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

New Demeter Win7 install (?) problems
by Latta, Drew E. 23 Apr '12

23 Apr '12

Bruce: I am having issues with getting the new Demeter release for Windows to work on my Win7 machine. The install program runs just fine and drops shortcuts to Artemis, Athena, Atoms, and Hephaestus on my desktop. However, when I click on the shortcuts to run these programs I get a very quick flash of a command line window saying something to the effect of: "The system cannot find the path specified." The shortcuts on the desktop point to, for example: "C:\demeter\perl\site\bin\dathena.bat" and there are batch files in the specified location with what appears to be useful text in them. Note that I get the same issue if I un-install and re-install to the default C:\strawberry directory. Running the batch files from their actual directory does the same thing, suggesting to me that the problem lies somewhere deeper than I have the wherewithal to de-bug. Did I miss a crucial step somewhere? Cheers, Drew Latta ----------------------------------- Drew E. Latta, Ph.D. Postdoctoral Associate Molecular Environmental Science Group Biosciences Division Argonne National Laboratory Building 203, Room E-105 9700 South Cass Avenue Argonne, IL 60439 Phone: 1-630-252-3985 dlatta(a)anl.gov<mailto:dlatta@anl.gov> http://www.mesg.anl.gov -----------------------------------

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Demeter
by Vanamee, Eva 23 Apr '12

23 Apr '12

Bruce, Demeter is a wonderful program and the GUI is beautiful! I am old enough to remember the time when we were doing things by commands. I am also rusty and have not done EXAFS in years. Is there an easy way to convert a PDB file into a feff.inp file? I am working on a protein with a [4Fe-4S] cluster. I have generated a PDB file with just the iron-sulfur cluster in it. File attached. I am having a hard time with ATOMS, even when I use a single Fe atom placed at the origin. Thanks, - Eva

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Re: [Ifeffit] Path problem in IFEFFIT
by Bruce Ravel 23 Apr '12

23 Apr '12

On Saturday, April 21, 2012 02:20:17 pm you wrote: > Dear Bruce, > > Attached is the file whcih gives me the Path problem (I posted on the > mailing list), I try to fot the br K edge for the AuBr4- complex. I also > have fitted the Au edge which worsk fine by then adding the Br edge > data, the problem start occuring, so I tried to putr it on its own.... > I might just miss something really easy, but I can t find it. > Hope you can help and thank you for your effort! Yvonne, There are a number of problems with your project file. Setting aside the inherent difficulty in measuring the Br K edge of a gold-bromine complex (the Au L2 edge is only 8.2 inverse Angstroms above the Br K edge), you have made a few mistakes in your feff input data. First, it would seem that you started from a feff.inp file you prepared for use with Feff8 or Feff9. The "XANES" keyword makes Feff6 (the version bundled with Ifeffit and Demeter) unhappy. I believe this is the proximate cause of the error message you initially reported last week. Unfortunately, Artemis does not provide a useful warning that Feff stopped without running properly to completion when it encountered the "XANES" keyword. That needs to be fixed. Thanks for bringing that to my attention. Second, you had an RMAX value in the Feff input data of 80. That's not a problem per se, but it does make Artemis issue a warning message since it's an oddly large value. Third, it seems that you started with Feff input data for the Au L3 edge then edited it to make one of the Br atoms the absorber. You did this 75% correctly. You did the right thing with the potentials list and the ipot values, but you forgot to change the HOLE value from 4 to 1. 4 is the value for the L3 edge, 1 is the value for the K edge. That is a common mistake -- indeed one that I make regularly -- that has come up on the list in the past. It tends to result in large E0 values since the phase of scattering an L3 photoelectron is so different from the K. In the end, I couldn't make much out of your fit, however. The data range is so limited that you have very little information to work with. And I suspect that the presence of the L2 edge is dominating the determination of the background function. I bet that the peak at 1 Angstrom is a background removal artifact. It is hard for me to believe that a gold scatterer at almost 2.5 Ang would make a peak at only 1 Ang in the Fourier transform. You might try restricting the range of the spline in Athena to something that does not include any of the Au L2 edge step. Even so, I am not so optimistic about being able to interpret these data. (Although, as part of multiple data set fit they may prove useful....) In any case, by making those fixes to the feff input data and re-clicking the run Feff button, I was able to make the program behave correctly. 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 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter

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first "official" relezse of my new software
by Bruce Ravel 22 Apr '12

22 Apr '12

Hi everyone, Today I am announcing my first official release of my latest version of my XAS data processing and analysis software. The package is called Demeter, the version number is 0.9.9, and it includes new versions of Athena, Artemis, and Hephaestus. In many ways, these are much like the versions of the software that have been in use for almost a decade. In many ways, however, they offer important improvements, including better plotting, prettier GUIs, and lots of new analysis features. For those using Windows, you can download the installer package from https://github.com/bruceravel/demeter/downloads For those using Linux, installation instructions can be found at http://bruceravel.github.com/demeter/pods/installation.pod.html I am hoping that installer packages for the Mac and for specific Linux distributions will become available in the coming months. The Demeter versions of the programs can coexist on a computer with the old versions. New Athena and old Athena peacefully coexist, indeed, they use the same project file format. The project file format for new Artemis is different, however new Artemis can import project files from old Artemis. I am no longer developing the old versions. I will no longer fix bugs or add new features to the old versions. All of my future develop efforts will be devoted to the new versions. Here are some useful links: Demeter's github page: https://github.com/bruceravel/demeter Demeter documentation: http://bruceravel.github.com/demeter/ Reporting bugs: http://bruceravel.github.com/demeter/pods/bugs.pod.html Artemis instruction videos: http://vimeo.com/channels/exafs It has been a joy to develop and support my software over the years. My interactions with the kind, engaged people in the community of Ifeffit users have been among the high points of my career. I hope that you enjoy my new software as much as I enjoyed writing it. Regards, Bruce -- 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 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter

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Re: [Ifeffit] first "official" relezse of my new software
by Enyuan Hu 21 Apr '12

21 Apr '12

So grateful for Bruce's efforts. Your generosity is one of the great joys of doing XAS. best, Enyuan

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Column label issue
by Vanamee, Eva 20 Apr '12

20 Apr '12

Hi Bruce, Somehow my earlier email bounced. I did try Erik's suggestion and renamed the columns with shorter names. It all works fine now after giving short Ch1, Ch2,... names for the columns. I am onto ARTEMIS and new issues. more soon.... On Apr 20, 2012, at 1:00 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: data processing - not all columns are visible (Bruce Ravel) > 2. Path file does not exist (Yvonne Grunder) > 3. Re: Path file does not exist (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 19 Apr 2012 17:51:49 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] data processing - not all columns are visible > Message-ID: <201204191751.49649.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-1" > > > Eva, > > It's been a busy week -- sorry for the pokey response. > > Erik is correct on all fronts -- the problem is the length of the line > of column labels. > > One rather irksome work-around I can suggest is to remove that line > with a text editor. > > The better work-around Erik alludes to is part of the newest version > of my software. However, I do not yet have a Mac installer for the > new version. > > B > > > On Tuesday, April 17, 2012 10:20:30 pm Erik Farquhar wrote: >> Hi Eva, >> >> It is also a good idea to mention that you are using OS X (as you told me). >> Are you using the iXAFS versions of Athena/Artemis? If so, which version >> #? >> >> To elaborate on Eva's e-mail, she collected data on NSLS X3B using a 31 >> element Ge detector. Datafiles are in the normal ASCII NSLS XDAC file >> format, with the individual Ge channel labeled as long strings XIA01FeK >> ... XIA31FeK. To date we've had no issues w/ these files using "classic >> Horae Athena/Artemis" on Windows machines. With Demeter on Windows, I did >> see the same problem as Eva, with the data file column selector dialog >> only displaying the first 25 columns or so. Bruce came up with a >> workaround at an early beta stage, so that long column name strings no >> longer cause the column selector dialog to puke. As I recall from Bruce's >> explanation, it had to do with IFEFFIT being unhappy with the long column >> labels, although evidently something in the code for the older programs >> overcame this limitation. >> >> If I had to guess, the OS X versions of "classic" Athena/Artemis are >> running into this issue with IFEFFIT disliking the long column labels. I >> don't have an OS X machine to test this, hence Eva's appeal to the wider >> IFEFFIT community. >> >> Cheers, >> Erik >> >> -- >> Erik Farquhar >> Case Center for Synchrotron Biosciences >> Brookhaven National Lab >> NSLS, Building 725A-X3 >> Upton, NY 11973 >> efarquhar(a)bnl.gov >> +1-631-344-8174 >> >> ________________________________ >> From: Bruce Ravel <bravel(a)bnl.gov> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Sent: Tuesday, April 17, 2012 5:55 PM >> Subject: Re: [Ifeffit] data processing - not all columns are visible >> >> On Tuesday, April 17, 2012 04:53:08 pm Vanamee, Eva wrote: >>> Greetings, >>> >>> I am using Artemis to read my data from a 31 channel detector. Only 25 of >>> them are shown in the column chooser. How can I make all columns show? >> >> Eva, >> >> Can we see an example data file? >> >> 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 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter > > > ------------------------------ > > Message: 2 > Date: Fri, 20 Apr 2012 12:59:48 +0100 > From: Yvonne Grunder <yvonne.grunder(a)manchester.ac.uk> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Path file does not exist > Message-ID: <4F914FB4.5080604(a)manchester.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Hallo, > > I have currently a problem with Artemis to fit my data. First, I import > the paths from the Feff calculation and define my fitting parameters. > Then I can run the fit exactly one time. If I try to fit the data a > second time, I get the following error message: > PATH: Au ( 9999 1 2.470 ---- @ Au > @ 2 2 single scattering) > The path file does not exist (perhaps the Feff > calculation was not run). > (and similar for all paths included...). > > Did anybody encounter a similar problem (I already reinstalled Demeter)? > > Best wishes, > Yvonne > > -- > Dr Yvonne Grunder > Chemistry Building - 6.09 > School of Chemistry > The University of Manchester > Manchester > M13 9PL > Tel.: +44 (0)161 306 4568 > > > > ------------------------------ > > Message: 3 > Date: Fri, 20 Apr 2012 08:25:03 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Path file does not exist > Message-ID: <201204200825.04031.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-1" > > > Yvonne, > > This is the sort of thing I cannot comment on without being able to > reproduce it on my own computer. Can you send me the project file > that demonstrates this problem? > > B > > > On Friday, April 20, 2012 07:59:48 am Yvonne Grunder wrote: >> Hallo, >> >> I have currently a problem with Artemis to fit my data. First, I import >> the paths from the Feff calculation and define my fitting parameters. >> Then I can run the fit exactly one time. If I try to fit the data a >> second time, I get the following error message: >> PATH: Au ( 9999 1 2.470 ---- @ Au >> @ 2 2 single scattering) >> The path file does not exist (perhaps the Feff >> calculation was not run). >> (and similar for all paths included...). >> >> Did anybody encounter a similar problem (I already reinstalled Demeter)? >> >> Best wishes, >> Yvonne > > -- > > 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 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/ifeffit/Demeter > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 110, Issue 16 > ****************************************

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Path file does not exist
by Yvonne Grunder 20 Apr '12

20 Apr '12

Hallo, I have currently a problem with Artemis to fit my data. First, I import the paths from the Feff calculation and define my fitting parameters. Then I can run the fit exactly one time. If I try to fit the data a second time, I get the following error message: PATH: Au ( 9999 1 2.470 ---- @ Au @ 2 2 single scattering) The path file does not exist (perhaps the Feff calculation was not run). (and similar for all paths included...). Did anybody encounter a similar problem (I already reinstalled Demeter)? Best wishes, Yvonne -- Dr Yvonne Grunder Chemistry Building - 6.09 School of Chemistry The University of Manchester Manchester M13 9PL Tel.: +44 (0)161 306 4568

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data processing - not all columns are visible
by Vanamee, Eva 19 Apr '12

19 Apr '12

Greetings, I am using Artemis to read my data from a 31 channel detector. Only 25 of them are shown in the column chooser. How can I make all columns show? Thanks in advance! - Eva

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data processing - colum issues
by Vanamee, Eva 18 Apr '12

18 Apr '12

Bruce, Attached is a data file. Erik, thanks for the helpful additional info. Yes, I am using Mac OS X and iXAFS3.0.3. I will shorten column names and will report on the result. Thanks, - Eva

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Re: [Ifeffit] Large XAFS data sets
by Jan Stötzel 16 Apr '12

16 Apr '12

Hi Matt, I solved it this way: In my code only the 1-5 reference component spectra for the LCF are permanently imported in IFEFFIT and one variable is reserved for all the spectra that I want to have fitted, which is done consecutively then. Each time a spectrum is fitted, the results are exported into arrays of my software and send to the plot pane. After that everything except the reference component spectra is resetted in IFEFFIT and the fitted spectrum is overwritten by the next one. Going that way IFEFFIT memory is never exceeded, neither when fitting 3000 spectra nor in principal with 3*10^6 spectra (although that would take more than a week I guess). Of course you need some time to code it but it works quite well. Nevertheless, a new IFEFFIT with faster fit routines would be most welcome of course :). Regards, Jan Zitat von Matt Newville <newville(a)cars.uchicago.edu>: > Hi Edmund, Jan, Matthew, > > On Thu, Apr 12, 2012 at 8:51 AM, Jan Stötzel > <j.stoetzel(a)uni-wuppertal.de> wrote: >> Hi Edmund, >> >> in my opinion evaluating 3000 spectra is neither a heroic attempt nor brute >> force. The LCF of 3000 spectra yields one beautiful plot with 3000 * >> components points, where the information of an enormous Gbyte data set is >> included - for me that is indeed very economical. With such a plot each >> reader can decide (or be convinced) which spectra are "boring" and if you >> want to study high order kinetics during your reaction you will be happy to >> have enough points to perform the required fits. Of course, one can also >> write a program that preselects a few spectra by evaluating the differences >> between the spectra. But then I guess you need at least one (avoidable) >> parameter to adjust the tolerance to distinguish between differences caused >> by noise and those due to real variations in sample composition. >> >> That´s why I´d prefer fitting all spectra and afterwards highlighting the >> interesting parts. That might take 2-3 hours for a few thosand spectra >> (extended lunch break) but it is still much more convenient than finding the >> "interesting" spectra manually by going through all spectra (or than finding >> the most suitable tolerance parameter). And the resulting plots are worth >> the time imo. I am rather going to check how much faster I can get by >> parallelizing the processes for multicores... >> >> Best regards, >> >> Jan Stötzel >> >> >> >> Zitat von Edmund Welter <edmund.welter(a)desy.de>: >> >>> Dear XAFS users >>> >>> recently I read several mails on this list which were dealing with the >>> problem of large data sets, as they are produced by Q-EXAFS scans or by >>> dispersive XAFS. The question was if there are tools available to handle >>> data sets of several 1000 spectra and perform a linear combination fit >>> or even a full EXAFS evaluation on each of them. Evaluating 3000 spectra >>> is a heroic attempt, but I wonder if it is also economical. >>> >>> >>> In most (that means not in ALL!) cases, the vast majority of these >>> spectra is boring, because the spectrum with the number X looks exactly >>> like the spectrum with the number X-1 looked and how the spectrum with >>> the number X+1 will look and so on. Evaluating all these (basically >>> identical) spectra is in principle a waste of time and working memory. >>> The interesting spectra are those which were measured when something was >>> happening in the sample. Since we do not always know at which time, or >>> temperature or reactant concentration etc. interesting things will >>> happen it is without any doubt justified to measure x-thousand spectra, >>> but after that we should use a more sophisticated approach than brute >>> force. >>> >>> I think that it would be much more useful to find procedures (that means >>> develop computer programs) that search for the (usually relatively small >>> number of) interesting spectra. The most obvious parameter is how >>> similar is a particular spectrum to the spectra measured before and >>> after. The next step would probably be to identify clusters of related >>> spectra using statistical methods. This is a problem which had to be >>> solved in other areas like the automated analysis of images before and >>> should also be possible with our kind of data. >>> >>> >>> Anyway, how to handle thousands of XAFS spectra will become a very >>> important problem in the future. With all these beamlines that provide >>> 10^12 photons per second we can measure a factor 100 -- 1000 faster than >>> >>> we did with 10^9 photons per second. So, I wonder if anything beyond the >>> brute force approach is going on in the EXAFS software universe to make >>> effective and economical use of the measured data. >>> >>> 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 >>> -------------------------------------------------------- > > > Sorry for the delay, but I just wanted to add my agreement to this > need to be able to work with larger data sets. Handling ~3000 XANES > spectra for linear analysis is definitely something that we need to be > able to do well, and it is not something that Ifeffit can do really at > all. This is a definite weakness. For reference, 3000 EXAFS spectra > can fit in well under 500 Mb of memory, and there really should be no > problem handling this amount of data as a multi-dimensional array in > memory on any modern machine -- in fact, expecting an order of > magnitude larger is not really that absurd. The main problem is > simply that the tools we have are not built with this is mind, and the > hardware + data collection have outpaced analysis software. > > I believe the Ifeffit2 approach will be much better suited for > handling such large datasets, and can easily use any of the linear > analysis tools from scipy (http://scipy.org/) If you or anyone else > has some suggested algorithms to include (PCA, non-negative > least-squares, etc), that would be very helpful. > > --Matt > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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