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

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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