[Ifeffit] Ifeffit Digest, Vol 167, Issue 11

Raj kumar rajrk37 at gmail.com
Sat Jan 7 09:17:10 CST 2017


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: Inline images 2]



Regards,
Raj

On 7 January 2017 at 01:06, <ifeffit-request at millenia.cars.aps.anl.gov>
wrote:

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> 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>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] error when fitting in Artemis
> Message-ID:
>         <CALoY8Yw=PYOKfKivpjFfeqmOALA95wJK++Yen+HAi70V3KH8_Q at mail.gm
> ail.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> 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
> >
> > 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
> >
> >  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/
> >  Software:    https://github.com/bruceravel
> >  Demeter:     http://bruceravel.github.io/demeter/
> >
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> Message: 2
> Date: Sat, 7 Jan 2017 00:06:46 +0000
> From: Scott Calvin <scalvin at sarahlawrence.edu>
> To: XAFS Analysis using Ifeffit <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>
> 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:rajr
> k37 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>_____________________
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> End of Ifeffit Digest, Vol 167, Issue 11
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