February 2007 - Ifeffit - millenia.cars.aps.anl.gov

why ss_2 is negative?
by hw26＠njit.edu 24 Feb '07

24 Feb '07

Dear all, I am doing model fitting using Artemis. My sample is uranium solution with an ionic liquid, 1-methoxyethyl-3-methyl imidazolium tetrafluoroborate (MOEMIMBF4). The Fitting seems ok except that the ss_2 is negative. I don't know how can I fix this problem. Can you get a chance to take a look? My fitting is simple, only three single scattering pathes which were produced by Six Pack. The fitting file is attached. I really appreciate it if you could take a look and give some advice! Best regards! Hao

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Re: [Ifeffit] Hephaestus
by Matt Newville 23 Feb '07

23 Feb '07

Hi Carloine, On 2/21/07, Caroline Peacock <clp(a)noc.soton.ac.uk> wrote: > Have just installed the Ifeffit package > (feffit-1.2.9-Mac10.4_horae64pre_pkg.dmg) on my Intel Mac > (OS X 10.4.8)... Upon double clicking Hephaestus (as instructed in the > readme) i am prompted to choose either X11 graphics or Aquaterm - either way > X11 opens and then nothing...Is this a UNIX based program - from the > screenshots i guessed it wasn't? > > Any ideas why it isn't working? I'm copying this to the Ifeffit mailing list, as I think someone else may have a better answer than I can give. Hephaestus does require X11, but I think the problem is that the Ifeffit-1.2.9 disk installers are all PPC only. That is, I think no one has made an installer for Intel Mac. --Matt

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(no subject)
by Ruwan Wijesundera 15 Feb '07

15 Feb '07

Dear Bruce We have used Athena and Artemis software to analyses the EXAFS. When we do the analysis, we used different S2o for each path for fitting of Cu2O data. I succeeded to obtain good fitting by this way. Documents related to percent EXAFS analysis have been mentioned S2o is one value for all paths. What I want to know is our fittings are correct or not. I am looking forward early response. About 10 years ago we had being using another program made by Tokyo University in Japan. In this program, the refined parameters also included S2oj and Nj to the each cells Thanks Ruwn

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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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