April 2012 - Ifeffit - millenia.cars.aps.anl.gov

related to previous mail
by John Farell 26 Apr '12

26 Apr '12

Hi, Related to previous mail that I sent, my question is which one I have to chose i.e., "guess" option or "set" option. Or is there any mistake I did?, Procedure that I have followed was not right ?. Suggest me....

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APS / IIT XAFS Summer School
by Matt Newville 26 Apr '12

26 Apr '12

Hi Folks, Several people have asked, so I'd like to announce here that there will be an XAFS Summer School in Chicago this summer, July 9 - 13, on the IIT Campus and at APS. Grant Bunker is organizing, and more details are at http://xafs.org/Workshops/IIT2012 Cheers, --Matt

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Fwd: P-EXAFS fitting results and multiple scattering
by Bruce Ravel 24 Apr '12

24 Apr '12

Hi Dalton, I am CCing this to you and to the ifeffit mailing list, which is, of course, the appropriate venue for asking questions about the software and about XAS fitting in general. Please use the mailing list in the future. First off, kudos for measuring EXAFS data of this quality on a phosphorous surface complex. That is a non-trivial measurement. All of your problems (O MS paths, uncertainties, fit quality) are all inter-related and, I think, could be addressed, at least in part, by considering a somewhat more sophisticated approach to the data analysis problem. For those who haven't opened up Dalton's project file, you'll find that Dalton has used Artemis' "quick first shell theory" tool to generate a Feff path for the phosphorous-oxygen path. He then rather abused that tool to try to get it to make MS paths involving the P and O atoms. I am not a big fan of trying to overuse the QFS tool beyond the intention implicit in its name. If you need to model an unknown species, you are much better off trying to find a more elaborate starting model. That is a topic that Shelly wrote about extensively in her papers from her days as a uranium biogeochemist. Her concept is that, while you don't necessarily know quite what your sample looks like, you can make some informed guesses. Her strategy, then, is to pick a crystal structure that resembles what you expect to find in the real sample and run Feff on that. Then parameterize those paths from the Feff calculation that you think represent your real structure. Here is one example of this http://dx.doi.org/10.1016/S0016-7037(02)00947-X In that paper, she models, for example, a uranyl-phosphoryl bond using some kind of uranyl phosphate mineral. She doesn't use every path from the mineral -- just the ones that describe the monodentate U-O-P ligand and its associated SS and MS paths. One big advantage of this approach is that you will have well formed potentials for all of your scatterers. Abusing the quick first shell tool from Artemis pretty pretty much guarantees that you will have a poorly formed potential surface. That is certainly true for the 5-atom cluster you ended up with in your Feff calculation. I also think that you need to examine your data rather more critically. Although your data are impressively good for phosphorous EXAFS, they are still pretty noisy data. Plot your chi(R) out to 10 Angstroms. Do you see how big the peaks are between 6 and 10 Ang? That indicates the level of noise in your data. The peaks between 1.5 and 3.5 Ang are not much bigger than the level of the noise. Regardless of how well you pick your starting model in Feff, there will be a limit to how much you can say about these data beyond the first coordination shell. I am not really clear quite what you did to fit your data. What you sent to me had all the parameters either set or skipped. Given that it is not clear how much signal between 1.5 and 3.5 is above the level of the noise, it is almost certainly not reasonable to think that you have anywhere near the 14 independent points your k- and R-range settings would suggest. You say that your colleagues tend to get smaller uncertainties than you are seeing. I imagine that is because their data are considerably less noisy that these P edge data. That might not be what you were hoping to hear. But data are what data are. Yours are of limited quality and there will be severe limits on how much information you will be able to extract from them. B ---------- Forwarded Message ---------- Subject: P-EXAFS fitting results and multiple scattering Date: Sunday, April 22, 2012, 05:08:14 pm From: "daltonabdala(a)gmail.com" <daltonabdala(a)gmail.com> To: bravel(a)bnl.gov Dear Bruce, I'm a Ph D student in Dr. Sparks group and currently doing my research work on P-EXAFS. I'm particularly interested in examining the surface load, pH and time effects on the formation of P surface complexes at the goethite/water interface. My EXAFS experiments have been carried out at the X15B beamline at BNL. I've employed Athena and Artemis to do data analysis and fitting. I've come across some issues that I would like to share with you and, perhaps, you could give me some advices or come up with a different procedure that I could use in order to fix some of the issues that have raised me some skepticism about my fitting results and hampered me drawing conclusions. First, I couldn't find a way to get a better fit for Oxygen multiple scattering. Second, the uncertainties found for all fitting parameters are way too high if I am to compare uncertainties for other systems that my co-workers are used to deal with. I'm attaching an Artemis project file so you can take a look at it. Thank you very much, - Dalton -- Dalton Belchior Abdala Ph D. Candidate Environmental Soil Chemistry University of Delaware 152 Townsend Hall, 19716 Newark, DE "Not everything that counts can be counted, and not everything that can be counted counts." Albert Einstein ----------------------------------------- -- 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] New Demeter Win7 install (?) problems
by fred.mosselmans＠diamond.ac.uk 24 Apr '12

24 Apr '12

Hi i dont know if this is relevant but the problem sounds similar to one i had at Diamond with Demeter that was covered on the list about six weeks ago. that was with XP hence i am not certain it's relevant. what was missing is the demeter folder for the log file to write to in the %appdata% folder. creating (for each user) a demeter folder in their %appdata% enables the log file to be written and the program to run. for my windows 7 home pc this appears to be uesername/appdata/roaming cheers Fred -- 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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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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