December 2013 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Launching Athena on Mountain Lion (Mac OS 10.8)
by Kyler Carroll 04 Dec '14

04 Dec '14

Hello, I had posted a comment/question a few months back when I had initially installed Mountain Lion on my mac regarding iXAFS compatibility with XQuartz and the new OS not supporting X11 anymore. Since then I have received a few comments back and I found one solution to be the best. This was originally sent by Tsu-Chien Weng from SSRL (tsuchien(a)slac.stanford.edu) Please find the following solution below. Once you install XQuartz the rest will be done in the Terminal.app. This is a one time solution and I havent had any trouble thus far with the program. Hope this works as well for everyone else as it did for me. 1. Install XQuartz from <http://xquartz.macosforge.org/landing/> 2. open Terminal.app 3. cd /Applications/Utilities 4. sudo mkdir X11.app 5. cd X11.app 6. sudo ln -s ../XQuartz.app/Contents Thank you, Kyler J. Carroll, Ph.D. Assistant Project Scientist Department of NanoEngineering University of California, San Diego

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Re: [Ifeffit] Athena deglitch problem
by Sathish Mayanna 16 Dec '13

16 Dec '13

*Dear Matt* > > > Now it seems working well except some minor things, I can remove the > points > > from the data, the random point selection by software works better for > > rebinned data. I think the only problem I have now is I still cannot move > > the cursor after double click (I can only remove the points which the > > software decides - at least now it choose the points where I double > click). > > When i move my mouse cursor on the plot, it shows the correct > coordinates. > > I'm still a bit confused about whether this actually working for you. > The data you sent has fairly large arrays (>2400 points), but all the > data was well-ordered in energy... I think that should "just work", > without needing re-binning. And it does for me, and I don't see how > re-binning would affect this. * If I don't rebin the data, Athena will not choose the point which I am intend to remove (I think i have some minor issues here). If I rebin the data from ~ 2400 to 350 points, Athena will work correctly.* > > I think it's always been the case that you double-click near the point > to be removed, and hope that Athena does select the one you intended. > *This works perfect for rebinned data. * > > > I have one clarifications, when u choose the option to deglitch the data > > (rebinned or non rebinned data), does the x(E) data plot looks like in > the > > attached file (line) or it looks like sets of blue round points same > size as > > cursor. > > For me, it looks very much like the image you attached. I do not see > a series of dots. > > > I think, the issue is solved except that I cannot move the randomly > chosen > > point. > > Why can't you remove the point chosen? That seems like it's not > working to me. Wasn't that the problem you were having? > *I mentioned "MOVE" in my above sentence, (Just to be more specific, when I double click on the plot to choose a point, sometimes Athena select its own random points away from the point where I clicked, when I try to drag that randomly chosen cursor to the point of my interest, it will not work), IS THIS NORMAL? * *I will try to figure out all the possible ways for non-rebinned data, if it does not work at least for now rebinned data works.* *Regards* *Sathish* > Again, it may be that I'm not understanding. Cheers, > > --Matt > > > ------------------------------ > > Message: 2 > Date: Mon, 16 Dec 2013 08:30:39 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Handling time resolved data > Message-ID: <52AF007F.4050600(a)bnl.gov> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 12/13/2013 09:00 AM, Ditty Dixon wrote: > > Dear Bruce, > > > > Recenetly we did some time resolved measurements, QEXAFS mode. While > > the old Athena arranged the file as we want i.e file 1, 2, 3 etc, the > > new did it bit different 1, 11 12 and again 2, 21 etc. Screenshot > > attached. Why is it doing diffrently for the two version? Can it be > > fixed some how. > > You haven't explained exactly where these data come from, so I am > assuming that each scan was written to its own file and these files were > imported into Athena. > > In Athena, data are imported in "ascii-betical" order, that is, sorted > in order of characters in the ASCII chart: > > http://en.wikipedia.org/wiki/ASCII#ASCII_printable_characters > > In that sense, Athena sorted your data as expected. As Chris pointed > out, if you want things like > > nr_1.spec > nr_2.spec > ... > nr_10.spec > > to sort numerically by the number between the _ and the .spec, you need > to format the them so that numerical and ascii-ordered sorting come out > the same. This is done as > > nr_01.spec > nr_02.spec > ... > nr_10.spec > > For a quick exafs experiment, two digits is probably not enough, so > you'd want something like > > nr_00001.spec > nr_00002.spec > ... > nr_00010.spec > > > I don't recall quite how the sorting worked in the old version of Athena > (it has been over 5 years since I stopped working on it), but my vague > memory is that, on Windows, they were imported in the order that they > were clicked upon the file selection dialog. The way it is currently > done is much better in that it is reproducible. > > > > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science 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 130, Issue 22 > **************************************** > -- Satty

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Handling time resolved data
by Ditty Dixon 16 Dec '13

16 Dec '13

Dear Bruce, Recenetly we did some time resolved measurements, QEXAFS mode. While the old Athena arranged the file as we want i.e file 1, 2, 3 etc, the new did it bit different 1, 11 12 and again 2, 21 etc. Screenshot attached. Why is it doing diffrently for the two version? Can it be fixed some how. Thank you, Ditty -- Ditty Dixon, Anorganische Chemie Karlsruhe Institute of Technology Kaiserstr 12 Karlsruhe, Germany Ph no: 004972160848093

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Re: [Ifeffit] Demeter deglitch problem
by Sathish Mayanna 15 Dec '13

15 Dec '13

Dear Matt and Bruce Thanks a lot for your help, I noticed your suggestions, regarding the deglitch problem, I installed the Demeter in another drive than in drive C. Now it seems working well except some minor things, I can remove the points from the data, the random point selection by software works better for rebinned data. I think the only problem I have now is I still cannot move the cursor after double click (I can only remove the points which the software decides - at least now it choose the points where I double click). When i move my mouse cursor on the plot, it shows the correct coordinates. I have one clarifications, when u choose the option to deglitch the data (rebinned or non rebinned data), does the x(E) data plot looks like in the attached file (line) or it looks like sets of blue round points same size as cursor. I think, the issue is solved except that I cannot move the randomly chosen point. Thanks a lot Sathish On Fri, Dec 13, 2013 at 5:10 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: Fwd: Re: Demeter deglitch problem (Matt Newville) > 2. Handling time resolved data (Ditty Dixon) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 12 Dec 2013 13:20:05 -0600 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov>, > Sathish Mayanna <satty334(a)gmail.com> > Subject: Re: [Ifeffit] Fwd: Re: Demeter deglitch problem > Message-ID: > <CA+7ESbpvTztp7Q8zTvShm8DO9yEjuo_2J6VuxtgnDWUNqk= > 1qQ(a)mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Sathish, Bruce, > > On Thu, Dec 12, 2013 at 12:51 PM, Bruce Ravel <bravel(a)bnl.gov> wrote: > > > > Sathish, > > > > I'm sorry, Sathish, but I simply don't see this behavior, on any of > > the computers I have tried. > > > > I have no trouble putting the cursor on the point in question. It can > > be a little tricky getting the cursor on, for example, one of the > > points from 6750 to 6770. That is because of the details of the > > algorithm that tries to find the actual data point that is closest to > > whatever point was clicked on. For a data point that is not a distant > > outlier, pretty good aim is required. > > > > That said, the two points near 6864 are distant outliers. Hitting one > > and not the other might be hard, but hitting one of them is easy. > > > > I am not disputing that you are having trouble. I am just saying that > > given the data you sent and the explanation you gave, I cannot > > reproduce the behavior, so I don't know what I can do to help. > > I made what I thought were two concrete suggestions / observations to > Satish, > a) I do not see k space data, and think you probably shouldn't either. > b) If you just move the mouse around on the plot window, > do you see the correct coordinates? > > I am sure Satish read Bruce's instructions on reporting bugs, but it > would have been polite if he had followed them. He did not answer the > questions designed to help diagnose the problem. He did not respond > not to the list, but directly to Bruce. In fact, he asked Bruce if > anyone else had seen the problem! > > Satish, it would be very much appreciated if this conversation > remained on the mailing list. If a problem happens for you, it is > possible that it will happen (or has happened) for someone else. > You'll get much better help and be helping others if you use the > mailing list. > > --Matt > > > ------------------------------ > > Message: 2 > Date: Fri, 13 Dec 2013 15:00:11 +0100 > From: Ditty Dixon <ditty.dixon(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Handling time resolved data > Message-ID: > <CABPBYUcg8DSWDnvdiK= > j9nfORORjG9n0RMYm4pVsaq6sYQYa3w(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear Bruce, > > Recenetly we did some time resolved measurements, QEXAFS mode. While the > old Athena arranged the file as we want i.e file 1, 2, 3 etc, the new did > it bit different 1, 11 12 and again 2, 21 etc. Screenshot attached. Why is > it doing diffrently for the two version? Can it be fixed some how. > > Thank you, > > Ditty > > > > -- > Ditty Dixon, > Anorganische Chemie > Karlsruhe Institute of Technology > Kaiserstr 12 > Karlsruhe, Germany > Ph no: 004972160848093 >

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Fwd: Re: Demeter deglitch problem
by Bruce Ravel 12 Dec '13

12 Dec '13

Sathish, I'm sorry, Sathish, but I simply don't see this behavior, on any of the computers I have tried. I have no trouble putting the cursor on the point in question. It can be a little tricky getting the cursor on, for example, one of the points from 6750 to 6770. That is because of the details of the algorithm that tries to find the actual data point that is closest to whatever point was clicked on. For a data point that is not a distant outlier, pretty good aim is required. That said, the two points near 6864 are distant outliers. Hitting one and not the other might be hard, but hitting one of them is easy. I am not disputing that you are having trouble. I am just saying that given the data you sent and the explanation you gave, I cannot reproduce the behavior, so I don't know what I can do to help. B -------- Original Message -------- Subject: Re: Demeter deglitch problem Date: Wed, 11 Dec 2013 14:59:09 +0100 From: Sathish Mayanna <satty334(a)gmail.com> To: Bruce Ravel <bravel(a)bnl.gov> Dear Bruce Thanks a lot for your time. I am sorry, I am a beginner in the field of XAS, thus was confused. Please find the attachment of one of my glitch data and an image showing the randomly chosen point at 6705 eV by software even though i double clicked at 6864 eV and in addition, I cannot move the position of randomly chosen point. I have tried both in my windows laptop and PC, it does not work in both cases. I hope this time I have provided the details you expected? Thanks Sathish On Tue, Dec 10, 2013 at 8:13 PM, Bruce Ravel <bravel(a)bnl.gov <mailto:bravel@bnl.gov>> wrote: On 12/10/2013 12:58 PM, Sathish Mayanna wrote: Dear Bruce I am sorry to contact you here, I watched your whole XAS workshop 2011 at Diamond, it was very helpful. Regarding the problem, I could not understand your message, I read the link to reports bug, I understand you cannot reproduce my problem also, I just wanted to know, if anybody had same problem like me and have any solutions. I am just wondering, does your message also means that I should send the rawdata or print screen? -- Sathish Look, I'm happy to help, but you have to give me something to work with. Obviously, I think deglitching works, otherwise I would have said something different. If you cannot give me some way of reproducing what you see on one my own computers, there is no way that I can help you. I'm not asking for a differently detailed explanation, I am asking for data and a recipe that reproduces the problem. Without that, what could I possibly do to help? B -- Bruce Ravel ------------------------------__------ bravel(a)bnl.gov <mailto:bravel@bnl.gov> National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel -- Satty

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error in ATOMS
by Julius Campecino 12 Dec '13

12 Dec '13

Hi Bruce, Here's the screen shot of my work in ATOMS. It's supposed to be more than 7 atoms in the core column but that's also one thing I do not know how to add change and add more atoms. When I click "Run Atoms", it gives me this error "Can't call method "tag" on an undefined value at C:/strawberry/perl/site/lib/Demeter/Atoms.pm line 668.'' I am using the recent version 0.9.18.2 of the Demeter installer. Thank you for your help! Julius

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Re: [Ifeffit] athena error message.....
by Bruce Ravel 10 Dec '13

10 Dec '13

On 11/30/2013 05:17 PM, William Nash wrote: > Heya Bruce, > > I'm trying to use Athena to process some XANES data from the Diamond > Synchrotron (UK). I went to the demeter webpage and downloaded/ran the > installer and the updater. However, when I try to run athena, I get an > error message: > > (Window Title: "perl.exe - Entry Point Not Found") > > The procedure entry point __gxx_personality_v0 could not be located in > the dynamic link library libstdc++-6.dll. > > Is this an error you are familiar with? I don't seem to be able to get > around it. It time permits, would you mind giving me some guidance. > > Grateful thanks, > William > First off, please use the Ifeffit mailing list http://cars9.uchicago.edu/mailman/listinfo/ifeffit/ which is the proper place to ask questions about and report problems with the software. As you can see, I have CCed my response to you and to the mailing list. Please continue correspondence on this topic via the mailing list. The most likely source of this problem is the one discussed here http://cars9.uchicago.edu/ifeffit/Demeter/MingwFix that is, that you have another version of MinGW installed on your computer, either that you yourself installed or that was installed by another application. This fellow, for example, had installed GnuPG and this triggered a similar conflict to what you see. http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04031.html Another possible problem is that you have another version of perl itself installed on you computer, again possibly as part of the installation of another package. HTH B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science 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] Ifeffit Digest, Vol 130, Issue 13
by Sathish Mayanna 10 Dec '13

10 Dec '13

Dear Matt and Bruce Thanks, I thought its a common problem, i will be more specific in this message. I am using windows 7, 64 bits and/or 32 bits Operating System, installed with updating 0.9.18.2 Demeter, its in the folder C:\strawberry. To deglitch the single point of EXAFS data using Athena, after CHOOSE A POINT option, when I double click on the plot of k space, it does choose a point randomly and I can remove that particular point, but unfortunately, I cannot move or select the point which I want to remove. It always choose a random point by its own. Do I miss something here ? Regards Sathish On Mon, Dec 9, 2013 at 8:49 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. Athena 0.9.18.2 deglitch option (Sathish Mayanna) > 2. Re: Athena 0.9.18.2 deglitch option (Bruce Ravel) > 3. Re: Athena 0.9.18.2 deglitch option (Matt Newville) > 4. Re: Itinerant vs localized XAFS (Latta, Drew E.) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 9 Dec 2013 19:24:33 +0100 > From: Sathish Mayanna <satty334(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Athena 0.9.18.2 deglitch option > Message-ID: > <CABVfawmnabGT= > S+iEwy-1bv0f6jSLRQc9gga+hSg0KjmaE5Cdg(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all > > I wondering, if anyone has problem with the option deglitch in Athena > especially for 32 or 64 bits Windows system? > > Would be really great, if anyone could help me to solve the problem, I have > a EXAFS data with huge glitch and the software do not choose/remove the > points and sometimes it crashes. > > Regards > Sathish >

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Artemis path like function crashing
by stephen.price＠diamond.ac.uk 10 Dec '13

10 Dec '13

Hi, I'm writing to report a crash of the path like function of Artemis, version 0.9.18 on Windows 7, 64 bit (the same thing also happened on my old windows XP machine). I have followed the procedure below several times on both machines and get the same result: · Load processed data from Athena of Pt nanoparticle, load and run Pt.inp in ATOMS (from atomsdb), run FEFF - click on path like tab · Make histograms from molecular dynamics time sequence - in this case from DL_POLY · Load HISTORY file from molecular dynamics - specify Rmin (e.g. 2.4 Å) Rmax (3.0) and bin size (0.005) · Plot RDF - in this case it loads in 503 time steps in increments of 10 and plots RDF after about 1 minute · I click on "Drag SS path from here" and drag to the path list - the message "making Fpaths n of 66" appears at the bottom of the window · As it is rebinning the last Fpath Artemis crashes with the log error "Can't locate object method "pathfinder_index" via package "Demeter::FPath" at C:/strawberry/perl/site/lib/Demeter/UI/Artemis/Path.pm line 254, <F> line 9" (dartemis.log attachment) · The final line mentioned in the dartemis.log sometimes varies e.g. <F> line 133 or <F> line 177 · This crash is independent of the Athena project, simulation HISTORY file (whether a 10 MB or a 100 MB file), choice of Rmin/max and bin size I can run a simple first/multi shell fit on the Pt nanoparticle, save and reopen the project (Pt test.fpj) but cannot save and reopen a project during any stage of the path like process as this crashes Artemis ("create RDF dartemis.log" and "Pt create RDF.fpj" attachments). I haven't attached a sample MD simulation file here as I don't want to fill everyone's inbox! Any help would be appreciated. Thank you, Steve Dr Stephen Price PDRA Beamline I18 Diamond Light Source -- 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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Itinerant vs localized XAFS
by Maurits Boeije 09 Dec '13

09 Dec '13

Dear XAFS specialists, We've performed an experiment at the ESRF in Grenoble to find experimental evidence of an electronic change in our system. We suspect, from ab initio calculations, that there is a change in how electrons are allocated in our Mn/Fe system. Calculations show that some electrons change from being itinerant at high temperatures, to being localized at low temperatures. We performed an XAFS experiment and hope to see a difference between the low and high temperatures measurements. There is always difference because the cell parameters change as function of temperature, and I used your Artemis program to investigate the influence of the cell parameters on the EXAFS signal. I can get a decent fit using the crystallographic data we have, but I'm not sure if I'm not throwing away any evidence of our electronic change. I can interpret a fitted interatomic distance of 2.1 A (compared to 2.0 A we got from diffraction) as being the mean interatomic distance in our sample, but I could also interpret it as a 0.1 A difference because of our suspected electronic change. The challenge now lies in seeing an electronic difference despite the crystallographic change. What we would ideally do, is to keep the (known) atomic positions and cell parameters fixed, fit the EXAFS parameters and see if we can predict either the high or low temperature spectrum. Do you think this is possible? Are there any parameters which are calculated by IFEFFIT who are not precise enough for such a conclusion? It could be that the effect we are looking for is so small that they are nullified by the assumptions in the EXAFS equation. I would appreciate any insight you could have in this particular problem. With kind regards, Drs. MFJ Boeije Fundamental Aspects of Materials and Energy TU Delft T +31 (0)15 27 83793 No trees were killed to send this message, but a large number of electrons were terribly inconvenienced

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