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

inp file - artemis crashing when running feff calc on manually generated inp file
by stephen.parry＠diamond.ac.uk 03 Nov '14

03 Nov '14

Can someone spot the problem with the attached inp file? I have manually reduced a cif file to remove multiple occupancy sites and cut down the unit cell from a large structure. I should be left with the first shell as Cartesian co-ords. I have then overwritten the co-ords and ipots into an old atoms generated inp file. I can't spot any formatting problems but when I run the feff calculation in artemis the program crashes. The feff.run error log file contains nothing obvious. "Feff 6L.02 TITLE Ga_c6h5f TITLE Ga TITLE S TITLE Gallium TITLE Note: mixed occ removed manually SP Calculating potentials and phases... 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 overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 overlapped potential and density for unique potential 2 muffin tin radii and interstitial parameters " Any help appreciated. Regards, Steve ================= Dr Stephen Parry Support Scientist, B18 Diamond Light Source Ltd. -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

2 1

Mac support for Demeter
by Bruce Ravel 28 Oct '14

28 Oct '14

Hi gang, I just heard from Frank Schima, the fellow who kindly provided packaging of Demeter via MacPorts. Frank is moving to a new position at NIST Boulder and will no longer be providing IT support for the group out there that does some XAS. That means his availability to maintain and update the MacPorts package will be somewhere between slim and non-existent. Here is what he said: I am no longer working for Quantum Devices as of Friday, 10/31/2014. So I will no longer be involved in updating Demeter and will be unsubscribing from the Ifeffit mailing list. For updates please follow the Macports procedures to request an update in Macports by opening a Trac ticket [1]. I may actually be able to perform the update but I cannot guarantee anything. [1] <https://trac.macports.org/newticket> I know that this support for the Mac was valued by many people in our community, so Frank will be missed. I am not able to provide packaging support for Mac users. Even if I had the time or energy to take on a new packaging responsibility, I simply don't own a Mac. This would be a good time for someone to step up and take over responsibility for the Mac package. It seems that Frank has done the bulk of the work. The MacPort ecosystem seems to be well supported and well documented, so I would think that someone else could readily step into that role. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

2 1

errors importing Artemis project with quick first shell paths
by Bruce Ravel 28 Oct '14

28 Oct '14

Ian, I am starting a new thread for your email. It is only peripherally related to the problem discussed in the other thread. The main problem was two mistakes in how a quick first shell path was brought back to life when importing the project file. I'll explain, although one of the problems is rather technical. Mistake #1 is related to the option for auto-generating variables. That flag was not turned off, so the auto-generated parameters got regenerated, over writing the ones you chose. Yikes! Mistake #2 involved an assumption about the order of entries in a hash data structure while bringing the QFS path back to life. That is extremely sloppy on my part because the order of hash entries is not predictable. This was leading to the intermittent aspects of the behavior. > Dear All, > Sorry for resurrecting this old thread but I've been experiencing a > bug that produces very similar symptoms and that I guess may be > related; but that won't be solved by Bruce's fix. Details are as > follows: > Software: Demeter 0.9.18.2 and 0.9.20 x64 (possibly earlier releases > too) on Windows 8.1 x64 (I've never observed this bug on Windows > versions before 8, but I've been using Windows 8 as my main OS for a > while now so that may be coincidental) > Steps to reproduce: I run a fitting project using quick first shell > fits and save it. When I re-open the project around 80% of the time > the problem occurs. > Symptoms: When I re-open the project around 80-90% of the time one or > more of the following occurs: > - One of the quick shell paths completely loses all its information > (including path information which isn't editable by the user, > parameter info etc; see attached screenshot) I believe that I have fixed this. > - Parameter info for one or more paths is reset to the default > (i.e. if I've named a path delrauau it's renamed dr_ag_au_1) Again, I believe that I have fixed this. > - In the GDS window starting values for parameters that have a > non-zero starting value are set to their previously guessed value, > rather than the starting value I set (ie. If I set ss as 0.003 and > during the fit it is guessed to be 0.001 when I reopen the project > the starting value will be set to 0.001) and "restrain" parameters > are changed to "guess". I have examined the history of your project. At no point is a fit saved with a restraint. The GDS windows is filled correctly according to the contents of your project file. Also, the initial guesses are all entered into the GDS window with the values I see in the history. Are you saying that you have made a restraint, saved the project, then had Artemis fail to remember that you had made a restraint? > - Phase correct fitting boxes are unticked (sometimes in an > "impossible fashion" where the "plot with phase correction" option > is set but no paths have the "use path for phase corrected plotting" > option set) I don't understand how that can be a problem. The default is not to plot with phase correction. I don't save the state of that button in the project file in any case. I need to do a bit more testing, hopefully I'll make a new trial release package for your to test before the end of the day. B > Attachments: > Noinfo.png - screenshot of Artemis when path info is lost > Reset.png - screenshot of Artemis when parameter names are reset > Dartemis.log - Artemis log file when opening a project that has this problem > Artemis.fpj - Artemis project file that displays these symptoms. > Please let me know if you need further info/files. > Thanks, > Ian > Ps: > OK, things got weird while preparing this bug report: The file in > question stopped opening at all - Artemis loaded and went through > loading fit x, x+1 etc., once it finished (not exactly sure what > stage) it just closed. And then, after several attempts, started > working again, as if by magic, before I'd saved a log file.... If I > can figure out how to reproduce this I'll send more info... -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

2 4

Saving data as chi(E) from Athena?
by Karina Mathisen 28 Oct '14

28 Oct '14

To whom it might concern The older version of Athena had the possibility to save the data as chi(E), which is sorely missed in the newer version. Is there an easy fix for this? Best regards Karina Mathisen ------------------------------------------------------------------------------- Karina Mathisen, PhD Deputy Head for teaching, Department of Chemistry NTNU - Norwegian University of Science and Technology Associate professor Karina.Mathisen(a)ntnu.no<mailto:Karina.Mathisen@ntnu.no> +47 735 96218 Realfagbygget E2-106, Høgskoleringen 5, Trondheim, Norway --------------------------------------------------------------------------------

2 1

Question about using a proper model
by pushkar shejwalkar 28 Oct '14

28 Oct '14

Dear All, I am new to XAFS data analysis and have very limited knowledge about using modelling structures for XAS analysis. I am not sure as to if this question is directly related to Demter or XAFS analysis as such but its a part of it for sure. * Question number one* I am trying to analyze the sample I recently collected at SPring-8 facility. The structure I am hoping to be formed during the reaction is more of a organometallic complex at silica interface. In order to establish the structure I was told that there are two methods I could use. 1) Use a counter part compound which is exact/looks like the structure I am hoping (so basically known compound) and then do traditional comparison method to establish the structure. UNFORTUNATELY I cannot synthesize such compound in lab nor such material is available in literature ( including crystal structure). 2) is to use the model. right now for modelling such structure I am using Spartan program (again I have not used it earlier in my graduate work) So I want to know as to how to generate the models in order to get the correct crystal parameters? (atoms positions?) Is spartan good enough to do job? is there any other method for doing such fitting? * Question number two* In order to get lower E0 values after the fitting, I read that there is a method to use in which delE value can be set to 0 intentionally and then recalibrating the spectra in athena again in order to accurately calibrate the E0. I read paper by Shelly kelly and Bruce Ravel. Also I have seen the steps in one of shelly kellys PDF formatted lecture, although I am still not sure about the exacts steps to take in order to do such calibration. Could someone explain me the steps in details (especially taking artemis files to athena and then using it as STD spectra for calibration purposes, I am confused about that) Thank you very much everyone in advance for your patience to go through such a long email and helping to solve my silly doubts. Your New Bee in this fantastic group Pushkar

3 5

Setting E0 for imported data
by Scott Bechler 27 Oct '14

27 Oct '14

Hello, I am trying to compare a sample with unknown lead bonding with some lead standards. After entering in all of the data and standard scans with reference channels, I aligned the reference channels, which shifted the data scans as well. My question regards the E0 of the data and standard scans. Even though the scan itself shifted, the E0 still remains where it was when I imported it, prior to aligning the reference channels. The peak itself shifted, but the program still marks the E0 at the previous peak position. Is this an issue? If so, how do I adjust the E0 of the scans the same amount that the reference channels shifted? It does say how much the scan shifted, so I went in and manually changed the E0 of each scan so that it correlated with this shift. Would this be an effective solution? If this does solve my problem, is there a less labor-intensive way to solve it in the program? Thanks so much for your help! -Scott

2 1

save Artemis project and cannot find Path List information when reopen
by huyanyun＠physics.utoronto.ca 26 Oct '14

26 Oct '14

Hi all, I encountered a serious problem with saving an Artermis project on my windows 8 64bit desktop. When I am ready to finish my fitting work, I click to save the log file, and go to main window to choose -File-'save project as...', and then close Artemis. But when I reopen this saved project, the Path Page lost all information for each path, and the 'Include path' button has been surprisingly unchecked for all path. The GDS page have all information there. This happened to me several times, but it seems sometime the PathPage data is saved and sometime is not, although I think I was doing the exact something. I attached one of my artemis project file and the most recent log file I saved before I close the program. Can anyone have a look and tell me what I did wrong? As my work is proceeding, this would be a very serious problem if I cannot save my 'hardwork'. Best, Yanyun ----- Attachments (links will expire on 28/02/15): 1. CoedgeforGa0.15 fitting.fpj (7.7 MB) [application/zip] Download link: https://webmail.physics.utoronto.ca/imp/attachment.php?id=53ffbffa-2424-413…

4 12

simulating As K edge XANES using full multi scatering method
by Shaofeng Wang 24 Oct '14

24 Oct '14

Dear all, Does anyone have experience for simulating As K edge XANES using multi-scatering method or some other methods. Please introduce some papers or articles to me. Any help is appreciated. Regards, Shaofeng

2 3

Artemis closes when I try to open a project file or import data
by Kurinji Krishnamoorthy 22 Oct '14

22 Oct '14

Hi, Artemis had been working well on my laptop for a while. But today when I attempted to open a saved project file ( with a *.fpj extension), the program tried to open it for a while but then ultimately closed without any error messages. A similar thing occurred when I tried to import an Athena data file into Artemis. I was wondering if anybody had any idea how to fix this problem? Thanks, Kurinji

4 7

Athena does not React after 2-4 steps
by Michael Kömm 22 Oct '14

22 Oct '14

Dear Bruce and dear mailing list, Athena stops working after doing a maximum of four steps (f.e. removing points, import data,...) when running on my PC with Windows 8. It either says "not responding" or just shuts down. Whenever Athena shuts down the errors in the .txt in the directory of the project differs. But it always looks like this: line 0: warning: Skipping unreadable file "C:\Users\Michael\AppData\Roaming\demeter\stash\gp_leqfnhqh" line 0: No data in plot only the file name changes. But there's never a file with that name in that directory. Sometimes there is as well a window opened that says: gnuplot.exe is not working anymore. I've deleted the Roaming\demeter folder but it didn't end the troubles. Hope there is a way to end this problem. Sincerely yours Michael Koemm PS: There is also one of my projects in the attachment.

2 1