August 2010 - Ifeffit - millenia.cars.aps.anl.gov

Manual update to iXAFS
by Paul Fons 31 Aug '10

31 Aug '10

Hi Bruce, Regards from a far too hot Japan, Thanks for the update suggestions for iXAFS Bruce. I managed to get it to work, but I found a couple of problems. 1. There is another intermediate directory in your steps (3,4,5), e.g. " /Applications/iXAFS/Contents/Resources/bin" should read " /Applications/iXAFS/Contents/Resources/Horae/bin" The intermediate directory Horae is missing in each case. 2. SVN is installed by default on the Mac. When I tried to run the mkartemis.pl and friends after downloading the latest svn release, however, I found that the rc.pl files were missing. How does one generate these from the svn files? I used a rc.pl from a horae-70 release I had around and it apparently worked. 3. The version numbers in the SVN release conflict within the files from the SVN (at least when following the procedure you mentioned above). Some of the files from the SVN release have (ArtemisLog) $VERSION set to 0.8.014 while others (e.g. Group.pm had $VERSION = "0.0.8.061"). This triggers an error in the athena and artemis of a version mismatch. I "fixed" this by disabling the check, as the logic of the versioning is not very clear from a simple examination of the files. What should the "$VERSION" string (and any other version related strings) be set to in each of the files? In any case it work, but it sure would be nice to have a nice new official release! paul

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Re: [Ifeffit] Methods to break correlations
by Brandon Reese 31 Aug '10

31 Aug '10

Hi Bruce, Thanks for the tip on updating iXAFS, I will give that a try. As to the plugin not working on Athena, apologies about the vagueness. I have tried to open the file using iXAFS (ifeffit v.1.2.10, Athena v.0.8.054) and received the attached error message. After clicking 'ok' Athena remains open. I have also tried to open the same data file on Parallels running WinXP SP3 using the standard *.exe installer (ifeffit v.1.2.11c, Athena v.0.8.061) and received the attached error message. After clicking 'ok' for the windows error, Athena quits (leaving the plot window open). According to the header of the file it was collected using "SSRL - EXAFS Data Collector 2.0". I have tried several combination's which plug-ins are selected and it didn't seem to make a difference. Thanks for the tips Brandon On Mon, Aug 30, 2010 at 11:00 AM, <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: Methods to break correlations (Bruce Ravel) > 2. Re: Methods to break correlations (Bruce Ravel) > 3. Re: Residual EXAFS spectra (Bruce Ravel) > 4. Re: Methods to break correlations (Jeff Terry) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 30 Aug 2010 10:08:13 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Methods to break correlations > Message-ID: <201008301008.13700.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-15" > > On Saturday 28 August 2010 02:47:11 pm Brandon Reese wrote: > > Does anyone have an Athena plugin for the SSRL data Collector > > v2.0? The SSRL plugins available make the program crash when I try and > use > > them. (moderators, let me know if these questions should have been in a > > separate posting) > > > > Here is the SSRL binary plugin from the svn repository > > > http://cars9.uchicago.edu/svn/horae/trunk/lib/Ifeffit/Plugins/Filetype/Athe… > > And here is the one for data files that have been converted to ascii > > > http://cars9.uchicago.edu/svn/horae/trunk/lib/Ifeffit/Plugins/Filetype/Athe… > > They should be placed in $HOME/.horae/Ifeffit/Plugins/Filetype/Athena/ > > > > I am willing to take a look at the problem you are seeing, but "it > crashes" doesn't give me much to work with. Obviously the plugins > worked for me otherwise I would not have considered them ready for > release. You need to provide some clue as to what the problem is. > Either supply a data file that triggers the problem or by cut and > paste what gets written after starting Athena in a terminal window or > (preferably) both. > > B > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/<http://cars9.uchicago.edu/%7Eravel/software/exafs/> > > > ------------------------------ > > Message: 2 > Date: Mon, 30 Aug 2010 10:11:06 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Cc: Jeff Terry <terryj(a)iit.edu> > Subject: Re: [Ifeffit] Methods to break correlations > Message-ID: <201008301011.06685.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-15" > > On Saturday 28 August 2010 02:47:11 pm Brandon Reese wrote: > > I am running iXAFS 2.1 b1, is there any way to update the > > Athena/Artemis versions, or would I have to an source install? > > That is actually a question I need to know the answer to as well. In > fact, our group's post-doc has the same question, so I plan to look > into it this week. (Since I did not make the iXAFS package, I am not > 100% clear on how it works -- which is actually true of most things on > a Mac!) > > I believe the answer is yes, but I'll let you know what I know more. > > B > > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/<http://cars9.uchicago.edu/%7Eravel/software/exafs/> > > > ------------------------------ > > Message: 3 > Date: Mon, 30 Aug 2010 10:20:02 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Residual EXAFS spectra > Message-ID: <201008301020.02497.bravel(a)bnl.gov> > Content-Type: Text/Plain; charset="iso-8859-1" > > On Monday 30 August 2010 09:57:09 am Bruce Ravel wrote: > > > Hi all, > > > I am doing an EXAFS spectra analysis of Eu(III) sorbed on mineral > oxides. > > > In course of this, I came across a lierature article(Geochimica et > > > cosmochimica Acta 64(16),2737,2000.) where a residual spectra (denoting > a > > > particular shell) was generated after subtracting four other different > > > paths contribution from the EXAFS spectra(k3.chi(k)). This procedure > was > > > adopted to identify and isolate different paths/shells informations > > > available in the EXAFS spectra. As the paper doesnot explain about the > > > procedure, I am little confused whether the author has adopted just the > > > linear subtraction methodology(i.e, sum of few selected paths minus the > > > original spectra) in creating the residual spectra or some other > > > mathematical approach. > > > > The caption to figure 5 in the article you cite says: > > > > "Residual EXAFS (produced by subtraction of U=Oax, U-Oeq, U-C, and > > U-U shells) ..." > > > > Seems pretty clear to me that what they show is the Fourier transform of > > > > data_chi(k) - sum_of_specified_paths(k) > > > > B > > > > Ummm... of course, I meant to say that the subtraction is done after > performing some kind of a fit to determine values of the parameters > affecting the paths included in the sum. > > Now I'll editorialize a bit ... the advantage of analyzing a > difference spectrum of this sort is that a small part of the data that > might get "lost" in the full fit gets emphasized. The disadvantage -- > and a big one at that -- is that you loose the ability to evaluate > correlations between the parameters of the fit to the residual and the > parameters that were used to determine the sum of paths used to make > the residual. Consequently, doing an analysis of the residual > spectrum requires a high level of confidence in the parameters used > for the subtracted paths. In my experience, that level of confidence > is rarely defensible. > > B > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > Building 535A > Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/<http://cars9.uchicago.edu/%7Eravel/software/exafs/> > > > ------------------------------ > > Message: 4 > Date: Mon, 30 Aug 2010 09:47:58 -0500 > From: Jeff Terry <terryj(a)iit.edu> > To: Bruce Ravel <bravel(a)bnl.gov> > Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Methods to break correlations > Message-ID: <FA839956-699F-4DB8-88FE-3B5E17E3AAAA(a)iit.edu> > Content-Type: text/plain; charset=us-ascii > > iXAFS originally started out as a wrapper to launch the individual > programs. At that time, it was a simple matter to replace any of the > individual programs. Ken McIvor has improved iXAFS so that it now builds > universal projects but has perl code embedded. This makes it more difficult > to update. > > That said there is a directory structure within iXAFS and I would guess > that replacing the individual programs would work. I make no guarantees > though as I am not sure of all the changes that Ken has made since I > initially wrote the cocoa wrapper. > > Jeff > > Sent from my iPhone > > On Aug 30, 2010, at 9:11 AM, Bruce Ravel <bravel(a)bnl.gov> wrote: > > > On Saturday 28 August 2010 02:47:11 pm Brandon Reese wrote: > >> I am running iXAFS 2.1 b1, is there any way to update the > >> Athena/Artemis versions, or would I have to an source install? > > > > That is actually a question I need to know the answer to as well. In > > fact, our group's post-doc has the same question, so I plan to look > > into it this week. (Since I did not make the iXAFS package, I am not > > 100% clear on how it works -- which is actually true of most things on > > a Mac!) > > > > I believe the answer is yes, but I'll let you know what I know more. > > > > B > > > > > > -- > > > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > National Institute of Standards and Technology > > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 > > Building 535A > > Upton NY, 11973 > > > > My homepage: http://xafs.org/BruceRavel > > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/<http://cars9.uchicago.edu/%7Eravel/software/exafs/> > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 90, Issue 24 > *************************************** >

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Methods to break correlations
by Brandon Reese 30 Aug '10

30 Aug '10

Hi all, I am performing EXAFS measurements on amorphous Indium Zinc Oxide (In and Zn edges) thin films and have a question about methods to break correlations. We have the films grown at several compositions ranging from 50/50 to 90/10 (In/Zn wt.%). We expect these films to display first NN shells very similar to their pure oxide cases, but the are interested in changes to the next-NN shells. I was wondering if folks on the mailing had some good references on multiple data set fits using doping fractions to break correlations. Would it be worth doing temperature dependent (or perhaps just cold) measurements to try and break correlations that way? Another couple unrelated questions... I am running iXAFS 2.1 b1, is there any way to update the Athena/Artemis versions, or would I have to an source install? Does anyone have an Athena plugin for the SSRL data Collector v2.0? The SSRL plugins available make the program crash when I try and use them. (moderators, let me know if these questions should have been in a separate posting) Regards, Brandon

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Residual EXAFS spectra
by sumitk＠barc.gov.in 30 Aug '10

30 Aug '10

Hi all, I am doing an EXAFS spectra analysis of Eu(III) sorbed on mineral oxides. In course of this, I came across a lierature article(Geochimica et cosmochimica Acta 64(16),2737,2000.) where a residual spectra (denoting a particular shell) was generated after subtracting four other different paths contribution from the EXAFS spectra(k3.chi(k)). This procedure was adopted to identify and isolate different paths/shells informations available in the EXAFS spectra. As the paper doesnot explain about the procedure, I am little confused whether the author has adopted just the linear subtraction methodology(i.e, sum of few selected paths minus the original spectra) in creating the residual spectra or some other mathematical approach. Any one having experience in this analysis will please repond to my problem. I would also like to know the best way to identify different shells contribution in the EXAFs spectra. Thanking in advance Sumit Kumar Scientific officer Radiochemistry Division Bhabha Atomic Research Centre Mumbai India-400 085. Phone: +91-22-2559 0640.

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Re: [Ifeffit] Ifeffit Digest, Vol 90, Issue 21
by Jatinkumar Rana 30 Aug '10

30 Aug '10

Dear Dominik, Thank you so much for your reply. However, i am not able to understand the logic behind removal of following atoms from Feff.inp file as mentioned by you **In principle, after running ATOMS, you just need to remove atoms from the generated feff.inp file so that the occupancy is correct. I.e., in this case, you need to remove roughly 1/4 of the Fe7, 1/2 of the Cr1, 1/3 of the P61, 2/3 of the P62, and 1/3 of the O614 atoms. Try finding those which are too close to other atoms. The FEFF output might help, so try deleting preferentially those causing FEFF to fail.** can you please give me the idea behind doing that and is it physically defendable to do such changes ?? Looking forward to your reply.. Best regards, Jatin On 27.08.2010 14:00, 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: Help with cif file (Dominik Samuelis) > 2. catalysis workshop at the karlsruher synchrotron ANKA > (Matthias Bauer) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 27 Aug 2010 10:09:05 +0200 > From: Dominik Samuelis<d.samuelis(a)fkf.mpg.de> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Help with cif file > Message-ID:<4C7772A1.2000307(a)fkf.mpg.de> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > Dear Jatin, > > in your original cif file, you have site occupancies as low as 0.5 (Cr1 > site) and 0.358 (P62). Just setting them to 1 will not help, because > ATOMS assumes them to be unity anyway. > > For such a complicated unit cell, the typical recipe with using > prototypical structures of course does not help, just because there is > not a simple prototype structure for arrojadite. > > In principle, after running ATOMS, you just need to remove atoms from > the generated feff.inp file so that the occupancy is correct. I.e., in > this case, you need to remove roughly 1/4 of the Fe7, 1/2 of the Cr1, > 1/3 of the P61, 2/3 of the P62, and 1/3 of the O614 atoms. Try finding > those which are too close to other atoms. The FEFF output might help, so > try deleting preferentially those causing FEFF to fail. > > Another solution might be loading the structure's cif file into a > structure editor such as DIAMOND. There, you can then check the bond > distance histograms and delete atoms accordingly. At the end, just > export the data in xyz format and use this as the atom positions list in > the feff.inp file. > > Regards, > Dominik > > > > On 20.08.2010 09:30, Jatinkumar Rana wrote: > >> Dear Dominic, Dear Bruce, >> >> I am also facing the same problem as experienced by Kleper. I am working >> on the EXAFS analysis of Arrojadite mineral. We have refined the >> strucutre using neutron diffraction to get crystallographic information >> which can be fed to ATOMS. The original .cif file contains the >> fractional occupancy so ATOMS give similar error report as mentioned by >> Kleper. After reading your post, i changed all site occupancy to 1 and >> then run ATOMS but still it gives me the error report. >> >> Can anybody tell me, why ATOMS report error ? >> >> I have attached both original .cif file (with fractional occupancy) and >> modified .cif file (all site occupancy = 1). I have EXAFS spectrum at Fe >> and Mn K-edge. >> >> Looking forward to your answer. >> >> Thanks a lot in advance... >> >> Best regards, >> Jatin >> >> >> >> >> >> On 18.08.2010 19:00, 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: Help with cif file (Dominik Samuelis) >>> 2. Re: Help with cif file (Bruce Ravel) >>> >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Wed, 18 Aug 2010 08:36:03 +0200 >>> From: Dominik Samuelis<d.samuelis(a)fkf.mpg.de> >>> To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> >>> Subject: Re: [Ifeffit] Help with cif file >>> Message-ID:<01A98ED5-00FE-4875-989A-C7663E57BF97(a)fkf.mpg.de> >>> Content-Type: text/plain; charset=iso-8859-1 >>> >>> Dear Kleper, >>> >>> even though I haven't tested it in detail, I'm sure the errors come >>> from the fact that ATOMS cannot handle site occupancies other than >>> unity. If you have a look in the cif file, you can see that both W >>> (0.23) and Ti (0.54) have a fractional occupancy: >>> >>> loop_ >>> _atom_site_label >>> _atom_site_type_symbol >>> _atom_site_symmetry_multiplicity >>> _atom_site_Wyckoff_symbol >>> _atom_site_fract_x >>> _atom_site_fract_y >>> _atom_site_fract_z >>> _atom_site_occupancy >>> _atom_site_attached_hydrogens >>> _atom_site_calc_flag >>> W1 W4+ 4 e 0. 0. 0.0564(2) 0.23 0 d >>> Ti1 Ti4+ 2 a 0. 0. 0. 0.54 0 d >>> O1 O2- 4 f 0.3007(6) 0.3007(6) 0. 1. 0 d >>> >>> To get it working, you need to use the prototypical structure (e.g. >>> TiO2) without mixed sites as ATOMS input. In the feff.inp file, you >>> can then change 46 out of 100 Ti atoms to W (5 out of 10 should be ok >>> as well for a smaller cluster). Don't forget to add the appropriate >>> POTENTIALS line for W to the feff.inp. The small shift of the W atoms >>> away from the Ti positions then could be handled by some additional >>> delR parameter for the W paths during fitting. >>> >>> All the best, >>> Dominik >>> >>> >>> Am 17.08.2010 um 15:27 schrieb Kleper Rocha: >>> >>> >>>> Please, >>>> >>>> Could someone help me with the cif file attached, get from the >>>> www.crystallographic.net shearch with the terms Ti, W, O. When I try >>>> to run the Feff the following message appears. >>>> >>>> "Feff 6L.02 >>>> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >>>> atoms 1 2 >>>> 1 0.00000 0.00000 0.00000 >>>> 2 0.00000 0.00000 -0.16378 >>>> Run continues... >>>> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >>>> atoms 1 3 >>>> 1 0.00000 0.00000 0.00000 >>>> 3 0.00000 0.00000 -0.32756 >>>> Run continues... >>>> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >>>> atoms 2 3 >>>> 2 0.00000 0.00000 -0.16378 >>>> 3 0.00000 0.00000 -0.32756 >>>> Run continues... >>>> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >>>> atoms 10 11 >>>> 10 0.00000 0.00000 2.57634 >>>> 11 0.00000 0.00000 2.74012 >>>> Run continues... >>>> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >>>> atoms 10 12 >>>> 10 0.00000 0.00000 2.57634 >>>> 12 0.00000 0.00000 2.90390 >>>> Run continues... >>>> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >>>> atoms 11 12 >>>> 11 0.00000 0.00000 2.74012 >>>> 12 0.00000 0.00000 2.90390 >>>> Run continues... >>>> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >>>> atoms 13 14 >>>> 13 0.00000 0.00000 -2.90390 >>>> 14 0.00000 0.00000 -3.06768 >>>> Run continues... >>>> Titanium tungsten oxide (0.54/0.46/2) >>>> Ti.54 W.46 O2 >>>> O2 Ti0.54 W0.46 >>>> Peters, E. >>>> Ueber ein niedervalentes Titan-Wolframoxid: Ti0,54 W0,46 O2 >>>> Calculating potentials and phases... >>>> 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 >>>> 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 >>>> muffin tin radii and interstitial parameters >>>> >>>> >>>> This warning indicates a problem in the Atoms list. For some >>>> reason you have atoms that are separated by than 0.93 Angstroms >>>> (or 1.75 Rydberg). >>>> >>>> This may be due to the presence of hydrogen atoms in your feff.inp >>>> file, in which case this is an innocuous warning and may be ignored. >>>> >>>> However, this may indicate a problem constructing the Atoms >>>> list. The most common cause of this problem is a mistake in the >>>> crystallographic data used on the Atoms page. You may have >>>> incorrect values for lattice constants or angles or incorrect >>>> values for site coordinates. You may need a shift vector to move >>>> the lattice into its standard setting. >>>> >>>> Please be aware that Atoms works with 5 digits of precision. >>>> Thus, if you have a site with a coordinate of 1/3, you should use >>>> either "1/3" or "0.33333" on the Atoms page. Using insufficient >>>> precision, say "0.333" is a common cause of this error message. >>>> >>>> Artemis has continued on the possibility that the warning is >>>> caused by hydrogen atoms, but be warned that the feff.inp may >>>> require your attention." >>>> >>>> Thanks in advance. >>>> >>>> >>>> >>>> Kleper de Oliveira Rocha >>>> >>>> <O2 Ti0.54 W0.46.cif>_______________________________________________ >>>> 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 >> > >

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catalysis workshop at the karlsruher synchrotron ANKA
by Matthias Bauer 27 Aug '10

27 Aug '10

Dear mailing list users, on behalf of the organising committee I would like to announce a workshop on catalysis at the Karlsruher synchrotron ANKA, please find attached the programm. Best regards, Matthias Bauer Workshop "Shining synchrotron light on catalysts - Needs and opportunities for the future" October 8th 2010 in Karlsruhe, Germany Catalysis is playing a major role in chemical industries considering that more than 90% of all chemical products have seen at least in one step a catalyst. With the challenges which we presently meet in fossil energy resources and CO2-emission, environmental catalysis and pharmaceuticals catalysis is one of the key areas. Rapid catalyst development by a rational approach requires a detailed understanding of their structure, where synchrotron light has significantly contributed in the past and will be even more powerful in the future. This is falling into the new developments also at ANKA with the establishment of a strengthened catalysis focus. During the workshop the needs and opportunities at synchrotron radiation sources will be discussed. Morning Session 1 8.30 Welcome (Tilo Baumbach, KIT Karlsruhe and Jan-Dierk Grunwaldt, KIT Karlsruhe) 8.40 9.00 Stefan Mangold (KIT, Karlsruhe) Spectroscopy and related techniques at ANKA 9.00 - 9.30 Anatoly Frenkel (NLSL, Brookhaven) "Multiple Length Scales in Nanocatalysts Probed in a Single Synchrotron Experiment: The Combined use of XAFS, XRD and DAFS" 9.30 10.00 Marc Newton (ESRF, Grenoble) "In situ hard X-ray studies of the dynamic behaviour of heterogeneous catalysts" 10.00 - 10.20 Ursula Bentrup (LIKAT, Rostock) Online monitoring of molybdate catalyst precursor synthesis and conditioning by coupled X-ray scattering and optical spectroscopic methods 10.20 - 10.40 Coffee Morning Session 2 10.40 11.10 Moniek Trompp (University of Southampton) 'Molecules in action - Developments in X-ray spectroscopy' 11.10 11.40 Anna Puig Molina (Haldor Topsøe, Lyngby) Synchrotron Radiation for Industrial Catalysis 11.40 - 12.10 Ronald Frahm (Universität Wuppertal) State of the art Quick-EXAFS: Applications in Catalysis 12.10 12.30 Olga Safonova (ESRF, Grenoble) Catalysis at SNBL and SLS 12.30 13.30 Lunch Future Developments 13.30 - 14.00 Wolfgang Caliebe (HASYLAB, Hamburg) Hard X-Ray Spectroscopy and Catalysis at DESY - Presence and Future 14.00 14.20 Jan-Dierk Grunwaldt (KIT, Karlsruhe) Shining X-rays on catalysts at ANKA: Present and Future 14.20 15.00 Discussion on Catalysis activities at ANKA and synchrotrons in general (Stefan Mangold, Matthias Bauer, Jan-Dierk Grunwaldt) Meeting site: The meeting will take place at the Akademie Hotel Karlsruhe (http://www.akademiehotel-karlsruhe.de/) Am Rüppurrer Schloß 40, 76199 Karlsruhe More info: http://anka.iss.kit.edu/english/448.php Admittance fee: Free of charge, but please register since the number of seats may be limited Organized by: Matthias Bauer, Jan-Dierk Grunwaldt, Stefan Mangold

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Re: [Ifeffit] Help with cif file
by Jatinkumar Rana 27 Aug '10

27 Aug '10

Dear Dominic, Dear Bruce, I am also facing the same problem as experienced by Kleper. I am working on the EXAFS analysis of Arrojadite mineral. We have refined the strucutre using neutron diffraction to get crystallographic information which can be fed to ATOMS. The original .cif file contains the fractional occupancy so ATOMS give similar error report as mentioned by Kleper. After reading your post, i changed all site occupancy to 1 and then run ATOMS but still it gives me the error report. Can anybody tell me, why ATOMS report error ? I have attached both original .cif file (with fractional occupancy) and modified .cif file (all site occupancy = 1). I have EXAFS spectrum at Fe and Mn K-edge. Looking forward to your answer. Thanks a lot in advance... Best regards, Jatin On 18.08.2010 19:00, 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: Help with cif file (Dominik Samuelis) > 2. Re: Help with cif file (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 18 Aug 2010 08:36:03 +0200 > From: Dominik Samuelis<d.samuelis(a)fkf.mpg.de> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Help with cif file > Message-ID:<01A98ED5-00FE-4875-989A-C7663E57BF97(a)fkf.mpg.de> > Content-Type: text/plain; charset=iso-8859-1 > > Dear Kleper, > > even though I haven't tested it in detail, I'm sure the errors come from the fact that ATOMS cannot handle site occupancies other than unity. If you have a look in the cif file, you can see that both W (0.23) and Ti (0.54) have a fractional occupancy: > > loop_ > _atom_site_label > _atom_site_type_symbol > _atom_site_symmetry_multiplicity > _atom_site_Wyckoff_symbol > _atom_site_fract_x > _atom_site_fract_y > _atom_site_fract_z > _atom_site_occupancy > _atom_site_attached_hydrogens > _atom_site_calc_flag > W1 W4+ 4 e 0. 0. 0.0564(2) 0.23 0 d > Ti1 Ti4+ 2 a 0. 0. 0. 0.54 0 d > O1 O2- 4 f 0.3007(6) 0.3007(6) 0. 1. 0 d > > To get it working, you need to use the prototypical structure (e.g. TiO2) without mixed sites as ATOMS input. In the feff.inp file, you can then change 46 out of 100 Ti atoms to W (5 out of 10 should be ok as well for a smaller cluster). Don't forget to add the appropriate POTENTIALS line for W to the feff.inp. The small shift of the W atoms away from the Ti positions then could be handled by some additional delR parameter for the W paths during fitting. > > All the best, > Dominik > > > Am 17.08.2010 um 15:27 schrieb Kleper Rocha: > > >> Please, >> >> Could someone help me with the cif file attached, get from the www.crystallographic.net shearch with the terms Ti, W, O. When I try to run the Feff the following message appears. >> >> "Feff 6L.02 >> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >> atoms 1 2 >> 1 0.00000 0.00000 0.00000 >> 2 0.00000 0.00000 -0.16378 >> Run continues... >> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >> atoms 1 3 >> 1 0.00000 0.00000 0.00000 >> 3 0.00000 0.00000 -0.32756 >> Run continues... >> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >> atoms 2 3 >> 2 0.00000 0.00000 -0.16378 >> 3 0.00000 0.00000 -0.32756 >> Run continues... >> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >> atoms 10 11 >> 10 0.00000 0.00000 2.57634 >> 11 0.00000 0.00000 2.74012 >> Run continues... >> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >> atoms 10 12 >> 10 0.00000 0.00000 2.57634 >> 12 0.00000 0.00000 2.90390 >> Run continues... >> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >> atoms 11 12 >> 11 0.00000 0.00000 2.74012 >> 12 0.00000 0.00000 2.90390 >> Run continues... >> WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. >> atoms 13 14 >> 13 0.00000 0.00000 -2.90390 >> 14 0.00000 0.00000 -3.06768 >> Run continues... >> Titanium tungsten oxide (0.54/0.46/2) >> Ti.54 W.46 O2 >> O2 Ti0.54 W0.46 >> Peters, E. >> Ueber ein niedervalentes Titan-Wolframoxid: Ti0,54 W0,46 O2 >> Calculating potentials and phases... >> 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 >> 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 >> muffin tin radii and interstitial parameters >> >> >> This warning indicates a problem in the Atoms list. For some >> reason you have atoms that are separated by than 0.93 Angstroms >> (or 1.75 Rydberg). >> >> This may be due to the presence of hydrogen atoms in your feff.inp >> file, in which case this is an innocuous warning and may be ignored. >> >> However, this may indicate a problem constructing the Atoms >> list. The most common cause of this problem is a mistake in the >> crystallographic data used on the Atoms page. You may have >> incorrect values for lattice constants or angles or incorrect >> values for site coordinates. You may need a shift vector to move >> the lattice into its standard setting. >> >> Please be aware that Atoms works with 5 digits of precision. >> Thus, if you have a site with a coordinate of 1/3, you should use >> either "1/3" or "0.33333" on the Atoms page. Using insufficient >> precision, say "0.333" is a common cause of this error message. >> >> Artemis has continued on the possibility that the warning is >> caused by hydrogen atoms, but be warned that the feff.inp may >> require your attention." >> >> Thanks in advance. >> >> >> >> Kleper de Oliveira Rocha >> >> <O2 Ti0.54 W0.46.cif>_______________________________________________ >> Ifeffit mailing list >> Ifeffit(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >

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Strange problems with Artemis
by Jatinkumar Rana 27 Aug '10

27 Aug '10

Dear users, I am facing a strange problem with Artemis and i don't know how to get rid of it. I hope any expert in the mailing lists would help me solving this problem. I have EXAFS data on Fe and Mn K-edge for Arrojadite mineral. Since the crystal structure of this mineral is not known we did neutron diffraction to refine the structure. To support the neutron diffraction results, we planned to do EXAFS on this mineral (Fe and Mn k-edge). We have around 8 different atomic species (i.e. Na,K,Fe,Mn,Al,Cr,O,P) in the mineral and some of the sites are fractionally occupied. Since ATOMS can not handle more than 7 potentials and site occupancy other than unity i have made following changes : 1) replaced Cr with Al, mainly because Cr is present in a few ppm only (relative importance). 2) set all site occupancy to 1 Even after doing the above changes, i got following error message when i run FEFF ************** Feff 6L.02 WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 11 20 11 -3.01973 -0.20361 1.44233 20 -3.54653 -0.05083 0.83053 Run continues... WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. atoms 46 62 46 -0.40014 -0.20361 5.03633 62 0.12666 -0.05083 5.64813 Run continues... Sodium Potassium Aluminium Chromium Iron Manganese Phosphate Hydrate Al Cr Fe7.53 H2 K1.21 Mn6 Na3 O50 P12 Kallfa\&s, Christoph Crystal structure, chemical composition and thermal behaviour of arrojadite Calculating potentials and phases... 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 free atom potential and density for atom type 6 free atom potential and density for atom type 7 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 overlapped potential and density for unique potential 4 overlapped potential and density for unique potential 5 overlapped potential and density for unique potential 6 overlapped potential and density for unique potential 7 muffin tin radii and interstitial parameters phase shifts for unique potential 0 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 1 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 2 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 3 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 4 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 5 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 6 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. phase shifts for unique potential 7 Hard tests failed in fovrg. Muffin-tin radius may be too large; coordination number too small. Preparing plane wave scattering amplitudes... nncrit in prcrit 9 Searching for paths... Rmax 7.0000 keep and heap limits 0.0000000 0.0000000 Preparing neighbor table nfound nheap nheapx nsc r 1000 469 469 3 5.2890 2000 730 730 3 5.7147 3000 907 907 3 5.9455 4000 1040 1040 3 6.1157 5000 1177 1177 3 6.2616 6000 1319 1319 3 6.3835 7000 1412 1413 3 6.4825 8000 1443 1444 3 6.5749 9000 1469 1473 3 6.6585 10000 1432 1474 3 6.7377 11000 1367 1474 3 6.8062 12000 1202 1474 3 6.8680 13000 870 1474 3 6.9289 14000 251 1474 3 6.9856 . . . . . .. . This warning indicates a problem in the Atoms list. For some reason you have atoms that are separated by than 0.93 Angstroms (or 1.75 Rydberg). This may be due to the presence of hydrogen atoms in your feff.inp file, in which case this is an innocuous warning and may be ignored. However, this may indicate a problem constructing the Atoms list. The most common cause of this problem is a mistake in the crystallographic data used on the Atoms page. You may have incorrect values for lattice constants or angles or incorrect values for site coordinates. You may need a shift vector to move the lattice into its standard setting. Please be aware that Atoms works with 5 digits of precision. Thus, if you have a site with a coordinate of 1/3, you should use either "1/3" or "0.33333" on the Atoms page. Using insufficient precision, say "0.333" is a common cause of this error message. Artemis has continued on the possibility that the warning is caused by hydrogen atoms, but be warned that the feff.inp may require your attention. ************************************ I have attached both *original.cif file* (with all 8 atomic species and fractional occupancy) and *modified.cif file* (Cr replaced by Al and all site occupancy set to 1) with this mail for your perusal. I hope some experts in the mailing list would suggest me some solutions. Many more thanks in advance for your valuable time and suggestions.... Best regards, Rana

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debye function
by Kleber Daum Machado 24 Aug '10

24 Aug '10

Hi, I'd like to know the explicit mathematical expressions that are represented by the functions debye(temp,thetad) and eins(temp,thetae). Are they given in some documentation file or article? Thank you very much Kleber

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Re: [Ifeffit] updating ifeffit manually
by hemantha aranwela 19 Aug '10

19 Aug '10

Hi Matt, Thanks for the information. I could not get the runner.exe to work. So installed the updates directly as you suggested. It works perfectly. Aranwela These were the steps I have followed. Updating Ifeffit manually (if, somehow, it does not update automatically) 1. Check the latest update installed (typically in C:\Program Files\Ifeffit\config\iff_xxx). In my case it was iff_009.2. Then check the current available update level from the cars webpage: http://cars9.uchicago.edu/~ifeffit/updates/current.datAt present it is at 013. 3. Download the missing updates from http://cars9.uchicago.edu/~ifeffit/updates/iff_XXX.zip Remember you need to change XXX to the appropriate file # (to 010 for an example). ( I had to download iff_010, iff_011, iff_012 and iff_013 and saved them on to the desktop). 4. These are zipped files. Need to unzip those into the C:\Program Files\Ifeffit folder. But one has to do this in sequence (it is said). ( In my case I unzipped 010 first then 011, next 012 and 013 after that. Unzipping is easy in windows 7. Just right click on the zipped folder and select ‘extract all’ then browse to the Ifeffit folder (In my case C:\Program Files\Ifeffit). It will prompt you to choose between two or three options. (In all cases I chose ‘copy and replace’ or just ‘replace’. That’a all. Everything should work perfectly. Date: Mon, 16 Aug 2010 14:06:47 -0500 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 90, Issue 7 Message-ID: <AANLkTinvBiq0ES9TLN2Air38tWw4VgCroOSJbsCSNU7X(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Aranwela, Thanks for the report. I do think this is a permissions problem. That's not to say it's not a real problem, just that it should be solvable. I just tested this by resetting the "update level" in config/current.dat, and forcing the updater to run. It worked fine to download and install the update. That was on a Mac running Windows 7 (64 bit) as a virtual machine. The account I used does have full Administrator control. The process running the updater definitely needs to be be able to write to C:\Program Files\Ifeffit (or wherever you installed to). Would you be willing to try to download the update zip file (say, iff_013.zip) and unzip it into your installation directory, as described at http://cars9.uchicago.edu/ifeffit/IfeffitOnWindows/WinUpdater and let us know what does and doesn't work? I'm sure that others would find your report helpful. Cheers, --Matt

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