October 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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Help: some operation using Athena and Artemis
by Bingjie Ouyang 26 Nov '12

26 Nov '12

Hi, I just joined the mailing list recommended by a friend, I hear this is a really good place to communicate and learn. So I'm here, actually I need help for some basic questions on Iffeffit software: 1, In Athena, how to make a fourier transform draft? 2, In Artemis, since I was told that each shell in R-space can be fitted separatly, is it OK to fit each shell in the R-range respectively, and then join up the fitted curve and just ignore the not match part in other R-ranges? And can a shell be comprised of several different paths (like Fe-O and Fe-S)? Thank you. Best wishes, Bingjie -- Bingjie Ouyang School of Earth Sciences and Engineering Nanjing University 22nd Hankou Road, Nanjing, Jiangsu, 210093 P. R. China Email: jessicaoy89(a)gmail.com

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Plot multiple fits in (D)Artemis and statistical errors
by Nilmar Camilo 26 Nov '12

26 Nov '12

Dear Bruce, I am new in the list and really don't know if the points raised below were already discussed. In the (D)Artemis (Demeter version 0.9.13) how may I: - Plot different fits with the experimental data (to visually compare the results) - I don't know if this is a (new) bug of the program but when I try to restore a fit the program closes. In the log file the following line is written: "Can't use an undefined value as a HASH reference at C:/Strawberry/perl/site/lib/Demeter/Fit.pm line 1558." Obs.: I am running Demeter in Windows 7 (Pro). Another problem is related to the statistical errors when constraining the S0^2 parameter to float between two limits. The program doesn't return the error for all others parameters (but just zero as the error value) as you can see below: guess parameters: amp = 0.79284158 # +/- 0.00000000 [0.95] enot = 5.29826510 # +/- 0.00000000 [0] delrIn11 = 0.00235278 # +/- 0.00000000 [0] ssIn11 = 0.00155959 # +/- 0.00000000 [0.00300] delrCe1 = -0.00231455 # +/- 0.00000000 [0] ssCe1 = 0.00192778 # +/- 0.00000000 [0.00300] delrIn11In11 = 0.02070081 # +/- 0.00000000 [0] delrIr1 = -0.00435502 # +/- 0.00000000 [0] ssIr1 = 0.00386517 # +/- 0.00000000 [0.00300] delrIn31 = 0.00648507 # +/- 0.00000000 [0] ssIn31 = 0.00669602 # +/- 0.00000000 [0.00300] delrIn12 = 0.00255704 # +/- 0.00000000 [0] ssIn12 = 0.00305432 # +/- 0.00000000 [0.00300] def parameters: b = 0.80000000 # [min(max(0.8,amp),1.0)] Thanks so much in advance. Nilmar

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Mac user
by Elena Mejia Likosova 30 Oct '12

30 Oct '12

Hi, I've been trying to download the IFEFFIT Mac version for my snow Leopard Mac. However, Athena doesn't work. Only Artemis seems to work. Do you have any new compatible version for my computer? Thanks, Elena Mejia Likosova PhD Student Advanced Water Management Centre at the University of Queensland Brisbane-Australia email: e.mejialikosova(a)uq.edu.au

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Linear combination fitting without normalization
by Stummelfinger 27 Oct '12

27 Oct '12

Hi there, Is there a way to do Linear combination fitting in Athena with data which were already proceeded (background corrected and normalized)? I don't want to do a double background correction /normalization on these data. However the Linear Combination Fitting dialog gives only the option "Norm(E)". Is there a work around? Thanks a lot, Cheers, Jan

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"deglitch many points" in D-Athena
by Jeremy Thorbahn 25 Oct '12

25 Oct '12

Hi Bruce, I noticed on the github to-do list you've written "plot margin lines for deglitching, deglitch many points" under the "weird stuff" section. just for clarification, is that to say that the deglitch many points feature is something you'd prefer not to implement? I attempted to use it earlier but noticed it was greyed out. I can get by without it, but would probably end up swapping project files between the old Athena and D-Athena to eliminate a few points of high-k glitching at once. The main point of my question: is this not a feature many people use? It seems awfully convenient to quickly tidy up data. Thanks as always, Jeremy -- ------------------------- Jeremy Thorbahn thorbahn(a)gmail.com

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command window
by Ravel, Bruce 24 Oct '12

24 Oct '12

> I am a beginner for xafs analysis. I installed the Demeter on my laptop. I found there was always a black command widow when I start > athena or artermis. If I close that window, the program was also closed. My operation system is windows 7. Why? A man walks into his doctor's office and says "Doctor! Doctor! It really hurts when I laugh! What should I do?" The doctor calmly responds, "Stop laughing." I haven't yet figured out how to reliably keep the pipe between my code and the plotting program open without an active command window. While I am sure that a solution exists, I have to prioritize my efforts. The presence of the command window just isn't a show-stopping problem. Have you tried ... ummm .... not closing the command window? B

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Re: [Ifeffit] Ifeffit Digest, Vol 116, Issue 13
by Tsuei, Ku-Ding 24 Oct '12

24 Oct '12

Thanks a lot, Bruce. I checked your new version 0.9.13.1 on my computers and both yield good fits. Now I can move on to work on real data. Ku-Ding On 2012/10/23 下午 06:24, 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: Running (D)Artemis yields different result from that > shown in (D)Artemis instruction videos (Bruce Ravel) > 2. release 0.9.13.1 (Bruce Ravel) > 3. DORIS III operation ended (Edmund Welter) > 4. Re: DORIS III operation ended (Voegelin, Andreas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 22 Oct 2012 16:12:43 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Running (D)Artemis yields different result from > that shown in (D)Artemis instruction videos > Message-ID: <3508041.vaaWmxvES8(a)lachesis.bnl.gov> > Content-Type: text/plain; charset="utf-8" > > > OK, you've convinced me. > > When I got into the lab this afternoon, I tried the same fit on a > Windows computer. Much to my surprise, the result on Windows was > quite different from the result on my linux computers at home. > > After a few hours of investigation, I found a problem in how Ifeffit > had been compiled on the Windows machine that I use to build the > Windows installer. > > I was able to come up with a short-term solution and then built a new > installer package for 0.9.13 which i think works correctly. > > I will be announcing a new release shortly. > > B > > > > On Monday, October 22, 2012 06:41:26 AM Tsuei, Ku-Ding wrote: >> Bruce, >> >> Perhaps you noticed the "Fit color" was red (large R-factor 0.074496, >> poor fit, also seen in the attached figure in the last email) when you >> loaded in the project file I sent you. When you hit Fit button again the >> "Fit color" might turn to green indicating good fit as shown in your >> result of a much smaller R-factor (0.004265). >> >> I did the following test on various versions of Demeter on my desktop >> and notebook computers both installed with Windows 7 SP1. Of course I >> uninstalled one version first before installing another. I tried to use >> Uninstall within the Program menu or use the Program manager. I tried to >> reboot or not to reboot after uninstallation or installation. Neither >> shows any difference. >> >> Fit color >> 0.9.10 green >> 0.9.11 red >> 0.9.12 red >> 0.9.13 red >> >> Only version 0.9.10 yields good fit. The latter versions would not give >> good fits even with repeated hitting the "Fit" button. I have no idea >> what causes these results but perhaps this observation provides a clue. >> >> Ku-Ding >> >> On 2012/10/22 ?? 01:00, 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: Running (D)Artemis yields different result from that >>> >>> shown in (D)Artemis instruction videos (Ravel, Bruce) >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Sun, 21 Oct 2012 12:36:10 +0000 >>> From: "Ravel, Bruce"<bravel(a)bnl.gov> >>> To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> >>> Subject: Re: [Ifeffit] Running (D)Artemis yields different result from >>> >>> that shown in (D)Artemis instruction videos >>> >>> Message-ID: >>> <47CED3CD722C2A439C0D1D1056B2132517C3B082(a)EX10-MB1.BNL.GOV> >>> >>> Content-Type: text/plain; charset="us-ascii" >>> >>> >>> Ku-Ding, >>> >>> I don't know what to tell you. On the computer I am sitting in front of >>> right now, I opened your two project files and hit the fit buttons, I get >>> the same fit with only numerical differences. Here I am cutting and >>> pasting from the two log files:> >>> old artemis: >>> Chi-square = 4334.684537717 >>> Reduced Chi-square = 691.819976095 >>> R-factor = 0.004250325 >>> >>> amp = 0.8649100 +/- 0.0412220 (1.0000) >>> enot = 5.6049380 +/- 0.2950270 (0.0000) >>> delr = -0.0226780 +/- 0.0023790 (0.0000) >>> ss = 0.0082230 +/- 0.0003250 (0.0030) >>> >>> new artemis: >>> Chi-square : 4348.7359268 >>> Reduced chi-square : 694.0625918 >>> R-factor : 0.0042652 >>> >>> amp = 0.86526150 # +/- 0.04129645 [1.00000] >>> enot = 5.61081742 # +/- 0.29527844 [0] >>> delr = -0.02266589 # +/- 0.00238341 [0] >>> ss = 0.00822546 # +/- 0.00032571 [0.00300] >>> >>> I don't acknowledge that there is a problem. >>> >>> B >>> >>> >>> ________________________________________ >>> From:ifeffit-bounces@millenia.cars.aps.anl.gov >>> [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of Tsuei, Ku-Ding >>> [tsuei(a)nsrrc.org.tw] Sent: Thursday, October 18, 2012 1:15 PM >>> To:ifeffit@millenia.cars.aps.anl.gov >>> Subject: [Ifeffit] Running (D)Artemis yields different result from that >>> shown in (D)Artemis instruction videos >>> >>> Hi Bruce, >>> >>> I went through your (D)Artemis instruction videos and ran the latest >>> Demetris 0.9.12 with 0.9.13 update side by side to reproduce the >>> results. However, my running yields much poorer fitting results on Au >>> foil EXAFS, even the first shell (video 03). Actually it happened using >>> the older 0.9.11 too. I also went through your Lecture videos shot at >>> Diamond and ran (D)Artemis but could reproduce your results closely. I >>> have felt puzzled for quite a while why the simplest case Au foil does >>> work well. Today I tried to run the same Au data and fitting by the old, >>> last version of Artemis 0.8.014. I could produce very good fitting on >>> the first shell with the R-factor very near that shown in the video. I >>> made sure the math expressions for the fitting parameters amp, enot, >>> delr and ss are set exactly the same, with fitting range exactly the >>> same, in both programs. Their screen outputs file is attached. The saved >>> respective project files are also attached. I copied the fit outputs >>> into their journals. I would appreciate if you may review these results >>> and help clear my puzzle. >>> >>> Best regards, >>> >>> Ku-Ding >>> >>> >>> >>> ------------------------------ >>> >>> _______________________________________________ >>> Ifeffit mailing list >>> Ifeffit(a)millenia.cars.aps.anl.gov >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >>> >>> >>> End of Ifeffit Digest, Vol 116, Issue 11 >>> **************************************** >>> . >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > -- > > 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 > > > > ------------------------------ > > Message: 2 > Date: Mon, 22 Oct 2012 16:20:16 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] release 0.9.13.1 > Message-ID: <2108483.PEeEN70mtK(a)lachesis.bnl.gov> > Content-Type: text/plain; charset="us-ascii" > > > Hi, > > As a result of a problem brought to my attention by Ku-Ding Tsuei, I > built a new installer of my software for Windows. The new installer, > release 0.9.13.1 can now be downloaded from > > http://bruceravel.github.com/demeter/ > > This is an installer package. There is not a package for updating > from 0.9.12. You must download and install the new installer package. > > This new installer is essential for anyone using Artemis. As Ku-Ding > discovered, versions 0.9.11 through 0.9.13 all suffer from the same > problem. If you are using Artemis from any of the affected versions, > you *must* upgrade. > > I apologize for making three flawed releases of my software and I hope > that no one has been too inconvenienced by my mistake. Once again, > this mailing list and its most excellent community proves to be the > best feature of our software! > > > As a bit of consolation, I want to direct your attention to the > Artemis Users' Guide. I have put a lot of effort into it in recent > weeks. It is still not complete, but it is much enhanced. > > http://bruceravel.github.com/demeter/artug/index.html > > > 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 > > > ------------------------------ > > Message: 3 > Date: Tue, 23 Oct 2012 09:35:25 +0200 > From: Edmund Welter <edmund.welter(a)desy.de> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] DORIS III operation ended > Message-ID: <508648BD.3020804(a)desy.de> > Content-Type: text/plain; charset="iso-8859-1" > > Dear fellow XAFS user, > > yesterday (October 22^nd 2012, 8 am) the DORIS III storage ring in > Hamburg was switched of for good. That means our 3 EXAFS beamlines are > left without photons and user operation at these beamlines had to end. > In the next 2 years we will build 2 new EXAFS beamlines at the PETRA III > storage ring that will hopefully equally well serve the demands of our > large user community as the 3 closed beamlines did during the last 20+ > years. > > I know this mailing list is mainly about software and number crunching, > but I thought the end of operation of a machine that produced so many > beautiful numbers to be crunched with IFEFFIT/Athena/Artemis etc. might > justify a short notice on this list. > > Anyway, to close the circle to the software, the end of user operation > of HASYLAB's DORIS beamlines finally gives our users the chance to use > this software and produce many nice papers during the coming months > (Ah,wait, that was something different, New York, July 1977 :-). > > I am looking forward to see you all back at our PETRA extension > beamlines in autumn 2014! Let me close this mail with the last line of > data ever measured at the A1 EXAFS beamline: > > 7893.277 0 0 0 0 0 0 0 0 0 0 0 0 0 > 5.489 13.22 > > > Best regards, > > Edmund Welter > > -- > -------------------------------------------------------- > Dr. Edmund Welter Deutsches Elektronen-Synchrotron > DESY FS-Do > > Notkestr. 85 Email: edmund.welter(a)desy.de > D-22607 Hamburg Phone: +49 40 8998 4510 > Germany Fax : +49 40 8998 2787 > -------------------------------------------------------- > >

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Re: [Ifeffit] Running (D)Artemis yields different result from that shown in (D)Artemis instruction videos
by Tsuei, Ku-Ding 24 Oct '12

24 Oct '12

Bruce, Perhaps you noticed the "Fit color" was red (large R-factor 0.074496, poor fit, also seen in the attached figure in the last email) when you loaded in the project file I sent you. When you hit Fit button again the "Fit color" might turn to green indicating good fit as shown in your result of a much smaller R-factor (0.004265). I did the following test on various versions of Demeter on my desktop and notebook computers both installed with Windows 7 SP1. Of course I uninstalled one version first before installing another. I tried to use Uninstall within the Program menu or use the Program manager. I tried to reboot or not to reboot after uninstallation or installation. Neither shows any difference. Fit color 0.9.10 green 0.9.11 red 0.9.12 red 0.9.13 red Only version 0.9.10 yields good fit. The latter versions would not give good fits even with repeated hitting the "Fit" button. I have no idea what causes these results but perhaps this observation provides a clue. Ku-Ding On 2012/10/22 上午 01:00, 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: Running (D)Artemis yields different result from that > shown in (D)Artemis instruction videos (Ravel, Bruce) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 21 Oct 2012 12:36:10 +0000 > From: "Ravel, Bruce"<bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Running (D)Artemis yields different result from > that shown in (D)Artemis instruction videos > Message-ID: > <47CED3CD722C2A439C0D1D1056B2132517C3B082(a)EX10-MB1.BNL.GOV> > Content-Type: text/plain; charset="us-ascii" > > > Ku-Ding, > > I don't know what to tell you. On the computer I am sitting in front of right now, I opened your two project files and hit the fit buttons, I get the same fit with only numerical differences. Here I am cutting and pasting from the two log files: > > old artemis: > > Chi-square = 4334.684537717 > Reduced Chi-square = 691.819976095 > R-factor = 0.004250325 > > amp = 0.8649100 +/- 0.0412220 (1.0000) > enot = 5.6049380 +/- 0.2950270 (0.0000) > delr = -0.0226780 +/- 0.0023790 (0.0000) > ss = 0.0082230 +/- 0.0003250 (0.0030) > > > new artemis: > > Chi-square : 4348.7359268 > Reduced chi-square : 694.0625918 > R-factor : 0.0042652 > > amp = 0.86526150 # +/- 0.04129645 [1.00000] > enot = 5.61081742 # +/- 0.29527844 [0] > delr = -0.02266589 # +/- 0.00238341 [0] > ss = 0.00822546 # +/- 0.00032571 [0.00300] > > > I don't acknowledge that there is a problem. > > B > > > ________________________________________ > From:ifeffit-bounces@millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of Tsuei, Ku-Ding [tsuei(a)nsrrc.org.tw] > Sent: Thursday, October 18, 2012 1:15 PM > To:ifeffit@millenia.cars.aps.anl.gov > Subject: [Ifeffit] Running (D)Artemis yields different result from that shown in (D)Artemis instruction videos > > Hi Bruce, > > I went through your (D)Artemis instruction videos and ran the latest > Demetris 0.9.12 with 0.9.13 update side by side to reproduce the > results. However, my running yields much poorer fitting results on Au > foil EXAFS, even the first shell (video 03). Actually it happened using > the older 0.9.11 too. I also went through your Lecture videos shot at > Diamond and ran (D)Artemis but could reproduce your results closely. I > have felt puzzled for quite a while why the simplest case Au foil does > work well. Today I tried to run the same Au data and fitting by the old, > last version of Artemis 0.8.014. I could produce very good fitting on > the first shell with the R-factor very near that shown in the video. I > made sure the math expressions for the fitting parameters amp, enot, > delr and ss are set exactly the same, with fitting range exactly the > same, in both programs. Their screen outputs file is attached. The saved > respective project files are also attached. I copied the fit outputs > into their journals. I would appreciate if you may review these results > and help clear my puzzle. > > Best regards, > > Ku-Ding > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 116, Issue 11 > **************************************** > . >

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DORIS III operation ended
by Edmund Welter 23 Oct '12

23 Oct '12

Dear fellow XAFS user, yesterday (October 22^nd 2012, 8 am) the DORIS III storage ring in Hamburg was switched of for good. That means our 3 EXAFS beamlines are left without photons and user operation at these beamlines had to end. In the next 2 years we will build 2 new EXAFS beamlines at the PETRA III storage ring that will hopefully equally well serve the demands of our large user community as the 3 closed beamlines did during the last 20+ years. I know this mailing list is mainly about software and number crunching, but I thought the end of operation of a machine that produced so many beautiful numbers to be crunched with IFEFFIT/Athena/Artemis etc. might justify a short notice on this list. Anyway, to close the circle to the software, the end of user operation of HASYLAB's DORIS beamlines finally gives our users the chance to use this software and produce many nice papers during the coming months (Ah,wait, that was something different, New York, July 1977 :-). I am looking forward to see you all back at our PETRA extension beamlines in autumn 2014! Let me close this mail with the last line of data ever measured at the A1 EXAFS beamline: 7893.277 0 0 0 0 0 0 0 0 0 0 0 0 0 5.489 13.22 Best regards, Edmund Welter -- -------------------------------------------------------- Dr. Edmund Welter Deutsches Elektronen-Synchrotron DESY FS-Do Notkestr. 85 Email: edmund.welter(a)desy.de D-22607 Hamburg Phone: +49 40 8998 4510 Germany Fax : +49 40 8998 2787 --------------------------------------------------------

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release 0.9.13.1
by Bruce Ravel 22 Oct '12

22 Oct '12

Hi, As a result of a problem brought to my attention by Ku-Ding Tsuei, I built a new installer of my software for Windows. The new installer, release 0.9.13.1 can now be downloaded from http://bruceravel.github.com/demeter/ This is an installer package. There is not a package for updating from 0.9.12. You must download and install the new installer package. This new installer is essential for anyone using Artemis. As Ku-Ding discovered, versions 0.9.11 through 0.9.13 all suffer from the same problem. If you are using Artemis from any of the affected versions, you *must* upgrade. I apologize for making three flawed releases of my software and I hope that no one has been too inconvenienced by my mistake. Once again, this mailing list and its most excellent community proves to be the best feature of our software! As a bit of consolation, I want to direct your attention to the Artemis Users' Guide. I have put a lot of effort into it in recent weeks. It is still not complete, but it is much enhanced. http://bruceravel.github.com/demeter/artug/index.html 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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Running (D)Artemis yields different result from that shown in (D)Artemis instruction videos
by Tsuei, Ku-Ding 21 Oct '12

21 Oct '12

Hi Bruce, I went through your (D)Artemis instruction videos and ran the latest Demetris 0.9.12 with 0.9.13 update side by side to reproduce the results. However, my running yields much poorer fitting results on Au foil EXAFS, even the first shell (video 03). Actually it happened using the older 0.9.11 too. I also went through your Lecture videos shot at Diamond and ran (D)Artemis but could reproduce your results closely. I have felt puzzled for quite a while why the simplest case Au foil does work well. Today I tried to run the same Au data and fitting by the old, last version of Artemis 0.8.014. I could produce very good fitting on the first shell with the R-factor very near that shown in the video. I made sure the math expressions for the fitting parameters amp, enot, delr and ss are set exactly the same, with fitting range exactly the same, in both programs. Their screen outputs file is attached. The saved respective project files are also attached. I copied the fit outputs into their journals. I would appreciate if you may review these results and help clear my puzzle. Best regards, Ku-Ding

2 1

feff800 path files
by Maria Zougrou 18 Oct '12

18 Oct '12

Hi, I'm trying to construct the heulandite structure running atoms and feff800 for the 3 Ca sites. Atoms gives me a feff8.inp I got the paths for Ca1 site, but it doesn't calculate the Ca2 paths. There doesn't seem to be a geometry problem, I don't get a message that some atoms are too close, what could be the problem? I'm attaching the files I'm using. Thank you

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possible bug: same Artemis project file, different results on 2 PCs
by Jeremy Thorbahn 10 Oct '12

10 Oct '12

Hi Bruce, I was putting together another post for the list (which is currently awaiting moderation since apparently my attached project files were too large) when I encountered some strange behaviour in Artemis. I tried opening my project file on my second PC to check that it would open fine for other members of the list. But by simply opening the project and clicking Fit, I was getting different results for my guess parameters on the two PCs. Both PCs are Windows 7 and updated to Demeter 0.9.13. Here is a link to the project file (trying to avoid size limitations for the list this time) http://dl.dropbox.com/u/10663174/ZnO.fpj and I will attach a screenshot of Artemis demonstrating what I am talking about from my two PCs. Since I am working to determine S02 and it is very different on each PC, I am hesitant to trust any of my results right now. Thanks Jeremy --

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determining S02 from ZnO vs. Zn foil
by Jeremy Thorbahn 09 Oct '12

09 Oct '12

[note: when putting together this post I discovered a possible bug regarding opening my project files on different PCs. I will submit that issue separately] Hi all: I am writing to probe the community's knowledge regarding my current problem in measuring S02. I have data on a series of glass samples containing ZnO. I also measured a ZnO crystalline powder, and a Zn foil was measured between detectors 2 and 3 (transmission mode) simultaneously with every run. My goal is to determine coordination numbers around Zn in the glass samples, which requires an accurate measurement of S02 for zinc. My main question is if there is any reason why the Zn foil would provide a more accurate result than the ZnO powder, or vice versa. I see no reason why it should be different, especially since this method depends entirely on the 'chemical transferability' of S02 in the first place. Nevertheless, I obtain different results from each, with S02 ~ 0.75 from the ZnO and ~0.88 from the foil. Statistically, the Zn foil dataset is "better" since it is a merge of all of my scans while there are only two scans of ZnO. However, part of me wants to trust the ZnO data more, for somewhat vague reasons such as that it is a "more similar" coordination environment to what I would expect in my samples, and that it was measured between the same two detectors, etc. If anyone has any experience that would indicate why one should be better than the other, I would love to hear about it. I will attach Artemis project files for each if you'd like to take a look at my fits. It is entirely possible that the discrepancy is due to an error in data processing or analysis on my part; I am by no means an expert. I hope the project files will not clog up anyone's mailbox, at a couple of megabytes each. Thanks, Jeremy

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Atoms bug & Athena request
by Bruce Ravel 04 Oct '12

04 Oct '12

Fred: Thanks for the bug report. It was a simple fix and I even uncovered another mistake in how crystal data that is entered by hand gets interpreted. Cool! Bradley: You'll be putin' on your dancing shoes after the next release. The combinatorial output files will be named as you requested. As always, thanks for the feedback. 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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possible minor bug in atoms in artemis probably just me
by fred.mosselmans＠diamond.ac.uk 04 Oct '12

04 Oct '12

Hi Bruce et al. I searched the mailing list for something similar as i feel this is so obvious it must be there to find. However i could n't find it so ... Also there's are easy workable workarounds so it's not very important. I was XAS data for atoms that sit in substituted sites in a known lattices - Sr in calcite, If i build the calcite lattice in atoms stand alone and save output from there and read into artemis then substitute Sr for Ca before running Feff etc. And import to Artemis the world is lovely (viewed on the perspective does the program continue working perspective and no wider one.) If i try to either read my Sr prj and then do the same (i.e. typing the xtal paras in) within artemis or just try to do that before reading in the Sr data the program crashes as soon as i try to run atoms. The log file error line is: Can't call method "element" without a package or object reference at C:/strawberry/perl/site/lib/Demeter/Atoms/Absorption.pm line 31. If i read the saved atoms input file (from stand-alone) into Demeter it runs fine. So i guess something is set up when i save it in stand alone atoms that ain't inputted by me and that helps out. Maybe this is meant to happen as people are supposed to read in cif files and the like and for slow people like myself who enter things by hand there are obstacles left strewn on the road. Fred The atoms inp file is attached. This works however entering these same xtal paras by hand doesn't if it's my hand(s) There are more recent calcite lattice paras but that doesn't affect the process. -- 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

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D-Athena Request
by BradleyW Miller 03 Oct '12

03 Oct '12

Hi, A minor (I hope) request for D-Athena on PC's. When running a LCF (eg collected a spectrum and named it AsScan1) and exporting the LCF predicted results to an excel file, the default name of the newly created xls file is "combinatorial.xls". In Athena (on PC) the default output file name was the name of the spectra you are fitting (eg AsScan1.cvs). If the default in D-Athena could be the name of the original spectra again that would be very appreciated. If it could be the name of the spectra and the name of the fit space (eg. AsScan1.derv.xls or AsScan1.norm.xls or AsScan1.Chi.xls)... I may have to dance a jig in your honor. Thanks for your time and the freeware. Respectfully, Bradley W. Miller, Ph.D. Post Doctoral Fellow Oak Ridge Institute for Science and Education U. S. Environmental Protection Agency National Risk Management Research Laboratory Land Remediation and Pollution Control Division 5995 Center Hill Avenue, Cincinnati, OH 45224-1702 Office: (513) 487-2889 Miller.BradleyW(a)epa.gov Fax: (513) 569-7879 www.epa.gov www.tinyurl.com/bwmiller The great tragedy of Science—the slaying of beautiful hypothesis by an ugly fact.— Thomas H. Huxley Views or Opinions expressed in this email is solely representative of the sender and does not represents those of the EPA or any other agency.

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Quick first shell (QFS) theory in Artemis
by Bruce Ravel 02 Oct '12

02 Oct '12

Hi all, One of the bugs reported last week involved a project file which made extensive use of the "quick first shell" -- or QFS -- feature of Artemis. The bug involved a problem importing such paths from a saved project file. That bug has been fixed in the 0.9.13 release that I announce a short while ago. This project file that triggered the bug reminded me of an issue that has come up at several recent XAS training courses that I have participated in. In situations where rather little is known about the structure of a material, there is a thought that the QFS tool could provide a model-independent way of generating scattering amplitudes and phase shifts for atoms suspected of being in the material. While the QFS tool is a reasonable thing for atoms in the first coordination shell (hence the name!), this is a dangerous practice for atoms at longer distances. Artemis does not police its misuse in this way beyond simply issuing a warning sugesting that you may be doing something inappropriate. A full discussion of this topic is rather lengthy, so I will refer you to a wiki page that I wrote: http://cars9.uchicago.edu/ifeffit/Demeter/QFS If you have considered using the QFS tool for atoms beyond the first coordination shell, please read that wiki page all the way to the end. 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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news + 0.9.13
by Bruce Ravel 02 Oct '12

02 Oct '12

Hi! I just gave Demeter's homepage a make-over. It's looking quite nice: http://bruceravel.github.com/demeter/ Links for downloading the windows packages are on the left. I also just posted version 0.9.13 on the downloads site and tagged the source code. I am trying something new with this release. Rather than rebuilding the whole Windows installer package with each release, I am now making Windows updater packages. It works like this: * Whenever I make a big change to Demeter or any of its dependencies, I will release a new Windows installer package. * For bug fixes and feature enhancements, I will release a new updater package. * The updater should be installed ON TOP OF the installer package. The current installer is Demeter 0.9.12. The current updater will update that to 0.9.13. If you have already installed 0.9.12 on your Windows computer, simply download and run the updater. If you have not yet installed 0.9.12, download both packages. Run the installer first, then run the updater. If that is not clear, everything is explained in detail at http://cars9.uchicago.edu/ifeffit/Demeter/WindowsUpdater This update fixes all of the problems that were reported last week on the mailing list. Here is the list of changes: https://github.com/bruceravel/demeter/blob/master/Changes.org 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] GDS parameters
by Matt Newville 01 Oct '12

01 Oct '12

John, On Mon, Oct 1, 2012 at 12:13 AM, John Farell <john_far(a)rediffmail.com> wrote: > > Dear friends, > > We are doing an experiment of temperature based phase transition. I need to get the values of all four GDS > parameters with errors. I know the theoretical model (i. e., atoms page). But to get all the four parameter > values with errors (amp, enot, delr, ss ). For this I cannot "set" all the parameters as well ass I cannot > guess all the parameters. Any suggestions for this problem ?. It's a bit hard for me to tell whether the question is about how to operate the program, or about some problem with operating it the way you think it should work. Why can't you set all the parameters? Are you unable to do this, or this something that you want to not do? Similarly, why can't you guess all the parameters? Is it that the Artemis GUI is not letting you do this? --Matt

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Athena closing on data import
by jiahui 01 Oct '12

01 Oct '12

Dear list, I have the problem of Athena closing on data import without any message. I went through the threads about this topic but fail to find the solution. I really appreciate that anyone can tell me how to fix it. Best regards, jiahui -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 28 September 2012 18:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 115, Issue 26 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: (D) Athena closing on data import (Bruce Ravel) 2. Re: Issue On Re-Open of File in Artemis (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Thu, 27 Sep 2012 13:05:32 -0400 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] (D) Athena closing on data import Message-ID: <1870787.0HCcKRKktn(a)lachesis.bnl.gov> Content-Type: text/plain; charset="us-ascii" On Thursday, September 27, 2012 01:22:36 PM Jeremy Thorbahn wrote: > I had not anticipated that the > turnaround time on getting a fix for my problem would be within the > hour Well, it's good timing to post to the list as I am walking back to my desk after a couple of hours at the beamline. :) Glad it worked out for you. 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 ------------------------------ Message: 2 Date: Thu, 27 Sep 2012 13:59:40 -0400 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Issue On Re-Open of File in Artemis Message-ID: <6179390.OcvHgOAaDK(a)lachesis.bnl.gov> Content-Type: text/plain; charset="us-ascii" Dan, Saving and reloading a project which uses a quick first shell path is very very broken right now. Getting it completely right may take a while. Sorry for that. B On Thursday, September 27, 2012 04:23:43 PM Daniel Whittaker wrote: > I am having an issue with a project i was working on yesterday - one i > hope can be resolved rather easily. > I was working on the project yesterday then i saved the file and > closed Artemis and all was well. > > However, today when i try and open the file and continue working on it > it instantly crashes the software on pressing FIT. First thing this > morning i updated to version 0.9.12. I am modelling using the first > shell fit that is built in - possible source of error? > I dont know the root cause of the issue as everything i have done here > i have done before with other datasets with no issue. I have tried > starting from scratch and reinstalling the software too but the issue > persists - it all works well (when startingg from scratch) until it > is saved and then tried to reopen. -- 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 ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 115, Issue 26 ****************************************

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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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