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

Open position at HASYLAB
by Welter, Edmund 01 Dec '09

01 Dec '09

Dear XAFS users, if you are interested or know someone who might be interested in a postdoc position in the field of spectroscopy with X-rays, please have a look at our recent job advertisement: http://www.desy.de/v2/docs/1257511440-e.pdf Regards, Edmund Welter

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Re: [Ifeffit] Ifeffit Digest, Vol 81, Issue 25
by Jasquelin Pena 30 Nov '09

30 Nov '09

Scott, .cif files for many minerals can be downloaded from the AMCSD: http://rruff.geo.arizona.edu/AMS/amcsd.php Jasquelin On Mon, 30 Nov 2009, 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: Request a .cif file for alpha & beta Nickel hydroxide > (Scott Wicker (Student)) > 2. Re: Request a .cif file for alpha & beta Nickel hydroxide > (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 29 Nov 2009 12:06:19 -0600 > From: "Scott Wicker (Student)" <scott_wicker_00(a)subr.edu> > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Request a .cif file for alpha & beta Nickel > hydroxide > Message-ID: > <301F55994159DB4682AA882A772707E1013EF192(a)primary14.subr.edu> > Content-Type: text/plain; charset="iso-8859-1" > > I would like to request a .cif file for the alpha & beta Nickel hydroxide. If someone also have .cif files for Cobalt hydroxide this will be greatly appreciated. Is there a single crystal data base for .cif files? > > thanks, > > Scott A. Wicker Sr. > Ph.d Graduate Student > Environmental Toxicology > Southern University A & M > Baton Rouge, LA 70813 > School: scott_wicker_00(a)cxs.subr.edu > Home: swicker(a)cox.net > > > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Frenkel, Anatoly > Sent: Fri 11/27/2009 1:12 PM > To: jswashin(a)ncsu.edu; XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Bond length determination EXAFS vs XRD > > XRD measures interplanar spacing, and XAFS - interatomic distances, and they are not the same if disorder is present. Look for articles by Boyce and Mikkelsen, Jr., in Phys Rev B in 1980's who were the first discussing these concepts in GaAs-InAs semiconductors and also KBr-RbBr ionic salts. > They showed that the average structure ascertained by diffraction differs from the local structure measured by EXAFS. > Modern day high energy XRD/PDF measures interatomic distances more accurately than Bragg peak analysis can do but how accurately it agrees with EXAFS is still subject of debates. > Anatoly > > > _____ > > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov on behalf of Joseph Washington > Sent: Fri 11/27/2009 2:08 PM > To: XAFS Analysis using Ifeffit > Subject: [Ifeffit] Bond length determination EXAFS vs XRD > > > > Happy Thanksgiving All! > > Can someone, send me some references which explains some of the reasons > why the bond lengths fitted in EXAFS would be different from that fitted > in XRD (assuming that we implemented the crystal model predicted by XRD > correctly in Artemis)? > > I would really appreciate this! > > Sincerely > -- > Joseph Washington > Research Assistant > Department of Physics > North Carolina State University > 431 Riddick Hall > Raleigh, NC 27695-8202 > email: jswashin(a)ncsu.edu > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > >

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Request a .cif file for alpha & beta Nickel hydroxide
by Eugenio Otal 30 Nov '09

30 Nov '09

Try with this database: http://www.icsd.iqfr.csic.es/ Regards, euG

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Bond length determination EXAFS vs XRD
by Joseph Washington 30 Nov '09

30 Nov '09

Happy Thanksgiving All! Can someone, send me some references which explains some of the reasons why the bond lengths fitted in EXAFS would be different from that fitted in XRD (assuming that we implemented the crystal model predicted by XRD correctly in Artemis)? I would really appreciate this! Sincerely -- Joseph Washington Research Assistant Department of Physics North Carolina State University 431 Riddick Hall Raleigh, NC 27695-8202 email: jswashin(a)ncsu.edu

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Re: [Ifeffit] Path degeneracy modification in feffNNN.dat
by Frenkel, Anatoly 21 Nov '09

21 Nov '09

It takes it from N. Anatoly ----- Original Message ----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Fri Nov 20 18:57:29 2009 Subject: Re: [Ifeffit] Path degeneracy modification in feffNNN.dat Hi ｔｈｅｒｅ, I have a general question about Artemis. I am going to split a degenerated path with degeneracy N=8 into twoｓ. I noticed that by cloning the path, the "N" in path math expression parameters was halved as "4". However, the degeneracy number in feffNNN.dat remains as "8". For fitting, where will Artemis exactly get this information? Or maybe I　ｓｈｏｕｌｄ　ｍｏｄｉｆｙ　ｆｅｆｆＮＮＮ．ｄａｔ　ｍａｎｕａｌｌｙ？　　Ｔｈａｎｋｓ　ｆｏｒ　ｙｏｕｒ　ｒｅｓｐｏｎｓｅ！＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝Ｄｒ．　Ｙｉｎｇ　ＺｏｕＲｅｓｅａｒｃｈ　Ａｓｓｏｃｉａｔｅ，ＵＷＭ／Ｐｈｙｓｉｃｓ，１９００　Ｅ．　Ｋｅｎｗｏｏｄ　Ｂｌｖｄ，Ｍｉｌｗａｕｋｅｅ，　ＷＩ５３２１７＝＝＝＝＝＝＝＝＝＝＝＝＝＝ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Re: [Ifeffit] Path degeneracy modification in feffNNN.dat
by Ying Zou 20 Nov '09

20 Nov '09

Hi ｔｈｅｒｅ, I have a general question about Artemis. I am going to split a degenerated path with degeneracy N=8 into twoｓ. I noticed that by cloning the path, the "N" in path math expression parameters was halved as "4". However, the degeneracy number in feffNNN.dat remains as "8". For fitting, where will Artemis exactly get this information? Or maybe I　ｓｈｏｕｌｄ　ｍｏｄｉｆｙ　ｆｅｆｆＮＮＮ．ｄａｔ　ｍａｎｕａｌｌｙ？　　Ｔｈａｎｋｓ　ｆｏｒ　ｙｏｕｒ　ｒｅｓｐｏｎｓｅ！＝＝＝＝＝＝＝＝＝＝＝＝＝＝＝Ｄｒ．　Ｙｉｎｇ　ＺｏｕＲｅｓｅａｒｃｈ　Ａｓｓｏｃｉａｔｅ，ＵＷＭ／Ｐｈｙｓｉｃｓ，１９００　Ｅ．　Ｋｅｎｗｏｏｄ　Ｂｌｖｄ，Ｍｉｌｗａｕｋｅｅ，　ＷＩ５３２１７＝＝＝＝＝＝＝＝＝＝＝＝＝＝

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E0 problems
by Chris Patridge 17 Nov '09

17 Nov '09

Hello, I am having some trouble with a first shell fitting. I have good reason to believe that the compound crystal structure should be quite similar to the starting input structure from other reliable analysis. The closest neighbor paths V-O is 1.61 A away so I set R to 0.8 as a start. I summed what I think are pertinent paths together and tried to fit these paths to a first shell. The bmp file attached contains the fit, summed paths, and the data all in R-space. The fit comes away with a small amplitude, huge E0 of close to -21 eV and negative delr & ss. I have included the artemis project. Is the k-space any indication that the data is too noisy? Any suggestions and or questions would be greatly appreciated. Thank you all, Chris Patridge UB Graduate Student Department of Chemistry Cell: 315-529-0501

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SO2 parameter for Cu2O
by abhijeet gaur 13 Nov '09

13 Nov '09

Hi all, I am fitting Cu2O EXAFS data taken at SSRL using the Artemis. But there is a problem with fitting results that SO2 parameter is coming very low around 0.50. I had also taken Cu2O data from different data bases to check whether theere some problem with my data, but after fitting them, the same problem of low SO2 is coming. In some research papers given SO2 parameter for Cu2O equal to 0.82. But I am unable to get that why all the Cu2O data giving low value of SO2. Is there any other fitting procedure to fit the compounds like Cu2O ?????? With thanks Abhijeet Gaur

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Re: [Ifeffit] Question about ATHENA software
by Bruce Ravel 13 Nov '09

13 Nov '09

Claudia, The implementation of the XANES self-absorption corrections follows the thing that Daniel Haskel wrote up here: http://www.aps.anl.gov/xfd/people/haskel/fluo.html The algorithm used is explained on pages 5-9 of the postscript file on that web page. The angles are defined relative to the surface, not the surface normal. HTH, B PS: You should consider joining the Ifeffit mailing list: (http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit) It is a very useful resource for siftware and for XAS in general. On Saturday 07 November 2009 02:22:45 pm you wrote: > Dear Bruce Ravel, > > I am a PhD student currently working with the ATHENA software. I came > across a question which I could not answer even after searching the > internet for hours. I hope you might have the time to briefly answer my > question. > > The self-absorption dialog requires the incoming (angle in) and the > outgoing angle (angle out) as an input. My basic question is: Are these > angles referenced to the sample surface or to the normal of the surface? > I would not worry about that if I had measured in 45deg geometry (as in > your tutorial example). However, I did not and therefore it makes a > large difference. > > I strongly apologize bothering you with such a basic question. > Many thanks in advance. > Best regards, > Claudia Fleischmann -- 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/~ravel/software/exafs/

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SO2 parameter problem
by abhijeet gaur 12 Nov '09

12 Nov '09

Hi all, I am fitting CuO2 EXAFS data taken at SSRL using the Artemis. But there is a problem with fitting results that SO2 parameter is coming very low around 0.50. I had also taken CuO2 data from different data bases to check whether theere some problem with my data, but after fitting them, the same problem of low SO2 is coming. In some research papers given SO2 parameter for CuO2 equal to 0.82. But I am unable to get that why all the CuO2 data giving low value of SO2. Is there any other fitting procedure to fit the compounds like CuO2 ?????? With thanks Abhijeet Gaur

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Why I can't install ifeffit?
by 康明亮 10 Nov '09

10 Nov '09

Dear, I don't konw why I can't intall ifeffit. As I run the Anthena programm, it prompted me the following message: Cannot execute grwnd.exe to open the graphics window. I don;t know how to resolve this problem. wish to obtain guidance. Thank you. Best regards Mingliang

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consultation
by 康明亮 10 Nov '09

10 Nov '09

Dear, I have encountered a problem when using IFEFFIT. As I double click the Athena icon on the desktop, it prompted the following concent: Cannot execute grwnd.exe to open the graphics window. How to resolve this problem? Thank you! Best regards Mingliang

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Athena User Guide—FCFS
by Julie Olmsted Cross 09 Nov '09

09 Nov '09

I have ten copies of the Athena User Guide leftover from the 2009 APS XAFS School. If you want one, send me your mailing address. First come, first served. ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~ Dr. Julie O. Cross User Technical Interface APS Engineering Support Division Argonne National Laboratory 9700 South Cass Ave., Bldg. 401/B4204 Argonne IL 60439-4801 tel: 630 252 0592 fax: 630 252 7187 ~^^~^~^~~^~^~^~^~^~^~^~^~~^~^~

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Re: [Ifeffit] Ifeffit Digest, Vol 81, Issue 7
by Khalid, Syed 09 Nov '09

09 Nov '09

The (Passivated Implanted Planar Silicon) PIPS detector that we purchase for our beamlines is model: PD 3000-55-300-AB AB is for BNC connector, if not specified they mail it with an AM (Axial Microdot) connector. PD is partially Depleted, 3000 mm square is the area of the detector. 55 KeV (FWHM) is the energy resolution for alpha particles, and 300 is the thickness of Si in microns. Syed Khalid -----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: Monday, November 09, 2009 1:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 81, Issue 7 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: python 2.6 wrapper (Carmelo Prestipino) 2. consultation (???) 3. Re: Question about ATHENA software (Bruce Ravel) 4. PIPs detectors (Bruce Ravel) 5. Re: PIPs detectors (Jeff Terry) ---------------------------------------------------------------------- Message: 1 Date: Mon, 09 Nov 2009 14:19:42 +0100 From: Carmelo Prestipino <carmelo.prestipino(a)esrf.fr> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] python 2.6 wrapper Message-ID: <20091109141942.0tdnvgz3ogcw0ckw(a)160.103.2.152> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Dear Matt and Carlo I was speaking about windows, sorry for the imprecision. I tested today the file sent by Matt, on my computer all seems to work fine with Python 2.6. Cheers Carmelo Quoting ifeffit-request(a)millenia.cars.aps.anl.gov: > 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. python 2.6 wrapper (Carmelo Prestipino) > 2. Re: python 2.6 wrapper (Carlo Segre) > 3. Re: python 2.6 wrapper (Matt Newville) > 4. Re: Ifeffit (Matt Newville) > 5. Re: Ifeffit (Cl?ment Levard) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 06 Nov 2009 10:50:25 +0100 > From: Carmelo Prestipino <carmelo.prestipino(a)esrf.fr> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] python 2.6 wrapper > Message-ID: <20091106105025.gifreaxeogoc440g(a)160.103.2.152> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Dear All > I upgraded my my python version on 2.6, I was wondering if is it > available a new Ifeffit wrapper for this version? > Best regards > Carmelo > > -- > > --------------------------------------- > Dr. Carmelo Prestipino > European Synchrotron Radiation Facility > BP220, 38043 Grenoble Cedex, > FRANCE > Tel: +33 (0)4 38 88 19 29 > --------------------------------------- > > > ------------------------------ > > Message: 2 > Date: Fri, 6 Nov 2009 07:46:55 -0600 (CST) > From: Carlo Segre <segre(a)iit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] python 2.6 wrapper > Message-ID: <alpine.DEB.1.10.0911060746230.3348(a)arsenide.iit.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > What is your operating system? The gifeffit progrm should work fine with > most versions of python. > > Carlo > > > On Fri, 6 Nov 2009, Carmelo Prestipino wrote: > >> Dear All >> I upgraded my my python version on 2.6, I was wondering if is it available a >> new Ifeffit wrapper for this version? >> Best regards >> Carmelo >> >> > > -- > Carlo U. Segre -- 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://www.iit.edu/~segre segre(a)debian.org > > > ------------------------------ > > Message: 3 > Date: Fri, 6 Nov 2009 10:46:46 -0600 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] python 2.6 wrapper > Message-ID: > <b8522e3d0911060846t6f7bea35j83dbff53c6c580d2(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Carmelo, Carlo, > > As Carlo says, on linux there should be no problem with the older > build system.... I'm using python2.6 and Ifeffit on linux. > > So, I'll assume you're asking about Windows. I do not yet have an > executable installer for Python2.6 on Windows. But, if you're brave, > I have something for you to try. In fact, just this past week, as > part of a move to a new Windows build system (see > http://cars9.uchicago.edu/ifeffit/MingwBuild) I've moved from using a > C extension for Python to using Python's ctypes library. This means > that the Ifeffit-Python interface is in pure Python and uses the DLL > directly, which is much better than the previous situation. > > I've tested this with python 2.6 and it works for me on both Windows > and linux, with very minor differences between them. The result > (Ifefffit.py attached) should be viewed as "beta testing" stage -- If > you try it out, I'd love to hear about any issues you have with it. I > don't have a nice installer for this, but you should be able to put > this in any folder that Python will find it. If you don't have > Ifeffit installed to C:\Program Files\Ifeffit, you may need to alter > the top of the script (the set_environ function). > > Cheers, > > --Matt > > > > > On Fri, Nov 6, 2009 at 3:50 AM, Carmelo Prestipino > <carmelo.prestipino(a)esrf.fr> wrote: >> Dear All >> I upgraded my my python version on 2.6, I was wondering if is it available a >> new Ifeffit wrapper for this version? >> Best regards >> Carmelo >> >> -- >> >> --------------------------------------- >> Dr. Carmelo Prestipino >> European Synchrotron Radiation Facility >> BP220, 38043 Grenoble Cedex, >> FRANCE >> Tel: +33 (0)4 38 88 19 29 >> --------------------------------------- >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >

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PIPs detectors
by Bruce Ravel 09 Nov '09

09 Nov '09

Hi all, A colleague at a company that, for some reason, blocks mail from this mailing list asked me a question the other day that I don't have an immediate answer for. I told him I would pass his question along to the list and forward him any answers. He asks: I've looked over the Canberra website, but I am a little confused about what specifications I should go for. To be absolutely honest, I have never seen a PIPs detector/chip in person as they have always has the Al/Mylar film attached. Would you happen to have a specifications/model list for one of these devices (and the requisite type of BNC connector that I need)? I would greatly appreciate any direction that you could offer. Thanks, 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/~ravel/software/exafs/

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Re: [Ifeffit] python 2.6 wrapper
by Carmelo Prestipino 09 Nov '09

09 Nov '09

Dear Matt and Carlo I was speaking about windows, sorry for the imprecision. I tested today the file sent by Matt, on my computer all seems to work fine with Python 2.6. Cheers Carmelo Quoting ifeffit-request(a)millenia.cars.aps.anl.gov: > 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. python 2.6 wrapper (Carmelo Prestipino) > 2. Re: python 2.6 wrapper (Carlo Segre) > 3. Re: python 2.6 wrapper (Matt Newville) > 4. Re: Ifeffit (Matt Newville) > 5. Re: Ifeffit (Cl?ment Levard) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 06 Nov 2009 10:50:25 +0100 > From: Carmelo Prestipino <carmelo.prestipino(a)esrf.fr> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] python 2.6 wrapper > Message-ID: <20091106105025.gifreaxeogoc440g(a)160.103.2.152> > Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; > format="flowed" > > Dear All > I upgraded my my python version on 2.6, I was wondering if is it > available a new Ifeffit wrapper for this version? > Best regards > Carmelo > > -- > > --------------------------------------- > Dr. Carmelo Prestipino > European Synchrotron Radiation Facility > BP220, 38043 Grenoble Cedex, > FRANCE > Tel: +33 (0)4 38 88 19 29 > --------------------------------------- > > > ------------------------------ > > Message: 2 > Date: Fri, 6 Nov 2009 07:46:55 -0600 (CST) > From: Carlo Segre <segre(a)iit.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] python 2.6 wrapper > Message-ID: <alpine.DEB.1.10.0911060746230.3348(a)arsenide.iit.edu> > Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed > > > What is your operating system? The gifeffit progrm should work fine with > most versions of python. > > Carlo > > > On Fri, 6 Nov 2009, Carmelo Prestipino wrote: > >> Dear All >> I upgraded my my python version on 2.6, I was wondering if is it available a >> new Ifeffit wrapper for this version? >> Best regards >> Carmelo >> >> > > -- > Carlo U. Segre -- 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://www.iit.edu/~segre segre(a)debian.org > > > ------------------------------ > > Message: 3 > Date: Fri, 6 Nov 2009 10:46:46 -0600 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] python 2.6 wrapper > Message-ID: > <b8522e3d0911060846t6f7bea35j83dbff53c6c580d2(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hi Carmelo, Carlo, > > As Carlo says, on linux there should be no problem with the older > build system.... I'm using python2.6 and Ifeffit on linux. > > So, I'll assume you're asking about Windows. I do not yet have an > executable installer for Python2.6 on Windows. But, if you're brave, > I have something for you to try. In fact, just this past week, as > part of a move to a new Windows build system (see > http://cars9.uchicago.edu/ifeffit/MingwBuild) I've moved from using a > C extension for Python to using Python's ctypes library. This means > that the Ifeffit-Python interface is in pure Python and uses the DLL > directly, which is much better than the previous situation. > > I've tested this with python 2.6 and it works for me on both Windows > and linux, with very minor differences between them. The result > (Ifefffit.py attached) should be viewed as "beta testing" stage -- If > you try it out, I'd love to hear about any issues you have with it. I > don't have a nice installer for this, but you should be able to put > this in any folder that Python will find it. If you don't have > Ifeffit installed to C:\Program Files\Ifeffit, you may need to alter > the top of the script (the set_environ function). > > Cheers, > > --Matt > > > > > On Fri, Nov 6, 2009 at 3:50 AM, Carmelo Prestipino > <carmelo.prestipino(a)esrf.fr> wrote: >> Dear All >> I upgraded my my python version on 2.6, I was wondering if is it available a >> new Ifeffit wrapper for this version? >> Best regards >> Carmelo >> >> -- >> >> --------------------------------------- >> Dr. Carmelo Prestipino >> European Synchrotron Radiation Facility >> BP220, 38043 Grenoble Cedex, >> FRANCE >> Tel: +33 (0)4 38 88 19 29 >> --------------------------------------- >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >

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modeling anti-site disorder
by Shashwat 08 Nov '09

08 Nov '09

Dear All, I am studying the local disorder caused in CoGa alloy (B2: CsCl structure) due to ball-milling; it is expected that Ga atoms substitute most of the Co atoms in the Co sublattice after prolonged milling. In order to model this "anti-site" disorder (occupation of Ga atoms on the Co sites) in ATOMS, I am considering to change the occupancies at the corresponding sites as given below: Before ball-milling: site a: occupancy of Ga = 1 site b: occupancy of Co = 1 (standard .cif data) After ball-milling (assuming 80% anti-site concentration): site a: occupancy of Ga = 0.2 (plus compensating vacancies) site b: occupancy of Co = 0.2 site b: occupancy of Ga = 0.8 Could anyone suggest if this approach is reasonable. Many thanks ... Regards, Shashwat

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Re: [Ifeffit] Ifeffit
by Matt Newville 06 Nov '09

06 Nov '09

Hi Clement, I don't have any experience with the windows emulator on Mac OS X, and have only heard reports that it does work. When running atoms.exe on the Windows emulator on Mac OS X, you see: Running "C:\Program Files\Ifeffit\bin\atoms.exe" MetaCinn.inp '\\.host\Shared Folders\Desktop' CMD.EXE was started with the above path as the current directory. UNC paths are not supported. Defaulting to Windows directory. MetaCinn.inp: not a valid input file for Atoms. My guesses are: a) you want to run atoms in a directory without a space in the name b) you want to be sure that the file is has Windows line endings, not Mac OS line endings. Those are guesses, so I'm also CC'ing this to the Ifeffit mailing list, as someone there may have experience with this issue. --Matt 2009/11/5 Clément Levard <clevard(a)stanford.edu> > > Hi Matt, > I am a new postdoc in Gordon Brown's group in Stanford and would like to use you package for XAS analysis. > I am working on Mac, have installed a Windows Emulator. Most of the programs works fine (Sixpack, Athena, Artemis) But I have troubles running Atoms and Feff6l. > Please find in attachment the message I get when I try to run atoms for example. note that the exact same input file works fine on a Windows computer. I have the same kind of error message while running feff6l. > Do you have an idea of what could be the problem ? > thanks a lot for your help! > > -- > Clément Levard > Postdoctoral Scholar > Cell # : 650-521-7096 > Mailing address: > Geological & Environmental Sciences > Green Earth Sciences > 367 Panama Street, room 305 > Stanford University > Stanford, CA 94305-2115

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python 2.6 wrapper
by Carmelo Prestipino 06 Nov '09

06 Nov '09

Dear All I upgraded my my python version on 2.6, I was wondering if is it available a new Ifeffit wrapper for this version? Best regards Carmelo -- --------------------------------------- Dr. Carmelo Prestipino European Synchrotron Radiation Facility BP220, 38043 Grenoble Cedex, FRANCE Tel: +33 (0)4 38 88 19 29 ---------------------------------------

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Two absorbing atom sites
by Yun Luo 05 Nov '09

05 Nov '09

Dear IFEFFIT List, I learned that IFEEFIT can model a single absorber in two different environment. Could anyone direct me to similar studies that have been done or related tutorials? Below are some thoughts and questions: For example, there is 2 wt% A in both M1 and M2 structural sites in crystal X as dopant. I first create 2 FEFF models in Artemis, one has absorbing atom A only in M1 site and the other one has A only in M2 site. In the fitting process, is it correct that I choose paths from both FEFF models and using different Eo and So^2 for M1 and M2 sites? And to model the site occupancy of A in each site, I can create a fraction parameter "a" (which means there are a*2 wt% A in M1 site and (1-a)*2 wt% A in M2 site). Is it correct to apply this fraction parameter only to So^2 to model the site occupancy of A in M1 and M2 site? I am worried this approach will use too many variables. Any suggestions on the constraints/restraints that I can use? Finally, is there anything else that I missed which needs to be considered to do the modeling for this case of two different absorbing atom sites? Any suggestion will be greatly appreciated! Thank you all in advance! Best regards! Yun

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Reference materials for Ca & Cd for XANES
by Varadarajan Sridharan 03 Nov '09

03 Nov '09

Dear Sir, I am planning to carryout the XANES measurements on Cd(1-x)Ca(x)O solid solution to determine the electronic state. Can you suggest me the reference materials for Ca(2+) K-edge and Cd(2+) L-edge for XANES studies. Thanking you in advance V. Sridharan --------- CMPD, IGCAR Kalpakkam, INdia

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Problem with EXAFS simulations: endless loop
by Cammelli Sebastiano 03 Nov '09

03 Nov '09

Dear feff user I try to simulate the EXAFS spectrum of a matrix composed of Fe and Cr (2 atoms on 35) at the Cr K edge. Well, I do not why, but feff (both 8.2 and 8.4) generates an endless loop. Here below I report the feff.inp used. I try even with different value of the SCF card (7.0 1 30 0.05 10) (4.0 1 30 0.05 10) (2.0 1 30 0.2 1) (3.0 1 30 0.2 1) but nothing changes. In order to solve the problem I should not use the SCF card, but this solution brings to a worse evaluation of the E0 and generally, from my little experience, I prefer to use it. The atoms coordinates were calculated by MD. Thank you very much for any help or suggestion. Best Sebastiano TITLE Cr in Fe matrix CONTROL 1 1 1 1 1 1 PRINT 0 0 0 0 0 0 RMULTIPLIER 1.003 LDOS -30 20 0.2 EDGE K S02 1.0 SCF 4.0 1 30 0.2 1 DEBYE 60 470 0 EXCHANGE 0 0 0 0 CORRECTIONS 0 2.5 EXAFS RPATH 10.0 POTENTIALS 0 24 Cr -1 -1 1 26 Fe -1 -1 2 24 Cr -1 -1 ATOMS -2.83900 -2.83700 -2.83600 1 Fe -1.41600 -1.41600 -1.41500 1 Fe 0.00000 0.00000 0.00000 0 Cr 2.84600 2.84500 2.84300 1 Fe 0.01340 2.84000 2.83900 1 Fe 2.84000 0.01200 2.83900 1 Fe 0.01200 0.01200 2.83200 1 Fe 2.84000 2.83900 0.01050 1 Fe 0.01200 2.83200 0.01000 1 Fe 2.83200 0.01000 0.01000 1 Fe 1.43000 1.42900 1.42800 2 Cr -2.83300 2.84500 2.84300 1 Fe -2.83900 0.01200 2.83900 1 Fe -2.83900 2.83900 0.01050 1 Fe -2.84700 0.01000 0.01000 1 Fe -1.40200 1.41900 1.41800 1 Fe 2.84300 -2.83400 2.84300 1 Fe 0.01050 -2.83900 2.83900 1 Fe 2.83700 -2.84100 0.01050 1 Fe 0.00900 -2.84700 0.01000 1 Fe 1.41800 -1.40300 1.41800 1 Fe -2.83600 -2.83400 2.84300 1 Fe -2.84200 -2.84100 0.01050 1 Fe -1.41000 -1.40900 1.41800 1 Fe 2.84300 2.84200 -2.83600 1 Fe 0.01050 2.83700 -2.84100 1 Fe 2.83700 0.00910 -2.84100 1 Fe 0.00900 0.00870 -2.84700 1 Fe 1.41800 1.41800 -1.40600 1 Fe -2.83600 2.84200 -2.83600 1 Fe -2.84200 0.00910 -2.84100 1 Fe -1.41000 1.41700 -1.41000 1 Fe 2.84100 -2.83700 -2.83600 1 Fe 0.00770 -2.84200 -2.84100 1 Fe 1.41700 -1.41100 -1.41000 1 Fe END

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Re: [Ifeffit] Installing Athena on a Mac
by Bruce Ravel 02 Nov '09

02 Nov '09

Minna, As I point out regularly on the mailing list, I am not a Mac user and do not maintain the mac packages. You really need to inquire on the mailing list for support in that area -- that way you will actually find the people who *can* help you. Here are some recent threads on the mailing list regarding Mac installation issues: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2009-September/009018.ht… http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2009-October/009077.html Perhaps your answer is there. If not, please feel free to make a new request for help on the list. Here is more information about the resources available to you: http://cars9.uchicago.edu/ifeffit/BruceRavel/FormLetters/HelpRequest As I explain there, the mailing list should always be your first stop when you have a question about the software. B PS: If any of the Mac users out there would like to update the Macintosh Issues section of http://cars9.uchicago.edu/ifeffit/FAQ/Installing_Ifeffit that would be really splendid. On Monday 02 November 2009 04:09:22 pm you wrote: > Hello Bruce, > > I'm trying to run Athena on a Mac, OS X Version 10.6.1. Following the > instructions at cars9.uchicago.edu/~ravel/software/downloads.html#mac for a > Macintosh OSX download, I went to SourceForge to download Ifeffit. The > latest version does not appear to be available for Mac download, so I > grabbed > Ifeffit-1.2.10.1-Mac10.4_Intel_horae66.dmg<http://sourceforge.net/projects/ >ifeffit/files/ifeffit/1.2.10/Ifeffit-1.2.10.1-Mac10.4_Intel_horae66.dmg/down >load> , because I'm on an Intel Mac, but the installation failed. I then > grabbed > Ifeffit-1.2.10-Mac10.4_PPC_horae066_pkg.dmg<http://sourceforge.net/projects >/ifeffit/files/ifeffit/1.2.10/Ifeffit-1.2.10-Mac10.4_PPC_horae066_pkg.dmg/do >wnload> and the installation appeared to work, but when I went to run > Athena, X11 opened but nothing else happened. I'm not really sure what the > problem is - can you at least give me a suggestion on where to start? > > Thanks for your help! > > Minna R. Krejci > PhD Candidate - Joester Group > Materials Science and Engineering > Northwestern University > > Cook Hall 3021 > Office: 847 491 3584 > Mobile: 330 603 8608 > minna(a)u.northwestern.edu -- 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/~ravel/software/exafs/

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Got Athena data plotted
by abhijeet gaur 28 Oct '09

28 Oct '09

Thanks a lot kicaj, I followed the procedure step by step and I got the data plotted in Excel. Thanks again Kicaj. Abhijeet

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Re: [Ifeffit] Normalization in Athena
by Gudrun Lisa Bovenkamp 27 Oct '09

27 Oct '09

Hi everybody, I am sure that Athena was tested a lot, but as Jeremy pointed out, which I think now is the answer: If the background is substracted before the fitting of the post edge. That is actually how we are normalizing XANES data in our group and that is what I tried in Athena. It is actually working much better with 2. order norm and flattening. Since I do not want to do it by hand for all spectra and import them back into Athena for LCF. This time I attached a the example Athena project file. But with this approach I rarely get the spectrum oscillating around one. I will think about it. Thanks for the hint, Matt, about "no points" in the range. But Athena is acutally complaining, if there are no points to fit the line. Of course, I read the chapter on Normalization in Athena. And what is giving me trouble, why I try the "1-point" approach, is that the small differences in the first post-edge normalization point make a great deal of difference in the normalization of the spectra respective to each other and thus LCF. Finally, I believe it is a very interesting question of taste how to determine the edge step for XANES data or when to substract the background. Or is there any specific reason for a special approach? Thank you all for your help!! Greetings, Lisa > Hi Lisa, > > Be sure that Athena has been rigorously tested and she does know how >to > normalize data. It is much more likely that the default values are >not > the "best" ones for your data. > > My book chapter goes over how Athena normalizes data in detail. If >you > send me your email address I'll send you a copy. In particular see > figure 14-16. > > Cheers, > Shelly > > Shelly, > > I agree that Athena applies its (her) algorithm correctly. Whether >that > algorithm is correct may be a matter of opinion. The apparent > discrepency Lisa sees is due to Athena's algorithm: > > i.e., fit preedge line, fit postedge function to normalization >range, > extrapolate both functions to edge energy to find edge step. > > Another option would be to fit predge line and subtract it. After >that, > fit the post edge normalization range. > > With Athena, if there is a non-zero slope to the preedge line and >you > choose norm order 1, you get Lisa's result. With normalization >order 2 > or 3, the results should either be the same, or at least, much >closer. > > Jeremy > > > > It is a little hard to evaluate your results, Lisa, without an > example. It may help to attach a small project file which > demonstrates your question. > > Without an actual example, I would have to guess that the bottom >line > is an odd choice of parameters. This page from the document might >be > helpful: > > http://cars9.uchicago.edu/~ravel/software/doc/Athena/html/bkg/norm.html > > B > > > > Lisa, > > I think the issue you're seeing is most likely due to telling athena > to fit the data between E0+199 and E0+200 with a constant. I'd > recommend expanding that range some to give Athena a chance -- if > there isn't any data between E=E0+199 and E0+200, Athena won't be >able > to figure out what the edge step should be. If you really want >the > edge step to be the value of pre-edge subtracted mu(E) at >E=E0+200eV, > you'll have to do that by hand. > > > --Matt > >

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