November 2009 - Ifeffit - millenia.cars.aps.anl.gov

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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