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

Re: XANES calculations
by John J. Rehr 17 Jan '06

17 Jan '06

Dear Antonio, It appears that you've just experienced a common problem with hexagonal space groups that one often needs a shift of the origin to get the "correct" crystal structure. According to the atoms documentation (click on SHIFT in Webatoms) there should be a note about this when you try to run, but I didn't see it anywhere when I tried WEBATOMS today. Anyway the fix is to introduce a MS shift vector of (0 0 .25), as in the atoms.inp file I sent you. I think it might be useful if an appropriate shift were introduced by default into the atoms database for very common lattice structures like graphite, or otherwise to detail more precisely the coordinates of the shift that one has to introduce by hand into atoms.inp (which is less desirable). Maybe Bruce Ravel can consider these friendly suggestions in future releases of atoms. I hope you don't mind, but I've forwarded this msg to the ifeffit list. Cheers, John ---------- Forwarded message ---------- Date: Mon, 16 Jan 2006 09:20:39 +0100 From: Antonio Politano <politano(a)fis.unical.it> To: 'John J. Rehr' <jjr(a)leonardo.phys.washington.edu> Subject: R: R: XANES calculations Yes, I understand about stoichiometry. But I don't have understood why using an atoms.inp file taken from the Atoms.inp archive I have six nearest neighbours of the central assorber at 1,42 A. In your feff.inp file under the ATOMS card there are only three nearest neighbours at 1,42 A (this is correct!!!). Thank you very much!!! Antonio Politano

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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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Pd data
by Kelly, Shelly D. 19 Dec '05

19 Dec '05

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] Mac installer for 10.4 with horae-048
by Matt Newville 15 Dec '05

15 Dec '05

Stefano, Paul, I just tried this on a fairly fresh OS 10.4 machine (Ifeffit had been installed over a year ago, when it was a 10.3 machine, and I wiped /Library/Perl/5.8.1 and /Applications/Ifeffit, and cleared the /Library/Receipt for Ifeffit....). I got the same behaviour as Stefano. It looks like everything did get installed this time, but that the resulting version of Ifeffit depends on Aquaterm. Downloading and installing Aquaterm from the disk-image package from sourceforge.net was simple (though it requires a privileged password) and made Athena and Artemis run fine. So my immediate recommendation is to install Aquaterm from Sourceforge. http://sourceforge.net/projects/aquaterm/ --Matt PS: We should probably also figure out how to not depend on Aquaterm, but telling people they need Aquaterm as well as X11.app seems simple enough.

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IFEFFIT installation problem
by Frenkel, Anatoly 15 Dec '05

15 Dec '05

On behalf of Joe Woicik (please reply to: woicik(a)bnl.gov) I downloaded version 1.2.8. Runner. exe gives me the following error and Athena does not run. Please let me know if anyone on the list has experienced similar problem. Joe Woicik Traceback (most recent call last): File "runner.py", line 753, in ? File "runner.py", line 184, in __init__ File "runner.py", line 275, in LookForUpdates File "runner.py", line 299, in read_web_version File "urllib.pyc", line 76, in urlopen File "urllib.pyc", line 181, in open File "urllib.pyc", line 297, in open_http File "httplib.pyc", line 712, in endheaders File "httplib.pyc", line 597, in _send_output File "httplib.pyc", line 564, in send File "httplib.pyc", line 538, in connect File "timeoutsocket.pyc", line 237, in connect timeoutsocket.Timeout: Attempted connect to ('164.54.160.111', 80) timed out. Traceback (most recent call last): File "runner.py", line 753, in ? File "runner.py", line 184, in __init__ File "runner.py", line 275, in LookForUpdates File "runner.py", line 299, in read_web_version File "urllib.pyc", line 76, in urlopen File "urllib.pyc", line 181, in open File "urllib.pyc", line 297, in open_http File "httplib.pyc", line 712, in endheaders File "httplib.pyc", line 597, in _send_output File "httplib.pyc", line 564, in send File "httplib.pyc", line 538, in connect File "timeoutsocket.pyc", line 237, in connect timeoutsocket.Timeout: Attempted connect to ('164.54.160.111', 80) timed out. Traceback (most recent call last): File "runner.py", line 753, in ? File "runner.py", line 184, in __init__ File "runner.py", line 275, in LookForUpdates File "runner.py", line 299, in read_web_version File "urllib.pyc", line 76, in urlopen File "urllib.pyc", line 181, in open File "urllib.pyc", line 297, in open_http File "httplib.pyc", line 712, in endheaders File "httplib.pyc", line 597, in _send_output File "httplib.pyc", line 564, in send File "httplib.pyc", line 538, in connect File "timeoutsocket.pyc", line 237, in connect timeoutsocket.Timeout: Attempted connect to ('164.54.160.111', 80) timed out.

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RE: [Ifeffit] my problem
by Frenkel, Anatoly 15 Dec '05

15 Dec '05

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 -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of Tadej Rojac Sent: Thursday, December 15, 2005 7:44 AM To: Ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] my problem 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. I'm looking forward t hearing from you...thank you... Tadej Rojac Jozef Stefan Institute Jamova 39 1000 Ljubljana Slovenia Tel.: +386 1 477 38 34 Fax: +386 1 477 38 87 E-mail: tadej.rojac(a)ijs.si

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RE: [Ifeffit] my problem
by Kelly, Shelly D. 15 Dec '05

15 Dec '05

Hi Tadej, ________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Tadej Rojac Sent: Thursday, December 15, 2005 6:44 AM To: Ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] my problem 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. [Kelly, Shelly D.] In the path page for each path of each feff calculation you need to have a variable that represents the occupancy. S02xN = abs(S02 * O1) ..... Then in the variable page (guess set def) Guess O1 = 0.15 Guess O2 = 0.15 Guess O3 = 0.15 .... Def O7 = 1 - abs(O1) -abs(O2) -abs(O3) - abs(O4) - abs(O5) -abs(O6) Hence you get one occupancy for free for knowing one more piece of information. Sounds like a tough problem. I'm looking forward t hearing from you...thank you... Tadej Rojac Jozef Stefan Institute Jamova 39 1000 Ljubljana Slovenia Tel.: +386 1 477 38 34 Fax: +386 1 477 38 87 E-mail: tadej.rojac(a)ijs.si

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my problem
by Tadej Rojac 15 Dec '05

15 Dec '05

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. I'm looking forward t hearing from you...thank you... Tadej Rojac Jozef Stefan Institute Jamova 39 1000 Ljubljana Slovenia Tel.: +386 1 477 38 34 Fax: +386 1 477 38 87 E-mail: tadej.rojac(a)ijs.si

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Re: [Ifeffit] statistical parameters
by Matt Newville 15 Dec '05

15 Dec '05

Hi Stefano, all, > same old question that emerges again: > > What formula is used by IFEFFIT to calculate the number of > independent points? Does it use the formula 2DkDR/pi? or 2DkDR/pi +1? > or 2DkDR/pi +2? And how does it approximate the resulting number to > integer? Ifeffit uses an approximation of 2*delta_k * delta_R / pi. Well, it could use a better approximation -- see below. But Ifeffit does not use 2dKdR/pi + 2. The Stern paper considers "independent points" to be discrete, counts the endpoints of this discrete array of "independent points", and neglects the rather significant problem of the limit dk->0. I find each of these to be problematic. The dk->0 limit problem makes it especially hard to implement in a meaningful way. Ifeffit uses n_idp = 2*delta_k * delta_R / pi, but is cautious (and probably overly so) in determining delta_k and delta_R. First, it puts these on the k- and R- grids (0.05 Ang^-1 and ~0.03067Ang). It is also works to avoid rounding incorrectly. Thus, currently your ranges: kmin=2.0, kmax=12, rmin=1.0, rmax=6.0 get mapped to kmin = 2.05, kmax=12.00 , rmin=1.012427, rmax=5.98525 Thus you should have n_idp = 31.4824. You can confirm that with 'print n_idp' from the command line. It sounds like that's what you're getting. And yes, I do think that having "kmin=2.00" map to "kmin=2.05" for this part of the calculation is overly cautious, and I will fix that in the next release (and n_idp will equal ~31.64). I could be persuaded to just use the user-supplied values, but the round-off errors shouldn't matter much. In general, I agree with most of the answers to not take N_idp too seriously. I would say to report it to 1 decimal place, just to emphasize that it is understood to be an estimate and not a discrete number. Saying "n_idp=12" implies "I could fit up to 12 parameters with confidence". It's easy enough to show this is usually NOT the case, but some people sure like a hard and fast rule. And, sadly, n_idp does influence the error bars some, so it seems wise to get it as close as we can. That's sort of rambly, but hope that helps --Matt PS: For autobk/spline(), the number of knots is actually chosen as n = 2 * int( rbkg * (kmax-kmin)/pi ) + 1 It turns out that for the b-spline algorithm used, the number of knots used needs to be an odd number greater than 4. So, the formula is convenient. Is it right? Well, it seems to work pretty well. As fitting variables, the spline y-values are somewhat correlated, so you might argue that you could have a few more variables. That's easy enough to try with spline(data.chi, rbkg=1, nknots=17) In my experience, this rarely helps but it might be worth re-visiting.

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RE: [Ifeffit] statistical parameters
by Kelly, Shelly D. 15 Dec '05

15 Dec '05

Hi Stephano > >Since 2dkdr/pi is not always an integer number, the degrees of freedom > >which is the NIP (number of independent points) - number of variables is > >not always an integer number. > > but I notice that in all papers this is reported as an integer > number, which makes sense. DOes it mean I have to round it up to the > closest integer? Plus, in the conversion from chi^2 to reduced-chi^2, > does IFEFFIT consider it as an integer number or not? [Kelly, Shelly D.] Well, In my opinion that depends on where you are publishing the data. If you are publishing the data in PRB then you should use the XX.X number. If you are publishing in Science Magazine then you should use the rounded number. If the answer depends on weather or not you round the number then I'd be suspicious. Often we round the number so that we don't have to explain why we have a non-integer numbers. You need ~ a factor of 2 for there to be a statistically significant difference in the reduced chi squared. So 33.5, 30, and 40 are all about the same number. Therefore I would round them all off to the nearest whole number that works. I like to show changes in the reduced chi square rather than the absolute value. Instead of showing a reduced-chi-square of 100 and 350, I show them as 1 and 3.5. Then you can say that 3.5 is much bigger than 1 so the model that gave 1 is the best. It is the relative change in the reduced chi square that matters. We get the absolute value wrong for a number of reasons. By showing the change you can side step all that explanation. > > > Plus, I have found a > >> few documents in which Matt reports Nidp as 2dkdr/pi, some others in > >> which he reports 2dkdr/pi+1. In SK's thesis, which is available on > >> the net (thanks Shelly :-)) she says +2. I was simply wondering which > >> is the right formula used in IFEFFIT, and if it is different from > >> what reported in Stern, Phys. Rev. B, 1993, 48, 9825-9827, why it is > >> so. > > > >Most importantly, all of these expressions for the number of independent > >points are similar. > > I know, but since I am reporting in a paper we are writing a table in > which we show chi^2, reduced chi^2, Nidp and Npar (and therefore the > degress of freedom) I was trying to be tidy and rigorous. But I am > facing numbers which I cannot make much sense of. [Kelly, Shelly D.] [Kelly, Shelly D.] That seems to be a problem. Are you processing the data with more than one k-weight in IFEFFIT? Try a test case were you use only one k-weight and see if you like the answers better. If you use more than one k-weight then the answers should be averages for all three data sets. > > >The most important part is that the number of > >independent points goes like 2dkdr/pi. When fitting EXAFS data you > >really need to have a lot more independent points than the number of > >fitted variables. In that case the +0, +1, or +2 doesn't really matter > >as long as you are consistent. > > of course, but see above. > > >The +1 and +2 come from the information at the beginning of the data > >set. I think of the raw chi(k) data as being chopped up into pieces > >with the length of each piece about dk ~ pi/dr. For every multiple of > >this length you get two data points representing an amplitude and phase, > >hence the 2dkdr/pi part. If this length is -- then a data set like this > >.--.--.--.--.- Has 4.5 independent points, plus the one at the > >beginning hence +1 (count the "."). Now often Fourier transforms are > >done from r=0 to some other bigger r value. At the special value of r=0 > >you only need one variable, the amplitude, since the phase is known, > >hence 2dkdr/pi + 1. For EXAFS analysis we never start at r=0 so we get > >two parameters for each length, hence 2drdk/pi + 2. > > OK. This is the sense of the paper by Stern, which now I understand > better, thanks! > Stefano > -- > ____________________________________________ > > Stefano Ciurli > Professor of Chemistry > Laboratory of Bioinorganic Chemistry > Department of Agro-Environmental Science and Technology > University of Bologna > Viale Giuseppe Fanin, 40 > I-40127 Bologna > Italy > Phone: +39-051-209-6204 > Fax: +39-051-209-6203 > > "Fatti non foste a viver come bruti, > ma per seguir virtute e canoscenza" > Dante Alighieri - Inferno - Canto XXVI > > "Ihr seid bestimmt, nicht Tieren gleich zu leben, > Nein, Tugend zu erringen und Erkenntnis" > "Ye were not form'd to live the life of brutes, > But virtue to pursue and knowledge high" > _______________________________________________ > 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] statistical parameters
by Kelly, Shelly D. 14 Dec '05

14 Dec '05

Hi Stephano, > Not sure I fully follow, as I am not talking about background > removal, but in any case, shouldn't the ratio between chi^2 and > reduced-chi^2 be an integer number, whichever? Since 2dkdr/pi is not always an integer number, the degrees of freedom which is the NIP (number of independent points) - number of variables is not always an integer number. > Plus, I have found a > few documents in which Matt reports Nidp as 2dkdr/pi, some others in > which he reports 2dkdr/pi+1. In SK's thesis, which is available on > the net (thanks Shelly :-)) she says +2. I was simply wondering which > is the right formula used in IFEFFIT, and if it is different from > what reported in Stern, Phys. Rev. B, 1993, 48, 9825-9827, why it is > so. Most importantly, all of these expressions for the number of independent points are similar. The most important part is that the number of independent points goes like 2dkdr/pi. When fitting EXAFS data you really need to have a lot more independent points than the number of fitted variables. In that case the +0, +1, or +2 doesn't really matter as long as you are consistent. The +1 and +2 come from the information at the beginning of the data set. I think of the raw chi(k) data as being chopped up into pieces with the length of each piece about dk ~ pi/dr. For every multiple of this length you get two data points representing an amplitude and phase, hence the 2dkdr/pi part. If this length is -- then a data set like this .--.--.--.--.- Has 4.5 independent points, plus the one at the beginning hence +1 (count the "."). Now often Fourier transforms are done from r=0 to some other bigger r value. At the special value of r=0 you only need one variable, the amplitude, since the phase is known, hence 2dkdr/pi + 1. For EXAFS analysis we never start at r=0 so we get two parameters for each length, hence 2drdk/pi + 2. HTH 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 Stefano Ciurli > Sent: Wednesday, December 14, 2005 11:16 AM > To: Ravel, Bruce D.; XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] statistical parameters > > Bruce, > > >According to what you said above, Nvar = 7, so nu=24.83, which is much > >closer to 23.54. > > of course. My mistake. But still... > > >That still seems bigger than rounding errors, though. > > that's what I am saying... > > >Here is my understanding of Ifeffit, but I am sure Matt can elaborate. > >Background removal uses the integer part of dk*dr*2/pi+1 to determine > >the number of knots. Fitting uses dk*dr*2/pi as a real number to > >determine Nidp. In any case, that's what Artemis reports when you ask > >it how many independent points in a project. My memory is that I > >checked it against Ifeffit's report of Nidp. > > > Stefano > -- > ____________________________________________ > > Stefano Ciurli > Professor of Chemistry > Laboratory of Bioinorganic Chemistry > Department of Agro-Environmental Science and Technology > University of Bologna > Viale Giuseppe Fanin, 40 > I-40127 Bologna > Italy > Phone: +39-051-209-6204 > Fax: +39-051-209-6203 > > "Fatti non foste a viver come bruti, > ma per seguir virtute e canoscenza" > Dante Alighieri - Inferno - Canto XXVI > > "Ihr seid bestimmt, nicht Tieren gleich zu leben, > Nein, Tugend zu erringen und Erkenntnis" > "Ye were not form'd to live the life of brutes, > But virtue to pursue and knowledge high" > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Re: statistical parameters (Josh Kas)
by joshua jason kas 14 Dec '05

14 Dec '05

Hi, I don't know what ifeffit does, but here is a nice paper by Ed Stern which goes through the theory Number of relevant independent points in x-ray-absorption fine-structure spectra. PRB V. 48 Number 13 The conlcusion is that if you are using r-space data that includes r=0 then Nidp = 2dkdR/pi + 1 otherwise, when r=0 is not included in the fit Nidp = 2dkdR/pi + 2 Hope this helps. Josh Kas

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phase shifts
by Stefano Ciurli 14 Dec '05

14 Dec '05

Hello, yet another one... sorry today is my day... With Athena it appears that I can simply (maybe too simply) click on a button and plot the phase shifted spectrum in R-space. How can I try to do the same using IFEFFIT from the command line? In practice, using IFEFFIT we can plot the fitted spectrum and the FT'ed experimental spectrum, but the plot does not consider the phase shift. We need to extract the phase shift in oder to translate the plot to show the phase shifted spectrum. How can we do that? What is the parameter in IFEFFIT that allows one - as in Athena - to add a constant number and shift the plot? Stefano PS: needless to say that we are learning... -- ____________________________________________ Stefano Ciurli Professor of Chemistry Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"

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statistical parameters
by Stefano Ciurli 14 Dec '05

14 Dec '05

Hello, same old question that emerges again: What formula is used by IFEFFIT to calculate the number of independent points? Does it use the formula 2DkDR/pi? or 2DkDR/pi +1? or 2DkDR/pi +2? And how does it approximate the resulting number to integer? Next: as far as I understand, the conversion from chi^2 to reduced-chi^2 involves dividing the first by the number of degrees of freedom. The latter is obtained by subtracting the number or floating parameters from the number of independent point right?. What if one fixes the value of one parameter, let's say S0^2 to unity? Does the number of parameters includes S0^2 in that case? We consider that it does not. Here is an example. We find with IFEFFIT (we use Dk= 10 (from 2 to 12), DR=5 (from 1 to 6). chi^2 = 87.1 reduced chi^2 = 3.7 parameters: E0, three distances and three sigma^2 we set S0^2 fixed to 1 R-factor: 1.15% The ratio between chi^2 and reduced chi^2 is 23.54, which is not an integer number as we would expect. Plus, this number does not correspond to Ninp -Nvar (31.83 - 5 = 26.83) What are we missing? Sorry if the question sounds silly to most of you. Stefano -- ____________________________________________ Stefano Ciurli Professor of Chemistry Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"

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Athena 0.8.046 and the "%" character
by Mauro Rovezzi 14 Dec '05

14 Dec '05

Hi folks, I've just noticed a strange behaviour in Athena. Please, let me know if you can reproduce this "error": - Open a project with two mu(E) - Merge them in chi(k) [noise weighted] - Rename the "merge" group in "something%something_else" - Save the new group as chi(k) - Save the project Well: 1. The generated .chi file contains nothing 2. Artemis fails to open the chi(k) from the Athena project (trapping an error and showing nothing). 3. Re-doing everything *without the "%" character, works!* Cheers, Mauro

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wiggly lines
by Stefano Ciurli 14 Dec '05

14 Dec '05

Hello all, I found this funny dialog on the web. I think it is worth a smile :-) Stefano "What is feff," You ask? "Well, I am glad that you asked that," I say. Then I continue, "Feff is a computer program that makes wiggly lines appear on your computer screen." "Not my computer screen," you say. "Yes, I suppose not YOUR computer screen- MY computer screen... Anyways, sometimes the lines are long and really very wiggly, and sometimes the lines are hardly very wiggly at all. But, there are always at least a few wiggles; you can count on that." "And another thing about the wiggly lines," I exclaim. "Sometimes those wiggly lines are pretty good wiggly lines, but then again, sometimes they are pretty bad." "How can you tell the difference," you ask? "Well, that's really very simple. Just go show the wiggly lines to your boss, and if he looks HAPPY then you have just shown him GOOD wiggly lines... If he looks SAD then you have just shown him BAD wiggly lines. And if he says, 'What the hell are all these wiggly lines?' then you probably just went into the wrong office; try down the hall a bit... ...just a little further... ...now on your left... ... next one... that's it! Good luck with those wiggly lines!" -- ____________________________________________ Stefano Ciurli Professor of Chemistry Laboratory of Bioinorganic Chemistry Department of Agro-Environmental Science and Technology University of Bologna Viale Giuseppe Fanin, 40 I-40127 Bologna Italy Phone: +39-051-209-6204 Fax: +39-051-209-6203 "Fatti non foste a viver come bruti, ma per seguir virtute e canoscenza" Dante Alighieri - Inferno - Canto XXVI "Ihr seid bestimmt, nicht Tieren gleich zu leben, Nein, Tugend zu erringen und Erkenntnis" "Ye were not form'd to live the life of brutes, But virtue to pursue and knowledge high"

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