September 2012 - Ifeffit - millenia.cars.aps.anl.gov

Fwd: Re: Use of feff8 with D-artemis?
by Bruce Ravel 20 Feb '13

20 Feb '13

On Thursday, July 12, 2012 05:31:19 PM you wrote: > > I wonder why the new Artemis (from Demeter) is limited to feff6 or feff7 as > the old ifeffit can deals with feff8 and feff9. > > Is it a wish? When you published data using feff7, the reviewers first note > that you should have used more actual version. I would challenge a reviewer to come up with a reliable study demonstrating that Feff8 or Feff9 provides a statistically significant improvement to EXAFS analysis. Obviously, I am not saying that full multiple scattering, self-consistency, and the various potential improvements in Feff9 are not relevant to XANES calculations or to Feff's treatment of other spectroscopies. What I am saying is that it has not been rigorously demonstrated that those things have an impact on the calculation of the extended EXAFS such that the analysis is improved in a statistically meaningful way. In short, I find that such arguments from reviewers boil down to "Feff8 is 33% better than Feff6 because 8 is 33% bigger than 6!" > Is it planned that D-Artemis will work with feff8 too? > > I am using the other programs of Demeter but still have to stick to the old > Artemis as none of my files can be read by D-Artemis (always error due to > feff8 or feff9 files by importing old project) That said, there is no good reason that artemis should not be able to use Feff8 or 9 if you want to do so. I suppose that laziness is the best explanation for why it doesn't yet. The Atoms portion of Demeter writes Feff8 files. The Atoms portion of Artemis simply has the line of code for using that part of Demeter commented out. That's trivial to fix. Getting Demeter to use Feff8 instead of Feff6 is not a lot of work, but it is also not a trivial amount of work. I will put this at the top of my to do list. Given that I will soon be leaving for conferences in distant places on the globe, I probably won't be able to release a version of Demeter that uses Feff8 effectively until Spetember. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel ----------------------------------------- -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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Importing Multiple Data Sets into Athena
by Daniel Whittaker 01 Oct '12

01 Oct '12

Hello all, I am having a small issue when importing multiple data sets into Athena all of which have a reference channel. The issue i am experiencing is that when importing multiple data sets together they do not all import correctly. The first data set (of all selected) imports fine (The data is Np and the reference Zr foil) - it imports the reference file which can be aligned to the calibration Zr foil file. However, the remainder of the files do not work at all, the reference channel does not import correctly at all. I have tried (best as i can tell) all of the pre-process options to no avail. When i import them individually it works although I have to tell it what element the ref channel is and the edge and E0 (couldn't the edge and E0 be linked such that selection of one filled the other?) but this isn't too much of an issue. It is by no means a massive problem but i thought i would ask if there is a way around it or if it is a real bug? All other multiple data processing - such as "align marked groups" - works fine. Regards, Dan Whittaker

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(D) Athena closing on data import
by Jeremy Thorbahn 27 Sep '12

27 Sep '12

Hi all, Since I upgraded to the Demeter version of Athena some months ago, I have been basically unable to use it for some of my data since immediately upon import, the program shuts itself down with no message. I have Athena 0.8.056 installed as well and do not have the same issue there, so I have been using that version just fine but I thought I should report this issue or seek advice if it is a fault of my data and not the program. I have 0.9.12 and the issue persists. It only occurs with my set of data from the HXMA beamline at the Canadian Light Source as well, I have successfully imported data from other beamlines. I am using Windows 7 Home 64-bit. I have attached a sample data file which causes the crash. Regards, Jeremy

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Demeter 0.9.12
by Bruce Ravel 26 Sep '12

26 Sep '12

Hi, I prefer not to make multiple releases of my software within a week. Unfortunately, there were just too many problems with last week's release, many of which were discussed right here on the mailing list. There are no new features, just a bunch of fixed bugs. The windows installer is available for download at https://github.com/bruceravel/demeter/downloads I tagged release 0.9.12 at github. For a complete list of changes see: https://github.com/bruceravel/demeter/blob/master/Changes.org Installation instructions: http://bruceravel.github.com/demeter/pods/installation.pod.html Reporting bugs: http://bruceravel.github.com/demeter/pods/bugs.pod.html or use the github issue tracker: https://github.com/bruceravel/demeter/issues As always, use this mailing list to report problems or to make suggestions. Regards, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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Re: [Ifeffit] Why different installations of Atoms generate different results?
by Tsuei, Ku-Ding 25 Sep '12

25 Sep '12

Dear Matt, Thanks for your positive reply. You are opening a door to solving my problem. Attached are the fpj file generated by (D)Artemis and the apj file by the old Artemis, respectively. They cannot be opened by Note Pad nor by Word Pad, so I do not know their contents. I actually generated these projects from scratch solely by File -> open project or data (Au.inp) in (D)Artemis (or alternatively from Feff calculations -> Add) or by File -> Open file in the old Artemis without inputting any data. I just wish to look at what kind of EXAFS spectra generated purely by calculation before using them for model fitting. For (D)Artemis I went through Run Atoms -> Run Feff and could select any path from the path list, click chi(k) and then Plot selection. Of course now I know how to change k-weighting in the Plot window. I know which path is plotted because each path corresponds to a single curve with its own color and the path names are included in the legend. For the old Artemis I went through Run Atoms -> Run Feff and clicked import All paths. Again I could select any path in the list and Plot k, R and q with a choice of k-wieghting. Similarly each path corresponds to a single curve with its own color and the path names are included in the legend. These steps illustrate how I copied these plots into the pdf file I sent to the mail list. The path page in the old Artemis contains some more information as Path parameter math expression side by side to the Data & Paths list. They are N:6, S02:amp, delE0:enot, delR:delr and sigma^2:ss. Indeed you are right that changing them to numbers results in different plots. But I thought I should keep the default path parameters intact because they are supposed to be from calculation . Moreover, many of these path parameters do not have similar math expressions in (D)Artemis. See the next paragraph. Yes, I followed Bruce's suggestion to go through the on line manual of (D)Artemis with loading the Au foil data first then up to The Path Page, aiming for fitting real data. I could generate paths from the Atoms and Feff window and plot their chi(k) and so on, identical to the previous project without loading in Au foil data. I could drag the selected paths from the Atoms window into the Data window. By selecting each path the associated parameters are displayed, but only N and (blank)=(S02)(?)=1, the rest fields are empty. Are they supposed to be filled like in the old Artemis? I then copied in math expression contents exactly the same as in the old Artemis. The plotting shows only the Au foil data. Then I pressed the yellow Fit button. A message box pops up: Fit cannot continue: You have not defined any fitting parameters. Could you offer more clues to continue? The (fit) project up to now is saved and attached. There are more problems running (D)Artemis on my Windows 7 Professional SP1. The program can load in the saved (fit) project described above but always crashes on loading the first project without Au foil data, no matter which compatibility mode I choose before starting. It may be worth noting that only the (D)Artemis DOS window appears when choosing None, Windows 7, Windows Vista SP2, Windows Vista SP1, Windows Vista, Windows 2000, and Windows NT 4.0 SP5. On choosing Windows XP SP3, Windows XP SP2, Windows 98 / Windows Me, and Windows 95 there appears another DOS window on startup, D:\strawberry\perl\bin\perl.exe. I am not sure if these information may help solving the cash problem of (D)Artemis. On the other hand, the old Artemis can load in the project file with no Au foil data without crashing. Your help is greatly appreciated. Ku-Ding Date: Mon, 24 Sep 2012 09:10:48 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Cc: bravel(a)bnl.gov Subject: Re: [Ifeffit] Why different installations of Atoms generate different results? Dear Ku-Ding, On Sat, Sep 22, 2012 at 8:13 AM, Tsuei, Ku-Ding <tsuei(a)nsrrc.org.tw> wrote: > Hi Bruce, > > Thanks a lot for your reply and comments particularly on how to change > k-weight in (D)Artemis-Atoms. Sorry for not being able to provide clear > results stating exactly where my confusion came from. I was not sure if an > attachment could be readable to this email list but let me try this time. > Certainly I do not know how to retrieve data values from these plots yet. > > The attached pdf file compares the output plots of k^n*chi(k) with n=0, 1, 2 > and 3 of the Au L3 EXAFS of the shortest path calculated from Artemis-Atoms > in Demeter and old Artemis. I suppose to read identical plots of k^n*chi(k) > from different programs but they are not. That is why I feel confused. > > Your help on clearing my confusion is appreciated. Then I can move on to do > model fit on real data. > > Ku-Ding The two results you show are quite different, but you don't tell us how you got them, expect to say the they were calculated by Artemis-Atom and D(Artemis)-Atoms. This is an incomplete description, allowing many possible differences. To be clear, Atoms only generates the feff.inp file. These should be the same between the two versions, especially for as simple a case as fcc Au. Next, Feff has to be run. This will be the same, assuming the input files are the same. Next, Artemis reads in the output files from Feff (you say you're using the first shell only, but I encourage you to verify that), applies Path Parameters to these, and generates chi(k). Are the number of Paths used, and the Path Parameters (N*S02, sigma2, e0, deltaR) the same in these two calculations? I'd guess that they are not. Providing plots of outputs is helpful, but as is said many times here, providing the project file is much more helpful as it shows not only the final result, but how you got there. Cheers, --Matt ------------------------------

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Opening (D)Artemis error
by Raimundo Lora Serrano 24 Sep '12

24 Sep '12

Dear Bruce or colleagues, Below is the error written in the log file after importing a saved (D)Artemis project. I cannot save an Artemis project and open it again. Just have to start (again) from the beginning. As stated previously, the program just fails to launch. Thanks in advance, Raimundo ------------- Attribute (initial) does not pass the type constraint because: Validation failed for 'Str' with value undef at constructor Demeter::GDS::new (defined at C:/strawberry/perl/site/lib/Demeter/GDS.pm line 189) line 185 Demeter::GDS::new('Demeter::GDS', 'gds', 'guess', 'expandsto', '', 'mark', 0, 'group', 'lxjcm', 'stored', '', 'error', 0, 'highlighted', 0, 'Use', 1, 'trouble', '', 'mathexp', 1.00000, ...) called at C:/strawberry/perl/site/lib/Demeter/Fit.pm line 1410 Demeter::Fit::__ANON__('Demeter::Fit=HASH(0xc46c914)', 'folder', 'C:\Users\Rai\AppData\Roaming\demeter\stash\_dem_rhysjijw\fits...', 'regenerate', 0) called at C:/strawberry/perl/site/lib/Moose/Meta/Method/Overridden.pm line 38 Demeter::Fit::deserialize('Demeter::Fit=HASH(0xc46c914)', 'folder', 'C:\Users\Rai\AppData\Roaming\demeter\stash\_dem_rhysjijw\fits...', 'regenerate', 0) called at C:/strawberry/perl/site/lib/Demeter/UI/Artemis/Project.pm line 359 Demeter::UI::Artemis::Project::read_project('HASH(0xa7b54d4)') called at C:/strawberry/perl/site/lib/Demeter/UI/Artemis.pm line 833 Demeter::UI::Artemis::OnMenuClick('Wx::Frame=HASH(0x4c0b39c)', 'Wx::CommandEvent=SCALAR(0xc46f51c)') called at C:/strawberry/perl/site/lib/Demeter/UI/Artemis.pm line 346 Demeter::UI::Artemis::__ANON__('Wx::Frame=HASH(0x4c0b39c)', 'Wx::CommandEvent=SCALAR(0xc46f51c)') called at C:\strawberry\perl\site\bin\dartemis.bat line 29 eval {...} called at C:\strawberry\perl\site\bin\dartemis.bat line 29

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Why different installations of Atoms generate different results?
by Tsuei, Ku-Ding 24 Sep '12

24 Sep '12

Hi Bruce, I am a novice of this community and actually have less than two weeks of experience using IFEFFIT (version 1.2.11 with iff_013 update) and its front end packages Demeter (version 0.9.11) and its predecessor Horae (Athena, Artemis etc. version 0.8.014) running under Windows 7 Professional SP1. They are excellent software guiding me quickly into this EXAFS world. Thanks a lot. However, I feel confused by viewing different results (chi(k)) calculated from three installations of Atoms, namely Atoms within (D)Artemis, stand alone (D)Atoms, and Atoms within the old Artemis. I then used the simplest Au.inp as the input for all. I checked the path outputs making sure the generated paths are identical and selected individual paths. To my surprise the chi(k) curves have different envelopes and magnitudes from 3 Atoms. It seems to me that chi(k) are calculated from the same feff6 program and should be identical from any installation; no FT range is involved to affect chi(R). Could you help clarify my confusion? Perhaps the new Demeter can be improved further. It seems that only k^2*chi(k) is plotted in Atoms within (D)Artemis, and only k*chi(k) is plotted in the stand alone (D)Atoms by viewing the vertical labels in plots. There seems no obvious place I can change k-weighting like in the old Artemis. I have not been able to find where, such as Edit preference in the old Artemis, I can change the default parameters, or learn what parameters are used in doing FT (kmin, kmax) or window function and so on. I learn these preference parameters quickly owing to the extensive documents built-in side by side with "action tabs" in the old Artemis and the link to html documents in the old Athena. By the way, watching your videos is an excellent way to learn Demeter but I had to pause to search related projects or files to run side by side with videos; some links with video download sites could be very helpful. Look forward to reading your answers and utilizing the more powerful Demeter. Thanks again. Best regards, Ku-Ding Tsuei ------------------------ Ku-Ding Tsuei, PhD Associate Scientist National Synchrotron Radiation Research Center 101 Hsin-Ann Road Hsinchu Science Park Hsinchu, TAIWAN 30076, ROC email: tsuei(a)nsrrc.org.tw

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Demeter 0.9.11
by Bruce Ravel 20 Sep '12

20 Sep '12

Hi, Yesterday I posted a new version of the Windows installer for Demeter at https://github.com/bruceravel/demeter/downloads and tagged version 0.9.11. A couple problems recently discussed on this mailing list that have been addressed: * I believe I fixed the problem of Demeter not co-existing on a windows computer with another version of perl. See this thread: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2012-August/010683.html * Athena now correctly imports data with a reference of another element. See this thread: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2012- September/010700.html * Improved import of project files from the old version of Artemis. See http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2012- September/010718.html There are several other improvements. For a complete list see: https://github.com/bruceravel/demeter/blob/master/Changes.org Installation instructions: http://bruceravel.github.com/demeter/pods/installation.pod.html Reporting bugs: http://bruceravel.github.com/demeter/pods/bugs.pod.html As always, use this mailing list to report problems or to make suggestions. Regards, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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path averaging in Artemis
by Simon Cassidy 19 Sep '12

19 Sep '12

Dear Bruce, I've run into a problem with the new artemis' path finder. When running the attached feff.inp file in atoms, two separate paths are merged together. The two paths it is merging are Se-Fe2 (N=4, reff=4.456) and Se-Fe3 (N=8, reff=4.465) which it gives as (N=12, reff=4.4621). The same problem occurs for these paths when starting with the Fe core. The same feff.inp file generates the right path list when run in the old version of artemis. Please could you take a look at this? Many thanks, Simon

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Mac OS X Mountain Lion iXAFS
by Kyler Carroll 19 Sep '12

19 Sep '12

Hello, I havent seen a post yet pertaining to this issue so I thought I would share and perhaps see if there are solutions to my problem. I have recently upgraded my mac to run the new OS X Mountain Lion and in the process noticed that apple no longer supports or includes X11. They instead have moved to XQuartz http://xquartz.macosforge.org. I downloaded the new XQuartz to my computer and obviously still cannot access iXAFS. I was wondering if someone could offer some advice for me so that I can still run iXAFS on my macbook (Macbook pro OS X version 10.8, 2.3 GHz intel core i5). Thank you, Kyler J. Carroll, Ph.D. Assistant Project Scientist Department of NanoEngineering University of California, San Diego

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