July 2005 - Ifeffit - millenia.cars.aps.anl.gov

Debye-Waller factors for metal oxides ?
by Ian James Drake 16 Apr '09

16 Apr '09

Hi, There is little discussion over the significance of fitted Debye-Waller factors (ss2) found for metal centers in metal oxides of heterogeneous catalysts. I am searching for a better way of determining how reasonable these values are in the fits I get. 1. Are phenomenological models like the correlated Debye model and Einstein model appropriate? It seems that Debye temperatures are hard to find for oxides. 2. Is there an equivalent value for ss2 in x-ray crystallography data that I can refer to for comparison in these materials? What should I look for in reviewing published x-ray crystallographic data? 3. Is the temperature dependence reported for the ss2 for some metals (like Cu and Al) similar to their respective oxides? For example, in Debye-Waller factor calculations reported for Al metal by R.C.G Killean (in J.Phys.F: Metal Phys., v. 4, pg. 1908, 1974), the ss2 changes by a factor of three between 25C and 300C. Would I expect a factor of three increase in crystalline zeolites (AlO4 structural units). 4. Specific to my work: I have studied Al containing oxides at temperatures between 25 and 300 C. I would like to quantify coordination changes by doing EXAFS fitting of the Al K-edge data. The EXAFS was taken at temperature and I observe no change in the broadening of the data. Likewise, the fitting shows no sensitivity in the Debye-Waller factor. It is nearly constant at 0.001 A over the temperatures of interest. Since ss2 and the coordination number (CN) are correlated, I would like a way to bind the error on the fitted CN by modeling real physical changes in the Debye-Waller factors. Do you have any suggestions? Looking forward to your thoughts. Ian Drake Graduate Student UC Berkeley

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Artemis- Loading up error
by Zohair Hussain 17 Apr '06

17 Apr '06

Hi! I recently had to install ifeffit software package on our network computer. The first time I ran Artemis I was asked to update which I did. However, Artemis did not start after that. The error message that I got is shown in the attached figures artemis-error1a and 1b. Please note that only Artemis doesn't work, all the other softwares (Athena, Hephaestus, TKAtoms etc.) work fine. I tried running the .bat file from the Ifeffit folder but that didn't work either. I also tried to run the artemis.exe file and received the error shown in figure "artemis-error2". Later I unisntalled and re-installed Ifeffit and chose not to do the updates and Artemis is now running fine. I was wondering if anyone has any idea why this is so or if there is a way around installing the updates and still being able to use Artemis??? Thanks, Zohair

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RE: [Ifeffit] R-factor
by Scott Calvin 20 Sep '05

20 Sep '05

Hi Alison, I agree entirely with Victor and Anatoly. In addition, I'd say that in my work an R-factor of above 0.1 is pretty sketchy. How sketchy depends on the complexity of the fit, of course; you're going over a big r-range, so if it takes you only two or three parameters to get an R-factor of 0.11, I guess that's not too bad. But if you have more parameters than that and it's still not fitting so well, I'd be concerned. As a referee, for example, that would be a much larger warning flag to me than the little discrepancy between the R-factors for the k- and q-space fits. Just to echo Victor and Anatoly again: it's quite easy for me to believe that the fitting algorithm just happened to find a somewhat different minimum in the fitting space in the two cases. They both suggested ways to test if that is the case. Although I've never fit in q-space, I've seen something that on the face of it is equally baffling: sometimes I've added an additional fitting parameter, changing nothing else, and seen the R-factor <italic>increase </italic>slightly. In some ideal sense, that shouldn't be--the fitting routine (this one happened to be Ifeffit) "should" at worst get the identical fit as to when the new parameter was constrained. But it is impossible to write a fitting routine that is guaranteed to find the closest possible fit, so all routines will occasionally generate those kinds of results. --Scott Calvin Sarah Lawrence College >-------------- Original message -------------- > >> Bruce, >> >> I've looked, and my R-factors for the back-transformed >> space are not necessarily twice the value of the R-factors >> for the k-space fits. In fact, they are often quite >> close. For example, just recently I had a k-space >> R-factor of 0.102 and a q-space R-factor of 0.113. Now, I >> realize those numbers are very close, but I'm afraid if I >> try to publish this, then I will get criticism for the >> q-space R-factors being larger. If I can explain it, then >> maybe it won't be a problem. >

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Icosahedral cluster coordinates
by Patrick Kluth 17 Aug '05

17 Aug '05

Hi All, Since this is my first message to the mailing list, I`d like to say thanks very much to Bruce, Matt and everyone else who is involved for this great piece of software. It makes life in the EXAFS world so much easier. I am working with metal clusters and would like to do some FEFF calculations on icosahedral clusters. Is there anyone out there who has a FEFF input file (or equivalently a list of coordinates) for an icosahedral cluster (147 atoms is probably sufficient for my purpuses). Thanks Patrick --------------------------------------------------------------------------------- Dr. Patrick Kluth ARC Australian Postdoctoral Fellow Department of Electronic Materials Engineering Research School of Physical Sciences and Engineering The Australian National University Canberra, ACT 0200 AUSTRALIA Phone: +61 2 6125 0358 Fax: +61 2 6125 0511 Mobile: +61 408 66 31 04 Email: Patrick.Kluth(a)anu.edu.au http://www.rsphysse.anu.edu.au/eme ---------------------------------------------------------------------------------

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ifeffit 1.2.7
by Matt Newville 26 Jul '05

26 Jul '05

Hi Folks, I've posted Ifeffit 1.2.7, including a new Windows installer, source code, and a Mac Binary installer (currently OS 10.3 only) on the IFeffit Web Page. I'll post these to sourceforge.net as soon as I can. For Windows users, there is also an automatic update that may be downloaded and installed. The changes to the ifeffit library are small: a few bugfixes, added a 'penalty()' math function (as per a discussion on this list about restraints) and an improved mechanism for ifeffit to report its status to a calling program like Athena and Artemis. The Windows and Mac installers also include the latest versions of Bruce's Athena, Artemis, and Hephaestus. There are still some known issues with "PAR-" files from Bruce's codes on Windows. Bruce and I think we can solve this, and are aiming to release a new Windows installer sometime in the next month (or so) that fixes this and cleans up some of the messiness of the Windows installer. --Matt

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RE: [Ifeffit] surface EXAFS
by Kelly, Shelly D. 21 Jul '05

21 Jul '05

Hi Matt, I should have given these details right away. My trick is to parameterize the feff paths in terms of an x, y, z coordinate for the atom on the surface. Then I refine three different polarization dependent data sets to find the best x, y, and z position of the atom on the surface. Thanks for the references! Shelly > -----Original Message----- > From: Matt Newville [mailto:newville@cars.uchicago.edu] > Sent: Thursday, July 21, 2005 11:13 AM > To: Kelly, Shelly D.; XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] surface EXAFS > > Hi Shelly, > > > I am working on a project were I trick feffit into moving an > > atom around on the surface of a plane to refine polarization > > dependent surface EXAFS data. I made a quick literature > > search and have not found any other EXAFS papers that do such > > a thing. Are you aware of similar work? I would like to give > > credit in our manuscript. > > I know of other work in progress (some in progress for a pretty > long time!!). I also believe there are a few surface XAFS > papers that used feffit. I think these may count, though I > don't have a copy of any of these in front of me: > > L. Y. Zhao et al, Applied Surface Science 228, p 257 (2004) > P. Luches et al, Surface Science 566, p 84 (2004) > L. Damoc, et al J. Applied Physics 92, p 1862 (2002) > S. K. Kim, et al, PRB 62, p 3025 (2000). > > I think there are probably others. > > I'm not sure what the 'trick' you're using is. Doing a polarized > calculation (with feff or in feffit) for an atom on a surface > doesn't seem like such a big deal, but maybe you're doing > something fancier. > > One paper that I know is in progress (and a just-completed > thesis) measures the 'height above the surface' of a sorbed atom > by defining several different distances in terms of this height. > > --Matt

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surface EXAFS
by Kelly, Shelly D. 21 Jul '05

21 Jul '05

Hello all, I am working on a project were I trick feffit into moving an atom around on the surface of a plane to refine polarization dependent surface EXAFS data. I made a quick literature search and have not found any other EXAFS papers that do such a thing. Are you aware of similar work? I would like to give credit in our manuscript. Shelly

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feff doesn't like cluster
by Juraj Majzlan 21 Jul '05

21 Jul '05

Hello, I collected As K EXAFS data and created a cluster which could represent the "probable geometry". I have an ATOMS file with coordinates of the atoms in a triclinic unit cell. ATOMS did its thing but FEFF refused to process the data and generated an error: Feff 6L.02 No atoms or overlap cards for unique pot 1 Cannot calculate potentials, etc. Fatal Error: at RDINP Then I filled the empty space around the cluster with hydrogen atoms on a grid, hoping that FEFF would like it more, but the same error came. Short of creating a complete structure (of some sort) with the cluster embedded in it, what can I do to make this work? Thank you, Juro Majzlan ---------------------------------- Juraj Majzlan Institute of Mineralogy and Petrology Albert-Ludwig-University of Freiburg Albertstrasse 23b Freiburg, D-79104, Germany telephone +49-761-203-6416 fax +49-761-203-6407 http://www.minpet.uni-freiburg.de

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RE: [Ifeffit] feff doesn't like cluster
by Kelly, Shelly D. 21 Jul '05

21 Jul '05

Oh well, I guess that could be fixed. Atoms assumes that the absorbing atom will also be a scattering atom, hence ipot 0 and ipot 1 are always defined with the same atom type. SK > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Juraj Majzlan > Sent: Thursday, July 21, 2005 10:14 AM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] feff doesn't like cluster > > Shelly, > > but why did ATOMS generate an ipot that doesn't exist? > > Juro > > On Jul 21, 2005, at 4:59 PM, Kelly, Shelly D. wrote: > > > > > Hi Juro, > > > > Feff is old fasioned. It requires that all ipot numbers are in order > > and that they exist, otherwise it just quits. In your example below > > ipot number 1 was not defined. > > > > Shelly > > > >> -----Original Message----- > >> From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > >> bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Juraj Majzlan > >> Sent: Thursday, July 21, 2005 9:51 AM > >> To: XAFS Analysis using Ifeffit > >> Subject: Re: [Ifeffit] feff doesn't like cluster > >> > >> Hello, > >> > >> thank you for the fast response. According to Norbert's > >> suggestion, I looked in the feff file. The problem seems to > >> be with the potential 1, assigned to As. Removing this line > >> and rewriting all potentials in the list makes feff like > >> the input. However, I don't understand why ATOMS has > >> generated these ipot values. The atoms.inp is below. > >> > >> Juro > >> > >> ----------------------------------part of feff.inp > >> POTENTIALS > >> * ipot Z element > >> 0 33 As > >> 1 33 As > >> 2 8 O > >> 3 26 Fe > >> > >> ATOMS * this list contains 24 > >> atoms > >> * x y z ipot tag > >> distance > >> 0.00000 0.00000 0.00000 0 As > >> 0.00000 > >> -1.40201 0.76410 -0.53997 2 O3_1 > >> 1.68554 > >> 0.00000 -1.59002 -0.56202 2 O4_1 > >> 1.68643 > >> 0.00000 -0.00003 1.68705 2 O1_1 > >> 1.68705 > >> 1.37801 0.79495 -0.56207 2 O2_1 > >> 1.68724 > >> -2.86303 -0.03582 -1.71095 3 Fe2_1 > >> 3.33550 > >> -1.39501 -2.50095 -1.71100 3 Fe3_1 > >> 3.33591 > >> -1.46101 -0.86989 -2.91804 2 O13_1 > >> 3.37731 > >> -2.86203 -1.70487 -0.55592 2 O12_1 > >> 3.37740 > >> 0.00000 -0.69408 3.59511 3 Fe1_1 > >> 3.66150 > >> 0.00000 -2.60210 2.90109 2 O7_1 > >> 3.89708 > >> 2.03002 -0.69418 3.59504 2 O9_1 > >> 4.18655 > >> -2.03002 -0.69397 3.59518 2 O8_1 > >> 4.18663 > >> -2.86503 1.63323 -2.86599 2 O11_1 > >> 4.36918 > >> 0.07200 -3.29702 -2.86609 2 O15_1 > >> 4.36921 > >> -4.26604 0.79825 -0.50387 2 O10_1 > >> 4.36923 > >> -1.32901 -4.13200 -0.50397 2 O14_1 > >> 4.36963 > >> 0.00000 1.21295 4.28913 2 O6_1 > >> 4.45734 > >> 0.00000 -1.38895 -4.49813 2 O5_1 > >> 4.70769 > >> -2.79603 -3.41087 -2.86399 2 O17_1 > >> 5.25873 > >> -4.33104 -0.83474 -2.86393 2 O16_1 > >> 5.25897 > >> 0.00000 -1.38912 5.50217 2 O5_2 > >> 5.67482 > >> 5.73406 0.79772 -0.50422 2 O10_2 > >> 5.81120 > >> 0.00000 1.21312 -5.71117 2 O6_2 > >> 5.83859 > >> END > >> > >> > >> ----------------------------------atoms.inp > >> title model6 > >> space P 1 > >> rmax=6.0 a=10.0001 b=10.0002 c=10.0003 alpha=90.001 > >> beta=90.002 gamma=90.003 > >> core=As > >> atom > >> ! At.type x y z tag > >> As 0.00000 0.00000 0.00000 As > >> Fe 0.00000 -0.06940 0.35950 Fe1 > >> Fe -0.28630 -0.00360 -0.17110 Fe2 > >> Fe -0.13950 -0.25010 -0.17110 Fe3 > >> O 0.00000 0.00000 0.16870 O1 > >> O 0.13780 0.07950 -0.05620 O2 > >> O -0.14020 0.07640 -0.05400 O3 > >> O 0.00000 -0.15900 -0.05620 O4 > >> O 0.00000 -0.13890 0.55020 O5 > >> O 0.00000 0.12130 0.42890 O6 > >> O 0.00000 -0.26020 0.29010 O7 > >> O -0.20300 -0.06940 0.35950 O8 > >> O 0.20300 -0.06940 0.35950 O9 > >> O -0.42660 0.07980 -0.05040 O10 > >> O -0.28650 0.16330 -0.28660 O11 > >> O -0.28620 -0.17050 -0.05560 O12 > >> O -0.14610 -0.08700 -0.29180 O13 > >> O -0.13290 -0.41320 -0.05040 O14 > >> O 0.00720 -0.32970 -0.28660 O15 > >> O -0.43310 -0.08350 -0.28640 O16 > >> O -0.27960 -0.34110 -0.28640 O17 > >> > >> > >> On Thu, 21 Jul 2005 08:53:27 -0500 (CDT) > >> Matt Newville <newville(a)cars.uchicago.edu> wrote: > >>> Juraj, > >>> > >>> Please post the feff.inp file. You might also > >>> send the atoms.inp file. > >>> > >>> -Matt > >>> > >>> On Thu, 21 Jul 2005, Juraj Majzlan wrote: > >>> > >>>> Hello, > >>>> > >>>> I collected As K EXAFS data and created a cluster which > >>>> could represent the "probable geometry". I have an > >>> ATOMS > >>>> file with coordinates of the atoms in a triclinic unit > >>>> cell. ATOMS did its thing but FEFF refused to process > >>> the > >>>> data and generated an error: > >>>> Feff 6L.02 > >>>> No atoms or overlap cards for unique pot 1 > >>>> Cannot calculate potentials, etc. > >>>> Fatal Error: at RDINP > >>>> > >>>> Then I filled the empty space around the cluster with > >>>> hydrogen atoms on a grid, hoping that FEFF would like > >>> it > >>>> more, but the same error came. > >>>> > >>>> Short of creating a complete structure (of some sort) > >>> with > >>>> the cluster embedded in it, what can I do to make this > >>>> work? > >>> > >>> > >>> _______________________________________________ > >>> Ifeffit mailing list > >>> Ifeffit(a)millenia.cars.aps.anl.gov > >>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > >> > >> > >> > >> ---------------------------------- > >> Juraj Majzlan > >> Institute of Mineralogy and Petrology > >> Albert-Ludwig-University of Freiburg > >> Albertstrasse 23b > >> Freiburg, D-79104, Germany > >> telephone +49-761-203-6416 > >> fax +49-761-203-6407 > >> http://www.minpet.uni-freiburg.de > >> _______________________________________________ > >> 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 > > > > ---------------------------------------------------------------------- > Juraj Majzlan > Institute of Mineralogy and Geochemistry > Albert-Ludwig-University of Freiburg > Albertstrasse 23b > D-79104 Germany > telephone +49-761-203-6416 > fax +49-761-203-6407 > http://www.minpet.uni-freiburg.de/Majzlan.html > > _______________________________________________ > 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] feff doesn't like cluster
by Kelly, Shelly D. 21 Jul '05

21 Jul '05

Hi Juro, Feff is old fasioned. It requires that all ipot numbers are in order and that they exist, otherwise it just quits. In your example below ipot number 1 was not defined. Shelly > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Juraj Majzlan > Sent: Thursday, July 21, 2005 9:51 AM > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] feff doesn't like cluster > > Hello, > > thank you for the fast response. According to Norbert's > suggestion, I looked in the feff file. The problem seems to > be with the potential 1, assigned to As. Removing this line > and rewriting all potentials in the list makes feff like > the input. However, I don't understand why ATOMS has > generated these ipot values. The atoms.inp is below. > > Juro > > ----------------------------------part of feff.inp > POTENTIALS > * ipot Z element > 0 33 As > 1 33 As > 2 8 O > 3 26 Fe > > ATOMS * this list contains 24 > atoms > * x y z ipot tag > distance > 0.00000 0.00000 0.00000 0 As > 0.00000 > -1.40201 0.76410 -0.53997 2 O3_1 > 1.68554 > 0.00000 -1.59002 -0.56202 2 O4_1 > 1.68643 > 0.00000 -0.00003 1.68705 2 O1_1 > 1.68705 > 1.37801 0.79495 -0.56207 2 O2_1 > 1.68724 > -2.86303 -0.03582 -1.71095 3 Fe2_1 > 3.33550 > -1.39501 -2.50095 -1.71100 3 Fe3_1 > 3.33591 > -1.46101 -0.86989 -2.91804 2 O13_1 > 3.37731 > -2.86203 -1.70487 -0.55592 2 O12_1 > 3.37740 > 0.00000 -0.69408 3.59511 3 Fe1_1 > 3.66150 > 0.00000 -2.60210 2.90109 2 O7_1 > 3.89708 > 2.03002 -0.69418 3.59504 2 O9_1 > 4.18655 > -2.03002 -0.69397 3.59518 2 O8_1 > 4.18663 > -2.86503 1.63323 -2.86599 2 O11_1 > 4.36918 > 0.07200 -3.29702 -2.86609 2 O15_1 > 4.36921 > -4.26604 0.79825 -0.50387 2 O10_1 > 4.36923 > -1.32901 -4.13200 -0.50397 2 O14_1 > 4.36963 > 0.00000 1.21295 4.28913 2 O6_1 > 4.45734 > 0.00000 -1.38895 -4.49813 2 O5_1 > 4.70769 > -2.79603 -3.41087 -2.86399 2 O17_1 > 5.25873 > -4.33104 -0.83474 -2.86393 2 O16_1 > 5.25897 > 0.00000 -1.38912 5.50217 2 O5_2 > 5.67482 > 5.73406 0.79772 -0.50422 2 O10_2 > 5.81120 > 0.00000 1.21312 -5.71117 2 O6_2 > 5.83859 > END > > > ----------------------------------atoms.inp > title model6 > space P 1 > rmax=6.0 a=10.0001 b=10.0002 c=10.0003 alpha=90.001 > beta=90.002 gamma=90.003 > core=As > atom > ! At.type x y z tag > As 0.00000 0.00000 0.00000 As > Fe 0.00000 -0.06940 0.35950 Fe1 > Fe -0.28630 -0.00360 -0.17110 Fe2 > Fe -0.13950 -0.25010 -0.17110 Fe3 > O 0.00000 0.00000 0.16870 O1 > O 0.13780 0.07950 -0.05620 O2 > O -0.14020 0.07640 -0.05400 O3 > O 0.00000 -0.15900 -0.05620 O4 > O 0.00000 -0.13890 0.55020 O5 > O 0.00000 0.12130 0.42890 O6 > O 0.00000 -0.26020 0.29010 O7 > O -0.20300 -0.06940 0.35950 O8 > O 0.20300 -0.06940 0.35950 O9 > O -0.42660 0.07980 -0.05040 O10 > O -0.28650 0.16330 -0.28660 O11 > O -0.28620 -0.17050 -0.05560 O12 > O -0.14610 -0.08700 -0.29180 O13 > O -0.13290 -0.41320 -0.05040 O14 > O 0.00720 -0.32970 -0.28660 O15 > O -0.43310 -0.08350 -0.28640 O16 > O -0.27960 -0.34110 -0.28640 O17 > > > On Thu, 21 Jul 2005 08:53:27 -0500 (CDT) > Matt Newville <newville(a)cars.uchicago.edu> wrote: > > Juraj, > > > > Please post the feff.inp file. You might also > > send the atoms.inp file. > > > > -Matt > > > > On Thu, 21 Jul 2005, Juraj Majzlan wrote: > > > > > Hello, > > > > > > I collected As K EXAFS data and created a cluster which > > > could represent the "probable geometry". I have an > > ATOMS > > > file with coordinates of the atoms in a triclinic unit > > > cell. ATOMS did its thing but FEFF refused to process > > the > > > data and generated an error: > > > Feff 6L.02 > > > No atoms or overlap cards for unique pot 1 > > > Cannot calculate potentials, etc. > > > Fatal Error: at RDINP > > > > > > Then I filled the empty space around the cluster with > > > hydrogen atoms on a grid, hoping that FEFF would like > > it > > > more, but the same error came. > > > > > > Short of creating a complete structure (of some sort) > > with > > > the cluster embedded in it, what can I do to make this > > > work? > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > ---------------------------------- > Juraj Majzlan > Institute of Mineralogy and Petrology > Albert-Ludwig-University of Freiburg > Albertstrasse 23b > Freiburg, D-79104, Germany > telephone +49-761-203-6416 > fax +49-761-203-6407 > http://www.minpet.uni-freiburg.de > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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