[Ifeffit] Ifeffit Digest, Vol 167, Issue 14
Raj kumar
rajkr3786 at gmail.com
Mon Jan 9 12:39:38 CST 2017
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-request at millenia.cars.aps.anl.gov>
wrote:
> Send Ifeffit mailing list submissions to
> ifeffit at 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 at millenia.cars.aps.anl.gov
>
> You can reach the person managing the list at
> ifeffit-owner at 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.calvin at gmail.com>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 11
> Message-ID: <00387E3A-5B7B-40C5-8C7D-F4053098816F at 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 <rajrk37 at 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-request at millenia.cars.aps.anl.gov
> <mailto:ifeffit-request at millenia.cars.aps.anl.gov>> wrote:
> > Send Ifeffit mailing list submissions to
> > ifeffit at millenia.cars.aps.anl.gov <mailto:ifeffit at 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-request at millenia.cars.aps.anl.gov <mailto:
> ifeffit-request at millenia.cars.aps.anl.gov>
> >
> > You can reach the person managing the list at
> > ifeffit-owner at 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 <GeorgeSterbinsky at u.northwestern.edu <mailto:
> GeorgeSterbinsky at u.northwestern.edu>>
> > To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov
> <mailto:ifeffit at millenia.cars.aps.anl.gov>>
> > Subject: Re: [Ifeffit] error when fitting in Artemis
> > Message-ID:
> > <CALoY8Yw=PYOKfKivpjFfeqmOALA95wJK++Yen+HAi70V3KH8_Q at 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 <bravel at bnl.gov <mailto:
> bravel at 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 ------------------------------------ bravel at bnl.gov
> <mailto:bravel at 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 at millenia.cars.aps.anl.gov <mailto:Ifeffit at 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 <scalvin at sarahlawrence.edu <mailto:
> scalvin at sarahlawrence.edu>>
> > To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov
> <mailto:ifeffit at millenia.cars.aps.anl.gov>>
> > Subject: Re: [Ifeffit] Problem with large so2: Updated
> > Message-ID: <4231DAE0-C9AF-49D8-82FB-B95F83465269 at sarahlawrence.edu
> <mailto:4231DAE0-C9AF-49D8-82FB-B95F83465269 at 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 <rajrk37 at gmail.com <mailto:
> rajrk37 at gmail.com><mailto:rajrk37 at gmail.com <mailto:rajrk37 at 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 at millenia.cars.aps.anl.gov <mailto:Ifeffit at millenia.cars.
> aps.anl.gov><mailto:Ifeffit at millenia.cars.aps.anl.gov <mailto:
> Ifeffit at 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 at millenia.cars.aps.anl.gov <mailto:Ifeffit at 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 at 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 at 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
> ****************************************
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20170109/707d999c/attachment-0001.html>
More information about the Ifeffit
mailing list