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

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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