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

Re: [Ifeffit] ERROR in getting feff8 input file for YBCO from Web atoms
by Barton, David (DG) 08 Feb '07

08 Feb '07

Feng, Matt, The problem appears to be caused by a error in parsing the Titles portion of this one particular ATOMS.INP file. If you delete the entire reference #2 in the titles area WEBAtoms runs fine. (refer2: Cava, et al, Physica C 165, p.419, (1990)). Error can be reproduced by: 1) Choose YBa2Cu3O7.inp : yttrium barium copper oxide ( 123 , ybco) entry in http://cars9.uchicago.edu/cgi-bin/atoms/Atoms-Search.cgi and run WebAtoms 2) Choose K-edge 3) Run ATOMS (You will see the ERROR ACCESS Denied) The work around: 1) Choose YBa2Cu3O7.inp : yttrium barium copper oxide ( 123 , ybco) entry in http://cars9.uchicago.edu/cgi-bin/atoms/Atoms-Search.cgi and run WebAtoms 2) Choose K-edge 3) Delete (refer2: Cava, et al, Physica C 165, p.419, (1990)) in the header. 4) Run ATOMS (and it now works fine). Dave >-----Original Message----- >From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf >Of Feng Wang >Sent: Wednesday, February 07, 2007 2:01 AM >To: XAFS Analysis using Ifeffit >Subject: Re: [Ifeffit] ERROR in getting feff8 input file for >YBCO from Webatoms > >Thank you, Paul, for clarifying this problem. > >Sincerely, > >Feng > > >> Just to follow on this -- I can access the YBCO atoms entry (via a >> search). The atoms.inp pops up correctly, but when I >attempted to run >> atoms, I got the same error message. The error doesn't come from my >> end (as far as I can tell). The problem seems to be with the >execution >> of atoms (e.g. hitting the button "Run atoms".). The cgi is >probably >> broken. >> >> Paul >> >> ERROR >> >> Access Denied >> >> Access Denied by security policy >> The security policy for your network prevents your request >from being >> allowed at this time. Please contact your administrator if you feel >> this is incorrect. >> >> On Feb 3, 2007, at 2:42 AM, Matt Newville wrote: >> >> > Hi Feng, >> > >> > Sorry for the trouble. I'm not sure where the problem >is. I can get >> > files from the Atoms archive from home (ie, outside the Argonne >> > network), and I don't see any recent errors in the logs, >suggesting >> > that both the server connections and the access through the Argonne >> > and APS firewalls are working. Could it be that the >trouble is at >> > your end? >> > >> > Perhaps we can troubleshoot this a little better. Does the 'search >> > for Atoms.inp' page >> > http://cars9.uchicago.edu/~newville/adb/search.html >> > appear for you? Is it responsive? >> > >> > Can you select a central atoms, a structure, and then hit 'Run >> > Webatoms'? >> > >> > Can you browse to http://cars9.uchicago.edu/atomsdb/ and >see a large >> > number of atoms.inp files? Can you select and download >some of these >> > files? >> > >> > Hope that helps, >> > >> > --Matt >> > _______________________________________________ >> > Ifeffit mailing list >> > Ifeffit(a)millenia.cars.aps.anl.gov >> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> _______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > >==================================== >EM group >Physics & NINT >Phone: (780)6411667 >http://www.phys.ualberta.ca/~fwang >_______________________________________________ >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] ERROR in getting feff8 input file for YBCO from Webatoms
by Feng Wang 07 Feb '07

07 Feb '07

Thank you, Paul, for clarifying this problem. Sincerely, Feng > Just to follow on this -- I can access the YBCO atoms entry (via a > search). The atoms.inp pops up correctly, but when I attempted to > run atoms, I got the same error message. The error doesn't come from > my end (as far as I can tell). The problem seems to be with the > execution of atoms (e.g. hitting the button "Run atoms".). The cgi > is probably broken. > > Paul > > ERROR > > Access Denied > > Access Denied by security policy > The security policy for your network prevents your request from being > allowed at this time. Please contact your administrator if you feel > this is incorrect. > > On Feb 3, 2007, at 2:42 AM, Matt Newville wrote: > > > Hi Feng, > > > > Sorry for the trouble. I'm not sure where the problem is. I can get > > files from the Atoms archive from home (ie, outside the Argonne > > network), and I don't see any recent errors in the logs, suggesting > > that both the server connections and the access through the Argonne > > and APS firewalls are working. Could it be that the trouble is at > > your end? > > > > Perhaps we can troubleshoot this a little better. Does the 'search for > > Atoms.inp' page > > http://cars9.uchicago.edu/~newville/adb/search.html > > appear for you? Is it responsive? > > > > Can you select a central atoms, a structure, and then hit 'Run > > Webatoms'? > > > > Can you browse to http://cars9.uchicago.edu/atomsdb/ and see a large > > number of atoms.inp files? Can you select and download some of these > > files? > > > > Hope that helps, > > > > --Matt > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ==================================== EM group Physics & NINT Phone: (780)6411667 http://www.phys.ualberta.ca/~fwang

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ERROR in getting feff8 input file for YBCO from Webatoms
by Feng Wang 07 Feb '07

07 Feb '07

Hi all, I used Webatoms (in http://cars9.uchicago.edu/~newville/adb/search.html) to get the feff8 input file for YBa2Cu3O7, but was given an error message, as shown below: ERROR Access Denied ------------------------------------------- Access Denied by security policy The security policy for your network prevents your request from being allowed at this time. Please contact your administrator if you feel this is incorrect I tried several other materials, there is no such kind error message. Could you please help with that? Thank you so much in advance. Sincerely, Feng ==================================== EM group Physics & NINT Phone: (780)6411667 http://www.phys.ualberta.ca/~fwang

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Re: [Ifeffit] statistical vicissitudes and dead links
by Kelly, Shelly D. 26 Jan '07

26 Jan '07

Hi Paul, Here is a PDF version of the relevant pages from Dani's thesis. Shelly --------------------------- Shelly Kelly Argonne National Laboratory Bldg 203, RM E113 9700 S. Cass Ave Argonne, IL 60439 Molecular Environmental Science Group www.mesg.anl.gov skelly(a)anl.gov phone: 630-252-7376 > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Paul Fons > Sent: Saturday, January 20, 2007 7:38 PM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] statistical vicissitudes and dead links > > Hi Shelly, > I noticed that the link you posted either is dead or doesn't work > from outside anl (the message from the server is ambiguous). > > Paul > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Multiple k-weight fitting
by David C. Schmitter 22 Jan '07

22 Jan '07

Hi everyone. I am currently trying to reduce the correlations between N and sigma squared. I have been told that multiple k-weight fitting is the way to go about this; but I am curious what the best method is to try and do this using Artemis. Is it simply a matter of clicking the other weighting options available? If so, what should I be looking for to determine whether my parameters are correct or not? I am not sure if this is a redundant question in terms of the mailing list; but I am a relatively new user and cannot remember seeing anything about it yet. Thanks. Dave Schmitter David C. Schmitter Dept. of Physics and Astronomy Nebraska Center for Materials and Nanoscience University of Nebraska Lincoln dschmitt(a)unlserve.unl.edu (402) 472-5094

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Re: [Ifeffit] statistical vicissitudes
by Kelly, Shelly D. 21 Jan '07

21 Jan '07

Hi Aaron, In EXAFS the expected deviation in RCS(reduced chi square) is sqrt(2/nu) So one fit is better than another fit if their difference is greater than twice the fluctuation in the RCS values (RCS1-RCS2)/RCS2 > 2 sqrt(2/nu) We divide by RCS2 because our RCS-values are poorly scaled. {in your link to the nist pages F = RCS1/RCS2 -1 and the statistically significant variation in F is 2 * sqrt(2/nu)} If there are different values for nu in the two models then (RCS1-RCS2) > 2sqrt(RCS2^2/nu2 + RCS1^2/nu1) I think that the best explanation of these tests are given in Dani Haskel's thesis pg 39 - 41 http://www.aps.anl.gov/xfd/people/haskel/dani.html and Bevington, P. R.; Robinson, D. K. Data Reduction and Error Analysis for the Physical Sciences; 2 ed.; McGraw-Hill: New York, 1992. HTH Shelly > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Aaron Slowey > Sent: Thursday, January 18, 2007 4:50 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] statistical vicissitudes > > Hello - > > The use of R-factors and reduced-chi-squared values, it's computations > by IFEFFIT have been made clear by past writings, but the use of > reduced-chi-squared as a comparative statistic has not, to my > knowledge, been completely well-documented. > > Not withstanding the three disconnects between classical statistics > and the realities of EXAFS mentioned in the IFEFFIT faq section > > http://cars9.uchicago.edu/iffwiki/FAQ/FeffitModeling#head- > ed63cbd00d0b85def31ada3a695873243d08a76a > > can > > Is the criterion provided by Kelly et al. (2001) J. Phys. Chem. B 105(27) > > http://www.mesg.anl.gov/pdf/JPC2001samms.pdf > > namely, redchi-sq_1 / redchi-sq_2) - 1 > 2 * (2 / deg_of_freedom)^0.5, > > derived from the F-test formalism and, if so, how? > > I tried to derive the above equation based on the F-test formalism > provided by NIST: > > http://www.itl.nist.gov/div898/handbook/prc/section3/prc32.htm > > but was unsuccessfull. The Kemner et al. paper referenced by Kelly et > al. to explain the statistical basis for the above equation does not > clearly do so. > > I request that someone please provide a reference to a *first > principles* basis for criteria to compare reduced-chi-square values of > alternate EXAFS fits. > > Aaron > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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statistical vicissitudes
by Aaron Slowey 18 Jan '07

18 Jan '07

Hello - The use of R-factors and reduced-chi-squared values, it's computations by IFEFFIT have been made clear by past writings, but the use of reduced-chi-squared as a comparative statistic has not, to my knowledge, been completely well-documented. Not withstanding the three disconnects between classical statistics and the realities of EXAFS mentioned in the IFEFFIT faq section http://cars9.uchicago.edu/iffwiki/FAQ/FeffitModeling#head-ed63cbd00d0b85def… can Is the criterion provided by Kelly et al. (2001) J. Phys. Chem. B 105(27) http://www.mesg.anl.gov/pdf/JPC2001samms.pdf namely, redchi-sq_1 / redchi-sq_2) - 1 > 2 * (2 / deg_of_freedom)^0.5, derived from the F-test formalism and, if so, how? I tried to derive the above equation based on the F-test formalism provided by NIST: http://www.itl.nist.gov/div898/handbook/prc/section3/prc32.htm but was unsuccessfull. The Kemner et al. paper referenced by Kelly et al. to explain the statistical basis for the above equation does not clearly do so. I request that someone please provide a reference to a *first principles* basis for criteria to compare reduced-chi-square values of alternate EXAFS fits. Aaron

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SSRL data format
by Matthew Ginder-Vogel 17 Jan '07

17 Jan '07

Hi All, Sam Webb's "SamView" which is part of SixPACK opens SSRL data files and you can then save them in ASCII format. I think he he has the source code posted on his website. Matt On 1/17/07, ifeffit-request(a)millenia.cars.aps.anl.gov < 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: opening SSRL data with Athena (Tsu-Chien Weng) > 2. Re: opening SSRL data with Athena (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 17 Jan 2007 09:57:05 +0100 > From: Tsu-Chien Weng <tsuchien.weng(a)esrf.fr> > Subject: Re: [Ifeffit] opening SSRL data with Athena > To: bravel(a)anl.gov > Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <45ADE4E1.9020902(a)esrf.fr> > Content-Type: text/plain; charset="iso-8859-1" > > Hi, Bruce, > > I have written codes in MATLAB to convert ASCII data into SSRL's binary > data in > order to use EXAFSPAK. The binary format is guessed by dumping the > data. Maybe > someone can use it as a start and come up with a plugin for Athena. > > > > Bruce Ravel wrote: > > > > Question 3 at this FAQ page: > > http://cars9.uchicago.edu/iffwiki/FAQ/HoraeQuestions > > explains in some detail what kind of data Athena is able to read. > > Obviously SSRL's binary format cannot be imported without the use of a > > plugin. > > > > It would be possible, in principle, to write a plugin that is capable > > of reading the SSRL binary format. However, to my knowledge (which > > certainly may be faulty) the technical details of the SSRL format are > > not published any place where I can find them. That's something of an > > impediment. ;-) > > > > It would most certainly help to convert to an ascii format. Not > > having worked at SSRL since my grad school days, I don't really know > > how to do so. Your beamline scientist should be able to help you with > > that. Perhaps someone on the list will know the details. > > > > B > > > > > -- > Tsu-Chien WENG > European Synchrotron Radiation Facility > 6, rue Jules Horowitz, EXPH Sect-26 > 38043 Grenoble, FRANCE > Tel: +33(0)438.88.19.82 > Fax: +33(0)476.88.27.84 >

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Re: opening SSRL data with Athena
by Bruce Ravel 17 Jan '07

17 Jan '07

On Friday 12 January 2007 15:20, Aaron Slowey wrote: > I'm running IFEFFIT, Athena, etc. on my Intel Mac after using the the > recent installer provided by MRCAT. I've opened Athena successfully > and was able to load a GSECARS data file, but I am unable to load > SSRL binary data files (original file from a VMS beamline computer). > > Would it help to convert the SSRL binaries to ASCII files? If so, how > can I do that? Aaron, There are enough people in the Ifeffit-using community who are SSRL users and who might be interested in this question. SO I am CCing my answer to the mailing list. Question 3 at this FAQ page: http://cars9.uchicago.edu/iffwiki/FAQ/HoraeQuestions explains in some detail what kind of data Athena is able to read. Obviously SSRL's binary format cannot be imported without the use of a plugin. It would be possible, in principle, to write a plugin that is capable of reading the SSRL binary format. However, to my knowledge (which certainly may be faulty) the technical details of the SSRL format are not published any place where I can find them. That's something of an impediment. ;-) It would most certainly help to convert to an ascii format. Not having worked at SSRL since my grad school days, I don't really know how to do so. Your beamline scientist should be able to help you with that. Perhaps someone on the list will know the details. B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advance Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/

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Projekt with the "flatten-problem"
by Jens Kruse 14 Jan '07

14 Jan '07

Hi, find attached an example with the "flatten-problem". thanks a lot, jens "Hi, I have a normalization problem with Athena. If I turn on the "flatten" option in the background removal section, Athena creates in some of the normalized spectra a step in the pre-edge range. How can I get rid of it? Thanks, jens"

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