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

Re: [Ifeffit] Ifeffit Digest, Vol 169, Issue 9
by Abhinav Prabhakar 05 Aug '20

05 Aug '20

Hello, Thank you for your reply. Attached is the CIF file in question. The crystal is Tobermorite 14A, taken from COD website. However, the structure has partial occupancy and it is modified to include full occupancy. The modified CIF file shows a space group of B11b (and cannot be recognized by Artemis). I tried a C1c1 space group (it works) but it shows the same structural values as a P11b. Regards, AP On Tue, Mar 14, 2017 at 1:00 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > 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: Space group type in Artemis (Bruce Ravel) > 2. Data export and coordination number (Abhinav Prabhakar) > 3. Re: Data export and coordination number (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 13 Mar 2017 09:20:14 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Space group type in Artemis > Message-ID: <3853f1f7-61fd-6886-306f-040c540ecae1(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 03/11/2017 05:56 AM, Abhinav Prabhakar wrote: > > Hello, > > > > I have a question about the working of Artemis as a new user. > > > > Artemis does not recognize the space group B11b. When importing a cif > > file of a crystal with this symmetry, it sends a prompt message that the > > space group symbol cannot be recognized. As a result, I changed it to > > P11b and it works. But would this change any crystal information (for > > eg. Degen, Reff values) significantly? > > I am not a crystallography expert in any sense. When I wrote Artemis, I > meticulously followed what I found in the fourth edition of the > International Tables for Crystallography, Volume A. Every symbol > defined in there is recognized by Artemis. (Well, I guess I should say > that every symbol is /supposed to be/ recognized by Artemis. If one is > missing, that's a bug and should be reported.) > > "B11b" is not a symbol that I found in my copy of ITC volume A. As > Robert suggested, there may be a way to rotate group 9 so that "B11b" is > an interpretable symbol in the abstract. But Artemis does not know how > to do that. (Nor do I.) > > "P11b" is a setting for space group #7. If, as Robert suggests, your > CIF file is for space group #9, then the answer to your last question is > yes. It is plainly obvious that using a different space group will > change the degeneracies and distances. > > > Of course, you did not bother to include a copy of the CIF file in > question to your original email, so it is not actually possible for > Robert or I or anyone else to actually help you effectively. > > At the risk of sounding like an annoyingly broken record, everyone > should take the time to ask a good question or write an actionable bug > report: > > http://bruceravel.github.io/demeter/documents/SinglePage/help.html > http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 743, Room 114 > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 2 > Date: Mon, 13 Mar 2017 21:48:31 +0800 > From: Abhinav Prabhakar <abhi.prabhakar(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Data export and coordination number > Message-ID: > <CA+nbL85FJReunY1Am1oeNTMtFskXMd8FmH_OgaO00mnmew2c-g(a)mail.gmail. > com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > As a new user, I have some questions related to the use of Athena and > Artemis: > > i) Is it possible to extract the normalized/background corrected data from > Athena (in E-,k- and R- space) and export it as numbers (to Excel perhaps)? > > ii) Using Artemis, how can coordination numbers (N) be expressed as 'guess' > parameters (Artemis allows only numerical values for N)? > > Thank you. > > Regards, > > Abhinav Prabhakar (Mr.) >

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Jupyter/python question for Larch
by Garret Bland 04 Aug '20

04 Aug '20

Hello! I have a Python/Larch related question. I have been developing some python script via jupyter and incorporating Larch as a module. I was able to read an athena prj file with the following code *import larch as lc* *athena_prj = lc.io.read_athena(prjfilename)* Python stores this object as a 'Group' object with each spectrum being an instance. I would like to go through more processing with all spectra. Example: *for spectrum in athena_prj:* * lc.xafs.find_e0(spectrum.energy, spectrum.mu <http://spectrum.mu>, group = spectrum)* This does not work since the 'Group' object is not iterable. I tried to look up some other built-in functionality with python, but couldn't find an efficient way other than manually typing out each spectrum (athena_prj.spectrum1, athena_prj.spectrum2, .... etc). Is there any built-in functionality in larch that can iterate this 'Group' object? Any help would be appreciated. Thank you for your time! Garret -- Garret Bland PhD Student Carnegie Mellon University Civil and Environmental Engineering Porter Hall 201 Pittsburgh, PA, 15213

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Writing a Script for MD Simulations / Scripting Atoms
by David Sprouster 28 Jul '20

28 Jul '20

Dear IFEFFIT Experts, My colleagues and I are working on preparing Python scripts which: 1) run about 20,000 cif files from MD simulations through Atoms, 2) produce feff.inp files, 3) run feff.inp files through Feff (for XANES), 4) average all the XANES spectra. We are having trouble opening the stand alone Atoms program through Python – we can get Athena and Artemis to open, but for some reason Atoms will not. A snipet of our code which includes the file path is attached below. *Code:* ### def openAtoms(): try: subprocess.run([r"C:\Users\ADIAZ\AppData\Roaming\DemeterPerl\perl\site\bin\datoms.bat"]) except: print('Error') openAtoms() ### We have searched the Ifeffit archive for some answers but came up short, and we were wondering if anybody on the list has any suggestions for a potential fix to this problem? Additionally, has anybody prepared a similar series of scripts (in Python) to generate XANES spectra from MD simulations? We note that Marcus Karolewski did discuss something similar in a past post: https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg02744.html Thanks in advance, Dave -- ---------------------------------------------------------------------------------- David J. Sprouster, Ph.D. Assistant Research Professor Department of Materials Science and Chemical Engineering Stony Brook University 222 Old Engineering Stony Brook, NY 11794 Phone: (631) 294-8983 web: http://stonybrook.edu/emrel ----------------------------------------------------------------------------------

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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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