the values reported in the "Value" field after the baseline fit, to which they were fixed. This appears to be the result of rounding of the baseline fit parameters at some point after the baseline fit. For example bline_slope was fixed to "-0.0024752483" but the best-fit value is "-0.00247500". I realize I am using XAS Viewer in a way that it was not exactly designed for, and perhaps no one anticipated someone fixing a parameter out to 10 decimal places. However, what I am doing still seems reasonable, and I would greatly appreciate it if XAS Viewer could be updated so that all digits entered in the Value field for a fixed parameter will be maintained for the fit. I am happy to provide a project file and instructions to reproduce my observation if they would be helpful. Thank you, George

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Reported W L3-edge and L2-edge energy
by Bare, Simon R 08 May '20

08 May '20

All: We are wondering if others agree that the reported values for the W L3 and W L2 edges are incorrect. We recently noticed the following: The "Edge" - defined by the inflection point of the absorption edge step When using the Ir L3 edge (11215.0 eV) as a calibration, the W L3- and L2-edges are 10203.4 eV and 11542.4 eV, respectively. When using the Pt L3 edge (11564.0 eV) as a calibration, the W L3- and L2-edges are 10203.3 eV and 11542.4 eV, respectively. These observations are thus different than the reported values of 10207.0 eV and 11544.0 eV for the L3 and L2 edges, respectively. Thanks in advance for the discussion and feedback. Simon R Bare Distinguished Scientist SSRL, MS69 SLAC National Accelerator Lab 2575 Sand Hill Road Menlo Park CA 94025 simon.bare(a)slac.stanford.edu<mailto:simon.bare@slac.stanford.edu> Ph: 650-926-2629 [co_access_logo_text]

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