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

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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