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

Re: possible bugs in Artemis
by Bruce Ravel 15 Jan '06

15 Jan '06

On Sunday 15 January 2006 03:22, you wrote: > When I push any of the 'Document' buttons, I get a blank window, a 'clunk' > and a bunch of error messages including a 'fileopen' error, suggesting that > the documentation pages aren't in the right places. Also, what determines > the k-range over which Artemis fits? If I ask for a longer k-range than > what it does by default, nothing seems to happen. Marcus is the second person to report this problem, which exists in the current versions of both Athena and Artemis. The problem exists in the tool that I use to display the document and falls into the category of obvious problems that I failed to test for before the last release. D'oh! The next release will fix this issue. Sadly, I might not have time to make a release in the next two weeks -- we'll see. In any case, the same documentation is available in a number of other places. On a Windows machine, there should be a Start menu entry labeled Ifeffit documentation that will lead you to html versions of the docs. Also, the html versions can be found at http://cars9.uchicago.edu/~ravel/software/docs.html 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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[HOWTO] Ifeffit f1f2() function
by Mauro Rovezzi 09 Jan '06

09 Jan '06

Hi to all, Is it correct to use as energy convolution width (in the f1f2 Ifeffit function) the natural widths of atomic levels tabulated by Krause & Oliver (J. Phys. Chem. Ref. Data, Vol. 8, No. 2, 1979)? My problem is to smooth (arctg-like) Cromer-Liberman f"(E) at the edge region [NOTE: I don't use feff8 because is too slow]. Thanks, Mauro -- Mauro Rovezzi <mauro.rovezzi(a)esrf.fr> PhD student - GILDA BM08 c/o ESRF (Grenoble, FR)

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new versions for the new year!
by Bruce Ravel 07 Jan '06

07 Jan '06

Happy New Year everyone! I have just released Athena 0.8.047, Artemis 0.8.004 and Hephaestus 0.12. You can read all about them at http://cars9.uchicago.edu/iffwiki/HoraeVersion059 New source code tarballs are at SourceForge and at my website. A Windows updater package has been made available and should be offered to the Windows users the next time you fire up one of the codes. Debian users can check Carlo's repository in the next few days -- he is usually quite punctual in making debian packages. The horae_update script has been fixed (I think). Those that want to use it can grab its newest version at http://cars9.uchicago.edu/~ravel/software/packages/horae_update and use it to install the software. As always, let me know about any problems or suggestions. Regards, B -- Bruce Ravel ---------------------------------------------- bravel(a)anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced 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/exafs/

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RE: [Ifeffit] my problem
by Scott Calvin 19 Dec '05

19 Dec '05

Hi Tadej, I agree with the general drift of Anatoly's comment--this is what Shelly meant by saying it sounds like a tough problem! But I think it came off sounding a little more harsh than I suspect Anatoly meant it to be, particularly considering some of the systems he himself has examined! Anatoly's description is fair IF only a nearest-neighbor fit is performed. But it's possible that inequivalent sites have very different environments at greater Reff, particularly since niobium is so much heavier than oxygen! For example, there's been a lot of work done that shows that there is a screamingly large difference in the EXAFS spectra of A and B sites in the spinel structure (Vince Harris did a lot of this, for example). In such a case, Artemis is able to find the site occupancy without too much trouble, using a strategy such as Shelly explained. Of course, =seven= freely-floating sites sounds likely to yield nonsense fits. It would help if you could use some physical intuition to try to simplify the problem, at least at first. Consider also using the "restraint" feature in Artemis/Ifeffit liberally in your early fits to keep the fit from wandering off into nonsensical territory. --Scott Calvin Sarah Lawrence College At 12:14 PM 12/15/2005, Anatoly wrote: >boundary="----_=_NextPart_001_01C6019A.F6711239" > >You cannot resolve these sites from EXAFS analysis. Even if you had >only 2 inequivalent sites of the same central atom with occupancies >N1 and N2, you would not be able to resolve N1 and N2 in the fit >because different Nb atoms would have similar environments (e.g., 4 >and 6 oxygens), and they will have similar Nb-O distances around >each site. The best you can do is to try to fit the first nearest >neighbor peak as an average Nb-O contribution (if it is a well >isolated peak) and try to make use of sigma2 that may turn out to be >larger than in some well known Nb oxide reference that you should >analyze first. > >Anatoly > >Dear collegues, > >my name is Tadej Rojac and I'm writing from the Institute Jozef >Stefan in Ljubljana, Slovenia. I work in the Department of >electronic ceramics. Actually, I'm working on a EXAFS spectra with >Artemis. What I am trying to do is mainly to describe an EXAFS >spectrum with a model concerning the structure of Nb2O5. I'm working >togheter with prof. Iztok Arcon, who is a specialist in the field. >My main problem is that I have to do some suppositions. In fact >Nb2O5 structure is quite complicated. It is composed of seven >different Nb positions which I took into account using 7 feffs in >Artemis. I don't know the exact occupancies of the seven positions. >In order to make the search easier I did at first a supposition >that all the occupancies must be positive, which is realistic. I set >this with the command "abs" in each feff file. Secondly, I need to >supose that the sum of all occupancies is 1. In that way the search >for the result is much easier, otherwise I get the sum greater than >one, which, for sure, is not the case. My question is how can I do >that? For example, if the occupancies are O1, O2, O3, O4, O5, O6 and >O7 and I define them with a starting value (let use say the same, so >1/7) than I can do O = O1+O2+O3+O4+O5+O6+O7. Finally I need to do O >=1, but here Artemis doesn't want to define the same parameter (O in >this case) twice. So, how can I insert the conditions, that the sum >of all the occupancies is 1, into Artemis? I hope you can help me.

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(no subject)
by Victor Krayzman 19 Dec '05

19 Dec '05

Hi Bruce, This is Victor Krayzman. I haven't seen you for ten years. Currently I am at NIST as a guest scientist. Besides other codes I work with Athena and Artemis and I have some troubles with Artemis. (It runs under Windows 2000) Last time I read a data file, made two FEFF calculations, read one more data file and made three FEFF calculations for it. Then I saved project, quit Artemis, open it again and tried to read the saved project. I found only data files and two FEFF calculations for the first data set. FEFF calculations for the second set disappeared. I met the same situation some time ago. To fix the problem I had to reinstall the Artemis. But now I have got the same thing. Could you help me? I attached the saved project and the message in a window. Thank you. Best regards to Ed. Sincerely. Victor

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RE: [Ifeffit] Pd data
by Barton, David (DG) 19 Dec '05

19 Dec '05

Sorry I meant to include that. The file at DND-CAT is a bit unwieldy. The key is: Col 4=energy, Col 25=Io, Col 26=It. Dave > -----Original Message----- > From: Kelly, Shelly D. [mailto:SKelly@anl.gov] > Sent: Monday, December 19, 2005 12:13 PM > To: XAFS Analysis using Ifeffit > Subject: RE: [Ifeffit] Pd data > > > Hi Dave, > > Thanks a bunch for the data file. Could I trouble you for a > key for the columns within the file? > > Shelly > > Shelly Kelly Bldg 203 RM E113 > Skelly(a)anl.gov Argonne National Laboratory > 630-252-7376 9700 S Cass Ave > www.mesg.anl.gov Argonne, IL 60439 > > > > > > -----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: Monday, December 19, 2005 10:11 AM > > To: 'XAFS Analysis using Ifeffit' > > Subject: RE: [Ifeffit] Pd data > > > > Shelly, > > > > Attached is a Pd foil data set. It was only collected out > to k=16A-1, > > otherwise the data looks great. Data was collected with > Si111 mono at > > DND-CAT (APS-ANL). > > > > Dave > > > > -----Original Message----- > > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Kelly, Shelly D. > > Sent: Monday, December 19, 2005 10:38 AM > > To: XAFS Analysis using Ifeffit > > Subject: [Ifeffit] Pd data > > > > > > Hello friends, > > > > Does anyone have Pd foil data or know of an EXAFS study that models > the > > data beyond the first shell? I have some data but it > doesn't seem to > > correspond to the crystallographic structure of Pd. I'm suspicious > that > > something about the foil sample caused the structure to become > non-ideal. > > > > Thanks > > 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] Pd data
by Kelly, Shelly D. 19 Dec '05

19 Dec '05

Hi Dave, Thanks a bunch for the data file. Could I trouble you for a key for the columns within the file? Shelly Shelly Kelly Bldg 203 RM E113 Skelly(a)anl.gov Argonne National Laboratory 630-252-7376 9700 S Cass Ave www.mesg.anl.gov Argonne, IL 60439 > -----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: Monday, December 19, 2005 10:11 AM > To: 'XAFS Analysis using Ifeffit' > Subject: RE: [Ifeffit] Pd data > > Shelly, > > Attached is a Pd foil data set. It was only collected out to k=16A-1, > otherwise the data looks great. Data was collected with Si111 mono at > DND-CAT (APS-ANL). > > Dave > > -----Original Message----- > From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit- > bounces(a)millenia.cars.aps.anl.gov] On Behalf Of Kelly, Shelly D. > Sent: Monday, December 19, 2005 10:38 AM > To: XAFS Analysis using Ifeffit > Subject: [Ifeffit] Pd data > > > Hello friends, > > Does anyone have Pd foil data or know of an EXAFS study that models the > data beyond the first shell? I have some data but it doesn't seem to > correspond to the crystallographic structure of Pd. I'm suspicious that > something about the foil sample caused the structure to become non-ideal. > > Thanks > Shelly > > > >

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RE: Ifeffit Digest, Vol 34, Issue 18
by Vivek Srinivasamurthi 19 Dec '05

19 Dec '05

Shelly, Sorry, forgot to attach the file before.. vivek -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Monday, December 19, 2005 11:12 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 34, Issue 18 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. Pd data (Kelly, Shelly D.) 2. RE: Pd data (Barton, David (DG)) ---------------------------------------------------------------------- Message: 1 Date: Mon, 19 Dec 2005 09:37:47 -0600 From: "Kelly, Shelly D." <SKelly(a)anl.gov> Subject: [Ifeffit] Pd data To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <A7B9B5614B54BE48B378DAE209FECC30ABE841(a)ROCKY.anl.gov> Content-Type: text/plain; charset="us-ascii" Hello friends, Does anyone have Pd foil data or know of an EXAFS study that models the data beyond the first shell? I have some data but it doesn't seem to correspond to the crystallographic structure of Pd. I'm suspicious that something about the foil sample caused the structure to become non-ideal. Thanks Shelly

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RE: Ifeffit Digest, Vol 34, Issue 18
by Vivek Srinivasamurthi 19 Dec '05

19 Dec '05

Shelly, Attached is a Pd nanoparticle sample on a carbon support. The data was taken upto 18 k-space. It also has a Pd foil in the reference channel. The data was collected with a Si(111) monochromator at BNL-NSLS -X18B. Vivek -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Monday, December 19, 2005 11:12 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 34, Issue 18 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. Pd data (Kelly, Shelly D.) 2. RE: Pd data (Barton, David (DG)) ---------------------------------------------------------------------- Message: 1 Date: Mon, 19 Dec 2005 09:37:47 -0600 From: "Kelly, Shelly D." <SKelly(a)anl.gov> Subject: [Ifeffit] Pd data To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <A7B9B5614B54BE48B378DAE209FECC30ABE841(a)ROCKY.anl.gov> Content-Type: text/plain; charset="us-ascii" Hello friends, Does anyone have Pd foil data or know of an EXAFS study that models the data beyond the first shell? I have some data but it doesn't seem to correspond to the crystallographic structure of Pd. I'm suspicious that something about the foil sample caused the structure to become non-ideal. Thanks Shelly

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RE: [Ifeffit] Pd data
by Barton, David (DG) 19 Dec '05

19 Dec '05

Shelly, Attached is a Pd foil data set. It was only collected out to k=16A-1, otherwise the data looks great. Data was collected with Si111 mono at DND-CAT (APS-ANL). 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: Monday, December 19, 2005 10:38 AM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] Pd data Hello friends, Does anyone have Pd foil data or know of an EXAFS study that models the data beyond the first shell? I have some data but it doesn't seem to correspond to the crystallographic structure of Pd. I'm suspicious that something about the foil sample caused the structure to become non-ideal. Thanks Shelly

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