Hi Scott, Thanks for the detailed comments on parameter usage in fitting. I have started evaluating/checking the used model and other possible model for meaningful fit. Once i achieve that, i will get back to you.
Regards, Raj On 8 January 2017 at 20:03, <ifeffit-requ...@millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit@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-requ...@millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-ow...@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: Ifeffit Digest, Vol 167, Issue 11 (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 8 Jan 2017 13:03:44 -0600 > From: Scott Calvin <dr.scott.cal...@gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 11 > Message-ID: <00387e3a-5b7b-40c5-8c7d-f40530988...@gmail.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Raj, > > The kind of thing I gather you did for #1 is almost always a bad idea. > Guessing parameters in one fit and then setting them to the results for > that fit in subsequent fits without further justification is asserting a > certainty about those parameters that you do not possess. Occasionally it > might be useful in an intermediate fit as a kind of diagnostic, but never > in fits from which you want to extract information.* Note that the fit in > which you set S02 is a different kind of constraint; rather than using the > result of a previous fit, you used an a priori plausible value. While that > can introduce its own biases, it at least is based on external information > (a ?reasonable" value for S02) rather than trying to do the fit in pieces > (I?ll run a fit, find values for guessed parameters, and then set those to > the first results for the next fit). > > Fundamentally, you just don?t have a good fit yet. Likely, something about > the system is a bit different than you envisioned it. But that?s part of > the point of using EXAFS, right? For fits to tell you that, and then you to > use your knowledge about the system to try out plausible modifications to > the model until you find something that works well, hopefully also > supporting it with other lines of evidence? > > That?s not something we?re going to be able to do for you on this list; > it?s the heart of the investigation you?re undertaking. > > Best, > > Scott Calvin > Lehman College of the City University of New York > > *I say ?never,? but I can think of one case where it might be justified, > and wouldn?t be surprised if there are others. If you were trying to decide > between a compound being 4-coordinated or 6-coordinated, and had some > reason for thinking it was purely one or the other, then a fitted > coordination number of, for example, 6.3 +/- 0.7 could reasonably be set to > 6 in future fits. But that?s not the kind of circumstance you have. > > > > On Jan 7, 2017, at 9:17 AM, Raj kumar <rajr...@gmail.com> wrote: > > > > Hi Scott, > > > > Thanks for your comments. Please see below for my answers. > > > > 1. Initially, i have started the fitting using single Eo but couldn't > achieve satisfactory fit. Hence, moved to use two Eo's, one for first two > shells and another for rest other shells, for fitting the curve. With this > strategy, I have varied all parameters, including Eo's, mentioned in the > previous table. As a result, i have identified appropriate Eo's for > respective paths. Subsequently, evaluated all other parameters keeping both > Eo's fixed. The result remains almost same irrespective of varying or > fixing Eo's. > > > > 2. YbVO4 belongs to zircon structure. In this kind of structure, only > the position of oxygen varies and leaving both metal atoms unmoved. The > atomic config, I have used (YbVO4-Demeter: @ standard zircon position) for > modelling is attached along with the COD database file. Both files having > different oxygen positions and hence different splitting distances for > first oxygen shell. Further, i have compared first two oxygen paths, > obtained from COD file, with experimental signal. It seems, the second > oxygen distance might be exaggerated. Again, please see attachment for the > confirmation. > > <image.png> > > > > > > > > Regards, > > Raj > > > > On 7 January 2017 at 01:06, <ifeffit-requ...@millenia.cars.aps.anl.gov > <mailto:ifeffit-requ...@millenia.cars.aps.anl.gov>> wrote: > > Send Ifeffit mailing list submissions to > > ifeffit@millenia.cars.aps.anl.gov <mailto:ifef...@millenia.cars. > aps.anl.gov> > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit < > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > > or, via email, send a message with subject or body 'help' to > > ifeffit-requ...@millenia.cars.aps.anl.gov <mailto: > ifeffit-requ...@millenia.cars.aps.anl.gov> > > > > You can reach the person managing the list at > > ifeffit-ow...@millenia.cars.aps.anl.gov <mailto:ifeffit-owner@ > 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: error when fitting in Artemis (George Sterbinsky) > > 2. Re: Problem with large so2: Updated (Scott Calvin) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Fri, 6 Jan 2017 16:32:45 -0600 > > From: George Sterbinsky <georgesterbin...@u.northwestern.edu <mailto: > georgesterbin...@u.northwestern.edu>> > > To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov > <mailto:ifeffit@millenia.cars.aps.anl.gov>> > > Subject: Re: [Ifeffit] error when fitting in Artemis > > Message-ID: > > <CALoY8Yw=PYOKfKivpjFfeqmOALA95wJK++Yen+HAi70V3KH8_Q@mail. > gmail.com <mailto:PYOKfKivpjFfeqmOALA95wJK%2B%2BYen%2BHAi70V3KH8_Q@ > mail.gmail.com>> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Robert and Bruce, > > > > Thank you for your replies and, Robert, for providing a work-around. I > too > > apologize for taking so long to respond. I was hoping to investigate the > > problem a bit further as to provide a more actionable bug report before > > responding to Robert, but in light of Bruce's message that no longer > seems > > as necessary. I also do not see a "phase.bin" file on my computer, and I > do > > see "0_Warning.txt". I will try to figure out when, in the history of the > > file, it became damaged and report back to the list if that information > > will help others prevent the problem or indicates a fix. > > > > Thanks again, > > George > > > > > > > > On Wed, Jan 4, 2017 at 10:05 AM, Bruce Ravel <bra...@bnl.gov <mailto: > bra...@bnl.gov>> wrote: > > > > > On 12/22/2016 12:11 PM, George Sterbinsky wrote: > > > > > >> I have attached an Artemis project. Upon opening the project, and > > >> clicking the fit button the error in the attached log file is > generated > > >> and the fit is not run. Looking at the history, fits have been run > > >> previously without error. The error message indicates Feff may need to > > >> be run again, but upon opening the Atoms and Feff window and then > > >> clicking on the Feff tab, I see the Run Feff button is grey and cannot > > >> be clicked. What steps are necessary in order to run a fit? > > >> > > > > > > Hi George, > > > > > > Sorry it has taken so long to respond. Partly holidays, partly that I > > > have been doing a bunch of work on Demeter that needed to get finished. > > > > > > So, the problem here does not seem to be a problem with Artemis. It > seems > > > to be an issue with someone's antivirus software. > > > > > > The artemis.fpj is simply a zip file with a different file extension. > > > Opening it up, one finds a folder called "feff". In the case of your > > > project file, the relevant subfolder is "azxqc" (that's a randomly > > > generated 5-character string, which is how Demeter names most things > > > internally). In that folder, there should be a "phase.bin" file from > the > > > Feff run. It's absent. Instead, I see a file called "0_Warning.txt", > the > > > contents of which read: > > > > > > BLOCKED FILE ALERT > > > > > > A file has been blocked due to the 'Blocked for exchange' rule. > > > Context: 'phase.bin' > > > Disallowed due to > > > Ticket Number: '09e8-5852-0da2-0001' > > > See your system administrator for further information. Copyright > 1999-2013 > > > McAfee, Inc.All Rights Reserved.http://www.mcafee.com < > http://www.mcafee.com/> > > > > > > Now, I do not know if this happened when you mailed the project file to > > > the list or if it happened at some other time. While the error > message is > > > certainly misleading in this case, I think that it is Artemis' way of > > > complaining about the missing phase.bin file. > > > > > > Perhaps there is some other problem at play. I don't know. But I > cannot > > > possibly troubleshoot that other problem given that an anti-virus > package > > > has, at some point, irretrievably damaged this project file. > > > > > > I think that the only plausible work-around is Robert's suggestion. > > > Reimport the feff.inp file, rerun Feff, exclude the existing path, > > > drag-and-drop the replacement path, then push path parameter values > from > > > the old path to the new one. Awkward, but I don't know what else to > > > suggest. > > > > > > B > > > > > > PS: If anyone has any kind of working knowledge of McAfee or any other > AV > > > software, I would be open to a suggestion for how to fix this. Is it a > > > file /name/ problem -- should phase.bin be called something else? Is > there > > > something in the phase.bin file that triggered McAfee? Any wisdom > would be > > > welcome. > > > > > > > > > -- > > > Bruce Ravel ------------------------------------ bra...@bnl.gov > <mailto:bra...@bnl.gov> > > > > > > National Institute of Standards and Technology > > > Synchrotron Science Group at NSLS-II > > > Building 743, Room 114 > > > Upton NY, 11973 > > > > > > Homepage: http://bruceravel.github.io/home/ < > http://bruceravel.github.io/home/> > > > Software: https://github.com/bruceravel < > https://github.com/bruceravel> > > > Demeter: http://bruceravel.github.io/demeter/ < > http://bruceravel.github.io/demeter/> > > > > > > _______________________________________________ > > > Ifeffit mailing list > > > Ifeffit@millenia.cars.aps.anl.gov <mailto:ifef...@millenia.cars. > aps.anl.gov> > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit < > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > <http://millenia.cars.aps.anl.gov/mailman/options/ifeffit> > > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/ > attachments/20170106/f7fdc0c9/attachment-0001.html < > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/ > attachments/20170106/f7fdc0c9/attachment-0001.html>> > > > > ------------------------------ > > > > Message: 2 > > Date: Sat, 7 Jan 2017 00:06:46 +0000 > > From: Scott Calvin <scal...@sarahlawrence.edu <mailto: > scal...@sarahlawrence.edu>> > > To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov > <mailto:ifeffit@millenia.cars.aps.anl.gov>> > > Subject: Re: [Ifeffit] Problem with large so2: Updated > > Message-ID: <4231dae0-c9af-49d8-82fb-b95f83465...@sarahlawrence.edu > <mailto:4231dae0-c9af-49d8-82fb-b95f83465...@sarahlawrence.edu>> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Raj, > > > > I don?t have an easy way to read Artemis files on my computer at the > moment, so I haven?t looked directly at those. But looking at your Word > document, I?m puzzled by a couple of things: > > > > > > * You have different E0?s for the nearby oxygens from more distant > shells. That can be defensible in some cases. But the strange thing is that > the values are identical in different fits, as if you?re setting them to > some value. How did you choose those values? > > * I downloaded a YbVO4 structure from the Crystallographic Open > Database and ran it in WebAtoms. While I wouldn?t expect it to generate > identical values to those from your model, it does show much greater > splitting between the nearest-neighbor oxygens (at 2.27 A) and the > next-nearest (2.56 A). Your model has 2.28 A and 2.39 A. That?s quite > different. Are you sure you entered the starting structure right? > > > > Best, > > > > Scott Calvin > > Lehman College of the City University of New York > > > > On Jan 5, 2017, at 3:12 PM, Raj kumar <rajr...@gmail.com <mailto: > rajr...@gmail.com><mailto:rajr...@gmail.com <mailto:rajr...@gmail.com>>> > wrote: > > > > Dear all, > > > > Earlier, I have posted few questions on large so2 value and got valuable > suggestions from Scott and Bruce. Here i am presenting my summary of > earlier emails and the present views. Could you please tell me whether am i > going in right direction. > > > > I have been trying to fit EXAFS signal of YbVO4 both in bulk and > nanoparticles form. Here, I would like to estimate so2 from bulk > (reference) and subsequently use the number, as normalization parameter, to > calculate the co-ordination number in all nanoparticles. Nanoparticles were > synthesized by solution route. First, I have modelled my reference (bulk > YbVO4) with two so2, N and R as free parameters. So2-1 is for first two > shell and so2-2 is for rest other shells. If I use single so2, the value is > obtained to be around 0.9 with unsatisfactory fit whereas second so2-2 > incorporation leads to satisfied fit with large uncertainty on the obtained > number i.e., (2.04 +/- 0.9). Using the same strategy, I could successfully > fit the nanoparticles again with large so2-2 (1.79). From literature and > IFEFFIT earlier discussion, i understood that so2 should be between 0.8-1.2 > value. Further, so2-2 is found to well correlated with ss1 and delc (a > parameter to define the movement of atoms! > i! > > n c direction). Among two, the former parameter (ss1) strongly > correlate with so2 and take value of 0.8 and 1.9 for fixed and varying > ss1, respectively, during the fit. This large value of so2 cannot be > controlled with the used model. Also, I have tried to fit the curve with > fixed so2 i.e., below 1 but leads to unsatisfactory fit. For your info, i > have tabulated various strategy and the resultant parameters. After > considering Scott suggestions (and previous posts), i have concluded the > following: Since, so2 is used as a normalization parameter and with the > estimated uncertainty, i would like to consider the obtained number as > reasonable value to normalize the unknown to calculate the CN in other > systems. Is this strategy good to calculate the CN in unknown? and later to > describe the trend on obtained parameters? > > > > Regards, > > Raj > > <Parameters comparison vs So2.docx>_____________________ > __________________________ > > Ifeffit mailing list > > Ifeffit@millenia.cars.aps.anl.gov <mailto:ifef...@millenia.cars. > aps.anl.gov><mailto:Ifeffit@millenia.cars.aps.anl.gov <mailto: > Ifeffit@millenia.cars.aps.anl.gov>> > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit < > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit < > http://millenia.cars.aps.anl.gov/mailman/options/ifeffit> > > > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/ > attachments/20170107/c4699fc5/attachment.html < > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/ > attachments/20170107/c4699fc5/attachment.html>> > > > > ------------------------------ > > > > Subject: Digest Footer > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit@millenia.cars.aps.anl.gov <mailto:ifef...@millenia.cars. > aps.anl.gov> > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit < > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit < > http://millenia.cars.aps.anl.gov/mailman/options/ifeffit> > > > > > > ------------------------------ > > > > End of Ifeffit Digest, Vol 167, Issue 11 > > **************************************** > > > > <YbVO4-Demeter.inp><COD.cif>________________________________ > _______________ > > Ifeffit mailing list > > Ifeffit@millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/ > attachments/20170108/73c70fc2/attachment.html> > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > ------------------------------ > > End of Ifeffit Digest, Vol 167, Issue 14 > **************************************** >
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