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

Most probably a bug or something.
by pushkar shejwalkar 02 Dec '15

02 Dec '15

Dear All, I have recently found this particular problem with plotting my graphs in k fitting. This is a problem with athena as well as artemis. When I plot the graphs in R or E or q there is no problem, but when I do so in k suddenly these four black circles show up on the left side of the graph. Interestingly this has appeared suddenly just now and after this (probably i can recollect exactly) I could not maximize my plotting window at all. although if I drag the corners it can be resized and these four circles then appears relatively smaller (basically it does not exapnds with the window. Anybody else have this problem? is there a quick fix? I am not sure if this is a bug or not so I am sending this here. my operating system is Windows 10, Athena and artemis 0.9.22 8GB RAM. (Please let me konw if anything else is needed) Pictures of these problem is attached below. I am attaching R-space just to show that it doesnt happen for the R-space. First picture is Athena, second is from Artemis fitting. [image: Inline image 4] [image: Inline image 2][image: Inline image 3] -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Tokyo-to Japan

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Re: [Ifeffit] Ifeffit Digest, Vol 154, Issue 5
by Enyuan Hu 02 Dec '15

02 Dec '15

Dear all, Thank you all for the kind help. I didn't know CuO is so useful in the sense that asking for its spectrum would reveal the abundant kindness in this community :) Enyuan On Wed, Dec 2, 2015 at 10:26 PM, <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: Ifeffit Digest, Vol 154, Issue 1 (Soma Chattopadhyay) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 2 Dec 2015 20:14:04 -0600 > From: Soma Chattopadhyay <soma.tifr(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 154, Issue 1 > Message-ID: > <CAMYsB8ucwLRpSNGFK1aA8LbuWb03t5fOajSjdPU= > SGerD30jQQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Enyuan > Attached is my athena project file with Cu foil, CuO and Cu2O data in > athena. > They have references foils with them. > best > Soma > > On Wed, Dec 2, 2015 at 7:38 PM, Enyuan Hu <enhu(a)bnl.gov> wrote: > > > Dear Matt, > > > > I'm sorry to be persistent but I noticed that the reference spectrum (Cu > > foil I assume) for these two CuO data doesn't seem to correct. I conclude > > this after I made comparison using the Cu foil data from the database and > > my own previous measurement. If it's not bothering you, can you help me > > look into that? Thanks. > > > > Enyuan > > > > On Wed, Dec 2, 2015 at 8:08 PM, Enyuan Hu <enhu(a)bnl.gov> wrote: > > > >> Dear Riti and Matt, > >> > >> Thank you two very much for the timely help. I didn't even know the > >> existence of these two libraries. Thanks again for letting me know such > a > >> valuable resource. > >> > >> regards, > >> Enyuan > >> > >> On Wed, Dec 2, 2015 at 7:40 PM, < > >> 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. CuO XAS spectrum (Enyuan Hu) > >>> 2. Re: CuO XAS spectrum (Ritimukta Sarangi) > >>> 3. Re: CuO XAS spectrum (Matthew Marcus) > >>> 4. Fwd: Most probably a bug or something. (pushkar shejwalkar) > >>> > >>> > >>> ---------------------------------------------------------------------- > >>> > >>> Message: 1 > >>> Date: Wed, 2 Dec 2015 18:32:11 -0500 > >>> From: Enyuan Hu <enhu(a)bnl.gov> > >>> To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > >>> Subject: [Ifeffit] CuO XAS spectrum > >>> Message-ID: > >>> < > >>> CAJud35MbtedoHtgoN3yFJgJ3squ+L5LCVpp1uNm0Tf4vwpWENA(a)mail.gmail.com> > >>> Content-Type: text/plain; charset="utf-8" > >>> > >>> Dear all, > >>> > >>> I'm analyzing some Cu compounds spectra and was wondering if anyone has > >>> the > >>> CuO XAS spectrum and is willing to share. Thanks. > >>> > >>> best regards, > >>> Enyuan > >>>

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Re: [Ifeffit] Ifeffit Digest, Vol 154, Issue 1
by Enyuan Hu 02 Dec '15

02 Dec '15

Dear Riti and Matt, Thank you two very much for the timely help. I didn't even know the existence of these two libraries. Thanks again for letting me know such a valuable resource. regards, Enyuan On Wed, Dec 2, 2015 at 7:40 PM, <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. CuO XAS spectrum (Enyuan Hu) > 2. Re: CuO XAS spectrum (Ritimukta Sarangi) > 3. Re: CuO XAS spectrum (Matthew Marcus) > 4. Fwd: Most probably a bug or something. (pushkar shejwalkar) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 2 Dec 2015 18:32:11 -0500 > From: Enyuan Hu <enhu(a)bnl.gov> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] CuO XAS spectrum > Message-ID: > < > CAJud35MbtedoHtgoN3yFJgJ3squ+L5LCVpp1uNm0Tf4vwpWENA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > > I'm analyzing some Cu compounds spectra and was wondering if anyone has the > CuO XAS spectrum and is willing to share. Thanks. > > best regards, > Enyuan >

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CuO XAS spectrum
by Enyuan Hu 02 Dec '15

02 Dec '15

Dear all, I'm analyzing some Cu compounds spectra and was wondering if anyone has the CuO XAS spectrum and is willing to share. Thanks. best regards, Enyuan

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Issue with Compatibility between versions of Athena
by Nirala Singh 26 Nov '15

26 Nov '15

Hello, I have recently downloaded Athena and was sending a project file to a colleague who uses an older version. When I sent it, I checked 'Backwards compatible project file', then saved the project and closed Athena, then sent the file. I had selected some normalization parameters as follows: [image: Inline image 2] When he opened the file, most of the parameters were the same, except the window type (changed from 'Hanning' to 'kaiser-bessel'). Is there any reason for this? Any way to maintain the window function between versions? [image: Inline image 1] Thank you,

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Fitting parameters corrleations between variables
by pushkar shejwalkar 24 Nov '15

24 Nov '15

Dear All, I am trying to fit in Pd compound and the fit that I obtained looks kinda good. I used Pd metal and Pd(OAc)2 shells for fitting. These standards were collected and fitted simultaneously and I got the SO2 value there as 0.67 with Pd foil coordination number as 12 which is correct when considered Pd foil CN. Next while fitting the actual sample (unknown) I used the formula in SO2 column as amp*N1 and put amp as 0.67 and N as 1. I kept N1 as variable (Guess). same I did for the second shell of Pd-O with N2. amp is kept on SET value of 0.67. After fitting I received the N1 and N2 value as 5.6 (0.5) and 1.6 (0.7) (roughly). however, when I checked the correlations between the variables I got the values as given in the log file attached. I saw there is some correlation between bkg01_01 and N2 and many such correlations between bkg values. I have so far never seen such correlations. What are the implications of these correlations? does this means that my fitting assumptions are incorrect. does correlations values in negative indicates something? Thank you very much for the input. By the way my RBKG is 1.2 in athena and I used this same file for fitting purpose and on artemis I used rmin 1.2 and rmax 3.4. All these information are in log file attached Any help in understanding this is appreciated. -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Tokyo-to Japan

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Zinc Sulfite Reference Spectrum
by Elisabeth E Feld 16 Nov '15

16 Nov '15

Dear All, I am studying the oxidation state of Sulfur using XANES and need a reference spectrum of Zinc Sulfite (ZnSO3) for comparison. I do not have access to taking the spectrum myself and currently do not have any spectrum grabber tool to pull the reference from a paper. If you could help me out by sending me a Zinc Sulfite spectrum, I would greatly appreciate it! Thank you, Elisabeth Elisabeth Feld Ph.D. Candidate Dellinger Research Group Chemistry Department Superfund Research Center Louisiana State University 338 Choppin Hall Baton Rouge, LA 70803 efeld1(a)lsu.edu

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Re: [Ifeffit] Ifeffit Digest, Vol 153, Issue 30
by Christopher Thomas Chantler 16 Nov '15

16 Nov '15

With Ifeffit-like, you can test these assumptions with an explicit chi^2_r, and indeed the answer does and must depend upon your actual individual error bars. The other factor here is how correlated your choice of parameters are which of course reaches that limit much faster. :) ------------------------------------------------------------ Christopher Chantler, Professor, FAIP Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS President, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au chantler(a)me.com http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html http://optics.ph.unimelb.edu.au/~chantler/home.html ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov [ifeffit-request(a)millenia.cars.aps.anl.gov] Sent: Tuesday, 17 November 2015 5:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 153, Issue 30 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: Problem with Perl interpreter (Bruce Ravel) 2. Re: Hello (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Mon, 16 Nov 2015 07:48:54 -0500 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Problem with Perl interpreter Message-ID: <5649D0B6.3050108(a)bnl.gov> Content-Type: text/plain; charset=windows-1252; format=flowed On 11/16/2015 02:53 AM, Wojciech Olszewski wrote: > The timeline of this problem was as follows: > 1) Demeter was working fine; > 2) One day I couldn't run any of the Demeter software - error message "Per interpreter has stopped working; > 3) Reinstallation of Demether - the problem is still there; > 4) Installation of perl (in other folder, not the same as Demeter) - the problem is still there; > 5) Mail to mailing list; > 6) Deinstallation of Demether and Perl; > 7) Installation of Demeter. > Unfortunately the problem is still there. I receive the same error message. Wojciech, Step 2 really suggests that this is a problem local to your computer. In recent weeks, there have been a few reports of anti-virus software blocking some component of perl or Demeter. In the time period between steps 1 and 2, was AV updated on this computer? Could you disable AV (as a test of course)? Or configure AV to explicitly allow Demeter to run? 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/ ------------------------------ Message: 2 Date: Mon, 16 Nov 2015 11:18:56 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Hello Message-ID: <CA+7ESbrzTzUkpPHj0CFZ6HErN5Hp_jMHJynJa0rUZ+XSM3dqPA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Riti, On Fri, Nov 13, 2015 at 6:25 PM, Ritimukta Sarangi <ritimukta(a)gmail.com> wrote: > Hi Bruce and Matt, > Are there any obvious examples of where Sterns criteria is shown to be > incorrect? Meaning that 2delkdelR/pi +2 has been shown to over predict the > number of available independent parameters? I have often been asked this by > students/users and failed to explain it well, except for taking of talking > sources or error such as systematic, spline, etc. > Thanks! > -Riti > > That's an excellent question. To be honest, I don't think this has been tested in great detail, with the main issue being "when can you truly tell that you've used too many parameters". We typically rely on "when adding a variable doesn't improve reduced chi-square" as that measure. But, the definition of reduced chi-square that we use includes a value for N_idp already, so we're more or less *imposing* the Stern rule. I think lots of us have observed cases where the Stern rule is definitely optimistic. And that might be understandable because the Stern rule doesn't include a separate measure of the noise in the data, or what the distribution of "the effect" of the parameters would be on the signal. That is, one can always increase the R range to 20 Angstroms, and so increase N_idp. But if you're trying to fit 25 variables for the part of the signal between 1.5 and 2.5 Ang, there is probably going to be very hard to get good measures of all 25 variables. The Stern rule sort of doesn't account for this, except in the sense of giving guidance. It would be interesting the revisit this with a better statistical treatments of information. There are, for example, statistical values like the Akaike Information criterion ( https://en.wikipedia.org/wiki/Akaike_information_criterion) and related values that might be useful for better understanding when one is using too many parameters. --Matt

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Problem with Perl interpreter
by Wojciech Olszewski 16 Nov '15

16 Nov '15

I have a problem with Demeter package. Up to yesterday everything was fine. Now when I try to start any program (Athena, Artemis...) I receive error message: Perl interpreter has stopped working (The application was unable to start correctly (0xc0000005)). Installation of perl (strawberry-perl-5.22.0.1-64bit.msi) didn't solve the problem. Unfortunately all the log files ("C:\Users\<username>\AppData\Roaming\Demeter\<name>.log") are empty. I am using the Demeter 0.9.24 on 64-bit Windows 7. I would be really grateful for help in solving this problem. Thank you in advance, Wojciech -- ALBA Synchrotron <http://www.albasynchrotron.es> Wojciech Olszewski BL22 - CLAESS: Core Level Absorption & Emission Spectroscopies - Experiments Division ALBA SYNCHROTRON LIGHT SOURCE Ctra. BP 1413 km. 3,3 | 08290 | Cerdanyola del Vallès| Barcelona | Spain <http://www.albasynchrotron.es/AboutUs/Access> (+34) 93 592 4059 www.albasynchrotron.es <http://www.albasynchrotron.es>| wolszewski(a)cells.es <mailto:wolszewski@cells.es> **Please, do not print this e-mail unless it is absolutely necessary. **Si heu rebut aquest correu per error, us informo que pot contenir informació confidencial i privada i que està prohibit el seu ús. Us agrairíem que ho comuniqueu al remitent i l'elimineu. Gràcies. Si ha recibido este correo por error, le informo de que puede contener información confidencial y privada y que está prohibido su uso. Le agradeceré que lo comunique a su remitente y lo elimine. Gracias. If you have received this e-mail in error, please note that it may contain confidential and private information, therefore, the use of this information is strictly forbidden. Please inform the sender of the error and delete the information received. Thank you.

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Re: [Ifeffit] Problem with Perl interpreter
by Wojciech Olszewski 16 Nov '15

16 Nov '15

On 11/13/2015 11:41 AM, Bruce Ravel wrote: >Hi Wojciech, > >Why are you installing perl independently of Demeter? Do you have some other use on your >computer that requires you to install perl? Installing another version of Strawberry Perl is >almost certain to clobber Demeter. Demeter is currently using perl 5.18, which is not binary >compatible with 5.22. So, when you install the other version of perl things will break. If you >take care to install a very recent version of Demeter to a different installation directory >than you use to install Strawberry 5.22, it is possible that the two can be made to co-exist. > >If you install them to the same installation folder -- say C:\strawberry -- then Demeter is >guaranteed to be broken be due to the binary incompatibility. So ... did you install the other >version of perl prior to noticing that Demeter was broken? If so, there are ways to proceed, >but it may get a bit complicated. At the very least, you can uninstall both packages completely >then resinstall Demeter. That should leave you with a functioning Demeter, but it may break >other software. Did you install Strawberry 5.22 because you have some other use for perl on >your computer? If so, can your other software work with the version of perl that comes with >Demeter? That is, do you really need Strawberry 5.22? Executive summary: I think you problem is >binary compatibility between perl version, of which you seem to have two on your computer. If >all of that doesn't solve your problem, it's going to take a lot more effort to troubleshoot >the problem. >Good luck! >B Dear Bruce, The timeline of this problem was as follows: 1) Demeter was working fine; 2) One day I couldn't run any of the Demeter software - error message "Per interpreter has stopped working; 3) Reinstallation of Demether - the problem is still there; 4) Installation of perl (in other folder, not the same as Demeter) - the problem is still there; 5) Mail to mailing list; 6) Deinstallation of Demether and Perl; 7) Installation of Demeter. Unfortunately the problem is still there. I receive the same error message. Best regards, Wojciech -- ALBA Synchrotron <http://www.albasynchrotron.es> Wojciech Olszewski BL22 - CLAESS: Core Level Absorption & Emission Spectroscopies - Experiments Division ALBA SYNCHROTRON LIGHT SOURCE Ctra. BP 1413 km. 3,3 | 08290 | Cerdanyola del Vallès| Barcelona | Spain <http://www.albasynchrotron.es/AboutUs/Access> (+34) 93 592 4059 www.albasynchrotron.es <http://www.albasynchrotron.es>| wolszewski(a)cells.es <mailto:wolszewski@cells.es> **Please, do not print this e-mail unless it is absolutely necessary. **Si heu rebut aquest correu per error, us informo que pot contenir informació confidencial i privada i que està prohibit el seu ús. Us agrairíem que ho comuniqueu al remitent i l'elimineu. Gràcies. Si ha recibido este correo por error, le informo de que puede contener información confidencial y privada y que está prohibido su uso. Le agradeceré que lo comunique a su remitente y lo elimine. Gracias. If you have received this e-mail in error, please note that it may contain confidential and private information, therefore, the use of this information is strictly forbidden. Please inform the sender of the error and delete the information received. Thank you.

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Re: [Ifeffit] Demeter under El Capitan
by Fowler, Joseph W. 15 Nov '15

15 Nov '15

Dear Matt, I’m the official MacPorts maintainer for Demeter. I am an amateur at this (i.e., at Ports), but I do have notes somewhere on how to update the port file (and, indeed, where to find it in the first place!). Concerning the long list of dependencies: I was unaware of the size of this list. I agree. It sounds crazy to think that we need THREE non-clang compilers to build demeter. I know the fellow who was the previous maintainer, and he has a bit of a superstitious belief in the powers of gcc. Perhaps he imposed this belief unnecessarily on us all? It sounds to me like you understand the internals of what demeter uses and how, much much better than I do. Let me suggest that you either contact me privately OR file a trac ticket at MacPorts about this. Either way, include details of what you think plausibly might be false dependencies. Of course, we’ll also want to add the new Perl dependencies that you pointed out. Perhaps then I can patch the port file and get your assistance in testing it in some way? Once we have a patch we like, I don’t have the powers to commit it to the MacPorts repository directly, but I can certainly make a request for a commit (they are pretty fast and responsive about that). I’d like to comment also on the time it takes to install MacPorts. The whole MacPorts concept supports installing from source AND installing pre-built binaries. The catch (as I understand it) is that the server resources that they use to build and serve the binaries are donated by a large corporation (one with a strong interest in selling more Macintosh computers, naturally). Thus the open-source Ports team cannot simply make the binary “buildbots” appear at will. An early adopter of an OS X version has to install every port, even the incredibly complex ones, from source. Again, I could be wrong, but I think that El Capitan is still in this state. See https://trac.macports.org/ticket/48609 and http://macports-dev.macosforge.narkive.com/tRq2luOR/el-capitan-buildbot for some additional info. Now, this is not to say that Homebrew is a worse solution than MacPorts. I have no basis for comparison (though here is one clue: many packages that I use within the Julia language depend on Homebrew for further dependencies, and I have noticed that they manage to Just Work). But I did want to defend MacPorts from the implied charge that it will always take all users ten hours to install a working system. If you can find a Homebrew expert to work with and develop a Demeter solution, that’s great. Here in my group at NIST, we use MacPorts for so many things that I’m sure we’ll continue to maintain the port file for the foreseeable future. Best wishes, Joe Fowler On Nov 13, 2015, at 11:00 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov>> <ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov>> wrote: From: Matt Newville <newville(a)cars.uchicago.edu<mailto:newville@cars.uchicago.edu>> Subject: Re: [Ifeffit] Demeter under El Capitan Date: November 13, 2015 at 9:34:31 AM MST To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov>> Reply-To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov>> Hi George, All, Some progress: The MacPorts folks fixed the problem with PDL so that a 'port selfupdate' will then allow PDL to build and then install. With that, Demeter then installs, though there are some warnings about missing dependencies (Heap, XMLRPC::Lite, File::Slurp::Tiny, Encoding::FixLatin::XS) which I'm guessing are relatively new dependencies, not included in the Portfile. I installed these missing perl modules using the 'perl -MCPAN -e shell' The basic Athena and Hephaestus and Artemis run OK, though I haven't done exhaustive testing. I did have to change the default gnuplot terminal from Qt to wxt for each of Athena and Artemis (I did not try plotting with Hephaestus). The settings page for Artemis is not easy to find -- it might be that the multiple-small-screen layout is difficult to map to the Mac window styling. As for Xorg vs XQuartz: The correct answer should be "neither". Neither Demeter nor gnuplot actually use X11 at all -- both are using wxWidgets, which does not use X11 on Mac. Similarly, I cannot understand the dependency on all of llvm, gcc4.9, and gcc5.2 from MacPorts. Most of the code even for MacPorts appears to be built with the *system* (ie, Apple-supplied) clang compiler. I can believe it "necessary" (well, really, "easiest") to build all of gcc to get gfortran, but not twice. And, yeah, if you have to install from source, it sort of matters. I do not know where to update the MacPorts Portfile. All links to the actual portfile scripts seem broken to me, but maybe they're available someplace. --Matt

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Demeter under El Capitan
by Fowler, Joseph W. 13 Nov '15

13 Nov '15

Bruce, Scott, Manuel: I’m the MacPorts maintainer for demeter and ifeffit, but I’m afraid I have not been much help lately. I’m sorry that I have not chimed in about any of the recent reports Mac / Macports problems under El Capitan. It so happens that my employer (US National Institute of Standards and Technology) does not let us upgrade to Yosemite OR El Capitan. They own the only Macs to which I have access, so I can only work under Mavericks. I’m afraid that artemis, hephaestus, and athena all start properly for me. To Manuel from Grenoble, all I can say is that xorg-server has a lot of dependencies, and it will take a long time to install the needed ports the first time. I would not think an entire hour is out of the question, depending on your connection speed and computer performance. To the others having trouble running (as opposed to installing), I wonder if anyone in the community is having success with the demeter suite under El Capitan? If so, we’d all be grateful if you could let us know what tricks were required. I am totally helpless on OS 10.10 and 10.11-specific problems. Joe Fowler NIST Boulder Laboratories

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Apparent bugs in Athena 0.9.24 running under Windows 7 64 bit
by Marcelo Eduardo Alves 13 Nov '15

13 Nov '15

I have run another example file (Au+Cyanobacteria) downloaded from https://github.com/bruceravel/XAS-Education in Athena 0.9.24 under Windows 7 64 bit using two different Dell computers and observed the following apparent bugs: In both computers the orange points that indicates the E0 and the limits of pre and post-edge fittings did not appear in the plots; In both computers the legends did not appear in all plots; the same for the axes's scales and titles. The LCF plot showed just the sample and the fitted normalized ones even when the standard ones were required; In one computer, there were just two choice options for the standards; in the other one these boxes worked normally and all standards could be considered. Some screenshots are attached to this message, Marcelo.

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Apparent bugs in Athena 0.9.24 under windows 7 64 bits - corrigendum
by Marcelo Eduardo Alves 13 Nov '15

13 Nov '15

Previous message: The LCF plot showed just the sample and the fitted normalized ones even when the standard ones were required Corrigendum: In fact, this is working in both computers, i.e., all plots appear in the graph; however, in one machine the legend, the axes´s scales, and the axes´s titles are not diplayed. M.

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Re: [Ifeffit] Problems with EXAFS Fitting of Metalloprotein Zinc Samples
by Carolyn Carr 12 Nov '15

12 Nov '15

Hi Bruce, Thanks so much for clarifying that for me! I have been basing my fitting in R-space off of XAFS spectroscopy; fundamental principles and data analysis DOI 10.1023/A:1019105310221 which has a section on fitting in R-space over k-space although it is very possible I misinterpreted its analysis. My zinc question is more of a query rather than a true problem, and so I am glad that you have taken time to correct my knowledge of how fitting works. Carolyn Carr

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LCF, Sayers & Bunker, R and ATHENA
by Florian Werner 12 Nov '15

12 Nov '15

Dear mailing list, we recently published a paper where we broke with the "Sayers & Bunker 1988 - Paradigm" to apply normalization as consistently as possible between samples and standards when performing linear combination fitting: http://pubs.acs.org/doi/abs/10.1021/acs.est.5b03096. There, we showed that for known mixtures of phosphorus standards the LCF of P K-edge XANES spectra delivers better results when changing the base-line and normalization parameters of the sample (in defined ranges, using the software /R/). I'm writing to the mailing list of several reasons: 1) A reviewer explicitly asked to contact Bruce Ravel so that the new insight could be implemented in ATHENA, 2) I was trying to combine my code with ATHENAs way of LCF before publishing the code. Unfortunately, I have not been able to resolve that a combination of both approaches results in large numbers of LCF procedures (sometimes Million or Billion). So many procedures are not fittable in reasonable time, maybe because my code is slow or maybe because /R/ isn't fast enough (or just the nlsLM-function that I'm using for LCF). I'm stuck and maybe programming in Perl would be a better choice (never programmed in Perl, yet)? Maybe a different kind of fitting algorithm would be faster?, 3) When using the nlsLM-function to perform LCF in /R/, I also have to provide portions of the standards before starting the fit. I used the same approach as ATHENA, dividing 1 by the number of standards so that every standard has the same portion. However, when playing with the code I realized that changing the starting portion can have an impact on the fitting result. Has this been observed or tested before by anyone else? How do you, in general, justify using the same starting portion for every standard? 4) Some minor question about LCF in ATHENA: a) Could the standards (the columns) in the output .csv-file after LCF be sorted alphabetically?, b) Does LCF in ATHENA sometimes produce negative numbers of a portion because the weight of any "last" standard in a set is always calculated by "1-sum(portions_of_other_standards)" (could it be this? https://github.com/bruceravel/demeter/blob/master/lib/Demeter/LCF.pm#L375-L…) To mimic "all samples sum to one" from ATHENA and to not produce negative portions, we used all LCF results which have a residual "absolute(1-sum(portions_of_all_standards)) < 0.0005"; maybe this is of interest also for ATHENA? Cheers, Florian

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Problems with EXAFS Fitting of Metalloprotein Zinc Samples
by Carolyn Carr 11 Nov '15

11 Nov '15

Hi, I have a general question rather than specific. I have only ever fit XAS data on metalloproteins and one feature that I see is that when fitting Zinc samples in R-space there is no local minima. For Cobalt and Nickel samples I typically get one or a few fits that are obviously significantly better in R-factor (with reasonable distances, sigma^2, etc) but for Zinc this is not the case. I can get many good fits and Zinc likes to increase the coordination up to 8 for all data sets I have ever fit, although there is obviously no physical basis in this. This is true of not just my own proteins but Zinc samples made by collaborators, and after looking through previous group members fit tables, they had similar issues. My understanding is that one of the benefits of fitting in R-space is that there is a local minima, whereas in k-space there are many minima. I was wondering if there was a physical basis for this feature in Zinc samples, or if perhaps my group is not aware of some experimental setup that we should be doing for Zinc that would resolve this problem. Thank you for any help regarding this matter, Carolyn Carr

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Problems with EXAFS Fitting of Metalloprotein Zinc Samples
by Carolyn Carr 10 Nov '15

10 Nov '15

Hi Robert, Thanks for your reply. We have done this with standard samples and we see the same thing. And of course, we can tell qualitatively from the XANES that our sample is not 8 coordinate, and not even 6 coordinate. We have never tried changing the temperature but we can try this the next time we go to SSRL. We actually do fit multiple scattering features as imidazoles which is one of the things we consider as a strength of Artemis for our basic needs. This is part of why we think this is strange, because putting 8 imidazoles around a zinc seems kind of silly but it likes it. 5 imidazoles and 3 sulfurs and I have an R-factor of 0.2% every time. If there is non standard multiple scattering that occurs in multiple unrelated proteins from different organisms then we would have no idea what this could be. Thanks for your comments! Carolyn Carr

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Re: [Ifeffit] Ifeffit Digest, Vol 153, Issue 12
by Marcelo Eduardo Alves 09 Nov '15

09 Nov '15

I have downloaded the zip-file containing the example files and extracted them into other subfolders (i.e. C:\Users\Marcelo\Documents\1.Athena Calibração e Alinhamento\Examples\Fe foil). I think that this was my error. When I use C:\Fe foil the file was opened in Athena without any issue. Thank you Robert and Guanghui 2015-11-09 16:24 GMT-02:00 <ifeffit-request(a)millenia.cars.aps.anl.gov>: > 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. Opening "older" data files in the latest Athena version > (Marcelo Eduardo Alves) > 2. Re: Opening "older" data files in the latest Athena version > (Robert Gordon) > 3. Re: Opening "older" data files in the latest Athena version > (Guanghui Zhang) > 4. Problems with EXAFS Fitting of Metalloprotein Zinc Samples > (Carolyn Carr) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 9 Nov 2015 15:41:33 -0200 > From: "Marcelo Eduardo Alves" <mealves.esalq(a)usp.br> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Opening "older" data files in the latest Athena > version > Message-ID: <97FB7D67CF2142A48FA29F9776D0A164@MarceloPC> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > > I am using the latest version of Demeter (0.9.24) and I have downloaded > the data files available at https://github.com/bruceravel/XAS-Education. > > However, I am not being able to open the example files in Athena (e.g., > Fe.060 of Fe foil folder). > > Please, would it be possible to open those example files in the latest > Athena version. > > Thank you. > > Marcelo. > > > _______________________________________ > Marcelo Eduardo Alves > Departamento de Ci?ncias Exatas - ESALQ/USP > Avenida P?dua Dias, 11 > 13418-900 Piracicaba-SP > Fone: 19-3429-4151- RAMAL 26 > Email: mealves.esalq(a)usp.br >

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Re: [Ifeffit] Ifeffit Digest, Vol 153, Issue 14
by Marcelo Eduardo Alves 09 Nov '15

09 Nov '15

Thanks a lot Robert! Marcelo. 2015-11-09 17:30 GMT-02:00 <ifeffit-request(a)millenia.cars.aps.anl.gov>: > 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: Ifeffit Digest, Vol 153, Issue 12 (Marcelo Eduardo Alves) > 2. Re: Ifeffit Digest, Vol 153, Issue 12 (Robert Gordon) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 9 Nov 2015 17:01:51 -0200 > From: Marcelo Eduardo Alves <mealves(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 153, Issue 12 > Message-ID: > < > CAAO6x+ZSKvPtdLYw1nvz-iPZec1+Hcin-my0mtJDKd27_8PRnw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > I have downloaded the zip-file containing the example files and extracted > them into other subfolders (i.e. C:\Users\Marcelo\Documents\1.Athena > Calibra??o e Alinhamento\Examples\Fe foil). > I think that this was my error. > When I use C:\Fe foil the file was opened in Athena without any issue. > Thank you Robert and Guanghui > > 2015-11-09 16:24 GMT-02:00 <ifeffit-request(a)millenia.cars.aps.anl.gov>: > > > 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. Opening "older" data files in the latest Athena version > > (Marcelo Eduardo Alves) > > 2. Re: Opening "older" data files in the latest Athena version > > (Robert Gordon) > > 3. Re: Opening "older" data files in the latest Athena version > > (Guanghui Zhang) > > 4. Problems with EXAFS Fitting of Metalloprotein Zinc Samples > > (Carolyn Carr) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 9 Nov 2015 15:41:33 -0200 > > From: "Marcelo Eduardo Alves" <mealves.esalq(a)usp.br> > > To: <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: [Ifeffit] Opening "older" data files in the latest Athena > > version > > Message-ID: <97FB7D67CF2142A48FA29F9776D0A164@MarceloPC> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear all, > > > > I am using the latest version of Demeter (0.9.24) and I have downloaded > > the data files available at https://github.com/bruceravel/XAS-Education. > > > > However, I am not being able to open the example files in Athena (e.g., > > Fe.060 of Fe foil folder). > > > > Please, would it be possible to open those example files in the latest > > Athena version. > > > > Thank you. > > > > Marcelo. > > > > > > _______________________________________ > > Marcelo Eduardo Alves > > Departamento de Ci?ncias Exatas - ESALQ/USP > > Avenida P?dua Dias, 11 > > 13418-900 Piracicaba-SP > > Fone: 19-3429-4151- RAMAL 26 > > Email: mealves.esalq(a)usp.br > >

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Re: [Ifeffit] Ifeffit Digest, Vol 153, Issue 11
by Marcelo Eduardo Alves 09 Nov '15

09 Nov '15

I have downloaded the zip-file containing the example files and extracted them into other subfolders (i.e. C:\Users\Marcelo\Documents\1.Athena Calibração e Alinhamento\Examples\Fe foil). When I use C:\Fe foil the file was opened in Athena without any issue. Thank you. 2015-11-09 15:55 GMT-02:00 <ifeffit-request(a)millenia.cars.aps.anl.gov>: > 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. Demeter under El Capitan (Fowler, Joseph W.) > 2. Re: Demeter under El Capitan (Zack Gainsforth) > 3. Opening "older" data files in the latest Athena version > (Marcelo Eduardo Alves) > 4. Re: Opening "older" data files in the latest Athena version > (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 9 Nov 2015 16:20:09 +0000 > From: "Fowler, Joseph W." <joe.fowler(a)nist.gov> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Demeter under El Capitan > Message-ID: <CAAD97E1-600B-43B3-B7AE-FAE9E373DC3E(a)nist.gov> > Content-Type: text/plain; charset="windows-1252" > > Bruce, Scott, Manuel: > > I?m the MacPorts maintainer for demeter and ifeffit, but I?m afraid I have > not been much help lately. > > I?m sorry that I have not chimed in about any of the recent reports Mac / > Macports problems under El Capitan. It so happens that my employer (US > National Institute of Standards and Technology) does not let us upgrade to > Yosemite OR El Capitan. They own the only Macs to which I have access, so I > can only work under Mavericks. I?m afraid that artemis, hephaestus, and > athena all start properly for me. > > To Manuel from Grenoble, all I can say is that xorg-server has a lot of > dependencies, and it will take a long time to install the needed ports the > first time. I would not think an entire hour is out of the question, > depending on your connection speed and computer performance. > > To the others having trouble running (as opposed to installing), I wonder > if anyone in the community is having success with the demeter suite under > El Capitan? If so, we?d all be grateful if you could let us know what > tricks were required. I am totally helpless on OS 10.10 and 10.11-specific > problems. > > Joe Fowler > NIST Boulder Laboratories > > >

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Re: [Ifeffit] Ifeffit Digest, Vol 153, Issue 9
by Matteo Busi 09 Nov '15

09 Nov '15

Dear Matt and Bruce, The problem is not with loading the files from the project, but instead to "load the loaded" files to the Data Summation. For example try to import all groups from the project of the example "Cu Metal" ( I will also attach it). Now go to data summation tab, in the components selection I'm able to select all groups except the first. (Shown in picture 1 attached). Now try to delete all groups and try to import groups from another project, let's say "Methylin" (attached). Now the groups avaiable for data summation work are still the previous ones (shown in picture 2). It seems that the data summation tab is not reading actively the groups loaded! I hope the situation it's clear now. Meanwhile I would also like to ask if there is a way to export the worked data ( for example, resulting from merges or sums) to new .dat files (in x-y coordinates). Regards, Matteo Busi 2015-11-06 19:00 GMT+01:00 <ifeffit-request(a)millenia.cars.aps.anl.gov>: > 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: Data Summation Bugs (Matt Newville) > 2. please remove me from the list (Jocelyn Koshinsky-Bissonnette) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 6 Nov 2015 07:53:37 -0600 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Data Summation Bugs > Message-ID: > <CA+7ESbo1MYOMO==BQ9g= > eVYC644iceLpsVvqNHudhQwCimPkvg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Matteo, > > It sounds like this issue is really about reading in data from saved > projects, not about summation of data. Is that correct or is there another > problem too? > > One of the main features of the Athena project files is that you can send > them in an email. Doing that would make it possible for someone to try to > reproduce and understand the problem you are having. > > Finally, not many of us have experience using Windows 10. Do you see the > same issue on other machines too? > > --Matt > > On Nov 6, 2015 5:39 AM, "Matteo Busi" <basebush(a)gmail.com> wrote: > > > > Hi, I'd like to report a few bugs I've encountered while using the Data > Summation of Athena. > > > > I've been working with multiple data sets and experienced some tecnical > difficulties. For example; when I'm importing multiple data from a project > saved beforem not all groups are selectable in the Components, and some > times even none of them are selectable. > > In the case I could see the groups imported selectable in the Components, > if I import new datasets as groups they will not be selectable as > Components, but the list will still be the first avaiable ( like it's > frozen) untill the reboot of the software. > > It's a pity because it's doing the rest of the job grandiosely. > > > > I'm running Athena from Windows 10. > > > > Regards, > > Matteo Busi, University of Stavanger, Norway > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >

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Opening "older" data files in the latest Athena version
by Marcelo Eduardo Alves 09 Nov '15

09 Nov '15

I have downloaded the worked examples available at https://github.com/bruceravel/XAS-Education However, I am not being able to open them in the latest Athena version (0.9.24) (e.g., Fe.060 of Fe foil folder). Could those files be opened in the last Athena version? Thank you. Marcelo.

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Opening "older" data files in the latest Athena version
by Marcelo Eduardo Alves 09 Nov '15

09 Nov '15

Dear all, I am using the latest version of Demeter (0.9.24) and I have downloaded the data files available at https://github.com/bruceravel/XAS-Education. However, I am not being able to open the example files in Athena (e.g., Fe.060 of Fe foil folder). Please, would it be possible to open those example files in the latest Athena version. Thank you. Marcelo. _______________________________________ Marcelo Eduardo Alves Departamento de Ciências Exatas - ESALQ/USP Avenida Pádua Dias, 11 13418-900 Piracicaba-SP Fone: 19-3429-4151- RAMAL 26 Email: mealves.esalq(a)usp.br

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Demeter installation on Mac El Capitan
by Muñoz Manuel 09 Nov '15

09 Nov '15

Dear Bruce, I try to instal Demeter on a Mac running El Capitan. I carefully followed the procedure (installation of Xcode and Macports), and I type the command: sudo port install xorg-server demeter in a terminal window. Unfortunately, after about 30 seconds, I am stuck with the following message: ---> Computing dependencies for xorg-server Would you have any suggestion? With my best regards, Manuel -- Manuel Muñoz Institut des Sciences de la Terre Université Joseph Fourier 1381 rue de la piscine – BP53 38041 Grenoble cedex 9 – France Tel.: 33 (0)4 76 51 40 54 – Fax: 33 (0)4 76 63 52 52

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