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

Theoretical value of S02 for different absorber
by Jatin Rana 04 Apr '12

04 Apr '12

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] Ifeffit Digest, Vol 110, Issue 2
by Carmelo Prestipino 02 Apr '12

02 Apr '12

I suppose the problem is about writing privilege on the folder Program files/Prestopronto. My script in Inno setup theoretically should change it, but evidently practically it doesn't work I'll solve it in the next upgrade. At this time you should change manually the writing privilege or install the program in a different directory. However, it is very difficult to understand what happen, and reproduce the error if the report is "it doesn't work ", (actually I'm not sure at all of diagnosis) normally, all the codes gives clear instruction how to report the error. Ciao Lello On Mon, Apr 2, 2012 at 11:24 AM, <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: Ifeffit Digest, Vol 110, Issue 1 (KONG Quingyu) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 2 Apr 2012 09:23:31 +0000 > From: KONG Quingyu <kong(a)synchrotron-soleil.fr> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 110, Issue 1 > Message-ID: > < > 30F62EE734A9EA45A3F211513CB620033621987A(a)SUN-DAG2.synchrotron-soleil.fr> > > Content-Type: text/plain; charset="iso-8859-1" > > Thanks a lot Santiago, by the way, does the program need windows Vista or > 7, I installed it in windows XP with different versions, b.0.7 or b.0.6, > but it did not work. > > Best regards, > Qingyu > > Beamline ODE > Soci?t? civile Synchrotron SOLEIL > L'Orme des Merisiers > Saint-Aubin - BP 48 > 91192 GIF-sur-YVETTE CEDEX > Tel: +33 (0)1 69 35 97 84 (office) > +33 (0)1 69 35 97 16 (beamline) > email: kong(a)synchrotron-soleil.fr > > ________________________________________ > 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: Monday, April 02, 2012 9:09 AM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 110, Issue 1 > > 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. Prestopronto links (Santiago Jos? Alejandro Figueroa) > 2. Re: Prestopronto links (Matt Newville) > 3. Re: Ifeffit Digest, Vol 109, Issue 24 (KONG Quingyu) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 1 Apr 2012 17:53:33 -0300 (BRT) > From: Santiago Jos? Alejandro Figueroa <figueroa(a)fisica.unlp.edu.ar> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Prestopronto links > Message-ID: > <37353.189.61.212.168.1333313613.squirrel(a)mail.fisica.unlp.edu.ar> > Content-Type: text/plain;charset=iso-8859-1 > > Hi > > I can add my two cent...(of REAIS) > > The web page of PRESTOPRONTO pointed out by Carmelo is: > > http://www.esrf.eu/computing/scientific/PRESTOPRONTO/Prestopronto.htm > > or > > http://code.google.com/p/prestopronto/ > > We start to use here at the LNLS in the dispersive beamline with > promissing results. > > > Best regards, > > Santiago > > > > ------------------------------ > > Message: 2 > Date: Sun, 1 Apr 2012 17:44:03 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Prestopronto links > Message-ID: > <CA+7ESbr73fkgSeBCGTZN=5HXZe3P9jHCVgZ36-aCd1PD=8X8VQ(a)mail.gmail.com > > > Content-Type: text/plain; charset=ISO-8859-1 > > Santago, Carmelo, > > 2012/4/1 Santiago Jos? Alejandro Figueroa <figueroa(a)fisica.unlp.edu.ar>: > > Hi > > > > I can add my two cent...(of REAIS) > > > > The web page of PRESTOPRONTO pointed out by Carmelo is: > > > > http://www.esrf.eu/computing/scientific/PRESTOPRONTO/Prestopronto.htm > > > > or > > > > http://code.google.com/p/prestopronto/ > > > > We start to use here at the LNLS in the dispersive beamline with > > promissing results. > > > > Looks great! Thanks for the links! > > --Matt > > > > ------------------------------ > > Message: 3 > Date: Mon, 2 Apr 2012 07:08:37 +0000 > From: KONG Quingyu <kong(a)synchrotron-soleil.fr> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 109, Issue 24 > Message-ID: > < > 30F62EE734A9EA45A3F211513CB6200336217807(a)SUN-DAG2.synchrotron-soleil.fr> > > Content-Type: text/plain; charset="us-ascii" > > Thanks a lot Lello and Matt, > > Now, it is clear to us that we anyway need our own program to > automatically treat the big data set. > > I tried XOP with XAID extension following your suggestions, it is nice to > have the graphic operation, but for a big data set with thousands of > spectra we need a program. Since we have already part of the program and > hope we will finish it soon to a kind of platform for automatic data > analysis. > > Regards, > Qingyu > > > > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto: > ifeffit-bounces(a)millenia.cars.aps.anl.gov] On Behalf Of > ifeffit-request(a)millenia.cars.aps.anl.gov > Sent: Saturday, March 31, 2012 9:47 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 109, Issue 24 > > 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 109, Issue 23 (Carmelo Prestipino) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 31 Mar 2012 21:47:19 +0200 > From: Carmelo Prestipino <carmelo.prestipino(a)univ-rennes1.fr> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 109, Issue 23 > Message-ID: > <CAHPDQqzGdbkRaXri5raNG60oiT+h1CPdgZVRHmWZ_CvVGML4ig(a)mail.gmail.com > > > Content-Type: text/plain; charset="iso-8859-1" > > Hi > if I can add my two cent...(of EURO) > > At the ESRF for this kind of studies some work has been done. > > There is the module XAID of the code XOP wrote by Manuel Sanchez del Rio > http://www.esrf.eu/computing/scientific/xop2.1/documentation.html > It is written in IDL from scratch. > It have normalization and linear combination fit features, it is fully > graphically interfaced and in terms of performances is quite impressive. > However, the program has a complicate structure that could difficult at > the first approach (but Manuel is very kind, don't hesitate to contact him > ). > > Otherwise there is the code PrestoPronto. > code.google.com/p/*prestopronto*/ > It is mainly a fully graphic python wrapping of ifeffit for sequential > analysis. > In terms of speed is very similar to Athena but it do automatically the > tricks of cleaning memory But it is still a very young code...... > It still has not any interface to linear combination analysis. > We never tested for more than 1000.. spectra > > Probably Mark Newton could give you some more suggestions Regards Lello > > > On Sat, Mar 31, 2012 at 7:00 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: Ifeffit Digest, Vol 109, Issue 21 (KONG Quingyu) > > 2. Re: Ifeffit Digest, Vol 109, Issue 21 (Matt Newville) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Fri, 30 Mar 2012 18:32:49 +0000 > > From: KONG Quingyu <kong(a)synchrotron-soleil.fr> > > To: "ifeffit(a)millenia.cars.aps.anl.gov" > > <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 109, Issue 21 > > Message-ID: > > < > > 30F62EE734A9EA45A3F211513CB6200324BD1922(a)SUN-DAG1.synchrotron-soleil.f > > r> > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > Thank you for all your helpful suggestions. > > > > Actually, our beamline has recently installed a fast detector with a > > repetation of 20KHz, which could collected data in a time resolution > > of few tens of microsecond and could easily produce a large amount of > > data. We have already accepted three users for microsecond time > > resolved studies, each of them collected millions of spectra. > > > > Together with the company that provide the detector and our software > > engineer we started to write a Python program to treat the data from > > November last year, however our engineer quitted recently, this make > > us to look for other solutions. > > > > If Demeter would works well for large amount of data treatment, it > > would be great. As I know ID24 at ESRF has also installed the same > > detector and would probably have similar demanding for such a program. > > > > Probably due to the limited memory of my pc, I can only open around > > 200 spectra simultanously with Athena. > > > > Best, > > Qingyu Kong > > > > > > Beamline ODE > > Soci?t? civile Synchrotron SOLEIL > > L'Orme des Merisiers > > Saint-Aubin - BP 48 > > 91192 GIF-sur-YVETTE CEDEX > > Tel: +33 (0)1 69 35 97 84 (office) > > +33 (0)1 69 35 97 16 (beamline) > > email: kong(a)synchrotron-soleil.fr > > > > ________________________________________ > > 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: Friday, March 30, 2012 3:29 PM > > To: ifeffit(a)millenia.cars.aps.anl.gov > > Subject: Ifeffit Digest, Vol 109, Issue 21 > > > > 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. delr and ss parameterization (Ebrahim Rezaei) > > 2. program (KONG Quingyu) > > 3. Re: program (Carlo Segre) > > 4. Re: program (Matt Newville) > > 5. Re: delr and ss parameterization (Bruce Ravel) > > 6. Re: program (Bruce Ravel) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Thu, 29 Mar 2012 21:57:21 -0700 (PDT) > > From: Ebrahim Rezaei <e_rezaei24(a)yahoo.com> > > To: ifeffit(a)millenia.cars.aps.anl.gov > > Subject: [Ifeffit] delr and ss parameterization > > Message-ID: > > > > <1333083441.66190.YahooMailClassic(a)web120501.mail.ne1.yahoo.com> > > Content-Type: text/plain; charset="utf-8" > > > > Hi everyone, > > > > > > I am working with bulk and nano structures of MnO, MnO2 and Mn2O3. I > > have two questions regarding how to parameterize delr and ss in > > Artemis. > > > > > > It is recommended to > > use either delr=alfa*Reff or relate it to unit cell structure. Can > > anybody tell me how to do the second approach? > > > > > > Also is that a good idea to let all ss to float? Or it should be > > constrained based on type and distance of atoms? I have seen an > > example about ZnO just letting the first two shell?s ss to float and > > let the rest to be the same. I would appreciate it very much if > > anybody could help me with this too. > > > > > > Regards, > > > > > > Ebrahim Rezaei > > > > PhD Candidate, Chem. Eng. Dep., University of Saskatchewan > > > > Saskatoon, SK, Canada > > -------------- next part -------------- An HTML attachment was > > scrubbed... > > URL: < > > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/2012032 > > 9/e13d64a5/attachment-0001.htm > > > > > > > ------------------------------ > > > > Message: 2 > > Date: Fri, 30 Mar 2012 06:46:38 +0000 > > From: KONG Quingyu <kong(a)synchrotron-soleil.fr> > > To: "ifeffit(a)millenia.cars.aps.anl.gov" > > <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: [Ifeffit] program > > Message-ID: > > < > > 30F62EE734A9EA45A3F211513CB6200324BD1794(a)SUN-DAG1.synchrotron-soleil.f > > r> > > > > Content-Type: text/plain; charset="iso-8859-1" > > > > We recently collected 3000 EXAFS spectra to follow a chemical reaction > > process, we would like to fit the experimental data with reference > > spectra using linear combination fitting. Does anyone know there are > > available or commercial program to normalize the data and make linear > > combination fitting. We tried to do it with Athena manually, but 3000 > > spectra take a long time for us and it is not a practical way. > > > > Thanks a lot. > > > > Qingyu Kong > > > > Beamline ODE > > Soci?t? civile Synchrotron SOLEIL > > L'Orme des Merisiers > > Saint-Aubin - BP 48 > > 91192 GIF-sur-YVETTE CEDEX > > Tel: +33 (0)1 69 35 97 84 (office) > > +33 (0)1 69 35 97 16 (beamline) > > email: kong(a)synchrotron-soleil.fr > > > > > > > > > > > > ------------------------------ > > > > Message: 3 > > Date: Fri, 30 Mar 2012 01:56:57 -0500 (CDT) > > From: Carlo Segre <segre(a)iit.edu> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] program > > Message-ID: <alpine.DEB.2.02.1203300154590.5339(a)hydride.phys.iit.edu> > > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > > > > Hi Qingyu > > > > On Fri, 30 Mar 2012, KONG Quingyu wrote: > > > > > We recently collected 3000 EXAFS spectra to follow a chemical > > > reaction process, we would like to fit the experimental data with > > > reference spectra using linear combination fitting. Does anyone know > > > there are available or commercial program to normalize the data and > > > make linear combination fitting. We tried to do it with Athena > > > manually, but 3000 spectra take a long time for us and it is not a > practical way. > > > > You might wish to look into Bruce Ravel's new suite of programs > > (called Demeter). I believe they are built to allow easy scripting of > > massive quantities of data such as yours. > > > > Carlo > > > > > > -- > > Carlo U. Segre -- Duchossois Leadership Professor of Physics Associate > > Dean for Graduate Admissions, Graduate College Illinois Institute of > > Technology > > Voice: 312.567.3498 Fax: 312.567.3494 > > segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org > > > > > > ------------------------------ > > > > Message: 4 > > Date: Fri, 30 Mar 2012 07:56:05 -0500 > > From: Matt Newville <newville(a)cars.uchicago.edu> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] program > > Message-ID: > > > > <CA+7ESbrjp46_kPw9F803MQOGdMRtFbDa-7oGem25+CL2bYznJg(a)mail.gmail.com > > > > > Content-Type: text/plain; charset=ISO-8859-1 > > > > Hi Qingyu, > > > > On Fri, Mar 30, 2012 at 1:46 AM, KONG Quingyu > > <kong(a)synchrotron-soleil.fr> wrote: > > > We recently collected 3000 EXAFS spectra to follow a chemical > > > reaction > > process, we would like to fit the experimental data with reference > > spectra using linear combination fitting. Does anyone know there are > > available or commercial program to normalize the data and make linear > > combination fitting. We tried to do it with Athena manually, but 3000 > > spectra take a long time for us and it is not a practical way. > > > > Ifeffit is designed to be scriptable for batch processing. This can > > be done with a raw Ifeffit script (which isn't very flexible) or from > > Perl or Python, which are more flexible. Carlo mentioned Demeter, > > which is a high-level Perl wrapping of the lower-level functionality. > > Working with 3000 spectra may be challenging with Ifeffit version > > 1.2, as the total amount of available memory is limited, but with some > > care it should be possible. > > > > FWIW, the next version of Ifeffit will eliminate this memory > > limitation, and make both scripting and extending the functionality > > much easier and better. This is still a work in progress (see > > https://github.com/xraypy/xraylarch) and poorly documented, but the > > essential idea is to write all of Ifeffit's functionality in Python, > > for all the reasons just stated, and this far enough along that I am > > confident it will be a big improvement. So far (for XAFS), this can > > read data, do simple pre-edge subtraction, normalization, remove > > backgrounds ala autobk, and do XAFS Fourier transforms. It can do > > simple "general purpose fitting", but does not yet expose a > > simple-to-use linear combination fitting functionality (shouldn't be > > too hard, as all the linear algebra pieces are readily available) or > > fitting spectra to Feff calculations (a bit more involved). Work is > > slow (mostly due to other obligations), but progress is being made, > > and it's close to ready for an initial release. If you are (or > > anyone else is) interested in trying this or helping out, let me know. > > > > --Matt > > > > > > > > ------------------------------ > > > > Message: 5 > > Date: Fri, 30 Mar 2012 09:13:11 -0400 > > From: Bruce Ravel <bravel(a)bnl.gov> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] delr and ss parameterization > > Message-ID: <201203300913.12166.bravel(a)bnl.gov> > > Content-Type: Text/Plain; charset="utf-8" > > > > On Friday, March 30, 2012 12:57:21 am Ebrahim Rezaei wrote: > > > I am working with bulk and nano structures of MnO, MnO2 and Mn2O3. I > > > have two questions regarding how to parameterize delr and ss in > > > Artemis. > > > > > > > > > It is recommended to > > > use either delr=alfa*Reff or relate it to unit cell structure. Can > > anybody > > > tell me how to do the second approach? > > > > > > > > > Also is that a good idea to let all ss to float? Or it should be > > > constrained based on type and distance of atoms? I have seen an > > example > > > about ZnO just letting the first two shell?s ss to float and let the > > > rest to be the same. I would appreciate it very much if anybody > > > could help me with this too. > > > > The alpha*reff trick is only strictly valid for cubic, monoatomic > > materials. For everything else in the world, it is an increasingly > > poor approximation. That's not to say it is not a helpful > > parameterization, just that you need to be mindful of its limitations. > > > > As for the sigma^2 parameter, you have to balance when is physically > > reasonable with what can be reliably extracted from a real data > > analysis. > > > > - Two atoms of a different species at the same distance should have > > different sigma^2 because they have different masses. > > > > - Two atoms of the same species at different distances should have > > different sigma^2 because sigma^2 is a mean square deviation in > > distance. > > > > So, in some sense, all scatterers might have their own sigma^2 > > parameters. But that is not to say that you data are sufficient to > > independently determine that many parameters. When you run up against > > the limited information content of your data, that is when you start > > making approximations of the sort that lead to setting sigma^2 > > parameters for different scatterers to be the same. > > > > However, there are sensible and physically justifiable reasons why the > > sigma^2 for certain multiple scattering paths should be related to > > those of single scattering paths. See > > http://dx.doi.org/10.1103/PhysRevB.54.156 > > > > Two of my favorite papers that show excellent data analysis solving > > real-world problems and which are written in a way that is of > > pedagogical value for XAS beginners are Scott Calvin's paper on doped > > ferrites (http://dx.doi.org/10.1103/PhysRevB.66.224405) and Shelly > > Kelly's paper on uranyl binding to biomass > > (http://dx.doi.org/10.1016/S0016-7037(02)00947-X) For more > > interesting papers, look through the archives of the mailing list and > > see who gives good answers to questions, then look up their papers. > > > > Another extremely useful resource which includes extensive discussion > > of the sorts of things you are asking about is Shelly's review > > chapter. Here's the amazon link to that book: > > > > http://www.amazon.com/Methods-Soil-Analysis-Part-Mineralogical/dp/0891 > > 188460/ The book is a bit pricy, but if you are a clever googler, you > > may find a PDF copy of her chapter. > > > > Regards, > > 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: 6 > > Date: Fri, 30 Mar 2012 09:29:10 -0400 > > From: Bruce Ravel <bravel(a)bnl.gov> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] program > > Message-ID: <201203300929.11143.bravel(a)bnl.gov> > > Content-Type: Text/Plain; charset="iso-8859-1" > > > > On Friday, March 30, 2012 02:46:38 am KONG Quingyu wrote: > > > We recently collected 3000 EXAFS spectra to follow a chemical > > > reaction process, we would like to fit the experimental data with > > > reference > > spectra > > > using linear combination fitting. Does anyone know there are > > > available or commercial program to normalize the data and make > > > linear combination fitting. We tried to do it with Athena manually, > > > but 3000 spectra take a long time for us and it is not a practical way. > > > > Hi Qingyu, > > > > Carlo is correct, Demeter could be used to write a special purpose > > program for automating this sort of thing. The performance in terms > > of speed may not be exactly what you want, but the performance in > > terms of quickly prototyping a program to process and analyze a large > > data volume is excellent. > > > > The Demeter code base comes with extensive (although still incomplete) > > documentation as well as plenty of example scripts, including examples > > for the individual chores you mention above. > > > > Here's Demeter's documentation: http://bruceravel.github.com/demeter/ > > > > > > As a closing comment, isn't it somehow strange that you and your > > colleagues went to all the trouble of building a fancy dispersive > > beamline without thinking ahead about how you were going to analyze > > your data? > > > > 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 > > > > > > ------------------------------ > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > End of Ifeffit Digest, Vol 109, Issue 21 > > **************************************** > > > > > > > > ------------------------------ > > > > Message: 2 > > Date: Fri, 30 Mar 2012 16:36:58 -0500 > > From: Matt Newville <newville(a)cars.uchicago.edu> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 109, Issue 21 > > Message-ID: > > > > <CA+7ESbrZir3zMWAKSx5HPpqjJ5H_qC-V0YAsnCXUzDO512q+aA(a)mail.gmail.com > > > > > Content-Type: text/plain; charset=ISO-8859-1 > > > > Hi Qingyu, > > > > On Fri, Mar 30, 2012 at 1:32 PM, KONG Quingyu > > <kong(a)synchrotron-soleil.fr> wrote: > > > Thank you for all your helpful suggestions. > > > > > > Actually, our beamline has recently installed a fast detector with a > > > repetation of 20KHz, which could collected data in a time resolution > > > of few tens of microsecond and could easily produce a large amount > > > of data. We have already accepted three users for microsecond time > > > resolved studies, each of them collected millions of spectra. > > > > > > Together with the company that provide the detector and our software > > > engineer we started to write a Python program to treat the data from > > > November last year, however our engineer quitted recently, this make > > > us to look for other solutions. > > > > Bruce wrote earlier, > > > > As a closing comment, isn't it somehow strange that you and your > > colleagues went to all the trouble of building a fancy dispersive > > beamline without thinking ahead about how you were going to analyze > > your data? > > > > Sadly, Bruce's observation is not unusual at all. Everyone is > > experiencing data overloads, and almost no one is investing in > > computing resources. Yours may be slightly larger than most XAFS > > users, but only by one or two orders of magnitude. Then again, you > > had a software engineer at your beamline at least for a while. > > > > To be clear, Ifeffit, Athena, Demeter, Sixpack, and so on are written > > primarily by beamline scientists like yourself. Your choices are to > > use what someone else gives you, write your own, or hire someone to do > > it for you. It appears that the last choice rarely works very well. > > That you get to use Bruce's codes at all (and for free!) is not an > > accident: it is part of the design, and an outcome of the programs > > being written by beamline scientists. > > > > The current software base is more than ten years old, and showing its > > age especially with respect to large data sets and multiple > > processors. This is a really good opportunity for you and your > > colleagues (and others in similar situations) to join in. That is, > > you should write code to deal with your fast data rates. If you write > > that with the Ifeffit family of programs, not only will people at ESRF > > be able to use it, but so will anyone else. > > > > > If Demeter would works well for large amount of data treatment, it > > > would be great. As I know ID24 at ESRF has also installed the same > > > detector and would probably have similar demanding for such a program. > > > > Looking into Demeter is one option, though I don't know exactly that > > is perfect for the linear combination analysis you want to use. Most > > of the core algorithms in Demeter still use Ifeffit 1.2, which are > > going to be limited for your needs, though they can be worked around > > if careful. Transferring Demeter to use the newer Ifeffit2 should be > > possible, but neither Bruce or I have done more than > > proof-of-principle tests. Looking into using Larch / IFeffit2 > > might be better for you, and I'd be happy to help you do that. For > > one thing, this approach has no memory limitations beyond your > > machine, is in Python and can read HDF5 files (which SOLEIL uses, as > > far as I understand) directly. It also has the possibility of using > > multicore machines well, but this has not yet been automated. It is > > also possible that the linear algebra techniques used for x-ray > > fluorescence map analysis, including code from Gerd Wellenreuther and > > Armando Sole would be useful for your needs. > > > > > Probably due to the limited memory of my pc, I can only open around > > > 200 spectra simultanously with Athena. > > > > You almost certainly want to not use Athena here anyway. You want > > automated processing programs. > > > > Like Bruce hinted at, you've invested heavily in a detector that > > allows you to collect data at a rate orders of magnitude faster than > > you could before. It would have been incredibly naive to believe that > > decade-old software would have been able to keep up with that. This > > is a good opportunity for you to help out yourself and others. > > > > Cheers, > > > > --Matt > > > > > > ------------------------------ > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > End of Ifeffit Digest, Vol 109, Issue 23 > > **************************************** > > > > > > -- > Carmelo Prestipino > Sciences Chimiques de Rennes UMR 6226 > Solid State and Materials Chemistry group (CSM) Campus de Beaulieu, B?t > 10B, bureau 122 > F-35042 RENNES > France > Tel: (+33) 22323 6531 > FAX: (+33) 22323 5959 >

1 0

data from 9.3.1
by Bruce Ravel 02 Apr '12

02 Apr '12

> Hi Dr. Bruce Ravel > > I have Cl K-edge XAS data (as attached for example) that I took from > beamline 9.3.1 ALS four years ago. I can’t import the data into the > Athena, what’s a problem. I want to study XANES of the data. > Thank you, > > Amphol Wongjamras > Department of Physics and Materials Science, Faculty of Science > Chiang Mai University > Chiang Mai, Thailand. Amphol, I am forwarding your question (and my answer) to the Ifeffit mailing list, which is the appropriate venue for asking questions about the software. Please subscribe to and use the mailing list in the future. The problem with the data file you attached is that there are lines with just numbers before the line with the column lables. This confuses Ifeffit and therefore confuses Athena. The simplest solution is to comment out (or, I suppose, delete) the first few lines in the file, like so: # 7 # 008 # # # Mono ev Isignal Izero Ph E 2800.000 -0.05113220 0.30488586 2799.981 2800.500 -0.05165100 0.30612183 2800.482 2801.000 -0.05169678 0.30537415 2800.976 Regards, 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

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 109, Issue 24
by KONG Quingyu 02 Apr '12

02 Apr '12

Thanks a lot Lello and Matt, Now, it is clear to us that we anyway need our own program to automatically treat the big data set. I tried XOP with XAID extension following your suggestions, it is nice to have the graphic operation, but for a big data set with thousands of spectra we need a program. Since we have already part of the program and hope we will finish it soon to a kind of platform for automatic data analysis. Regards, Qingyu -----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: Saturday, March 31, 2012 9:47 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 109, Issue 24 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 109, Issue 23 (Carmelo Prestipino) ---------------------------------------------------------------------- Message: 1 Date: Sat, 31 Mar 2012 21:47:19 +0200 From: Carmelo Prestipino <carmelo.prestipino(a)univ-rennes1.fr> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Ifeffit Digest, Vol 109, Issue 23 Message-ID: <CAHPDQqzGdbkRaXri5raNG60oiT+h1CPdgZVRHmWZ_CvVGML4ig(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi if I can add my two cent...(of EURO) At the ESRF for this kind of studies some work has been done. There is the module XAID of the code XOP wrote by Manuel Sanchez del Rio http://www.esrf.eu/computing/scientific/xop2.1/documentation.html It is written in IDL from scratch. It have normalization and linear combination fit features, it is fully graphically interfaced and in terms of performances is quite impressive. However, the program has a complicate structure that could difficult at the first approach (but Manuel is very kind, don't hesitate to contact him ). Otherwise there is the code PrestoPronto. code.google.com/p/*prestopronto*/ It is mainly a fully graphic python wrapping of ifeffit for sequential analysis. In terms of speed is very similar to Athena but it do automatically the tricks of cleaning memory But it is still a very young code...... It still has not any interface to linear combination analysis. We never tested for more than 1000.. spectra Probably Mark Newton could give you some more suggestions Regards Lello On Sat, Mar 31, 2012 at 7:00 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: Ifeffit Digest, Vol 109, Issue 21 (KONG Quingyu) > 2. Re: Ifeffit Digest, Vol 109, Issue 21 (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 30 Mar 2012 18:32:49 +0000 > From: KONG Quingyu <kong(a)synchrotron-soleil.fr> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 109, Issue 21 > Message-ID: > < > 30F62EE734A9EA45A3F211513CB6200324BD1922(a)SUN-DAG1.synchrotron-soleil.f > r> > > Content-Type: text/plain; charset="iso-8859-1" > > Thank you for all your helpful suggestions. > > Actually, our beamline has recently installed a fast detector with a > repetation of 20KHz, which could collected data in a time resolution > of few tens of microsecond and could easily produce a large amount of > data. We have already accepted three users for microsecond time > resolved studies, each of them collected millions of spectra. > > Together with the company that provide the detector and our software > engineer we started to write a Python program to treat the data from > November last year, however our engineer quitted recently, this make > us to look for other solutions. > > If Demeter would works well for large amount of data treatment, it > would be great. As I know ID24 at ESRF has also installed the same > detector and would probably have similar demanding for such a program. > > Probably due to the limited memory of my pc, I can only open around > 200 spectra simultanously with Athena. > > Best, > Qingyu Kong > > > Beamline ODE > Soci?t? civile Synchrotron SOLEIL > L'Orme des Merisiers > Saint-Aubin - BP 48 > 91192 GIF-sur-YVETTE CEDEX > Tel: +33 (0)1 69 35 97 84 (office) > +33 (0)1 69 35 97 16 (beamline) > email: kong(a)synchrotron-soleil.fr > > ________________________________________ > 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: Friday, March 30, 2012 3:29 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 109, Issue 21 > > 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. delr and ss parameterization (Ebrahim Rezaei) > 2. program (KONG Quingyu) > 3. Re: program (Carlo Segre) > 4. Re: program (Matt Newville) > 5. Re: delr and ss parameterization (Bruce Ravel) > 6. Re: program (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 29 Mar 2012 21:57:21 -0700 (PDT) > From: Ebrahim Rezaei <e_rezaei24(a)yahoo.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] delr and ss parameterization > Message-ID: > > <1333083441.66190.YahooMailClassic(a)web120501.mail.ne1.yahoo.com> > Content-Type: text/plain; charset="utf-8" > > Hi everyone, > > > I am working with bulk and nano structures of MnO, MnO2 and Mn2O3. I > have two questions regarding how to parameterize delr and ss in > Artemis. > > > It is recommended to > use either delr=alfa*Reff or relate it to unit cell structure. Can > anybody tell me how to do the second approach? > > > Also is that a good idea to let all ss to float? Or it should be > constrained based on type and distance of atoms? I have seen an > example about ZnO just letting the first two shell?s ss to float and > let the rest to be the same. I would appreciate it very much if > anybody could help me with this too. > > > Regards, > > > Ebrahim Rezaei > > PhD Candidate, Chem. Eng. Dep., University of Saskatchewan > > Saskatoon, SK, Canada > -------------- next part -------------- An HTML attachment was > scrubbed... > URL: < > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/2012032 > 9/e13d64a5/attachment-0001.htm > > > > ------------------------------ > > Message: 2 > Date: Fri, 30 Mar 2012 06:46:38 +0000 > From: KONG Quingyu <kong(a)synchrotron-soleil.fr> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] program > Message-ID: > < > 30F62EE734A9EA45A3F211513CB6200324BD1794(a)SUN-DAG1.synchrotron-soleil.f > r> > > Content-Type: text/plain; charset="iso-8859-1" > > We recently collected 3000 EXAFS spectra to follow a chemical reaction > process, we would like to fit the experimental data with reference > spectra using linear combination fitting. Does anyone know there are > available or commercial program to normalize the data and make linear > combination fitting. We tried to do it with Athena manually, but 3000 > spectra take a long time for us and it is not a practical way. > > Thanks a lot. > > Qingyu Kong > > Beamline ODE > Soci?t? civile Synchrotron SOLEIL > L'Orme des Merisiers > Saint-Aubin - BP 48 > 91192 GIF-sur-YVETTE CEDEX > Tel: +33 (0)1 69 35 97 84 (office) > +33 (0)1 69 35 97 16 (beamline) > email: kong(a)synchrotron-soleil.fr > > > > > > ------------------------------ > > Message: 3 > Date: Fri, 30 Mar 2012 01:56:57 -0500 (CDT) > From: Carlo Segre <segre(a)iit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] program > Message-ID: <alpine.DEB.2.02.1203300154590.5339(a)hydride.phys.iit.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > Hi Qingyu > > On Fri, 30 Mar 2012, KONG Quingyu wrote: > > > We recently collected 3000 EXAFS spectra to follow a chemical > > reaction process, we would like to fit the experimental data with > > reference spectra using linear combination fitting. Does anyone know > > there are available or commercial program to normalize the data and > > make linear combination fitting. We tried to do it with Athena > > manually, but 3000 spectra take a long time for us and it is not a practical way. > > You might wish to look into Bruce Ravel's new suite of programs > (called Demeter). I believe they are built to allow easy scripting of > massive quantities of data such as yours. > > Carlo > > > -- > Carlo U. Segre -- Duchossois Leadership Professor of Physics Associate > Dean for Graduate Admissions, Graduate College Illinois Institute of > Technology > Voice: 312.567.3498 Fax: 312.567.3494 > segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org > > > ------------------------------ > > Message: 4 > Date: Fri, 30 Mar 2012 07:56:05 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] program > Message-ID: > > <CA+7ESbrjp46_kPw9F803MQOGdMRtFbDa-7oGem25+CL2bYznJg(a)mail.gmail.com > > > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Qingyu, > > On Fri, Mar 30, 2012 at 1:46 AM, KONG Quingyu > <kong(a)synchrotron-soleil.fr> wrote: > > We recently collected 3000 EXAFS spectra to follow a chemical > > reaction > process, we would like to fit the experimental data with reference > spectra using linear combination fitting. Does anyone know there are > available or commercial program to normalize the data and make linear > combination fitting. We tried to do it with Athena manually, but 3000 > spectra take a long time for us and it is not a practical way. > > Ifeffit is designed to be scriptable for batch processing. This can > be done with a raw Ifeffit script (which isn't very flexible) or from > Perl or Python, which are more flexible. Carlo mentioned Demeter, > which is a high-level Perl wrapping of the lower-level functionality. > Working with 3000 spectra may be challenging with Ifeffit version > 1.2, as the total amount of available memory is limited, but with some > care it should be possible. > > FWIW, the next version of Ifeffit will eliminate this memory > limitation, and make both scripting and extending the functionality > much easier and better. This is still a work in progress (see > https://github.com/xraypy/xraylarch) and poorly documented, but the > essential idea is to write all of Ifeffit's functionality in Python, > for all the reasons just stated, and this far enough along that I am > confident it will be a big improvement. So far (for XAFS), this can > read data, do simple pre-edge subtraction, normalization, remove > backgrounds ala autobk, and do XAFS Fourier transforms. It can do > simple "general purpose fitting", but does not yet expose a > simple-to-use linear combination fitting functionality (shouldn't be > too hard, as all the linear algebra pieces are readily available) or > fitting spectra to Feff calculations (a bit more involved). Work is > slow (mostly due to other obligations), but progress is being made, > and it's close to ready for an initial release. If you are (or > anyone else is) interested in trying this or helping out, let me know. > > --Matt > > > > ------------------------------ > > Message: 5 > Date: Fri, 30 Mar 2012 09:13:11 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] delr and ss parameterization > Message-ID: <201203300913.12166.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="utf-8" > > On Friday, March 30, 2012 12:57:21 am Ebrahim Rezaei wrote: > > I am working with bulk and nano structures of MnO, MnO2 and Mn2O3. I > > have two questions regarding how to parameterize delr and ss in > > Artemis. > > > > > > It is recommended to > > use either delr=alfa*Reff or relate it to unit cell structure. Can > anybody > > tell me how to do the second approach? > > > > > > Also is that a good idea to let all ss to float? Or it should be > > constrained based on type and distance of atoms? I have seen an > example > > about ZnO just letting the first two shell?s ss to float and let the > > rest to be the same. I would appreciate it very much if anybody > > could help me with this too. > > The alpha*reff trick is only strictly valid for cubic, monoatomic > materials. For everything else in the world, it is an increasingly > poor approximation. That's not to say it is not a helpful > parameterization, just that you need to be mindful of its limitations. > > As for the sigma^2 parameter, you have to balance when is physically > reasonable with what can be reliably extracted from a real data > analysis. > > - Two atoms of a different species at the same distance should have > different sigma^2 because they have different masses. > > - Two atoms of the same species at different distances should have > different sigma^2 because sigma^2 is a mean square deviation in > distance. > > So, in some sense, all scatterers might have their own sigma^2 > parameters. But that is not to say that you data are sufficient to > independently determine that many parameters. When you run up against > the limited information content of your data, that is when you start > making approximations of the sort that lead to setting sigma^2 > parameters for different scatterers to be the same. > > However, there are sensible and physically justifiable reasons why the > sigma^2 for certain multiple scattering paths should be related to > those of single scattering paths. See > http://dx.doi.org/10.1103/PhysRevB.54.156 > > Two of my favorite papers that show excellent data analysis solving > real-world problems and which are written in a way that is of > pedagogical value for XAS beginners are Scott Calvin's paper on doped > ferrites (http://dx.doi.org/10.1103/PhysRevB.66.224405) and Shelly > Kelly's paper on uranyl binding to biomass > (http://dx.doi.org/10.1016/S0016-7037(02)00947-X) For more > interesting papers, look through the archives of the mailing list and > see who gives good answers to questions, then look up their papers. > > Another extremely useful resource which includes extensive discussion > of the sorts of things you are asking about is Shelly's review > chapter. Here's the amazon link to that book: > > http://www.amazon.com/Methods-Soil-Analysis-Part-Mineralogical/dp/0891 > 188460/ The book is a bit pricy, but if you are a clever googler, you > may find a PDF copy of her chapter. > > Regards, > 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: 6 > Date: Fri, 30 Mar 2012 09:29:10 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] program > Message-ID: <201203300929.11143.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-1" > > On Friday, March 30, 2012 02:46:38 am KONG Quingyu wrote: > > We recently collected 3000 EXAFS spectra to follow a chemical > > reaction process, we would like to fit the experimental data with > > reference > spectra > > using linear combination fitting. Does anyone know there are > > available or commercial program to normalize the data and make > > linear combination fitting. We tried to do it with Athena manually, > > but 3000 spectra take a long time for us and it is not a practical way. > > Hi Qingyu, > > Carlo is correct, Demeter could be used to write a special purpose > program for automating this sort of thing. The performance in terms > of speed may not be exactly what you want, but the performance in > terms of quickly prototyping a program to process and analyze a large > data volume is excellent. > > The Demeter code base comes with extensive (although still incomplete) > documentation as well as plenty of example scripts, including examples > for the individual chores you mention above. > > Here's Demeter's documentation: http://bruceravel.github.com/demeter/ > > > As a closing comment, isn't it somehow strange that you and your > colleagues went to all the trouble of building a fancy dispersive > beamline without thinking ahead about how you were going to analyze > your data? > > 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 > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 109, Issue 21 > **************************************** > > > > ------------------------------ > > Message: 2 > Date: Fri, 30 Mar 2012 16:36:58 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 109, Issue 21 > Message-ID: > > <CA+7ESbrZir3zMWAKSx5HPpqjJ5H_qC-V0YAsnCXUzDO512q+aA(a)mail.gmail.com > > > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Qingyu, > > On Fri, Mar 30, 2012 at 1:32 PM, KONG Quingyu > <kong(a)synchrotron-soleil.fr> wrote: > > Thank you for all your helpful suggestions. > > > > Actually, our beamline has recently installed a fast detector with a > > repetation of 20KHz, which could collected data in a time resolution > > of few tens of microsecond and could easily produce a large amount > > of data. We have already accepted three users for microsecond time > > resolved studies, each of them collected millions of spectra. > > > > Together with the company that provide the detector and our software > > engineer we started to write a Python program to treat the data from > > November last year, however our engineer quitted recently, this make > > us to look for other solutions. > > Bruce wrote earlier, > > As a closing comment, isn't it somehow strange that you and your > colleagues went to all the trouble of building a fancy dispersive > beamline without thinking ahead about how you were going to analyze > your data? > > Sadly, Bruce's observation is not unusual at all. Everyone is > experiencing data overloads, and almost no one is investing in > computing resources. Yours may be slightly larger than most XAFS > users, but only by one or two orders of magnitude. Then again, you > had a software engineer at your beamline at least for a while. > > To be clear, Ifeffit, Athena, Demeter, Sixpack, and so on are written > primarily by beamline scientists like yourself. Your choices are to > use what someone else gives you, write your own, or hire someone to do > it for you. It appears that the last choice rarely works very well. > That you get to use Bruce's codes at all (and for free!) is not an > accident: it is part of the design, and an outcome of the programs > being written by beamline scientists. > > The current software base is more than ten years old, and showing its > age especially with respect to large data sets and multiple > processors. This is a really good opportunity for you and your > colleagues (and others in similar situations) to join in. That is, > you should write code to deal with your fast data rates. If you write > that with the Ifeffit family of programs, not only will people at ESRF > be able to use it, but so will anyone else. > > > If Demeter would works well for large amount of data treatment, it > > would be great. As I know ID24 at ESRF has also installed the same > > detector and would probably have similar demanding for such a program. > > Looking into Demeter is one option, though I don't know exactly that > is perfect for the linear combination analysis you want to use. Most > of the core algorithms in Demeter still use Ifeffit 1.2, which are > going to be limited for your needs, though they can be worked around > if careful. Transferring Demeter to use the newer Ifeffit2 should be > possible, but neither Bruce or I have done more than > proof-of-principle tests. Looking into using Larch / IFeffit2 > might be better for you, and I'd be happy to help you do that. For > one thing, this approach has no memory limitations beyond your > machine, is in Python and can read HDF5 files (which SOLEIL uses, as > far as I understand) directly. It also has the possibility of using > multicore machines well, but this has not yet been automated. It is > also possible that the linear algebra techniques used for x-ray > fluorescence map analysis, including code from Gerd Wellenreuther and > Armando Sole would be useful for your needs. > > > Probably due to the limited memory of my pc, I can only open around > > 200 spectra simultanously with Athena. > > You almost certainly want to not use Athena here anyway. You want > automated processing programs. > > Like Bruce hinted at, you've invested heavily in a detector that > allows you to collect data at a rate orders of magnitude faster than > you could before. It would have been incredibly naive to believe that > decade-old software would have been able to keep up with that. This > is a good opportunity for you to help out yourself and others. > > Cheers, > > --Matt > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 109, Issue 23 > **************************************** > -- Carmelo Prestipino Sciences Chimiques de Rennes UMR 6226 Solid State and Materials Chemistry group (CSM) Campus de Beaulieu, B?t 10B, bureau 122 F-35042 RENNES France Tel: (+33) 22323 6531 FAX: (+33) 22323 5959

2 1

Re: [Ifeffit] Ifeffit Digest, Vol 110, Issue 1
by KONG Quingyu 02 Apr '12

02 Apr '12

Thanks a lot Santiago, by the way, does the program need windows Vista or 7, I installed it in windows XP with different versions, b.0.7 or b.0.6, but it did not work. Best regards, Qingyu Beamline ODE Société civile Synchrotron SOLEIL L'Orme des Merisiers Saint-Aubin - BP 48 91192 GIF-sur-YVETTE CEDEX Tel: +33 (0)1 69 35 97 84 (office) +33 (0)1 69 35 97 16 (beamline) email: kong(a)synchrotron-soleil.fr ________________________________________ 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: Monday, April 02, 2012 9:09 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 110, Issue 1 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. Prestopronto links (Santiago Jos? Alejandro Figueroa) 2. Re: Prestopronto links (Matt Newville) 3. Re: Ifeffit Digest, Vol 109, Issue 24 (KONG Quingyu) ---------------------------------------------------------------------- Message: 1 Date: Sun, 1 Apr 2012 17:53:33 -0300 (BRT) From: Santiago Jos? Alejandro Figueroa <figueroa(a)fisica.unlp.edu.ar> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Prestopronto links Message-ID: <37353.189.61.212.168.1333313613.squirrel(a)mail.fisica.unlp.edu.ar> Content-Type: text/plain;charset=iso-8859-1 Hi I can add my two cent...(of REAIS) The web page of PRESTOPRONTO pointed out by Carmelo is: http://www.esrf.eu/computing/scientific/PRESTOPRONTO/Prestopronto.htm or http://code.google.com/p/prestopronto/ We start to use here at the LNLS in the dispersive beamline with promissing results. Best regards, Santiago ------------------------------ Message: 2 Date: Sun, 1 Apr 2012 17:44:03 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Prestopronto links Message-ID: <CA+7ESbr73fkgSeBCGTZN=5HXZe3P9jHCVgZ36-aCd1PD=8X8VQ(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Santago, Carmelo, 2012/4/1 Santiago Jos? Alejandro Figueroa <figueroa(a)fisica.unlp.edu.ar>: > Hi > > I can add my two cent...(of REAIS) > > The web page of PRESTOPRONTO pointed out by Carmelo is: > > http://www.esrf.eu/computing/scientific/PRESTOPRONTO/Prestopronto.htm > > or > > http://code.google.com/p/prestopronto/ > > We start to use here at the LNLS in the dispersive beamline with > promissing results. > Looks great! Thanks for the links! --Matt ------------------------------ Message: 3 Date: Mon, 2 Apr 2012 07:08:37 +0000 From: KONG Quingyu <kong(a)synchrotron-soleil.fr> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 109, Issue 24 Message-ID: <30F62EE734A9EA45A3F211513CB6200336217807(a)SUN-DAG2.synchrotron-soleil.fr> Content-Type: text/plain; charset="us-ascii" Thanks a lot Lello and Matt, Now, it is clear to us that we anyway need our own program to automatically treat the big data set. I tried XOP with XAID extension following your suggestions, it is nice to have the graphic operation, but for a big data set with thousands of spectra we need a program. Since we have already part of the program and hope we will finish it soon to a kind of platform for automatic data analysis. Regards, Qingyu -----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: Saturday, March 31, 2012 9:47 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 109, Issue 24 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 109, Issue 23 (Carmelo Prestipino) ---------------------------------------------------------------------- Message: 1 Date: Sat, 31 Mar 2012 21:47:19 +0200 From: Carmelo Prestipino <carmelo.prestipino(a)univ-rennes1.fr> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Ifeffit Digest, Vol 109, Issue 23 Message-ID: <CAHPDQqzGdbkRaXri5raNG60oiT+h1CPdgZVRHmWZ_CvVGML4ig(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" Hi if I can add my two cent...(of EURO) At the ESRF for this kind of studies some work has been done. There is the module XAID of the code XOP wrote by Manuel Sanchez del Rio http://www.esrf.eu/computing/scientific/xop2.1/documentation.html It is written in IDL from scratch. It have normalization and linear combination fit features, it is fully graphically interfaced and in terms of performances is quite impressive. However, the program has a complicate structure that could difficult at the first approach (but Manuel is very kind, don't hesitate to contact him ). Otherwise there is the code PrestoPronto. code.google.com/p/*prestopronto*/ It is mainly a fully graphic python wrapping of ifeffit for sequential analysis. In terms of speed is very similar to Athena but it do automatically the tricks of cleaning memory But it is still a very young code...... It still has not any interface to linear combination analysis. We never tested for more than 1000.. spectra Probably Mark Newton could give you some more suggestions Regards Lello On Sat, Mar 31, 2012 at 7:00 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: Ifeffit Digest, Vol 109, Issue 21 (KONG Quingyu) > 2. Re: Ifeffit Digest, Vol 109, Issue 21 (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 30 Mar 2012 18:32:49 +0000 > From: KONG Quingyu <kong(a)synchrotron-soleil.fr> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 109, Issue 21 > Message-ID: > < > 30F62EE734A9EA45A3F211513CB6200324BD1922(a)SUN-DAG1.synchrotron-soleil.f > r> > > Content-Type: text/plain; charset="iso-8859-1" > > Thank you for all your helpful suggestions. > > Actually, our beamline has recently installed a fast detector with a > repetation of 20KHz, which could collected data in a time resolution > of few tens of microsecond and could easily produce a large amount of > data. We have already accepted three users for microsecond time > resolved studies, each of them collected millions of spectra. > > Together with the company that provide the detector and our software > engineer we started to write a Python program to treat the data from > November last year, however our engineer quitted recently, this make > us to look for other solutions. > > If Demeter would works well for large amount of data treatment, it > would be great. As I know ID24 at ESRF has also installed the same > detector and would probably have similar demanding for such a program. > > Probably due to the limited memory of my pc, I can only open around > 200 spectra simultanously with Athena. > > Best, > Qingyu Kong > > > Beamline ODE > Soci?t? civile Synchrotron SOLEIL > L'Orme des Merisiers > Saint-Aubin - BP 48 > 91192 GIF-sur-YVETTE CEDEX > Tel: +33 (0)1 69 35 97 84 (office) > +33 (0)1 69 35 97 16 (beamline) > email: kong(a)synchrotron-soleil.fr > > ________________________________________ > 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: Friday, March 30, 2012 3:29 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 109, Issue 21 > > 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. delr and ss parameterization (Ebrahim Rezaei) > 2. program (KONG Quingyu) > 3. Re: program (Carlo Segre) > 4. Re: program (Matt Newville) > 5. Re: delr and ss parameterization (Bruce Ravel) > 6. Re: program (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 29 Mar 2012 21:57:21 -0700 (PDT) > From: Ebrahim Rezaei <e_rezaei24(a)yahoo.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] delr and ss parameterization > Message-ID: > > <1333083441.66190.YahooMailClassic(a)web120501.mail.ne1.yahoo.com> > Content-Type: text/plain; charset="utf-8" > > Hi everyone, > > > I am working with bulk and nano structures of MnO, MnO2 and Mn2O3. I > have two questions regarding how to parameterize delr and ss in > Artemis. > > > It is recommended to > use either delr=alfa*Reff or relate it to unit cell structure. Can > anybody tell me how to do the second approach? > > > Also is that a good idea to let all ss to float? Or it should be > constrained based on type and distance of atoms? I have seen an > example about ZnO just letting the first two shell?s ss to float and > let the rest to be the same. I would appreciate it very much if > anybody could help me with this too. > > > Regards, > > > Ebrahim Rezaei > > PhD Candidate, Chem. Eng. Dep., University of Saskatchewan > > Saskatoon, SK, Canada > -------------- next part -------------- An HTML attachment was > scrubbed... > URL: < > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/2012032 > 9/e13d64a5/attachment-0001.htm > > > > ------------------------------ > > Message: 2 > Date: Fri, 30 Mar 2012 06:46:38 +0000 > From: KONG Quingyu <kong(a)synchrotron-soleil.fr> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] program > Message-ID: > < > 30F62EE734A9EA45A3F211513CB6200324BD1794(a)SUN-DAG1.synchrotron-soleil.f > r> > > Content-Type: text/plain; charset="iso-8859-1" > > We recently collected 3000 EXAFS spectra to follow a chemical reaction > process, we would like to fit the experimental data with reference > spectra using linear combination fitting. Does anyone know there are > available or commercial program to normalize the data and make linear > combination fitting. We tried to do it with Athena manually, but 3000 > spectra take a long time for us and it is not a practical way. > > Thanks a lot. > > Qingyu Kong > > Beamline ODE > Soci?t? civile Synchrotron SOLEIL > L'Orme des Merisiers > Saint-Aubin - BP 48 > 91192 GIF-sur-YVETTE CEDEX > Tel: +33 (0)1 69 35 97 84 (office) > +33 (0)1 69 35 97 16 (beamline) > email: kong(a)synchrotron-soleil.fr > > > > > > ------------------------------ > > Message: 3 > Date: Fri, 30 Mar 2012 01:56:57 -0500 (CDT) > From: Carlo Segre <segre(a)iit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] program > Message-ID: <alpine.DEB.2.02.1203300154590.5339(a)hydride.phys.iit.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > Hi Qingyu > > On Fri, 30 Mar 2012, KONG Quingyu wrote: > > > We recently collected 3000 EXAFS spectra to follow a chemical > > reaction process, we would like to fit the experimental data with > > reference spectra using linear combination fitting. Does anyone know > > there are available or commercial program to normalize the data and > > make linear combination fitting. We tried to do it with Athena > > manually, but 3000 spectra take a long time for us and it is not a practical way. > > You might wish to look into Bruce Ravel's new suite of programs > (called Demeter). I believe they are built to allow easy scripting of > massive quantities of data such as yours. > > Carlo > > > -- > Carlo U. Segre -- Duchossois Leadership Professor of Physics Associate > Dean for Graduate Admissions, Graduate College Illinois Institute of > Technology > Voice: 312.567.3498 Fax: 312.567.3494 > segre(a)iit.edu http://phys.iit.edu/~segre segre(a)debian.org > > > ------------------------------ > > Message: 4 > Date: Fri, 30 Mar 2012 07:56:05 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] program > Message-ID: > > <CA+7ESbrjp46_kPw9F803MQOGdMRtFbDa-7oGem25+CL2bYznJg(a)mail.gmail.com > > > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Qingyu, > > On Fri, Mar 30, 2012 at 1:46 AM, KONG Quingyu > <kong(a)synchrotron-soleil.fr> wrote: > > We recently collected 3000 EXAFS spectra to follow a chemical > > reaction > process, we would like to fit the experimental data with reference > spectra using linear combination fitting. Does anyone know there are > available or commercial program to normalize the data and make linear > combination fitting. We tried to do it with Athena manually, but 3000 > spectra take a long time for us and it is not a practical way. > > Ifeffit is designed to be scriptable for batch processing. This can > be done with a raw Ifeffit script (which isn't very flexible) or from > Perl or Python, which are more flexible. Carlo mentioned Demeter, > which is a high-level Perl wrapping of the lower-level functionality. > Working with 3000 spectra may be challenging with Ifeffit version > 1.2, as the total amount of available memory is limited, but with some > care it should be possible. > > FWIW, the next version of Ifeffit will eliminate this memory > limitation, and make both scripting and extending the functionality > much easier and better. This is still a work in progress (see > https://github.com/xraypy/xraylarch) and poorly documented, but the > essential idea is to write all of Ifeffit's functionality in Python, > for all the reasons just stated, and this far enough along that I am > confident it will be a big improvement. So far (for XAFS), this can > read data, do simple pre-edge subtraction, normalization, remove > backgrounds ala autobk, and do XAFS Fourier transforms. It can do > simple "general purpose fitting", but does not yet expose a > simple-to-use linear combination fitting functionality (shouldn't be > too hard, as all the linear algebra pieces are readily available) or > fitting spectra to Feff calculations (a bit more involved). Work is > slow (mostly due to other obligations), but progress is being made, > and it's close to ready for an initial release. If you are (or > anyone else is) interested in trying this or helping out, let me know. > > --Matt > > > > ------------------------------ > > Message: 5 > Date: Fri, 30 Mar 2012 09:13:11 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] delr and ss parameterization > Message-ID: <201203300913.12166.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="utf-8" > > On Friday, March 30, 2012 12:57:21 am Ebrahim Rezaei wrote: > > I am working with bulk and nano structures of MnO, MnO2 and Mn2O3. I > > have two questions regarding how to parameterize delr and ss in > > Artemis. > > > > > > It is recommended to > > use either delr=alfa*Reff or relate it to unit cell structure. Can > anybody > > tell me how to do the second approach? > > > > > > Also is that a good idea to let all ss to float? Or it should be > > constrained based on type and distance of atoms? I have seen an > example > > about ZnO just letting the first two shell?s ss to float and let the > > rest to be the same. I would appreciate it very much if anybody > > could help me with this too. > > The alpha*reff trick is only strictly valid for cubic, monoatomic > materials. For everything else in the world, it is an increasingly > poor approximation. That's not to say it is not a helpful > parameterization, just that you need to be mindful of its limitations. > > As for the sigma^2 parameter, you have to balance when is physically > reasonable with what can be reliably extracted from a real data > analysis. > > - Two atoms of a different species at the same distance should have > different sigma^2 because they have different masses. > > - Two atoms of the same species at different distances should have > different sigma^2 because sigma^2 is a mean square deviation in > distance. > > So, in some sense, all scatterers might have their own sigma^2 > parameters. But that is not to say that you data are sufficient to > independently determine that many parameters. When you run up against > the limited information content of your data, that is when you start > making approximations of the sort that lead to setting sigma^2 > parameters for different scatterers to be the same. > > However, there are sensible and physically justifiable reasons why the > sigma^2 for certain multiple scattering paths should be related to > those of single scattering paths. See > http://dx.doi.org/10.1103/PhysRevB.54.156 > > Two of my favorite papers that show excellent data analysis solving > real-world problems and which are written in a way that is of > pedagogical value for XAS beginners are Scott Calvin's paper on doped > ferrites (http://dx.doi.org/10.1103/PhysRevB.66.224405) and Shelly > Kelly's paper on uranyl binding to biomass > (http://dx.doi.org/10.1016/S0016-7037(02)00947-X) For more > interesting papers, look through the archives of the mailing list and > see who gives good answers to questions, then look up their papers. > > Another extremely useful resource which includes extensive discussion > of the sorts of things you are asking about is Shelly's review > chapter. Here's the amazon link to that book: > > http://www.amazon.com/Methods-Soil-Analysis-Part-Mineralogical/dp/0891 > 188460/ The book is a bit pricy, but if you are a clever googler, you > may find a PDF copy of her chapter. > > Regards, > 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: 6 > Date: Fri, 30 Mar 2012 09:29:10 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] program > Message-ID: <201203300929.11143.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-1" > > On Friday, March 30, 2012 02:46:38 am KONG Quingyu wrote: > > We recently collected 3000 EXAFS spectra to follow a chemical > > reaction process, we would like to fit the experimental data with > > reference > spectra > > using linear combination fitting. Does anyone know there are > > available or commercial program to normalize the data and make > > linear combination fitting. We tried to do it with Athena manually, > > but 3000 spectra take a long time for us and it is not a practical way. > > Hi Qingyu, > > Carlo is correct, Demeter could be used to write a special purpose > program for automating this sort of thing. The performance in terms > of speed may not be exactly what you want, but the performance in > terms of quickly prototyping a program to process and analyze a large > data volume is excellent. > > The Demeter code base comes with extensive (although still incomplete) > documentation as well as plenty of example scripts, including examples > for the individual chores you mention above. > > Here's Demeter's documentation: http://bruceravel.github.com/demeter/ > > > As a closing comment, isn't it somehow strange that you and your > colleagues went to all the trouble of building a fancy dispersive > beamline without thinking ahead about how you were going to analyze > your data? > > 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 > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 109, Issue 21 > **************************************** > > > > ------------------------------ > > Message: 2 > Date: Fri, 30 Mar 2012 16:36:58 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 109, Issue 21 > Message-ID: > > <CA+7ESbrZir3zMWAKSx5HPpqjJ5H_qC-V0YAsnCXUzDO512q+aA(a)mail.gmail.com > > > Content-Type: text/plain; charset=ISO-8859-1 > > Hi Qingyu, > > On Fri, Mar 30, 2012 at 1:32 PM, KONG Quingyu > <kong(a)synchrotron-soleil.fr> wrote: > > Thank you for all your helpful suggestions. > > > > Actually, our beamline has recently installed a fast detector with a > > repetation of 20KHz, which could collected data in a time resolution > > of few tens of microsecond and could easily produce a large amount > > of data. We have already accepted three users for microsecond time > > resolved studies, each of them collected millions of spectra. > > > > Together with the company that provide the detector and our software > > engineer we started to write a Python program to treat the data from > > November last year, however our engineer quitted recently, this make > > us to look for other solutions. > > Bruce wrote earlier, > > As a closing comment, isn't it somehow strange that you and your > colleagues went to all the trouble of building a fancy dispersive > beamline without thinking ahead about how you were going to analyze > your data? > > Sadly, Bruce's observation is not unusual at all. Everyone is > experiencing data overloads, and almost no one is investing in > computing resources. Yours may be slightly larger than most XAFS > users, but only by one or two orders of magnitude. Then again, you > had a software engineer at your beamline at least for a while. > > To be clear, Ifeffit, Athena, Demeter, Sixpack, and so on are written > primarily by beamline scientists like yourself. Your choices are to > use what someone else gives you, write your own, or hire someone to do > it for you. It appears that the last choice rarely works very well. > That you get to use Bruce's codes at all (and for free!) is not an > accident: it is part of the design, and an outcome of the programs > being written by beamline scientists. > > The current software base is more than ten years old, and showing its > age especially with respect to large data sets and multiple > processors. This is a really good opportunity for you and your > colleagues (and others in similar situations) to join in. That is, > you should write code to deal with your fast data rates. If you write > that with the Ifeffit family of programs, not only will people at ESRF > be able to use it, but so will anyone else. > > > If Demeter would works well for large amount of data treatment, it > > would be great. As I know ID24 at ESRF has also installed the same > > detector and would probably have similar demanding for such a program. > > Looking into Demeter is one option, though I don't know exactly that > is perfect for the linear combination analysis you want to use. Most > of the core algorithms in Demeter still use Ifeffit 1.2, which are > going to be limited for your needs, though they can be worked around > if careful. Transferring Demeter to use the newer Ifeffit2 should be > possible, but neither Bruce or I have done more than > proof-of-principle tests. Looking into using Larch / IFeffit2 > might be better for you, and I'd be happy to help you do that. For > one thing, this approach has no memory limitations beyond your > machine, is in Python and can read HDF5 files (which SOLEIL uses, as > far as I understand) directly. It also has the possibility of using > multicore machines well, but this has not yet been automated. It is > also possible that the linear algebra techniques used for x-ray > fluorescence map analysis, including code from Gerd Wellenreuther and > Armando Sole would be useful for your needs. > > > Probably due to the limited memory of my pc, I can only open around > > 200 spectra simultanously with Athena. > > You almost certainly want to not use Athena here anyway. You want > automated processing programs. > > Like Bruce hinted at, you've invested heavily in a detector that > allows you to collect data at a rate orders of magnitude faster than > you could before. It would have been incredibly naive to believe that > decade-old software would have been able to keep up with that. This > is a good opportunity for you to help out yourself and others. > > Cheers, > > --Matt > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 109, Issue 23 > **************************************** > -- Carmelo Prestipino Sciences Chimiques de Rennes UMR 6226 Solid State and Materials Chemistry group (CSM) Campus de Beaulieu, B?t 10B, bureau 122 F-35042 RENNES France Tel: (+33) 22323 6531 FAX: (+33) 22323 5959

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Prestopronto links
by Santiago José Alejandro Figueroa 01 Apr '12

01 Apr '12

Hi I can add my two cent...(of REAIS) The web page of PRESTOPRONTO pointed out by Carmelo is: http://www.esrf.eu/computing/scientific/PRESTOPRONTO/Prestopronto.htm or http://code.google.com/p/prestopronto/ We start to use here at the LNLS in the dispersive beamline with promissing results. Best regards, Santiago

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Re: [Ifeffit] Ifeffit Digest, Vol 109, Issue 23
by Carmelo Prestipino 31 Mar '12

31 Mar '12

Hi if I can add my two cent...(of EURO) At the ESRF for this kind of studies some work has been done. There is the module XAID of the code XOP wrote by Manuel Sanchez del Rio http://www.esrf.eu/computing/scientific/xop2.1/documentation.html It is written in IDL from scratch. It have normalization and linear combination fit features, it is fully graphically interfaced and in terms of performances is quite impressive. However, the program has a complicate structure that could difficult at the first approach (but Manuel is very kind, don't hesitate to contact him ). Otherwise there is the code PrestoPronto. code.google.com/p/*prestopronto*/ It is mainly a fully graphic python wrapping of ifeffit for sequential analysis. In terms of speed is very similar to Athena but it do automatically the tricks of cleaning memory But it is still a very young code...... It still has not any interface to linear combination analysis. We never tested for more than 1000.. spectra Probably Mark Newton could give you some more suggestions Regards Lello On Sat, Mar 31, 2012 at 7:00 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: Ifeffit Digest, Vol 109, Issue 21 (KONG Quingyu) > 2. Re: Ifeffit Digest, Vol 109, Issue 21 (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 30 Mar 2012 18:32:49 +0000 > From: KONG Quingyu <kong(a)synchrotron-soleil.fr> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 109, Issue 21 > Message-ID: > < > 30F62EE734A9EA45A3F211513CB6200324BD1922(a)SUN-DAG1.synchrotron-soleil.fr> > > Content-Type: text/plain; charset="iso-8859-1" > > Thank you for all your helpful suggestions. > > Actually, our beamline has recently installed a fast detector with a > repetation of 20KHz, which could collected data in a time resolution of few > tens of microsecond and could easily produce a large amount of data. We > have already accepted three users for microsecond time resolved studies, > each of them collected millions of spectra. > > Together with the company that provide the detector and our software > engineer we started to write a Python program to treat the data from > November last year, however our engineer quitted recently, this make us to > look for other solutions. > > If Demeter would works well for large amount of data treatment, it would > be great. As I know ID24 at ESRF has also installed the same detector and > would probably have similar demanding for such a program. > > Probably due to the limited memory of my pc, I can only open around 200 > spectra simultanously with Athena. > > Best, > Qingyu Kong > > > Beamline ODE > Soci?t? civile Synchrotron SOLEIL > L'Orme des Merisiers > Saint-Aubin - BP 48 > 91192 GIF-sur-YVETTE CEDEX > Tel: +33 (0)1 69 35 97 84 (office) > +33 (0)1 69 35 97 16 (beamline) > email: kong(a)synchrotron-soleil.fr > > ________________________________________ > 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: Friday, March 30, 2012 3:29 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 109, Issue 21 > > 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. delr and ss parameterization (Ebrahim Rezaei) > 2. program (KONG Quingyu) > 3. Re: program (Carlo Segre) > 4. Re: program (Matt Newville) > 5. Re: delr and ss parameterization (Bruce Ravel) > 6. Re: program (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 29 Mar 2012 21:57:21 -0700 (PDT) > From: Ebrahim Rezaei <e_rezaei24(a)yahoo.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] delr and ss parameterization > Message-ID: > <1333083441.66190.YahooMailClassic(a)web120501.mail.ne1.yahoo.com> > Content-Type: text/plain; charset="utf-8" > > Hi everyone, > > > I am working with bulk and nano structures of MnO, MnO2 > and Mn2O3. I have two questions regarding how to > parameterize delr and ss in Artemis. > > > It is recommended to > use either delr=alfa*Reff or relate it to unit cell structure. Can anybody > tell > me how to do the second approach? > > > Also is that a good idea to let all ss to float? Or it should > be constrained based on type and distance of atoms? I have seen an example > about ZnO just letting the first two shell?s ss to float and let the rest > to be > the same. I would appreciate it very much if anybody could help me with > this too. > > > Regards, > > > Ebrahim Rezaei > > PhD Candidate, Chem. Eng. Dep., University of Saskatchewan > > Saskatoon, SK, Canada >

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Re: [Ifeffit] Ifeffit Digest, Vol 109, Issue 21
by KONG Quingyu 30 Mar '12

30 Mar '12

Thank you for all your helpful suggestions. Actually, our beamline has recently installed a fast detector with a repetation of 20KHz, which could collected data in a time resolution of few tens of microsecond and could easily produce a large amount of data. We have already accepted three users for microsecond time resolved studies, each of them collected millions of spectra. Together with the company that provide the detector and our software engineer we started to write a Python program to treat the data from November last year, however our engineer quitted recently, this make us to look for other solutions. If Demeter would works well for large amount of data treatment, it would be great. As I know ID24 at ESRF has also installed the same detector and would probably have similar demanding for such a program. Probably due to the limited memory of my pc, I can only open around 200 spectra simultanously with Athena. Best, Qingyu Kong Beamline ODE Société civile Synchrotron SOLEIL L'Orme des Merisiers Saint-Aubin - BP 48 91192 GIF-sur-YVETTE CEDEX Tel: +33 (0)1 69 35 97 84 (office) +33 (0)1 69 35 97 16 (beamline) email: kong(a)synchrotron-soleil.fr ________________________________________ 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: Friday, March 30, 2012 3:29 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 109, Issue 21 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. delr and ss parameterization (Ebrahim Rezaei) 2. program (KONG Quingyu) 3. Re: program (Carlo Segre) 4. Re: program (Matt Newville) 5. Re: delr and ss parameterization (Bruce Ravel) 6. Re: program (Bruce Ravel) ---------------------------------------------------------------------- Message: 1 Date: Thu, 29 Mar 2012 21:57:21 -0700 (PDT) From: Ebrahim Rezaei <e_rezaei24(a)yahoo.com> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] delr and ss parameterization Message-ID: <1333083441.66190.YahooMailClassic(a)web120501.mail.ne1.yahoo.com> Content-Type: text/plain; charset="utf-8" Hi everyone, I am working with bulk and nano structures of MnO, MnO2 and Mn2O3. I have two questions regarding how to parameterize delr and ss in Artemis. It is recommended to use either delr=alfa*Reff or relate it to unit cell structure. Can anybody tell me how to do the second approach? Also is that a good idea to let all ss to float? Or it should be constrained based on type and distance of atoms? I have seen an example about ZnO just letting the first two shell?s ss to float and let the rest to be the same. I would appreciate it very much if anybody could help me with this too. Regards, Ebrahim Rezaei PhD Candidate, Chem. Eng. Dep., University of Saskatchewan Saskatoon, SK, Canada

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program
by KONG Quingyu 30 Mar '12

30 Mar '12

We recently collected 3000 EXAFS spectra to follow a chemical reaction process, we would like to fit the experimental data with reference spectra using linear combination fitting. Does anyone know there are available or commercial program to normalize the data and make linear combination fitting. We tried to do it with Athena manually, but 3000 spectra take a long time for us and it is not a practical way. Thanks a lot. Qingyu Kong Beamline ODE Société civile Synchrotron SOLEIL L'Orme des Merisiers Saint-Aubin - BP 48 91192 GIF-sur-YVETTE CEDEX Tel: +33 (0)1 69 35 97 84 (office) +33 (0)1 69 35 97 16 (beamline) email: kong(a)synchrotron-soleil.fr

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delr and ss parameterization
by Ebrahim Rezaei 30 Mar '12

30 Mar '12

Hi everyone, I am working with bulk and nano structures of MnO, MnO2 and Mn2O3. I have two questions regarding how to parameterize delr and ss in Artemis. It is recommended to use either delr=alfa*Reff or relate it to unit cell structure. Can anybody tell me how to do the second approach? Also is that a good idea to let all ss to float? Or it should be constrained based on type and distance of atoms? I have seen an example about ZnO just letting the first two shell’s ss to float and let the rest to be the same. I would appreciate it very much if anybody could help me with this too. Regards, Ebrahim Rezaei PhD Candidate, Chem. Eng. Dep., University of Saskatchewan Saskatoon, SK, Canada

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