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

Re: [Ifeffit] question about Eo and simultaneous fitting
by tony vitova 15 Feb '07

15 Feb '07

Hi again to everybody, Thank you for the answers. They are all helpful. Just to specify a little more: all samples are measured at the K edge of the doped metal oxide. I expect relation between the coordination environments of the different samples as the reduced and oxidized samples are mixture of two formal oxidation states. I will try with different Eo and the Shelly's aligning-suggestion. Tony ----- Original Message ---- From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Wednesday, February 14, 2007 9:01:29 PM Subject: Re: [Ifeffit] question about Eo and simultaneous fitting Tony -- > Should I fit EXAFS spectra of a doped material and the same material, but > oxidized and reduced (three spectra) simultaneously? In my opinion: yes, as > I am looking for small differences. Is varying one Eo for the three samples > the right approach? > I am also wondering, should I vary one Eo for samples with different doping > concentrations? > I think you need to be more specific about what your samples are and what you're trying to learn from them. For example, I could read your question as meaning you have samples of Mn K edge for Mn doped into silicon ("a doped material") Si K edge of pure silicon ("same material, reduced") Si K edge of quartz ("same material, oxidized") In which case, I don't see that see much to be gained by fitting the spectra together. In general, one fits multiple spectra together when it is expected that there is a relationship between the different coordination environments, most usually a simple relationship between the g(R)'s for the different samples. E0 is typically different for each sample. There are situations where they can be constrained to be the same, such as spectra are all on the same sample at different temperatures. For more specific answers, please ask more specific questions. --Matt _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ____________________________________________________________________________________ Looking for earth-friendly autos? Browse Top Cars by "Green Rating" at Yahoo! Autos' Green Center. http://autos.yahoo.com/green_center/

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question about Eo and simultaneous fitting
by tony vitova 14 Feb '07

14 Feb '07

Hi, first I would like to thank all experienced people answering in this forum!! I have learned really a lot from you. And now my question: Should I fit EXAFS spectra of a doped material and the same material, but oxidized and reduced (three spectra) simultaneously? In my opinion: yes, as I am looking for small differences. Is varying one Eo for the three samples the right approach? I am also wondering, should I vary one Eo for samples with different doping concentrations? Thank you for any hint! Tony ____________________________________________________________________________________ It's here! Your new message! Get new email alerts with the free Yahoo! Toolbar. http://tools.search.yahoo.com/toolbar/features/mail/

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Re: [Ifeffit] question about Eo and simultaneous fitting
by Scott Calvin 14 Feb '07

14 Feb '07

Hi Shelly, Interesting--I've never tried that method with samples that I expect to differ in oxidation state. If it's differing in oxidation state, the local environment is probably different too...particularly, nearest-neighbor distances should be changed significantly. So how do you align the chi(k) data with each other, when they oscillate at a different frequency? --Scott Calvin Sarah Lawrence College At 10:38 AM 2/14/2007, you wrote: >The approach that I like to take, is to vary the choice of E0 in the >background subtraction step so that the chi(k) spectra are well aligned >with each other and the theory. Then only one Ezero parameter is >needed. > >Cheers, >Shelly

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Re: [Ifeffit] question about Eo and simultaneous fitting
by Kelly, Shelly D. 14 Feb '07

14 Feb '07

Hi Scott, The change in frequency is a bigger affect at high k than the energy shift parameter. The energy shift parameter affects the data more strongly at low k. So I align the data to each other at low k, and then they become out of phase with each other at high k. A similar effect is seen for pressure dependent data where the oxidation state doesn't change but the bond length changes. I also look at how well the data are both aligned to the theory used to describe the data sets independently. The energy shift values should overlap within the uncertainty to justify using a single parameter for them. I suppose that my method might not work for all systems. But if the data are similar enough so that a multiple data set fit has significant overlap in the models used to describe the spectra, then it has worked. Shelly > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin > Sent: Wednesday, February 14, 2007 9:55 AM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] question about Eo and simultaneous fitting > > Hi Shelly, > > Interesting--I've never tried that method with samples that I expect > to differ in oxidation state. If it's differing in oxidation state, > the local environment is probably different too...particularly, > nearest-neighbor distances should be changed significantly. So how do > you align the chi(k) data with each other, when they oscillate at a > different frequency? > > --Scott Calvin > Sarah Lawrence College > > At 10:38 AM 2/14/2007, you wrote: > > >The approach that I like to take, is to vary the choice of E0 in the > >background subtraction step so that the chi(k) spectra are well aligned > >with each other and the theory. Then only one Ezero parameter is > >needed. > > > >Cheers, > >Shelly > > _______________________________________________ > 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] question about Eo and simultaneous fitting
by Kelly, Shelly D. 14 Feb '07

14 Feb '07

Hi Tony, The approach that I like to take, is to vary the choice of E0 in the background subtraction step so that the chi(k) spectra are well aligned with each other and the theory. Then only one Ezero parameter is needed. Cheers, Shelly > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin > Sent: Wednesday, February 14, 2007 7:52 AM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] question about Eo and simultaneous fitting > > Hi Tony, > > A quick answer before I try to fight my way through an ice storm to > get to work. :) > > Fitting the three spectra simultaneously makes sense, but if > oxidation state is expected to be different, then you really need > different E0's. > > As far as doping, it depends on the details. In some cases, it may > require a different E0's, in others, not. Of course, you can try it > both ways, and see what the fits think. > > --Scott Calvin > Sarah Lawrence College > > At 05:04 AM 2/14/2007, you wrote: > >Hi, > > > >first I would like to thank all experienced people answering in > >this forum!! I have learned really a lot from you. > > > >And now my question: > >Should I fit EXAFS spectra of a doped material and the same > >material, but oxidized and reduced (three spectra) simultaneously? > >In my opinion: yes, as I am looking for small differences. Is > >varying one Eo for the three samples the right approach? > >I am also wondering, should I vary one Eo for samples with different > >doping concentrations? > > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Debian packages
by Carlo Segre 13 Feb '07

13 Feb '07

Hello All: I have set up a new repository for the Debian packages of IFEFFIT & friends. I have also begun to build Ubuntu packages as well. Of course, whenever possible the packages are in the Debian archive. The following are available to use in your /etc/apt/sources.list # backported packages for sarge (will stop supporting this once etch # releases) deb http://debian-xray.iit.edu sarge main contrib non-free # backported packages for etch (now that etch is in freeze, any new # versions will be placed here) deb http://debian-xray.iit.edu etch main contrib non-free # additional software not yet in Debian (you can see what is there just # for grins!) deb http://debian-xray.iit.edu sid main contrib non-free # packages made for Ubuntu (I will support only the last three releases) deb http://debian-xray.iit.edu dapper main contrib non-free deb http://debian-xray.iit.edu edgy main contrib non-free deb http://debian-xray.iit.edu feisty main contrib non-free The old repositories at fermi.phys.iit.edu/debian are still there but not being updated. I will probably remove them in 2007. Cheers, Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, 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

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feff and xanes calculation troubles
by Paul Fons 13 Feb '07

13 Feb '07

Hello all, I am working with a colleague who is working on some High-Tc materials. He has data taken at the F K-edge and is trying to simulate these spectra using feff8 (the same problem occurs from feff8.1 to feff8.5). To make a short story short, the SCF routine never terminates (converges). A bit of the output is attached below. The problem is a little nasty in that while the data is being taken from the F K-edge, the material contains heavy atoms (Ba). I am pretty much at a loss of what to try to improve the situation. I have attempted to change the augmentation sphere overlap using both the AFOLP and FOLP cards to no avail (same problem). I have also tried to use smaller steps and change the amount of mixing in the initial SCF step (using the options on the SCF card). I am running out of ideas of what to try next and was wondering if anyone had any suggestions. The SCF radius is set to the second coordination shell, but moving it around doesn't help with the lack of convergence. The calculation does run to completion without the SCF step, but this leaves a lot to be desired. Thanks for any help out there. I submitted this to the feff mailing list last week, but all is quiet, so I am trying here (sorry for the duplication if that counts). Paul Number of processors = 4 Feff 8.50 XANES: 0234F2.0 (0234f_j2) Executing pot on 4 Number of processors = 4 Calculating potentials ... free atom potential and density for atom type 0 free atom potential and density for atom type 1 free atom potential and density for atom type 2 free atom potential and density for atom type 3 free atom potential and density for atom type 4 free atom potential and density for atom type 5 initial state energy overlapped potential and density for unique potential 0 overlapped potential and density for unique potential 1 overlapped potential and density for unique potential 2 overlapped potential and density for unique potential 3 atomic xmu,vint,rhoint -0.209299551987679 -0.698008117675781 0.410117955794590 atomic xmu,vint,rhoint -0.209299551987679 -0.698008117675781 0.410117955794590 atomic xmu,vint,rhoint -0.209299551987679 -0.698008117675781 0.410117955794590 overlapped potential and density for unique potential 4 overlapped potential and density for unique potential 5 muffin tin radii and interstitial parameters atomic xmu,vint,rhoint -0.209299551987679 -0.698008117675781 0.410117955794590 iph, rnrm(iph)*bohr, rmt(iph)*bohr, folp(iph) 0 1.10153E+00 1.07171E+00 1.06941E+00 1 1.97019E+00 1.91470E+00 1.07252E+00 2 1.69963E+00 1.64348E+00 1.08663E+00 3 1.27604E+00 1.18970E+00 1.15000E+00 4 1.10566E+00 1.05671E+00 1.12119E+00 5 1.14759E+00 1.11204E+00 1.08060E+00 Core-valence separation mu_old= -3.671 SCF ITERATION NUMBER 1 OUT OF 30 Calculating energy and space dependent l-DOS. It takes time ... point # 1 energy = -42.000 Doing FMS for a cluster of 19 atoms around iph = 0 0 FMS matrix (LUD) at point 1, number of state kets = 106 Doing FMS for a cluster of 19 atoms around iph = 1 0 FMS matrix (LUD) at point 1, number of state kets = 126 Doing FMS for a cluster of 23 atoms around iph = 2 0 FMS matrix (LUD) at point 1, number of state kets = 167 Doing FMS for a cluster of 23 atoms around iph = 3 0 FMS matrix (LUD) at point 1, number of state kets = 162 Doing FMS for a cluster of 20 atoms around iph = 4 0 FMS matrix (LUD) at point 1, number of state kets = 120 Doing FMS for a cluster of 19 atoms around iph = 5 0 FMS matrix (LUD) at point 1, number of state kets = 106 point # 20 energy = -30.938 point # 40 energy = -10.825 point # 60 energy = -6.803 point # 80 energy = -6.553 Electronic configuration iph il N_el 0 0 2.047 0 1 5.690 0 2 0.000 0 3 0.000 0 4 0.000 1 0 2.330 1 1 6.314 1 2 2.163 1 3 0.000 1 4 0.000 2 0 0.370 2 1 6.565 2 2 2.462 2 3 0.000 2 4 0.000 3 0 0.489 3 1 0.602 3 2 6.195 3 3 0.000 3 4 0.000 4 0 1.898 4 1 5.097 4 2 0.000 4 3 0.000 4 4 0.000 5 0 2.052 5 1 5.493 5 2 0.000 5 3 0.000 5 4 0.000 mu_new= -6.564 Charge transfer: iph charge(iph) 0 0.053 1 -0.161 2 -0.280 3 0.741 4 -0.198 5 -0.108 SCF ITERATION NUMBER 2 OUT OF 30 Calculating energy and space dependent l-DOS. It takes time ... point # 1 energy = -42.000 Doing FMS for a cluster of 19 atoms around iph = 0 0 FMS matrix (LUD) at point 1, number of state kets = 106 Doing FMS for a cluster of 19 atoms around iph = 1 0 FMS matrix (LUD) at point 1, number of state kets = 126 Doing FMS for a cluster of 23 atoms around iph = 2 0 FMS matrix (LUD) at point 1, number of state kets = 167 Doing FMS for a cluster of 23 atoms around iph = 3 0 FMS matrix (LUD) at point 1, number of state kets = 162 Doing FMS for a cluster of 20 atoms around iph = 4 0 FMS matrix (LUD) at point 1, number of state kets = 120 Doing FMS for a cluster of 19 atoms around iph = 5 0 FMS matrix (LUD) at point 1, number of state kets = 106 point # 20 energy = -30.863 point # 40 energy = -10.614 point # 60 energy = -6.564 point # 80 energy = -6.814 point # 100 energy = -7.064 point # 120 energy = -7.314 point # 140 energy = -7.564 point # 160 energy = -7.814 point # 180 energy = -8.064 point # 200 energy = -8.314 point # 220 energy = -8.564 point # 240 energy = -8.814 point # 260 energy = -9.064 point # 280 energy = -9.314 point # 300 energy = -9.564 point # 320 energy = -9.814 point # 340 energy = -10.064 point # 360 energy = -10.314 point # 380 energy = -10.564 point # 400 energy = -10.814 point # 420 energy = -11.064 point # 440 energy = -11.314 point # 460 energy = -11.564 point # 480 energy = -11.814 point # 500 energy = -12.064 Electronic configuration iph il N_el 0 0 1.953 0 1 5.525 0 2 0.000 0 3 0.000 0 4 0.000 1 0 2.185 1 1 6.138 1 2 0.633 1 3 0.000 1 4 0.000 2 0 0.296 2 1 6.452 2 2 0.726 2 3 0.000 2 4 0.000 3 0 0.511 3 1 0.579 3 2 10.062 3 3 0.000 3 4 0.000 4 0 1.853 4 1 4.537 4 2 0.000 4 3 0.000 4 4 0.000 5 0 1.941 5 1 5.032 5 2 0.000 5 3 0.000 5 4 0.000 mu_new= -12.053 Charge transfer: iph charge(iph) 0 0.137 1 0.054 2 -0.136 3 0.582 4 -0.233 5 -0.084 SCF ITERATION NUMBER 3 OUT OF 30 Calculating energy and space dependent l-DOS. It takes time ... point # 1 energy = -42.000 Doing FMS for a cluster of 19 atoms around iph = 0 0 FMS matrix (LUD) at point 1, number of state kets = 106 Doing FMS for a cluster of 19 atoms around iph = 1 0 FMS matrix (LUD) at point 1, number of state kets = 126 Doing FMS for a cluster of 23 atoms around iph = 2 0 FMS matrix (LUD) at point 1, number of state kets = 167 Doing FMS for a cluster of 23 atoms around iph = 3 0 FMS matrix (LUD) at point 1, number of state kets = 162 Doing FMS for a cluster of 20 atoms around iph = 4 0 FMS matrix (LUD) at point 1, number of state kets = 120 Doing FMS for a cluster of 19 atoms around iph = 5 0 FMS matrix (LUD) at point 1, number of state kets = 106 point # 20 energy = -31.019 point # 40 energy = -12.053 point # 60 energy = -11.990 point # 80 energy = -11.740 point # 100 energy = -11.490 point # 120 energy = -11.240 point # 140 energy = -10.990 point # 160 energy = -10.740 Electronic configuration iph il N_el 0 0 1.960 0 1 5.591 0 2 0.000 0 3 0.000 0 4 0.000 1 0 2.194 1 1 6.168 1 2 0.690 1 3 0.000 1 4 0.000 2 0 0.311 2 1 6.485 2 2 0.838 2 3 0.000 2 4 0.000 3 0 0.493 3 1 0.564 3 2 9.770 3 3 0.000 3 4 0.000 4 0 1.858 4 1 4.581 4 2 0.000 4 3 0.000 4 4 0.000 5 0 1.947 5 1 5.142 5 2 0.000 5 3 0.000 5 4 0.000 mu_new= -10.658 Charge transfer: iph charge(iph) 0 0.419 1 0.862 2 0.317 3 0.212 4 -0.419 5 -0.088 SCF ITERATION NUMBER 4 OUT OF 30 Calculating energy and space dependent l-DOS. It takes time ... point # 1 energy = -42.000 Doing FMS for a cluster of 19 atoms around iph = 0 0 FMS matrix (LUD) at point 1, number of state kets = 106 Doing FMS for a cluster of 19 atoms around iph = 1 0 FMS matrix (LUD) at point 1, number of state kets = 126 Doing FMS for a cluster of 23 atoms around iph = 2 0 FMS matrix (LUD) at point 1, number of state kets = 167 Doing FMS for a cluster of 23 atoms around iph = 3 0 FMS matrix (LUD) at point 1, number of state kets = 162 Doing FMS for a cluster of 20 atoms around iph = 4 0 FMS matrix (LUD) at point 1, number of state kets = 120 Doing FMS for a cluster of 19 atoms around iph = 5 0 FMS matrix (LUD) at point 1, number of state kets = 106 point # 20 energy = -30.879 point # 40 energy = -10.658 point # 60 energy = -10.608 point # 80 energy = -10.358 dot ... dot ... dot point # **** energy = 371.142 point # **** energy = 371.392 point # **** energy = 371.642 point # **** energy = 371.892 point # **** energy = 372.142 point # **** energy = 372.392 point # **** energy = 372.642 point # **** energy = 372.892 point # **** energy = 373.142 crash! bang!

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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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Re: [Ifeffit] Re: opening SSRL data with Athena
by Silvio Levy 14 Jan '07

14 Jan '07

Here is how I converted my SSRL-collected data so as to be able to import them into Athena. (By the way, when you collect the data you can specify that you want them in ASCII, but I did not know that at the time.) 1. Install EXAFSPAK, the SSRL-grown Exafs data analysis suite. 2. Run the MVIEW command on each file with instructions to save the output in ASCII. Although the command is interactive, you can run it in quasi-batch mode -- you just have to quit from each window as pops up. This way you can cycle through 100 files or more in a couple of minutes. For example, on Linux, I ran the following shell script for files collected in transmission mode. The key command is mview /num=1-6 /den=1 /write=output-file input-file ********************** #!/bin/sh cd Raw # directory where the SSRL binary files reside for i in `cat list-of-files-to-be-converted` do mview /num=1-6 /den=1 /write=../ASCII/$i $i done # this prints 7 columns (the first being a repeat of energy) # In Athena, select num=5,den=6 for sample, num=6,den=7 for reference ********************** Hope this helps! Silvio Levy

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RE: [Ifeffit] Projekt with the "flatten-problem"
by Kelly, Shelly D. 11 Jan '07

11 Jan '07

Good going Dave. I think that you are correct. Shelly > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Barton, David (DG) > Sent: Thursday, January 11, 2007 10:49 AM > To: 'XAFS Analysis using Ifeffit' > Subject: RE: [Ifeffit] Projekt with the "flatten-problem" > > Jens, > > It appears to me that the E-shift is causing the problems with the step in > the pre-edge data. Shelly's data only appears to remove the step because > the pre-edge and the extrapolated post-edge plots are nearly parallel. If > you adjust the Normalization range in Shelly's data you will see the step > appear again. > > However, if you set the E-shift to zero and reset Eo, pre-edge range, and > normalization range (to your liking) you will see that the step is goes > away. So the work around would be to subtract the E-shift from your Raw > data, then import into Athena and do not use any E-shift. > > Bruce or Matt may have to comment, but it appears to me that the > normalization/flatten routine may not be dealing with the E-shift > appropriately. > > Dave > > >-----Original Message----- > >From: ifeffit-bounces(a)millenia.cars.aps.anl.gov > >[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf > >Of Kelly, Shelly D. > >Sent: Thursday, January 11, 2007 11:11 AM > >To: XAFS Analysis using Ifeffit > >Subject: RE: [Ifeffit] Projekt with the "flatten-problem" > > > >Hi Jens, > > > >I believe the problem is related to the structure in the data > >before E0. > >If you choose e0 to be at the beginning of the structure then > >the normalization is handled better by Athena. Take a look at > >the attached project file. The first data set with e0 on the > >edge as you would choose for EXAFS analysis (e1) shows the > >error that Jens reported. The second data set with a lower > >value for e0 at the beginning of the structure (e2) gets the job done. > > > >Cheers, > >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 Jens Kruse > >> Sent: Thursday, January 11, 2007 2:38 AM > >> To: Athena mailing List > >> Subject: [Ifeffit] Projekt with the "flatten-problem" > >> > >> 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" > > > _______________________________________________ > 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] Projekt with the "flatten-problem"
by Barton, David (DG) 11 Jan '07

11 Jan '07

Jens, It appears to me that the E-shift is causing the problems with the step in the pre-edge data. Shelly's data only appears to remove the step because the pre-edge and the extrapolated post-edge plots are nearly parallel. If you adjust the Normalization range in Shelly's data you will see the step appear again. However, if you set the E-shift to zero and reset Eo, pre-edge range, and normalization range (to your liking) you will see that the step is goes away. So the work around would be to subtract the E-shift from your Raw data, then import into Athena and do not use any E-shift. Bruce or Matt may have to comment, but it appears to me that the normalization/flatten routine may not be dealing with the E-shift appropriately. Dave >-----Original Message----- >From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf >Of Kelly, Shelly D. >Sent: Thursday, January 11, 2007 11:11 AM >To: XAFS Analysis using Ifeffit >Subject: RE: [Ifeffit] Projekt with the "flatten-problem" > >Hi Jens, > >I believe the problem is related to the structure in the data >before E0. >If you choose e0 to be at the beginning of the structure then >the normalization is handled better by Athena. Take a look at >the attached project file. The first data set with e0 on the >edge as you would choose for EXAFS analysis (e1) shows the >error that Jens reported. The second data set with a lower >value for e0 at the beginning of the structure (e2) gets the job done. > >Cheers, >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 Jens Kruse >> Sent: Thursday, January 11, 2007 2:38 AM >> To: Athena mailing List >> Subject: [Ifeffit] Projekt with the "flatten-problem" >> >> 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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RE: [Ifeffit] Projekt with the "flatten-problem"
by Kelly, Shelly D. 11 Jan '07

11 Jan '07

Hi Jens, I believe the problem is related to the structure in the data before E0. If you choose e0 to be at the beginning of the structure then the normalization is handled better by Athena. Take a look at the attached project file. The first data set with e0 on the edge as you would choose for EXAFS analysis (e1) shows the error that Jens reported. The second data set with a lower value for e0 at the beginning of the structure (e2) gets the job done. Cheers, 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 Jens Kruse > Sent: Thursday, January 11, 2007 2:38 AM > To: Athena mailing List > Subject: [Ifeffit] Projekt with the "flatten-problem" > > 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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Re: ZnO Artemis demo - problem with "dr" parameter
by Scott Calvin 11 Jan '07

11 Jan '07

Hi Craig, I'm cc'ing this to the Ifeffit mailing list, as others may encounter similar problems. It's not your novice-ness that's causing the problem; it's a version issue. I wrote the ZnO example when an older version of the software was current. Since then, "dr" became a reserved variable, and can't be user defined. (Bruce could probably give the reason for that change.) I fixed that, but it looks like the older version of the tutorial is being included with the current distributions of Ifeffit and friends. We'll fix that. In the meanwhile, though, you can just change the variable names by hand to "delr" or something like that (you have to change them in both the GDS screen and the path screens, or course). Sorry about that. Incidentally, there's a related bug in Artemis itself. If you have it automatically come up with variables for you on a new fit, it will name one "dr", and then can't do the fit! :( --Scott Calvin Sarah Lawrence College At 01:24 AM 1/9/2007, Craig Klauber wrote: >Dear Scott, > Sorry to bug you on what may be a very trivial issue - but if >its a quick fix a bit of guidance would be very much appreciated. > I've been working through your ZnO demo tutorial on Artemis and >everything worked well until I received the following warning message from >Artemis after trying to Fit at the beginning of part 2. The Fit then aborts. > >"This parameter uses a name which has special meaning in Ifeffit: > dr >You must change this parameter name before attempting to fit. >One common example of this sort is a variable named "dr1", which >should be changed to something like "dr_1" or "drone"." > >The warning message doesn't make a great deal of sense as "dr" is a defined >parameter within Artemis. > >Running ifeffit-1.2.9-mac10.4_horae64pre_pkg on a Mac PPC G5 Dual 2GHz under >OS X 10.4.8. Presumably I'm doing something dumb (very much the novice EXAFS >is not my area). Have checked a number of the Ifeffit Archives, but so far >have not spotted a reference to this. > >Kind Regards >Craig Klauber > > > >__________________________________________________ >Craig Klauber >CSIRO Minerals >PO Box 90 >Bentley WA 6982 >AUSTRALIA >Ph: +61 8 9334 8060 >Fax: +61 8 9334 8001 >craig.klauber(a)csiro.au >CSIROTEL: 99 8060 >http://www-wf.minerals.csiro.au >__________________________________________________

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N_ind
by m.bauer 10 Jan '07

10 Jan '07

good evening everybody, i just started exposing myself to the nyqvist-topic and even i might be on the risk of boring the specialists out there i have another question for my better understanding: if i fit my data in k-space without any fourier filtering and backtransforming etc. what value of /dr/ do i have to use when calculating the N_ind? i hope it is just that range in the r-space, which contains significant (or according to my structural model used reasonable) structural data, i.e. the range i would use if i would filter the data....!? thanks for your help, regards matthias -- Matthias Bauer Universität Stuttgart Institut für Physikalische Chemie Arbeitskreis Prof. Dr. H. Bertagnolli Pfaffenwaldring 55 70569 Stuttgart (Vaihingen) Telefon: (+49) 0711-685-64472 Fax: (+49) 0711-685-64443 E-Mail: m.bauer(a)ipc.uni-stuttgart.de homepage: http://www.ipc.uni-stuttgart.de/~matthias/index.htm

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Problems with the >flatten< option in Athena
by Jens Kruse 10 Jan '07

10 Jan '07

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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RE: [Ifeffit] Problems with the >flatten< option in Athena
by Kelly, Shelly D. 10 Jan '07

10 Jan '07

Hi Jens, You can try moving e0. E0 should be on the edge. Is E0 at the position of the step? You could also send us an example. Then we can help more directly. I'd guess that the step is caused by some background parameters that are set incorrectly. SK > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Jens Kruse > Sent: Wednesday, January 10, 2007 8:56 AM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Problems with the >flatten< option in Athena > > 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 > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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