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

Demeter 0.9.10
by Bruce Ravel 17 Jul '12

17 Jul '12

Hi everyone, I just uploaded a new version of the Demeter installer for Windows -- which includes the programs Athena, Artemis, and Hephaestus -- to its download site at https://github.com/bruceravel/demeter/downloads The current version number is 0.9.10. I also tagged this version in the github repository for anyone interested in a tagged version of the source code. Installation instructions for all platforms are at http://bruceravel.github.com/demeter/pods/installation.pod.html While there are no major new features in this release, the list of bug fixes and improvements is rather lengthy. Here are the details: https://github.com/bruceravel/demeter/blob/master/Changes.org Here are hints for making helpful bugs reports: http://bruceravel.github.com/demeter/pods/bugs.pod.html Documentation about Demeter in various kinds of media can found at http://bruceravel.github.com/demeter/ As a closing note, I want to mention that I am about 2/3 done with the long-awaited users' guide for Artemis. There is a link to the current (but incomplete) draft at the Documentation site. I will update that as I work it. Once it is complete, I will work on a PDF version. Once that is complete (and assuming I still have energy for such things!), I will work on updating the Athena Users' Guide for the new Demeter-based version. Whew! As always, thanks to everyone who uses my software. Your enthusiasm is a huge inspiration for me. Bruce PS: If, in the last few months, you have reported a bug or requested a feature that is not in this release, please remind me! -- 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 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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"Re: Contents of Ifeffit digest..."
by johnny huertas 15 Jul '12

15 Jul '12

Anatoly: Thanks so much. Jhonny Huertas Flores Rio de Janeiro-Brasil > From: ifeffit-request(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 113, Issue 13 > To: ifeffit(a)millenia.cars.aps.anl.gov > Date: Sat, 14 Jul 2012 16:19:14 -0500 > > 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: Ifeffit Digest, Vol 113, Issue 11 (Anatoly I Frenkel) > 2. "RE: Contents of Ifeffit digest..." (johnny huertas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 14 Jul 2012 19:13:01 +0000 > From: Anatoly I Frenkel <afrenke2(a)yu.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 113, Issue 11 > Message-ID: > <545F89325F51764C902D37B42C9F4D53135B1B44(a)YUWEXCPM12.yuad.uds.yu.edu> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Jhonny, > > This article on AgBr(x)Cl(1-x) explains how to do this type of analysis, and if there are still questions, look for other articles (in Phys. Rev. B and Phys. Rev. Lett.) on mixed ionic salts, by the same authors: > > https://pubweb.bnl.gov/~frenkel/BUCKLING-PHB/buckledPHB.pdf > > It is a model independent way to find local composition of Br and Cl around Ag. You are better off doing that (limit it to the 1st shell analysis) rather than using particular configurations you are proposing, and then see if you get the same composition (x) for Ag-Br as you obtain for composition y corresponding to the Br-Br coordination number found from Br K-edge. That will mean that your alloy is random. Otherwise, there may be either short range order or segregation that you will be able to identify by comparing x and y in each individual case. Rely on XRD results also, to tell whether you really have a solid solution or not. > > If you only measured Ag edge, you still can make some conclusions but you should rely on the bulk composition to compare the "x" and "y". > > Anatoly > > > ________________________________ > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of johnny huertas [johnnyhf(a)hotmail.com] > Sent: Saturday, July 14, 2012 1:51 PM > To: Lista fe IFEFFIT > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 113, Issue 11 > > Hi Matt: > Thanks for your response. First of all I am beginner in this issue. Because of my little experience I don't know exactly how to specify my problem but I think you write an interesting phrase in your response: "are you asking if you can distinguish random substitution from ordered substitution? I'm not sure why the Ag-Br and Ag-Cl parameters would be the same". > I don't know how to create a robust fitting model to distinguish random substitution from ordered substitution of the example found in Bruce site about AgBr(1-x)Clx. What are the parameters that I must consider to fit the spectra and to verify if exist random or ordered substitution? I am attaching a document very explicit about this. Thanks again. > > > > > Jhonny Huertas Flores > Rio de Janeiro-Brasil > > > > > From: ifeffit-request(a)millenia.cars.aps.anl.gov > > Subject: Ifeffit Digest, Vol 113, Issue 11 > > To: ifeffit(a)millenia.cars.aps.anl.gov > > Date: Sat, 14 Jul 2012 12:00:01 -0500 > > > > 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. problems (johnny huertas) > > 2. Re: problems (Matt Newville) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Fri, 13 Jul 2012 22:21:50 +0000 > > From: johnny huertas <johnnyhf(a)hotmail.com> > > To: <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: [Ifeffit] problems > > Message-ID: <BAY167-W124DD69B56D1526E67FEC05D5D70(a)phx.gbl> > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Members of list: > > I have some problems to resolve a question. I have been working a lot in fit the AgBr(1-x)Clx example of FEFFIT site. My fits were good in my opinion, but I don't know how to identify the Br and Cl atomic distribution around Ag (random or specific?). I didn't find any example about this in the site. Conversely I have made some attempts to identify such distribution. I have made two fits preparing for each one feff file, a feff file puting Br and Cl atoms in face and other in medirian position around Ag knowing the CN=6 of this central atom and fiting only the first shell. Unfortunatelly I don't have found satisfactory results because the paremeter are equal in both cases. I would like you help showing a similar example. Thanks. > > Jhonny Huertas Flores > > Rio de Janeiro-Brasil > > > > > >

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"RE: Contents of Ifeffit digest..."
by johnny huertas 15 Jul '12

15 Jul '12

Hi Matt: Thanks for your response. First of all I am beginner in this issue. Because of my little experience I don't know exactly how to specify my problem but I think you write an interesting phrase in your response: "are you asking if you can distinguish random substitution from ordered substitution? I'm not sure why the Ag-Br and Ag-Cl parameters would be the same".I don't know how to create a robust fitting model to distinguish random substitution from ordered substitution of the example found in Bruce site about AgBr(1-x)Clx. What are the parameters that I must consider to fit the spectra and to verify if exist random or ordered substitution? I am attaching a document very explicit about this. Thanks again. Jhonny Huertas Flores Rio de Janeiro-Brasil > From: ifeffit-request(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 113, Issue 12 > To: ifeffit(a)millenia.cars.aps.anl.gov > Date: Sat, 14 Jul 2012 13:42:01 -0500 > > 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: Ifeffit Digest, Vol 113, Issue 11 (johnny huertas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 14 Jul 2012 17:51:20 +0000 > From: johnny huertas <johnnyhf(a)hotmail.com> > To: Lista fe IFEFFIT <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 113, Issue 11 > Message-ID: <BAY167-W39E4C96CF961ED74CD8924D5D60(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi Matt:Thanks for your response. First of all I am beginner in this issue. Because of my little experience I don't know exactly how to specify my problem but I think you write an interesting phrase in your response: "are you asking if you can distinguish random substitution from ordered substitution? I'm not sure why the Ag-Br and Ag-Cl parameters would be the same".I don't know how to create a robust fitting model to distinguish random substitution from ordered substitution of the example found in Bruce site about AgBr(1-x)Clx. What are the parameters that I must consider to fit the spectra and to verify if exist random or ordered substitution? I am attaching a document very explicit about this. Thanks again. > > Jhonny Huertas Flores > Rio de Janeiro-Brasil > > > > From: ifeffit-request(a)millenia.cars.aps.anl.gov > > Subject: Ifeffit Digest, Vol 113, Issue 11 > > To: ifeffit(a)millenia.cars.aps.anl.gov > > Date: Sat, 14 Jul 2012 12:00:01 -0500 > > > > 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. problems (johnny huertas) > > 2. Re: problems (Matt Newville) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Fri, 13 Jul 2012 22:21:50 +0000 > > From: johnny huertas <johnnyhf(a)hotmail.com> > > To: <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: [Ifeffit] problems > > Message-ID: <BAY167-W124DD69B56D1526E67FEC05D5D70(a)phx.gbl> > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Members of list: > > I have some problems to resolve a question. I have been working a lot in fit the AgBr(1-x)Clx example of FEFFIT site. My fits were good in my opinion, but I don't know how to identify the Br and Cl atomic distribution around Ag (random or specific?). I didn't find any example about this in the site. Conversely I have made some attempts to identify such distribution. I have made two fits preparing for each one feff file, a feff file puting Br and Cl atoms in face and other in medirian position around Ag knowing the CN=6 of this central atom and fiting only the first shell. Unfortunatelly I don't have found satisfactory results because the paremeter are equal in both cases. I would like you help showing a similar example. Thanks. > > Jhonny Huertas Flores > > Rio de Janeiro-Brasil > > > > > >

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Re: [Ifeffit] Ifeffit Digest, Vol 113, Issue 11
by johnny huertas 14 Jul '12

14 Jul '12

Hi Matt:Thanks for your response. First of all I am beginner in this issue. Because of my little experience I don't know exactly how to specify my problem but I think you write an interesting phrase in your response: "are you asking if you can distinguish random substitution from ordered substitution? I'm not sure why the Ag-Br and Ag-Cl parameters would be the same".I don't know how to create a robust fitting model to distinguish random substitution from ordered substitution of the example found in Bruce site about AgBr(1-x)Clx. What are the parameters that I must consider to fit the spectra and to verify if exist random or ordered substitution? I am attaching a document very explicit about this. Thanks again. Jhonny Huertas Flores Rio de Janeiro-Brasil > From: ifeffit-request(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 113, Issue 11 > To: ifeffit(a)millenia.cars.aps.anl.gov > Date: Sat, 14 Jul 2012 12:00:01 -0500 > > 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. problems (johnny huertas) > 2. Re: problems (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 13 Jul 2012 22:21:50 +0000 > From: johnny huertas <johnnyhf(a)hotmail.com> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] problems > Message-ID: <BAY167-W124DD69B56D1526E67FEC05D5D70(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > > Members of list: > I have some problems to resolve a question. I have been working a lot in fit the AgBr(1-x)Clx example of FEFFIT site. My fits were good in my opinion, but I don't know how to identify the Br and Cl atomic distribution around Ag (random or specific?). I didn't find any example about this in the site. Conversely I have made some attempts to identify such distribution. I have made two fits preparing for each one feff file, a feff file puting Br and Cl atoms in face and other in medirian position around Ag knowing the CN=6 of this central atom and fiting only the first shell. Unfortunatelly I don't have found satisfactory results because the paremeter are equal in both cases. I would like you help showing a similar example. Thanks. > Jhonny Huertas Flores > Rio de Janeiro-Brasil > > >

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problems
by johnny huertas 14 Jul '12

14 Jul '12

Members of list: I have some problems to resolve a question. I have been working a lot in fit the AgBr(1-x)Clx example of FEFFIT site. My fits were good in my opinion, but I don't know how to identify the Br and Cl atomic distribution around Ag (random or specific?). I didn't find any example about this in the site. Conversely I have made some attempts to identify such distribution. I have made two fits preparing for each one feff file, a feff file puting Br and Cl atoms in face and other in medirian position around Ag knowing the CN=6 of this central atom and fiting only the first shell. Unfortunatelly I don't have found satisfactory results because the paremeter are equal in both cases. I would like you help showing a similar example. Thanks. Jhonny Huertas Flores Rio de Janeiro-Brasil

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Re: [Ifeffit] Referencing Demeter
by Bruce Ravel 13 Jul '12

13 Jul '12

Daniel, Please use the Ifeffit mailing list questions and comments on the software. http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > My name is Daniel Whittaker, I am PhD student at the University of > Manchester, UK. I have used your Demeter software (Athena and Artemis - i > used the first shell fit method as reading in crystal data was very > problematic) to model some EXAFS data. I am now preparing the manuscript > for publication and was wondering how you would like referencing (other > than Bruce Ravels Demeter software package) and if there is anything in > particular you would like in the experimental section about how the > software works? I have looked on your page and couldn't seem to find > anything that explicit requests referencing in a particular format. Ravel, B. & Newville, M. athena and artemis: data analysis for X-ray absorption spectroscopy using ifeffit, Journal of Synchrotron Radiation 12, 537–541 (2005) http://dx.doi.org/10.1107/S0909049505012719 > Thanks for your help with this and for producing the package in the first > place, as someone who knew literally nothing when i started i have managed > to model quite a few spectra to a satisfactory level. > > Regards, > > Daniel Whittaker, MChem > Nuclear FiRST DTC PhD Student > The University of Manchester > Oxford Road > Manchester > M13 9PL -- 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 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel

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Manganese oxide EXAFS modelin
by Ebrahim Rezaei 13 Jul '12

13 Jul '12

Hi everyone, I am working with bulk and nano-particles manganese oxides. Basically I have collected EXAFS of Mn K-edge for my reference material (Mn2O3, bixibyite) and also the catalyst (Mn supported on alumina). The catalyst shows formation of nanoparticles of bixibyite on alumina with size around 20 nm. My first question is about modeling the reference material in order to find So which will be used as a fixed parameter to find oxygen and manganese first and second shell CNs for the catalyst. The difficulty with modeling the reference material arises due to the rather complex atomic coordinates of Mn2O3 containing oxygen atoms at different but very close distances. Basically Mn2O3 has two sites (25% and 75% occupancy for site 1 and 2 respectively) with the following coordinates: Site 1 Site 2 Atom R (Å) CN Atom R (Å) CN O 1.993 6 O 1.899 2 Mn 3.104 6 O 1.985 2 Mn 3.565 6 O 2.249 2 Mn 3.115 6 Mn 3.575 6 I am aware that in order to fit the EXAFS equation I should considers paths from both sites and multiply their amplitudes by their site occupancy. But to make the life easier I simplified the atom coordinates of Mn2O3 to be able to extract the CNs from the catalyst. To my understanding one can expect to have 6 oxygen atoms in average at the first shell (0.25*6 + 0.75*6 = 6), 6 Mn atoms at the second shell and 6 Mn atoms at the third shell regardless of the site occupancy. Therefore I ignored the site occupancy and considered the following atomic coordinates assuming that there is only one site in the in the model developed for the reference material: Atom R (Å) CN O 1.985 4 O 2.249 2 Mn 3.115 6 Mn 3.565 6 The model works fairly acceptable and I am able to get CN from the catalysts as well. But I am not sure if my assumptions could be acceptable or not. I was wondering if I can have idea of the EXAFS community experts on this. My other question is about dealing with σ2 as a fixed parameter. I have noticed that after fitting the catalysts, σ2 of paths in the catalysts are almost close to that of the reference material. Therefore I tried to fix the values of σ2 for the catalyst and use the ones I have obtained from the reference material. This increases the degree of freedom of the fit and results in smaller error bars in CN while χ2 increases by 2.5%. Basically I have always kept number of variables to almost less than half of the number of the independent points either with fixing or relaxing σ2. I was wondering if estimation of σ2 in the catalysts from the reference material might be a good assumption in my case or not. I think it should not be a bad idea since size of Mn2O3 nano-particles on alumina is fairly large (around 20 nm) showing formation of complete crystalline of Mn2O3 on the catalyst. I have my project file in hand and I can send it for further discussion as well. I appreciate your time and help in advance. Best Regards, Ebrahim Rezaei, PhD Student, Chemical Engineering Department, University of Saskatchewan, Saskatoon, SK, Canada

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Athena Request
by BradleyW Miller 11 Jul '12

11 Jul '12

Hi, If my memory is correct there was a period of time you were taking request for improvements on Athena. This may be too late however I would like to see the LCF function of Athena capable of running multiple models (sequential models e.g. Sample A followed by B, C...) using a similar set of standards. For instances, I may have 25-40 spectra (environmental samples), one set of standards which may be plausible, and currently I have to run the model wait for the LCF model for sample A to finish before starting Sample B. If there was a way to write a script or add the functionality of multiple scans from the same set of standards, I (and maybe others) could set up a computer and leave for several hours instead of returning every 5-30 mins to execute a new LCF model. A conversation was posted about running models with a large number of standards (and whether it was appropriate), similarly running multiple samples is cumbersome. In a related comment I have tried to take advantage of access to high speed computing, but Athena's code does not appear to be capable of taking advantage of increased resources (either RAM and CPU) in order to decrease computational time. All the same thanks (to the many of you working on Ifeffit) for the shareware and all your support. Thanks for your time. Respectfully, Bradley W. Miller, Ph.D. Post Doctoral Fellow Oak Ridge Institute for Science and Education U. S. Environmental Protection Agency National Risk Management Research Laboratory Land Remediation and Pollution Control Division 5995 Center Hill Avenue, Cincinnati, OH 45224-1702 Office: (513) 487-2889 Miller.BradleyW(a)epa.gov Fax: (513) 569-7879 www.epa.gov www.tinyurl.com/bwmiller The great tragedy of Science—the slaying of beautiful hypothesis by an ugly fact.— Thomas H. Huxley Views or Opinions expressed in this email is solely representative of the sender and does not represents those of the EPA or any other agency.

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Crash when Discarding Feff Calculation
by Andrew Korinda 08 Jul '12

08 Jul '12

I have an Arthemis project (started in Demeter) with several feff calculations with the input written by me into a feff.inp boiler plate. The calculations themselves were fine but now when I show a calculation and click discard, I get the pop-up asking me if I want to discard this calculation, I click yes, then everything closes. Attached is the log file, project file, and demeter.mru. Let me know if there's anything I can do to help debug this. Andy Korinda

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FEFF83 question
by Pal, Rhitankar 05 Jul '12

05 Jul '12

Dear Professor Ravel, I am using FEFF83 and IFEFFIT recently to calculate the EXAFS spectra of Mn-cluster in PhotosystemII. I would like to know what is the E0 value FEFF83 uses for a Mn atom. Does it use the same E0 for all the absorbing atoms if there are multiple Mn atoms in a cluster. Please let me know if you or any of your group member can help me with this. Thanks and best regards Rhitankar Pal Postdoc, Batista Group Yale University

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