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@millenia.cars.aps.anl.gov> wrote:
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   1. Re: Ifeffit Digest, Vol 167, Issue 11 (Scott Calvin)


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Message: 1
Date: Sun, 8 Jan 2017 13:03:44 -0600
From: Scott Calvin <dr.scott.calvin@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-F4053098816F@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@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@millenia.cars.aps.anl.gov <mailto:ifeffit-request@millenia.cars.aps.anl.gov>> wrote:
> Send Ifeffit mailing list submissions to
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> or, via email, send a message with subject or body 'help' to
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> 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@u.northwestern.edu <mailto:GeorgeSterbinsky@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 <bravel@bnl.gov <mailto:bravel@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@bnl.gov <mailto:bravel@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
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> >
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> ------------------------------
>
> Message: 2
> Date: Sat, 7 Jan 2017 00:06:46 +0000
> From: Scott Calvin <scalvin@sarahlawrence.edu <mailto:scalvin@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-B95F83465269@sarahlawrence.edu <mailto:4231DAE0-C9AF-49D8-82FB-B95F83465269@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@gmail.com <mailto:rajrk37@gmail.com><mailto:rajrk37@gmail.com <mailto:rajrk37@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>_______________________________________________
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