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

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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difference spectra function in (D)Athena
by Christopher Patridge 12 Apr '12

12 Apr '12

Hello Mailing List, I have a question about the difference spectrum function. I chose difference spectrum in norm mu(E) in the Demeter pull down menu. I set the standard and chose another spectrum. Plotting both the difference and spectra gives me the image attached. Is the difference shifted significantly to lower energy? If so, why does it change its energy scale relative to the plotted spectra? Is there a setting I can change or could this be a small bug? Thank you all, buena salud, Chris Patridge -- Christopher J. Patridge PhD. Contact: (315)-529-0501

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Re: [Ifeffit] Theoretical value of S02 for different absorber
by Rana, Jatinkumar Kantilal 05 Apr '12

05 Apr '12

Dear Dr. Newville, Thank you so much for your reply. Things are very much clear now. With best regards, Jatin ________________________________________ 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: Thursday, April 05, 2012 7:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 110, Issue 6 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: Theoretical value of S02 for different absorber (Rana, Jatinkumar Kantilal) 2. Results Reporting (John Farell) 3. Re: Results Reporting (Bruce Ravel) 4. Re: Theoretical value of S02 for different absorber (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Thu, 5 Apr 2012 10:44:05 +0000 From: "Rana, Jatinkumar Kantilal" <jatinkumar.rana(a)helmholtz-berlin.de> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Theoretical value of S02 for different absorber Message-ID: <6FCB59A6A97E13429B863B7014B57E4B10E2E8@didag1> Content-Type: text/plain; charset="utf-8" Dear Dr. Ravel, Thank you very much for your prompt reply. I followed the instruction on (http://leonardo.phys.washington.edu/feff/wiki/index.php?title=EXAFS_calcula…) and activated S02 card by making S02 0.0 in feff.inp file. As a result, FEFF calculated S02. However, I get confused when I compare FEFF calculated S02 with reported value in literature and the one obtained from my own fit. For example, S02 for Mn absorber FEFF calculated 0.94 Fitted value for my sample ~0.75 Fitted value for various Mn-oxides ~0.75 Other reported value from Mn fit ~0.70-0.80 (http://www.sciencedirect.com/science/article/pii/S0020169397057496) S02 for Fe absorber FEFF calculated ~0.94 Fitted value for Fe-foil ~0.70 Fitted value for various Fe-oxides ~0.70 Reported value by calculation 0.69 (http://prola.aps.org/abstract/PR/v169/i1/p27_1) It is well known that S02 is a property of central absorbing atom and is considered to be constant between 0.7 - 1.0. However, in real world, S02 is affected by various systematic errors like thicker samples (in transmission), absorption by other elements in sample at given energy range and many more. These factors can suppress the amplitudes of EXAFS oscillations resulting in lower value of fitted S02 than it should be for a given absorber. The reason I am so much curious about S02 is, if I know what should be (or should be considered) the value of S02 for a given absorber than I can possibly understand the reasons of fitted S02 being too low or too high. For instance, S02 and Sigma2 are highly correlated for first shell. So from fitted value of S02 and Sigma2 of first shell, I could possibly understand changes in local structure. So I would like to put forward very simple but still confusing question that which value of S02 should be considered, FEFF calculated or the one obtained by fitting standards (either reference foils or reference compounds measured on same beamline) and why. Many thanks in advance !!! With best regards, Jatin -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Mittwoch, 4. April 2012 19:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 110, Issue 5 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. Theoretical value of S02 for different absorber (Jatin Rana) 2. Re: Theoretical value of S02 for different absorber (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Wed, 4 Apr 2012 17:45:13 +0800 (SGT) From: Jatin Rana <jatin_rana2002(a)yahoo.com> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Theoretical value of S02 for different absorber Message-ID: <1333532713.14873.YahooMailNeo(a)web193501.mail.sg3.yahoo.com> Content-Type: text/plain; charset="utf-8" Dear Ifeffit users, Can anyone recommend a reference where I can get calculated value of S02 for various elements ? I would like to compare them with my fitted values. Many thanks in advance !! With best regards, Jatin Rana

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Re: [Ifeffit] Theoretical value of S02 for different absorber
by Rana, Jatinkumar Kantilal 05 Apr '12

05 Apr '12

Dear Dr. Ravel, Thank you very much for your prompt reply. I followed the instruction on (http://leonardo.phys.washington.edu/feff/wiki/index.php?title=EXAFS_calcula…) and activated S02 card by making S02 0.0 in feff.inp file. As a result, FEFF calculated S02. However, I get confused when I compare FEFF calculated S02 with reported value in literature and the one obtained from my own fit. For example, S02 for Mn absorber FEFF calculated 0.94 Fitted value for my sample ~0.75 Fitted value for various Mn-oxides ~0.75 Other reported value from Mn fit ~0.70-0.80 (http://www.sciencedirect.com/science/article/pii/S0020169397057496) S02 for Fe absorber FEFF calculated ~0.94 Fitted value for Fe-foil ~0.70 Fitted value for various Fe-oxides ~0.70 Reported value by calculation 0.69 (http://prola.aps.org/abstract/PR/v169/i1/p27_1) It is well known that S02 is a property of central absorbing atom and is considered to be constant between 0.7 - 1.0. However, in real world, S02 is affected by various systematic errors like thicker samples (in transmission), absorption by other elements in sample at given energy range and many more. These factors can suppress the amplitudes of EXAFS oscillations resulting in lower value of fitted S02 than it should be for a given absorber. The reason I am so much curious about S02 is, if I know what should be (or should be considered) the value of S02 for a given absorber than I can possibly understand the reasons of fitted S02 being too low or too high. For instance, S02 and Sigma2 are highly correlated for first shell. So from fitted value of S02 and Sigma2 of first shell, I could possibly understand changes in local structure. So I would like to put forward very simple but still confusing question that which value of S02 should be considered, FEFF calculated or the one obtained by fitting standards (either reference foils or reference compounds measured on same beamline) and why. Many thanks in advance !!! With best regards, Jatin -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Mittwoch, 4. April 2012 19:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 110, Issue 5 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. Theoretical value of S02 for different absorber (Jatin Rana) 2. Re: Theoretical value of S02 for different absorber (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Wed, 4 Apr 2012 17:45:13 +0800 (SGT) From: Jatin Rana <jatin_rana2002(a)yahoo.com> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Theoretical value of S02 for different absorber Message-ID: <1333532713.14873.YahooMailNeo(a)web193501.mail.sg3.yahoo.com> Content-Type: text/plain; charset="utf-8" Dear Ifeffit users, Can anyone recommend a reference where I can get calculated value of S02 for various elements ? I would like to compare them with my fitted values. Many thanks in advance !! With best regards, Jatin Rana

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Results Reporting
by John Farell 05 Apr '12

05 Apr '12

Hi.. Can you please explain me how to report the errors of EXAFS parameters like bond length, Co - ordination number, disorder etc. (Or how to obtain those errors ??) with regards John

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