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

RE: XAFS 12
by Wojciech Gawelda 04 Mar '04

04 Mar '04

Hi Bruce, I wondered about the same thing but it seems like editors of Physica Scripta are very reluctant to say anything. I tried repeatedly to send e-mails to them asking about any approximation when the topical issue on XAFS 12 will come out but I got no response. So it seems like we have to patiently wait and check their web site from time to time. I know it doesn't sound great... Greetings, Wojciech Gawelda ********************************************************************* Wojciech Gawelda Laboratoire de Spectroscopie Ultrarapide (LSU) Institut des Sciences et Ingénierie Chimiques (ISIC), Faculté des Sciences de Base (SB-BSP) Ecole Polytechnique Fédérale de Lausanne (EPFL) CH-1015 Lausanne-Dorigny, Switzerland Tel.: +41 (21) 693 0452 Fax.: +41 (21) 693 0422 E-mail: wojciech.gawelda(a)epfl.ch WWW: http://lsu.epfl.ch ********************************************************************* -----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: mercredi, 3. mars 2004 19:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 13, Issue 3 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. references for fluorescence corrections (Grant Bunker) 2. XAFS12 (Bruce Ravel) 3. Chi^2-Map question (Norbert Weiher) ---------------------------------------------------------------------- Message: 1 Date: Tue, 2 Mar 2004 22:21:17 -0600 (CST) From: Grant Bunker <bunker(a)biocat1.phys.iit.edu> Subject: [Ifeffit] references for fluorescence corrections To: ifeffit(a)millenia.cars.aps.anl.gov Message-ID: <Pine.LNX.4.44.0403022219160.32516-100000(a)biocat1.phys.iit.edu> Content-Type: TEXT/PLAIN; charset=US-ASCII Greetings, All - I'll make another effort to get this by the ANL Spam filters. A references for fluorescence corrections can be found in Booth and Bridge's paper http://xxx.lanl.gov/abs/cond-mat/0306252 they have refs to earlier work also. thanks - grant On Tue, 2 Mar 2004 ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: question about S02 (passive electron reduction factor) > (Matt Newville) > 2. *****SPAM***** references for self-absorption correction > (Grant Bunker) > 3. Correlations (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 1 Mar 2004 12:16:38 -0600 (CST) > From: Matt Newville <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] question about S02 (passive electron reduction > factor) > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <Pine.LNX.4.44.0403011211200.10753-100000(a)millenia.cars.aps.anl.gov> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Hi Scott, > > First, I'm not sure how your message got tagged as Spam by Argonne's > SpamAssassin (words or phrases selling drugs??? huh???), but that > happens well before I can do anything about it. I've forwarded this > message on as a false positive for spam. For better archiving, I > also included the full message you sent below. > > > Good point. It is much more straightforward to check the uncertainty than > > the correlation to determine if that could be responsible for the > > anomalous S02...so I should have said that Yu-Chuan should check the > > uncertainty of the S02 parameter. If it is very large (say 0.8), then > > Ifeffit is in effect reporting that it cannot determine S02 well for some > > reason. At that point, I think it is helpful to see if there is a high > > correlation, since that may give a clue as to the reason for the large > > uncertainty. > > Knowing the correlations always helps. And stating a best-fit value > without an uncertainty is dangerous (one might take an implicit > uncertainty, which may not be what you mean). > > This is probably a bit off-topic from the original question (where > I'd guess self-absorption to be the main issue,....), but let's > consider typical fit results: S02= 0.9 +/- 0.1, sigma2= 0.015 +/- > 0.005, and a correlation between S02 and sigma2 C_S02_sigma2= +0.90. > One could conclude from these that a true value of S02= 1.0 was > reasonable. But in order to get to S02= 1.0, sigma2 has to go up to > ~= 0.019 (~= sigma2_best + C_S02_sigma2 * delta_sigma2). S02= 0.80 > is also reasonable, but this implies sigma2 would drop to around > 0.011. The correlation means that, although having either S02= 0.80 > OR sigma2= 0.020 would be reasonable,t having both S02= 0.80 AND > sigma2= 0.020 is much less likely. > > The correlation by itself says nothing about the likelihood of > having a true value for S02 of, say, 0.5. There is a chance this > can happen, but it's small because the uncertainty in S02 is 0.1. > The correlation simply tells you how sigma2 would respond if S02 > were 0.5, but nothing more. > > > So this brings up a (possibly contentious) point. In their reporting > > recommendations, the IXS suggests reporting high correlations, > > particularly when they are between parameters that do not routinely show > > high correlations. What is the reason for this suggestion? I'm not > > criticizing it...just looking for the rationale. > > It's hard to speak for the IXS, but I'd say that correlations are > recommended to be reported because they're important statistics. The > correlations, along with the best-fit values and uncertainties, help > more fully describe the range of plausible results. > > It's generally well-known that the parameters (S02,sigma2) and > (E0,R) are highly correlated for a single shell of a single data > set, and the implications of these are generally understood, I > think. Sometimes other variables are correlated, and some people > even do complex fits with multiple data sets or generalized > variables that are not the simple XAFS parameters ;). In these > cases, it may not be obvious how the variables are correlated. I > think the IXS committee was concerned about this, and so recommended > reporting correlations in such cases. That seems sensible to me. > > --Matt > > > > On Sat, 28 Feb 2004, Scott Calvin wrote: > > > > Matt, > > > > Good point. It is much more straightforward to check the uncertainty than > > the correlation to determine if that could be responsible for the anomalous > > S02...so I should have said that Yu-Chuan should check the uncertainty of > > the S02 parameter. If it is very large (say 0.8), then Ifeffit is in effect > > reporting that it cannot determine S02 well for some reason. At that point, > > I think it is helpful to see if there is a high correlation, since that may > > give a clue as to the reason for the large uncertainty. > > > > So this brings up a (possibly contentious) point. In their reporting > > recommendations, the IXS suggests reporting high correlations, particularly > > when they are between parameters that do not routinely show high > > correlations. What is the reason for this suggestion? I'm not criticizing > > it...just looking for th erationale. > > > > --Scott Calvin > > Sarah Lawrence College > > > > > ------------------------------ > > Message: 2 > Date: Mon, 1 Mar 2004 13:53:53 -0600 (CST) > From: Grant Bunker <bunker(a)biocat1.phys.iit.edu> > Subject: [Ifeffit] *****SPAM***** references for self-absorption > correction > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <Pine.LNX.4.44.0403011343220.6220-100000(a)biocat1.phys.iit.edu> > Content-Type: text/plain; charset="us-ascii" > > -------------------- Start SpamAssassin results ---------------------- > Content analysis details: (7.1 hits, 5.6 required) > -4.9 BAYES_00 BODY: Bayesian spam probability is 0 to 1% > [score: 0.0000] > 6.0 PORN_4 URI: URL uses words/phrases which indicate porn > 6.0 DRUGS_APS BODY: Words and phrases selling drugs > > -------------------- End of SpamAssassin results --------------------- > > >

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XAFS12
by Bruce Ravel 03 Mar '04

03 Mar '04

Hi folks! Does anyone have any information on when the volume of Physica Scripta containing the proceedings of the last XAFS conference will be published? Is there at least a volume number yet? Thanks, B -- Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu Code 6134, Building 3, Room 405 Naval Research Laboratory phone: (1) 202 767 2268 Washington DC 20375, USA fax: (1) 202 767 4642 NRL Synchrotron Radiation Consortium (NRL-SRC) Beamlines X11a, X11b, X23b National Synchrotron Light Source Brookhaven National Laboratory, Upton, NY 11973 My homepage: http://feff.phys.washington.edu/~ravel EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/

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references for fluorescence corrections
by Grant Bunker 02 Mar '04

02 Mar '04

Greetings, All - I'll make another effort to get this by the ANL Spam filters. A references for fluorescence corrections can be found in Booth and Bridge's paper http://xxx.lanl.gov/abs/cond-mat/0306252 they have refs to earlier work also. thanks - grant On Tue, 2 Mar 2004 ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: question about S02 (passive electron reduction factor) > (Matt Newville) > 2. *****SPAM***** references for self-absorption correction > (Grant Bunker) > 3. Correlations (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 1 Mar 2004 12:16:38 -0600 (CST) > From: Matt Newville <newville(a)cars.uchicago.edu> > Subject: Re: [Ifeffit] question about S02 (passive electron reduction > factor) > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <Pine.LNX.4.44.0403011211200.10753-100000(a)millenia.cars.aps.anl.gov> > Content-Type: TEXT/PLAIN; charset=US-ASCII > > Hi Scott, > > First, I'm not sure how your message got tagged as Spam by Argonne's > SpamAssassin (words or phrases selling drugs??? huh???), but that > happens well before I can do anything about it. I've forwarded this > message on as a false positive for spam. For better archiving, I > also included the full message you sent below. > > > Good point. It is much more straightforward to check the uncertainty than > > the correlation to determine if that could be responsible for the > > anomalous S02...so I should have said that Yu-Chuan should check the > > uncertainty of the S02 parameter. If it is very large (say 0.8), then > > Ifeffit is in effect reporting that it cannot determine S02 well for some > > reason. At that point, I think it is helpful to see if there is a high > > correlation, since that may give a clue as to the reason for the large > > uncertainty. > > Knowing the correlations always helps. And stating a best-fit value > without an uncertainty is dangerous (one might take an implicit > uncertainty, which may not be what you mean). > > This is probably a bit off-topic from the original question (where > I'd guess self-absorption to be the main issue,....), but let's > consider typical fit results: S02= 0.9 +/- 0.1, sigma2= 0.015 +/- > 0.005, and a correlation between S02 and sigma2 C_S02_sigma2= +0.90. > One could conclude from these that a true value of S02= 1.0 was > reasonable. But in order to get to S02= 1.0, sigma2 has to go up to > ~= 0.019 (~= sigma2_best + C_S02_sigma2 * delta_sigma2). S02= 0.80 > is also reasonable, but this implies sigma2 would drop to around > 0.011. The correlation means that, although having either S02= 0.80 > OR sigma2= 0.020 would be reasonable,t having both S02= 0.80 AND > sigma2= 0.020 is much less likely. > > The correlation by itself says nothing about the likelihood of > having a true value for S02 of, say, 0.5. There is a chance this > can happen, but it's small because the uncertainty in S02 is 0.1. > The correlation simply tells you how sigma2 would respond if S02 > were 0.5, but nothing more. > > > So this brings up a (possibly contentious) point. In their reporting > > recommendations, the IXS suggests reporting high correlations, > > particularly when they are between parameters that do not routinely show > > high correlations. What is the reason for this suggestion? I'm not > > criticizing it...just looking for the rationale. > > It's hard to speak for the IXS, but I'd say that correlations are > recommended to be reported because they're important statistics. The > correlations, along with the best-fit values and uncertainties, help > more fully describe the range of plausible results. > > It's generally well-known that the parameters (S02,sigma2) and > (E0,R) are highly correlated for a single shell of a single data > set, and the implications of these are generally understood, I > think. Sometimes other variables are correlated, and some people > even do complex fits with multiple data sets or generalized > variables that are not the simple XAFS parameters ;). In these > cases, it may not be obvious how the variables are correlated. I > think the IXS committee was concerned about this, and so recommended > reporting correlations in such cases. That seems sensible to me. > > --Matt > > > > On Sat, 28 Feb 2004, Scott Calvin wrote: > > > > Matt, > > > > Good point. It is much more straightforward to check the uncertainty than > > the correlation to determine if that could be responsible for the anomalous > > S02...so I should have said that Yu-Chuan should check the uncertainty of > > the S02 parameter. If it is very large (say 0.8), then Ifeffit is in effect > > reporting that it cannot determine S02 well for some reason. At that point, > > I think it is helpful to see if there is a high correlation, since that may > > give a clue as to the reason for the large uncertainty. > > > > So this brings up a (possibly contentious) point. In their reporting > > recommendations, the IXS suggests reporting high correlations, particularly > > when they are between parameters that do not routinely show high > > correlations. What is the reason for this suggestion? I'm not criticizing > > it...just looking for th erationale. > > > > --Scott Calvin > > Sarah Lawrence College > > > > > ------------------------------ > > Message: 2 > Date: Mon, 1 Mar 2004 13:53:53 -0600 (CST) > From: Grant Bunker <bunker(a)biocat1.phys.iit.edu> > Subject: [Ifeffit] *****SPAM***** references for self-absorption > correction > To: ifeffit(a)millenia.cars.aps.anl.gov > Message-ID: > <Pine.LNX.4.44.0403011343220.6220-100000(a)biocat1.phys.iit.edu> > Content-Type: text/plain; charset="us-ascii" > > -------------------- Start SpamAssassin results ---------------------- > Content analysis details: (7.1 hits, 5.6 required) > -4.9 BAYES_00 BODY: Bayesian spam probability is 0 to 1% > [score: 0.0000] > 6.0 PORN_4 URI: URL uses words/phrases which indicate porn > 6.0 DRUGS_APS BODY: Words and phrases selling drugs > > -------------------- End of SpamAssassin results --------------------- > > >

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Correlations
by Scott Calvin 01 Mar '04

01 Mar '04

Thanks, Matt. That clarifies a few things...in particular, I found the example you gave (quoted below) to be quite helpful. --Scott Calvin Sarah Lawrence College At 12:16 PM 3/1/2004 -0600, you wrote: >This is probably a bit off-topic from the original question (where >I'd guess self-absorption to be the main issue,....), but let's >consider typical fit results: S02= 0.9 +/- 0.1, sigma2= 0.015 +/- >0.005, and a correlation between S02 and sigma2 C_S02_sigma2= +0.90. >One could conclude from these that a true value of S02= 1.0 was >reasonable. But in order to get to S02= 1.0, sigma2 has to go up to >~= 0.019 (~= sigma2_best + C_S02_sigma2 * delta_sigma2). S02= 0.80 >is also reasonable, but this implies sigma2 would drop to around >0.011. The correlation means that, although having either S02= 0.80 >OR sigma2= 0.020 would be reasonable,t having both S02= 0.80 AND >sigma2= 0.020 is much less likely. >> >--Matt > >

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*****SPAM***** references for self-absorption correction
by Grant Bunker 01 Mar '04

01 Mar '04

-------------------- Start SpamAssassin results ---------------------- Content analysis details: (7.1 hits, 5.6 required) -4.9 BAYES_00 BODY: Bayesian spam probability is 0 to 1% [score: 0.0000] 6.0 PORN_4 URI: URL uses words/phrases which indicate porn 6.0 DRUGS_APS BODY: Words and phrases selling drugs -------------------- End of SpamAssassin results ---------------------

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question about S02 (passive electron reduction factor)
by hsnuboy 01 Mar '04

01 Mar '04

Dear Ifeffit folks, This is Yu-Chuan. I am now trying to fit my sample, magnesium orthovanadate. I try to follow Bruce's Cu example and Scott's ZnO example steps and I found a problem come to my fitting. At the beginning of the fitting, the S02(amp) are far away from 0.9 (just about 0.3). It's much different than Bruce's and Scott's examples. For Cu and ZnO examples, the fitting results of amp are close to 0.9 at the beginning even if you set just four parameters (guess:amp, e0, delr, and ss). Also, John have said that the S02 value should be around 0.9. That's why I am wondering if there is anything wrong with my data processing? Does anyone happen to have this kind of problem? Thank you for your help. Good day Yu-Chuan

4 4

RE: [Ifeffit] question about S02 (passive electron reduction factor)
by hsnuboy 29 Feb '04

29 Feb '04

Scott, Bruce, Matt, Kelly, Grant and all, Thank you for your advice. I am really appreciate that.I think I have to give more detail about my analysis results and make it more clear. 1. I took the fluorescence spectrum. 2. I checked the pre-edge and post-edge lines and they looked reasonable. 3. I took the three first shell paths(Vanadium-Oxide) to fit the data. and I set amp, e0, delr, ss for the variables. 4. The degeneracy of the paths are the same as calculated by FEFF6 5. the following results amp = 0.316 +/- 0.108 e0 = 5.053 +/- 4.321 delr= 0.003 +/- 0.025 ss = -0.003 +/- 0.004 6. the correlations between amp and ss =0.88 e0 and delr = 0.86 I don't know if any other information can help to solve this problem. Thank you for your help. By the way, Grant, the papaer you mentioned, is that from " J. J. Rehr, C. H. Booth, F. Bridges, and S.I. Zabinsky, Physical review B, 49,12347, 1994"? Or other else? Can you give me more detail about that? Good day Yu-Chuan

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*****SPAM***** Re: [Ifeffit] question about S02 (passive electron reduction factor)
by SCalvin100＠aol.com 28 Feb '04

28 Feb '04

-------------------- Start SpamAssassin results ---------------------- Content analysis details: (5.7 hits, 5.6 required) 0.2 NO_REAL_NAME From: does not include a real name 1.0 FROM_ENDS_IN_NUMS From: ends in numbers -1.5 BAYES_01 BODY: Bayesian spam probability is 1 to 10% [score: 0.0180] 0.1 HTML_MESSAGE BODY: HTML included in message 6.0 DRUGS_APS BODY: Words and phrases selling drugs -------------------- End of SpamAssassin results --------------------- The original message was not completely plain text, and may be unsafe to open with some email clients; in particular, it may contain a virus, or confirm that your address can receive spam. If you wish to view it, it may be safer to save it to a file and open it with an editor.

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RE: [Ifeffit] question about S02 (passive electron reduction factor)
by Kelly, Shelly D. 27 Feb '04

27 Feb '04

Yu-Chuan, Matt and all, > >> Yu-Chuan wrote: > >> > >> At the beginning of the fitting, the S02(amp) are far away > from 0.9 > >> (just about 0.3). It's much different than Bruce's and Scott's > >> examples. [...] Also, John have said that the S02 value should be > >> around 0.9. That's why I am wondering if there is anything > wrong with > >> my data processing? Does anyone happen to have this kind > of problem? > > > > > > There are several possibilities. One is sample prep. [...] [...] > > Another is normalization.[...] Finally, look at the correlation > > between S02 and sigma2...if it is very high (say 0.95 or > above) it may > > simply be coming up with low estimates for each. > > Yu-Chuan didn't give details of sample prep or data > collection, and I agree with Scott that these are most likely > cause of low S02 factors (Scott mentioned problems with > transmission measurements, and Grant mentioned how > self-absorption can cause similarly low S02 factors for > fluorescence measurements). I also agree with Scott that > poor normalization will affect S02, though S02~0.3 would > indicate an edge step off by a factor of ~3, which is a > pretty big error for normalization. I doubt that is the culprit. > > But: the correlation between S02 and sigma2 is NOT the cause > of a value for S02 being low by a factor of 3. A high > correlation means that a reasonably good fit could also be > found by changing both S02 and sigma2 away from their > best-fit value. This is not at all the same as saying that > either parameter has the wrong best-fit value. In fact, the > correlation between pair of variables says nothing about the > trustworthiness of the best-fit values, only how much the > uncertainties in the best-fit values depend on other variables. > And, just to be clear, the reported uncertainties already > take these correlation into account. > > Yu-Chuan didn't actually say what the reported uncertainties > in S02 were, but it seems that it was small enough so that > S02~=0.3 could be distinguished from S02~=0.9. > > --Matt The degeneracy of the paths included in the fit were not mentioned, and could easily cause the S02 value to be off by a factor of 3. Especially, if you forget that feff has already taken the degeneracy of the path into account, and then you set some N-value to 2 or 3 or 4. I have seen others make this mistake before... Shelly

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Re: [Ifeffit] question about S02 (passive electron reduction factor)
by Grant Bunker 26 Feb '04

26 Feb '04

As a follow-on to Scott's and Bruce's responses, if the samples were measured in fluorescence, the sample self-absorption effects would be a likely explanation for the problem. At the Vanadium edge the absorption length of the sample would probably be short (microns) and you would have to go to some trouble to avoid those problems. There are good correction procedures for that problem (e.g. see papers by Booth and Bridges, Haskell...). grant bunker On Thu, 26 Feb 2004 ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: question about S02 (passive electron reduction factor) > (Scott Calvin) > 2. Re: question about S02 (passive electron reduction factor) > (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 25 Feb 2004 13:18:29 -0500 > From: Scott Calvin <scalvin(a)slc.edu> > Subject: Re: [Ifeffit] question about S02 (passive electron reduction > factor) > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <3.0.1.32.20040225131829.00acff58(a)mail.slc.edu> > Content-Type: text/plain; charset="us-ascii" > > Hi Yu-Chuan, > > There are several possibilities. One is sample prep. If you have an > extremely uneven sample (lots of pinholes, etc.) in transmission it can > lead to results like you're describing. Another is normalization. If you're > using Athena for background subtraction make sure you look at the pre-edge > line and post-edge curve and see that they look reasonable. Sometimes if > the background has a funny shape to it Athena can create a post-edge curve > that shoots way up at the edge energy; this could also lead to the effect > you're describing. Finally, look at the correlation between S02 and > sigma2...if it is very high (say 0.95 or above) it may simply be coming up > with low estimates for each. There are, of course, other possibilities as > well, but in my experience those are the most common. > > --Scott Calvin > Sarah Lawrence College > > >This is Yu-Chuan. I am now trying to fit my sample, magnesium > orthovanadate. > >I try to follow Bruce's Cu example and Scott's ZnO example steps and I > found a > >problem come to my fitting. At the beginning of the fitting, the S02(amp) > are > >far away from 0.9 (just about 0.3). It's much different than Bruce's and > >Scott's examples. For Cu and ZnO examples, the fitting results of amp are > >close to 0.9 at the beginning even if you set just four parameters > (guess:amp, > >e0, delr, and ss). Also, John have said that the S02 value should be around > >0.9. That's why I am wondering if there is anything wrong with my data > >processing? Does anyone happen to have this kind of problem? Thank you for > >your help. > > > > > ------------------------------ > > Message: 2 > Date: Thu, 26 Feb 2004 10:43:48 -0500 > From: Bruce Ravel <ravel(a)phys.washington.edu> > Subject: Re: [Ifeffit] question about S02 (passive electron reduction > factor) > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: <200402261043.48841.ravel(a)phys.washington.edu> > Content-Type: text/plain; charset="iso-8859-1" > > > Hi, > > Yesterday we had a question about oddly small S02 values. In his > thorough summary of possible explanations, Scott mentioned this: > > On Wednesday 25 February 2004 01:18 pm, Scott Calvin wrote: > > Another is normalization. If you're using Athena for background > > subtraction make sure you look at the pre-edge line and post-edge > > curve and see that they look reasonable. Sometimes if the background > > has a funny shape to it Athena can create a post-edge curve that > > shoots way up at the edge energy; this could also lead to the effect > > you're describing. > > I thought that a word of explanation about why Athena does what she > does might be helpful to folks. In this email I am going to refer to > data taken on an iron foil. To follow along, fire up Athena and > select "Import a demo project" from the Help menu. Select the > `calibrate.prj' file. This contains an iron foil spectrum. > > Set the plotting range in energy to [-200:1500]. Set the upper bound > of the normalization range to 400. Click on the "post-edge line" > button in the plotting options section. This will plot the data, the > background, and the post-edge line. Note that the post-edge line is > U-saped, diverging from the data a bit at low energy and significantly > at high energy. Note also that the edge step is about 3.05. > > Now set the upper bound of the normalization range to 1700 and click > the red E plotting button. Now the post-edge line goes through the > data and the edge step is about 2.86. > > So what's going on? Well, the post-edge line is determined by > regressing a quadratic polynomial to the data in the user-specified > normalization range. When the upper bound was set to 400, the square > term in the polynomial was quite large because *that* was the > regression to the data over that short data range. When the upper > bound was set to 1700, the square term was a lot smaller, the > post-edge line was closer to linear and it was constrained by the > regression to follow the data over the entire data range. > > Setting the upper bound of the normalization range had the effect of > increasing the edge step by about 6%. Remember that the edge step is > the value of the post-edge line extrapolated back to E0 after the > pre-edge line is removed from the data. With the short energy range, > the edge step is too large and the chi(k) is attenuated. In the > subsequent fit, S02 will have to be similarly smaller to compensate. > In this case it was a 6% effect, but if the post-edge line is really > screwy, the attenuation could be much larger. > > So this was the long-winded way of repeating what Scott said -- plot > the post-edge line and make sure the regression was done such that the > post-edge line goes through the entire data in a way that seems > sensible. It is also, as Scott said, prudent to check the pre-edge > line as well. > > B > > > > -- > ********* PLEASE NOTE MY NEW PHONE, FAX, & ROOM NUMBERS ****************** > > Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu > Code 6134, Building 3, Room 405 > Naval Research Laboratory phone: (1) 202 767 2268 > Washington DC 20375, USA fax: (1) 202 767 4642 > > NRL Synchrotron Radiation Consortium (NRL-SRC) > Beamlines X11a, X11b, X23b > National Synchrotron Light Source > Brookhaven National Laboratory, Upton, NY 11973 > > My homepage: http://feff.phys.washington.edu/~ravel > EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/ > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 12, Issue 14 > *************************************** >

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