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

Artemis Bug
by mattie.peck＠huskers.unl.edu 29 Aug '13

29 Aug '13

Hello, I've got another bug I think. Like I said I'm using the new version of Artemis to open old .apj files and I've noticed that the path information isn't importing correctly. I have opened several .apj files and this problem happens with all of them. I have attached the .apj file and a pdf with screen shots pointing out the discrepancies. I have the latest version of demeter 0.9.18 and I am running Windows XP. Thanks for the help. Sincerely, Mattie Peck

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Artemis Crash
by mattie.peck＠huskers.unl.edu 28 Aug '13

28 Aug '13

Hello, I'm using the new version of Artemis to open old .apj files and when I try to run a fit the program completely shuts down. It allows me to start Artemis and load plots but as soon as I click the "fit" button it crashes. I have attached the .apj file and the dartemis log file and I have copied the text from the log file below. I have the latest version of demeter 0.9.18 and I am running Windows XP. Thanks for the help. Sincerely, Mattie Peck LOG FILE CONTENTS BELOW: Started at 2013-08-28T14:18:37 WinXP/.NetMedia Center Edition Service Pack 3 Service Pack 35126002302561 PATH: C:\GPIB_32\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\Program Files\QuickTime\QTSystem\;C:\strawberry\perl\bin;C:\strawberry\perl\site\bin;C:\strawberry\c\bin;C:\GPIB_32\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\Zone Labs\ZoneAlarm\MailFrontier;C:\Program Files\Microsoft SQL Server\90\Tools\binn\;C:\Program Files\QuickTime\QTSystem\;C:\FullProf_Suite perl version: v5.12.3 @INC: C:/strawberry/perl/site/lib C:/strawberry/perl/vendor/lib C:/strawberry/perl/lib . At line 55 of file rdffdt.f (unit = 1, file = 'fort.1') Fortran runtime error: End of file

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a caveat for Demeter 0.9.18 and Athena project files
by Bruce Ravel 27 Aug '13

27 Aug '13

Hi everyone, There is one feature of the new version of Athena that requires some explanation. I discovered a programming error in Athena that has existed for a long time and which made it difficult to add new features to Athena. In order to accommodate three features in this release (as well as future improvements), I had to make a change to the contents of the Athena project file and a corresponding change to how Athena reads them. The result of this is that a project file written by version 0.9.18 cannot be read by earlier versions of Athena. To manage a situation where you need to send a project file to someone who has not yet upgraded to 0.9.18, it is possible to explicitly ask Athena to write a project file that is backwards compatible. This is done by checking the "Backwards compatibility" check button in the File menu, as shown in the attached screenshot. Check that button, then re-save the project file. Athena project files exported this way will lose a small amount of information, but they will be imported without trouble by earlier versions of Athena. I apologize in advance for any confusion. I would not have made this decision were I not convinced that the new functionality was worth the potential confusion. Regards, B PS: For the technical-minded, I'll explain the situation in more detail. The change involves dropping the use of this Perl module: https://metacpan.org/module/MooseX::StrictConstructor I had been using that module to restrict the creation of new attributes for the objects that contain a data group. The effect of that module is to terminate the program when it encounters an unknown attribute. I don't quite recall why I decided that was the preferred behavior, but it has been in place since the early releases of Demeter. In 0.9.18 I needed to add three new attributes: an uncertainty in energy shift after aligning, a normalization parameter that is in Larch but not Ifeffit, and a flag related to processing dispersive XAS data. As I integrate Larch into Demeter, there will be more new Data attributes. Having made this change for this release, I do not anticipate a similar problem in the future. So, I had to bite the bullet and make this change that affects backwards compatibility. The check button for backwards compatible project files simply filters out the three new attributes before writing the project file, hence the small amount of information loss. -- 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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Demeter 0.9.18
by Bruce Ravel 27 Aug '13

27 Aug '13

Hi everyone, I just tagged release 0.9.18 of Demeter on github and posted a new Windows updater package. This is, by any measure, a big update. The list of new features and fixed bugs is quite lengthy -- here's the complete list: http://bruceravel.github.io/demeter/Changes.html#sec-1.1 There's a lot of great new stuff in Athena and Artemis, including a lot of fulfilled feature requests. Please check it out! I have also updated both Users' Guides to reflect many of these new features. The Users' Guides can be found at Demeter's home page: http://bruceravel.github.io/demeter/ For the Windows users, I have added a item to the Start Menu that opens the folder containing the log files that are written when one of the programs runs into a problem. Hopefully that will make it easier and more convenient to find them and include them in bug reports. Cheers, 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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amorphous metal alloys EXAFS spectra to be fitted with Artemis
by "Piotr J. Bardziński" 25 Aug '13

25 Aug '13

Dear Sir or Madam, I got a normalized Fe K-edge EXAFS spectrum for my amorphous 7-component alloy sample, for which I know its atomic percent composition. I need to find out the interatomic distances between the Fe and the other atoms present in the alloy (identify the peaks in R-space) as well as how many atoms of each element is surrounding the absorbing iron atom (coordination number). To meet my goal, I think I need to fit the R-space Fourier transform of my EXAFS spectrum in a program like Artemis. Unfortunately, I haven`t found any tutorial discussing how to deal with amorphous sample with unknown organization of the atoms. When you are about to prepare an atomic model in Artemis for fitting, you need to build a model with an initial interatomic distances, atomic coordination number, etc, but all that is obviously unknown to me. I know nothing about the short range order in my material and I want to learn it from the experiment itself (note that itcan be and most probably is different from the one present in crystalline structures). So, my question is, could somebody tell me how to deal with such system using the Artemis, what type of initial models for fitting should be prepared? All of your help will be greatly appreciated. Best regards, Piotr Bardziński,

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Recommendations for DFT/computational chemistry software?
by Scott Calvin 22 Aug '13

22 Aug '13

Hi all, I know many of you use DFT calculations to help model EXAFS data for molecular compounds. Do you have recommendations for good computational chemistry packages, commercial or otherwise, to use for that purpose? --Scott Calvin Sarah Lawrence College

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Lecture/tutorials required on FeFF 9.x
by S. Gautam 22 Aug '13

22 Aug '13

Dear All, I have been trying to find out some lectures/tutorials on FeFF 9.x (J.J. Rehr) to deliver my XAFS users, other than it's UserGuide as available on the website. If someone has made for their users, it would help me to deliver with acknowledging you. thanks in advance sincerely Sanjeev ----- Dr. Sanjeev Gautam KIST -PAL , South Korea -------------- http://orcid.org/0000-0003-3123-9906 -----

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(D) Atoms crashing while running feff
by Matt Frith 18 Aug '13

18 Aug '13

Dear All, I have been trying to run a feff calculation on FeAl2O4 with Fe as the absorbing atom. Every time I attempt the calculation in Artemis crashes. Atoms also crashes if it is run independently. The dartemis and datoms log files both read: "At line 90 of file istprm.f Fortran runtime error: End of file Can't close(GLOB(0x931c6cc)) filehandle: '' at C:/strawberry/perl/site/lib/Demeter/Feff.pm line 1015" Can someone please tell me what I need to edit to solve this problem? Can editing something on the input file fix this problem? The cif file and datoms log file for the problem are attached. Problem occurred on Win 7 32bit computer. Thank you for your time. Sincerely, Matt Frith Graduate Student Princeton University

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Linear Combination Fitting using ATHENA
by Teck Kwang Choo 15 Aug '13

15 Aug '13

Hello, I have been using ATHENA to perform Linear Combination Fitting (LCF) on my XANES spectrum to quantify the amounts of Fe (II) and Fe (III) in my samples using only FeO and Fe2O3 as standards. The results showed a majority of Fe (II), which is contrary to what was expected. This made me wonder if the LCF results from XANES is a molar percentage (mol %) or weight percentage (wt%). Could anyone enlighten me on this matter? Thanks! -- Teck Kwang Choo PhD Student Department of Chemical Engineering Room 225, Building 36 Monash University Mobile No.: 04-11489904

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Re: [Ifeffit] Recommendations for DFT/computational chemistry software?
by Ryan Nelson 12 Aug '13

12 Aug '13

Hi Scott, Gaussian is a pretty solid program. The input files are easy to write, and it's popularity make it easy to find support. It is a commercial product, though, which can be a problem if your on a tight budget. Several years back, I tried Gamess, which worked fine. Its biggest drawback for me was writing input files. It was cumbersome to use mixed/custom basis sets, which is probably key for anything you'll be doing for EXAFS. I haven't tried Gamess recently, so the situation may have changed. I hear good things about Orca as well. I think this package does a lot of interesting stuff related to XAS, but I haven't spent much time with it. A couple years back, Orca couldn't do analytical frequency calculations, which, in my experience, led to very slow frequency calculations. However, according to the website, it seems like that feature will be coming soon, so I would like to find some time to really play around with this program again. My colleague uses WebMO, which is a web-based frontend to many electronic structure packages. I haven't used it myself, but it may make for a more unified experience for many of these packages. Just my two cents... Good luck. Ryan > Hi all, > > I know many of you use DFT calculations to help model EXAFS data for > molecular compounds. Do you have recommendations for good computational > chemistry packages, commercial or otherwise, to use for that purpose? > > --Scott Calvin > Sarah Lawrence College > > >

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Re: [Ifeffit] Recommendations for DFT/computational chemistry software?
by Eric Breynaert 12 Aug '13

12 Aug '13

Dear Scott, The answer to this question depends on the compounds you're interested with and probably also on the software you have access to. In principle all computational chemistry software can export a molfile of the optimised structure. Using xyz coordinates in the molfile you can easily rig a feff input file. Best advice is probably to get in touch with a molecular modelling group and ask them to do the structure optimisations. If that's not an option, you could try Gaussian. Fairly expensive, but in combination with Gaussview it's reasonably easy to get the structure optimisation going. Gamess should do the trick for free. ADF is also an option and VASP can even handle periodic systems decently. But as i said initially, the best advice is to collaborate with a good molecular modelling group. Regards, Eric -- Eric Breynaert Centrum voor Oppervlaktechemie en Katalyse Departement Microbiële en moleculaire systemen (M²S) - KU Leuven Kasteelpark Arenberg 23 - bus 2461 B-3001 Leuven Tel: +3216321598 Fax: +3216321998

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issues with Athena (new Demeter package)
by Adrian Gainar 12 Aug '13

12 Aug '13

Hi All, I experience two issues with Athena of the updated new Demeter package, which it would be easier to describe: 1) when I open successively two .prj files that contain each a fitted spectrum, Athena seems to remember only the positions, widths and amplitudes of arctan and gaussian curves of the spectrum I open first; this translates to the fact that for the other fitted spectra that I open afterwards, it remembers the peak positions, widths and amplitudes of the curves belonging to the initially opened spectrum. The result of this issue is that I need to enter manually each time these values in order to get the fits back again - do you have any suggestions how this can be fixed?; 2) another issue is that after spectra calibrations, the spectrum does not appear to be calibrated. More specifically, when one checks the centroid positions of arctan or gaussian curves directly on the spectrum, the values don't correspond with the ones in the boxes, which I believe that means the calibration did not happen after all. Thank you very much in advance for any suggestions or ideas! Best wishes, Adrian ******************* Adrian Gainar PhD student Office: D37 School of Chemical Engineering and Analytical Science Jackson's Mill University of Manchester Manchester M13 9PL UK e-mail address contact: adrian.gainar(a)postgrad.manchester.ac.uk<mailto:adrian.gainar@postgrad.manchester.ac.uk> office telephone no.: +44(0)161 306 4362

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Fwd: Linear Combination Fitting using ATHENA
by Scott Calvin 09 Aug '13

09 Aug '13

I just noticed part of this thread went off-list. That's easy to do by mistake sometimes. I'm forwarding this part of the exchange to the list so that we don't start talking too much in circles. --Scott Calvin Sarah Lawrence College Begin forwarded message: From: Scott Calvin <scalvin(a)sarahlawrence.edu<mailto:scalvin@sarahlawrence.edu>> Subject: Re: [Ifeffit] Linear Combination Fitting using ATHENA Date: August 9, 2013 8:54:59 AM EDT To: Teck Kwang Choo <teck.kwang.choo(a)monash.edu<mailto:teck.kwang.choo@monash.edu>> Hi Teck Kwang, An Fe3O4 spectrum is available at the CARS XAFS database: http://cars.uchicago.edu/~newville/ModelLib/search.html --Scott Calvin Sarah Lawrence College On Aug 9, 2013, at 8:35 AM, Teck Kwang Choo <teck.kwang.choo(a)monash.edu<mailto:teck.kwang.choo@monash.edu>> wrote: Hi Scott, My spectrum standard fits extremely well with FeO: the sample spectrum's conformation to FeO's can be seen even by just superimposing both spectra together. Through XRD, it was confirmed that Ferrite (-Fe2O4) is the primary form of Fe but unfortunately I did not have any Ferrite standard compound with me during the actual XANES analysis. I am now suspecting that both FeO and -Fe2O4's spectra might be similar to each other. Do you have the spectrum for ferrite (Mg-ferrite if possible) by any chance? Thanks and kind regards. Teck Kwang On 9 August 2013 21:00, Scott Calvin <scalvin(a)sarahlawrence.edu<mailto:scalvin@sarahlawrence.edu>> wrote: Hi Teck Kwang, Molar percent by absorbing atom. In other words, if the best fit is 60% Fe(II), that corresponds to 60% of the iron atoms being Fe(II). But note that XANES depends on more than just valence state. Does the FeO and Fe2O3 combination fit the XANES well? Do those compounds correspond well to the actual compounds expected in the material? Did you try other iron standards? --Scott Calvin Sarah Lawrence College On Aug 8, 2013, at 11:37 PM, Teck Kwang Choo <teck.kwang.choo(a)monash.edu<mailto:teck.kwang.choo@monash.edu><mailto:teck.kwang.choo@monash.edu<mailto:teck.kwang.choo@monash.edu>>> wrote: Hello, I have been using ATHENA to perform Linear Combination Fitting (LCF) on my XANES spectrum to quantify the amounts of Fe (II) and Fe (III) in my samples using only FeO and Fe2O3 as standards. The results showed a majority of Fe (II), which is contrary to what was expected. This made me wonder if the LCF results from XANES is a molar percentage (mol %) or weight percentage (wt%). Could anyone enlighten me on this matter? Thanks! --

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tracking atom positions
by Bruce Ravel 08 Aug '13

08 Aug '13

Matthew said: > As it is now, if you want to describe your unknown structure as a > distorted version of the one for which FEFF was run, you have to > enter formulas for distances by hand. For instance, suppose you're > doing a substitutional dopant and you want to use Artemis to fit the > displacement of the impurity off-site and the dilation/contraction > of the first-neighbor shell. As it is now, you have to do the > algebra yourself to compute all the distances in terms of the > distortion parameters. It would be really nice if there were some > syntax for describing the alteration of atom positions, from which > Artemis would automatically compute the displacements. This might > have to be a new class of parameters. Such a computation would > cover the MS paths as well. What it would still NOT do is account > for the effect of leg-to-leg angles on MS paths (deviation from > focusing/backscatter), but it would be a step. I realize that this > would be a big job to implement in a nice way that wouldn't break > everything that came before, but it would be super useful and make > the IFEFFIT team (yet again) heros to the community It's nice to start a new thread when you start a new thread, so I'm starting a new thread. :) I understand exactly what you are asking for. In short, you would like to be able to parameterize atom positions, possibly even crystallographic parameters, and have those propagated through to the math expressions for delta_R for the paths. In fact, Demeter has some of what's needed already built in. There are two things needed to implement that with the way things currently work. 1. The pathfinder needs to remember the all the scattering geometries that contribute to a degenerate set of paths so that a parameterization has the possibility of breaking degeneracies. 2. In the case of using crystal data, Atoms needs to remember the symmetry operations that were done to place each atom in the cluster. This would allow Demeter to propagate a change in a crystal parameter through to delta_R. #1 already exists in Demeter. #2 is something I worked on in the past, but never got working to my satisfaction. The point is that most of #2 is in there, but commented out. That is, it's reasonably close. As you suggest, the hard part is presenting this to the user. I have actually been thinking about this problem lately and am interested in getting back to it. I have another big feff-interface improvement to work on first (an idea for dealing with Feff calculations over multiple, inequivalent sites in a user-friendly and user-efficient way), but I'll think about it. I should mention that Shelly has implemented something like this before for use with Matt's ancient feffit program. You might be able to get her to chime in.... 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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FEFF report: Hard tests failed in fovrg.
by Naumova, Maria 07 Aug '13

07 Aug '13

Dear EXAFS people, I have a question that appeared in FEFF and IFEFFIT several times. Still I didn't get an answer. Here are some links to this question discussed or asked previously: http://cars9.uchicago.edu/feff/feffusers/msg00255.html http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg02675.html http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg01532.html http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2005-October/002080.html I have EXAFS of several similar organic complexes - copper which has S, N and Hal (Cl or I), and sometimes copper in its first coordination shell and more C and N in ligands. I have structural data for them which I use as a model for FEFF. When I run FEFF via Artemis I get the following report for all my substances (I have 6 potentials in the list): Calculating potentials and phases... free atom potential and density for atom type 0 free atom potential and density for atom type 1 ...and so on... overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 ...and so on... muffin tin radii and interstitial parameters phase shifts for unique potential 0 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 1 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. ...and so on... Feff done. Have a nice day. In FEFF documentation I read the following: "To save time the code calculates the overlapped atom potential for each unique potential only once, using as a sample geometry the first atom in the atom list with a given unique potential index. Thus it is essential that the neighborhood of that sample atom be representative. Failure to do so may cause the code to perform poorly. " http://leonardo.phys.washington.edu/feff/Docs/feff6/feff6-4.html#pot I think that at least for copper and halogen or sulfur geometry of every atom in the atom list is representative. "Often we receive reports by users of older versions of FEFF of bugs that are fixed in the latest releases. Other code failures can often be traced to input file errors, sometimes quite subtle. An example would be non-physical widely spaced distributions of atoms. Symptoms of this common problem are very large muffin-tin radii (see the header of any .dat file) and possibly a failure of the phase-shift program to converge." http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2005-October/002080.html Here the reason is explained. Since it's an organic complex local distances between neighrours are small, but distances between parts of molecule can be quite big. Still it's not "non-physical widely spaced distributions of atoms". For example distance from copper to the first shell is 2 - 2.3 A (2.6-2.7 to I and Cu). To the "second shell" (ligand atoms connected to the first shell atoms or not connected but close to central atom) - 2.9 - 3.4 A. Finally what I want to know: May I use this FEFF calculation as a valid base for future fit? Or this error means that FEFF doesn't work correct and I can't rely on its output? If the phase-shift program failed to converge does it mean that it could stop in some completely unrealistic result? I attach several FEFF inp files which have this problem. Thanks for your help, Maria Naumova PhD student in DESY

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linear combination fitting
by Shaofeng Wang 07 Aug '13

07 Aug '13

Dear Bruce, I am using Dathena to do some linear combination fitting. In your program, you give three methods for fitting, nomal, derivate and chi(k). I got three different results using these methods. My question is which one is better to obtain more reasonable result or what the purpose of each method is. Regards, Shaofeng

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Re: [Ifeffit] linear combination fitting (Matt Newville)
by fred.mosselmans＠diamond.ac.uk 07 Aug '13

07 Aug '13

Matt wrote "Please avoid asking "why is the blue curve always lower than the red curve"?" By using a negative offset in Athena you can get the red curve below the blue curve :-) cheers Fred I hope Matt doesn't have the monopoly on jokes. -- 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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. Re: Split white line in TcO2 spectra and similar Tc(IV)
by fred.mosselmans＠diamond.ac.uk 07 Aug '13

07 Aug '13

Dear Wayne Thanks for your explanation 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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Split white line in TcO2 spectra and similar Tc(IV) octahedral environments
by fred.mosselmans＠diamond.ac.uk 06 Aug '13

06 Aug '13

Hi, Tc(IV) which is a d3 configuration ion, when octahedrally coordinated by O ligands eg TcO2 has what I would call a split white line (see attached image) in the K-edge XANEs. Others might call it a very strong second resonance . The image is from TC in an iron oxide phase by the way. One of my collaborators asked me why does the edge have two peaks.? This is a simple question but is there a simple answer? In a literature search although the shape seems accepted I couldn't find a straightforward explanation. Ce(IV) L3 spectra have a split white line due to some sort of crystal field effect but there the transition (L3-edge) is direct to d states so it's a bit more obvious. Here it's an s-p transition formally so you'd think it must be some sort of split p state explanation , but I am not sure why? I am sure you could XANES simulate this to reproduce it but that doesn't answer the question why in simple terms. It may be it 's a complicated band structure explanation and so there is no simple answer but if anyone has read or knows one , I 'd be interested,. There are some similar effects in the white lines of Zr K-edge spectra , when the Zr is also octahedral but I can only find reports of that not the reason for it. BTW This is definitely pure Tc(IV) so the answer is not multiple oxidation states., which has been used to explain different Tc split white lines in other situations. Thanks Fred Prof. J F W Mosselmans Principal Beamline Scientist I18 Diamond Light Source Diamond House Harwell Campus Didcot Oxon OX11 ODE UK T 00 44 1235 778568 M 00 44 7785510211 E fred.mosselmans(a)diamond.ac.uk F 00 44 1235 778448 Never mind the W it's the tax that counts -- 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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Re: [Ifeffit] Some doubts about Artemis (Scott Calvin and Bruce Ravel)
by Miguel A. Gómez 06 Aug '13

06 Aug '13

Thank you Scott and Bruce for your answers. From now, I will always take a look to the mail archive before to do any question. I guess it should be annoying to have to answer the same everytime. Sorry for that. Related to my second doubt (the possible bug of Artemis), please find attach my work project in case you could take a brief look of this. Maybe the problem is in my computer, so don't waste too much time with this... Best regards, Miguel > Message: 3 > Date: Mon, 05 Aug 2013 23:06:51 +0200 > From: "Miguel A. =?utf-8?b?R8OzbWV6?=" <miguel.gomez(a)ica.csic.es> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Some doubts about Artemis > Message-ID: > <20130805230651.Horde.tJbhajp6yHZSABPrpsjx4gA(a)webmail.csic.es> > Content-Type: text/plain; charset=UTF-8; format=flowed; DelSp=Yes > > > Hi everyone, > > I have two doubts about the use of the Artemis software: > > 1) Is it possible to use the coordination number of one path (N) as a > variable? Because I tried to do it, but I am unable to write any > letter in the path parameters set. > > 2) When I change the 'Fourier transform parameters' in order to > perform a new fit, the "window range" (green line) in the plotting > screen wont change the range (at least visually) and remains between > the defaut values (r from 1 to 3 or k from 2 to 10). Is there any form > to modify this? > > Thank you in advance, > Miguel > ________________________________________________________________________________ > > Miguel Angel Gomez Gonzalez > > PhD. Student > Institute of Agricultural Sciences (ICA) > Spanish National Research Council (CSIC) > > > > ------------------------------ > > Message: 4 > Date: Mon, 5 Aug 2013 17:25:22 -0400 > From: Scott Calvin <scalvin(a)sarahlawrence.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Some doubts about Artemis > Message-ID: <7DAE38F1-36DF-47C8-83DB-6FC250D4C553(a)slc.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Miguel, > > On Aug 5, 2013, at 5:06 PM, Miguel A. G?mez <miguel.gomez(a)ica.csic.es> wrote: >> >> 1) Is it possible to use the coordination number of one path (N) as a >> variable? Because I tried to do it, but I am unable to write any >> letter in the path parameters set. > > Because N only appears in the EXAFS equation as part of the product > S02*N, coordination number can be fit by putting the variable in the > S02 field. For example, the coordination number in the N box can be > changed to 1, and the entry in the N field can be changed to S02*N, > with N then made a "guess" variable. Of course, you can't sensibly > fit every N and fit S02...something has to be set. > >> >> 2) When I change the 'Fourier transform parameters' in order to >> perform a new fit, the "window range" (green line) in the plotting >> screen wont change the range (at least visually) and remains between >> the defaut values (r from 1 to 3 or k from 2 to 10). Is there any form >> to modify this? > > Usually it changes the next time you plot. If it doesn't, you are > experiencing a bug that is specific to your circumstances (hardware > + OS + project). Those kinds of bugs are, unfortunately, difficult > to track down. > > --Scott Calvin > Sarah Lawrence College > > > > > > ------------------------------ > > Message: 5 > Date: Mon, 05 Aug 2013 17:27:22 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Some doubts about Artemis > Message-ID: <520018BA.7020306(a)bnl.gov> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed" > > On 08/05/2013 05:06 PM, Miguel A. G?mez wrote: >> >> Hi everyone, >> >> I have two doubts about the use of the Artemis software: >> >> 1) Is it possible to use the coordination number of one path (N) as a >> variable? Because I tried to do it, but I am unable to write any letter >> in the path parameters set. > > See > http://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg03646.html > and the responses that follow. > > We've been answering questions on the mailing list for many years now. > Searching through the archives is a really good use of time. > >> 2) When I change the 'Fourier transform parameters' in order to perform >> a new fit, the "window range" (green line) in the plotting screen wont >> change the range (at least visually) and remains between the defaut >> values (r from 1 to 3 or k from 2 to 10). Is there any form to modify this? > > As described, this is certainly not correct. Attached are two screen > shots. For the first one, I imported a project file and immediately > clicked the "Rk" button. I changed the values of kmax and Rmax, then > clicked the "Rk" button again. The values were clearly updated > correctly for the second plot. > > Please see my post to the mailing list from only 30 hours ago (!!) > about the difference between an actionable bug report and complaining > into the wind: > > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2013-August/011284.html > > 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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Some doubts about Artemis
by Miguel A. Gómez 05 Aug '13

05 Aug '13

Hi everyone, I have two doubts about the use of the Artemis software: 1) Is it possible to use the coordination number of one path (N) as a variable? Because I tried to do it, but I am unable to write any letter in the path parameters set. 2) When I change the 'Fourier transform parameters' in order to perform a new fit, the "window range" (green line) in the plotting screen wont change the range (at least visually) and remains between the defaut values (r from 1 to 3 or k from 2 to 10). Is there any form to modify this? Thank you in advance, Miguel ________________________________________________________________________________ Miguel Angel Gomez Gonzalez PhD. Student Institute of Agricultural Sciences (ICA) Spanish National Research Council (CSIC)

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data point limits in Athena?
by Göttlicher, Jörg 05 Aug '13

05 Aug '13

Hello, does someone now if there is a limit of data points for Athena/Athena-Demeter? I have realized that a XAFS data file containing about 2500 data points is not read in properly in Athena (v. 0.8.061) and is started at zero energy and cutted of before the end of the data rows in Athena-Demeter v. 0.9.9, whereas the same file reduced to about 1600 data points was read in without any problems in both Athena versions. I hope that someone has an idea about the reason(s) and how to manage the read in of such data without prior treatment? Using the binning mode or truncation (to cut off the zero energy point, that occured when reading in with Demeter 0.9.9), did not succeed because the data were not treated correctly during the import. Best regards Joerg

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Postdoc Position
by Jeff Terry 30 Jul '13

30 Jul '13

Hi All, Hope this is ok to post. I have an open postdoc position in my group. Chemistry, physics, materials science, nuclear engineering, or similar fields will be considered. Synchrotron measurements will involve EXAFS, XRD, PES, and others. You can see the details at: http://t.co/xNnYrMgMly Thanks, Jeff Jeff Terry Associate Professor of Physics Illinois Institute of Technology Sent from my iPhone

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Two-Phase EXAFS fitting
by Taehoon Kim 29 Jul '13

29 Jul '13

Dear users in Ifeffit forum, I'm working at a cathode material represented by xLi2MnO3.(1-x)LiMO2 (M = Mn, Ni, and Co). This material can be described as a solid solution between Li2MnO3 and LiMO2. The main phase is the LiMO2 (M = Mn, Ni, and Co), which shows a trigonal crystal structure (R-3m). The integrated phase is the Li2MnO3, which exhibits a monoclinic structure (C2/m). What would be the right way to perform the EXAFS fitting using Artemis for the multi-phase materials ? I was thinking creating two crystal structure set using ATOMS, and perform feff calculation for each, and then choose scattering path from each atom set. I wonder whether this is an appropriate approach ? and how can I apply the ratio of each phase (let's say x is 0.6) in the fitting process ? Thank you in advance ! Kind Regards Taehoon

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DAthena crashes when reconstructing data from PCA
by Scott Calvin 29 Jul '13

29 Jul '13

Hi Bruce, Athena is crashing every time I try to "Reconstruct Data" in the PCA dialog. It doesn't seem to matter what data I use, or what space I'm working in (mu or chi), or how many components I use in the reconstruction. I'm using Demeter 0.9.17 with Ifeffit 1.2.11d, under Windows 8 running in Parallels 8 running under OS 10.8.4 on a MacBook Pro. The log file for the latest crash is below. If you'd like a project file too, let me know, but it happens, e.g., with the gold cyanobacteria project file, and with every data set I've tried. --Scott Calvin Sarah Lawrence College

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