[Ifeffit] Amplitude ratios greater than 100%
Dear All, With the attached CIF file, i have generated chi and other files. In turn, for some paths, i have found amplitude ratios are greater than 100% (even it is reaching few thousands % for some paths - chi file also attached with this email). I know, it is meaningless. I would like to know, why am i getting these weird ratios? What is wrong with the CIF file? Thanks, Raj chi.dat Description: Binary data feff.inp Description: Binary data ___ 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
Re: [Ifeffit] Ifeffit Digest, Vol 189, Issue 8
Thanks for the clarification, Anatoly! Regards, Raj On Fri, Nov 2, 2018 at 4:04 PM 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: EXAFS of wine (Anatoly Frenkel) >2. Re: Ifeffit Digest, Vol 189, Issue 2 (Anatoly Frenkel) > > > -- > > Message: 1 > Date: Fri, 2 Nov 2018 06:36:57 -0400 > From: Anatoly Frenkel > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] EXAFS of wine > Message-ID: <45d3d1e4-6749-463c-9fe3-259b77345...@stonybrook.edu> > Content-Type: text/plain; charset="utf-8" > > John, > > Since when theorists started to need real samples? I thought a simulation > is equally enjoyable. > > Anatoly > > > On Nov 2, 2018, at 12:17 AM, John J Rehr wrote: > > > > Hi everyone > > > > The spectrum is pretty noisy with all the super Tuscano grapes ( > Alicante, Merlot etc) in the mix to give it?s complex berry character and > the 2016 is supposedly better. > > How about we take some samples to the lab ... ? > > > > John > > > > > >> On Thu, Nov 1, 2018 at 16:07 Anatoly Frenkel < > anatoly.fren...@stonybrook.edu> wrote: > >> I thought this mailing list is an appropriate venue to post a picture > of the bottle of wine I bought yesterday in a store on Long Island. > >> > >> > >> > >> Anatoly___ > >> 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 > > ___ > > 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/20181102/b637c308/attachment-0001.html > > > > -- > > Message: 2 > Date: Fri, 2 Nov 2018 09:13:52 -0400 > From: Anatoly Frenkel > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 189, Issue 2 > Message-ID: > Content-Type: text/plain; charset="utf-8" > > If the sample is not homogeneous, it doesn?t matter if you use EXAFS or > XANES spectra, they originate from the same atoms. > > Anatoly > > > On Nov 2, 2018, at 2:39 AM, Raj kumar wrote: > > > > Dear Anatoly and Marcus, > > > > Thanks for your answers. So in this case, i understood, I shouldn't use > the extended XAFS region for the analysis. In the other hand, is it allowed > to cut the region till 9150 eV and use the data for the XANES analysis? > > > > Regards, > > Raj > > > > > >> On Thu, Nov 1, 2018 at 11:37 PM < > 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: Bump/oscillating pattern at high energies of EXAFS > >> (Anatoly Frenkel) > >>2. Re: Bump/oscillating pattern at high energies of EXAFS > >> (Matthew Marcus) > >>3. EXAFS of wine (Anatoly Frenkel) > >> > >> > >>
Re: [Ifeffit] Ifeffit Digest, Vol 189, Issue 2
Dear Anatoly and Marcus, Thanks for your answers. So in this case, i understood, I shouldn't use the extended XAFS region for the analysis. In the other hand, is it allowed to cut the region till 9150 eV and use the data for the XANES analysis? Regards, Raj On Thu, Nov 1, 2018 at 11:37 PM 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: Bump/oscillating pattern at high energies of EXAFS > (Anatoly Frenkel) >2. Re: Bump/oscillating pattern at high energies of EXAFS > (Matthew Marcus) >3. EXAFS of wine (Anatoly Frenkel) > > > -- > > Message: 1 > Date: Thu, 1 Nov 2018 17:47:56 -0400 > From: Anatoly Frenkel > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] Bump/oscillating pattern at high energies of > EXAFS > Message-ID: > < > cafsmozbm2rmvuermuoryw9ehvrzqcvx60zhqufmk39olroy...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > It is an effect of inhomogeneity of the sample, that is, the variation in > the metal density throughout the X-ray beam footprint. > Anatoly > > > > On Thu, Nov 1, 2018 at 5:34 PM Raj kumar wrote: > > > Dear All, > > > > I have monitored the growth process of YbVO4 nanoparticles using EXAFS. > > Here, nanoparticles were synthesized in water medium. Both initial and > > final products (EXAFS) of the synthesis were measured using the > continuous > > flow approach whereas the intermediate products were recorded, in the > glass > > capillary, using the stopped flow. In the attached figure, you can find > the > > same (all products). At high energies of EXAFS, both initial and final > > measurements show smooth behavior whereas the oscillating pattern/bump > was > > observed for the intermediate states. > > > > Here, my question is: Is the oscillating pattern appearing in the > > intermediate states due to the sedimentation/in-homogeneity of the > product > > in the capillary or it is the characteristic of the synthesis? > > > > With regards, > > Raj > > ___ > > 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/20181101/431f9b86/attachment-0001.html > > > > -- > > Message: 2 > Date: Thu, 1 Nov 2018 14:55:12 -0700 > From: Matthew Marcus > To: ifeffit@millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Bump/oscillating pattern at high energies of > EXAFS > Message-ID: > Content-Type: text/plain; charset=utf-8; format=flowed > > Agreed. The low frequency and high amplitude at the end is implausible as > EXAFS. > > Sincerely, > Matthew Marcus > > It is an effect of inhomogeneity of the sample, that is, the variation > in the metal density throughout the X-ray beam footprint. > > Anatoly > > > > > > > > On Thu, Nov 1, 2018 at 5:34 PM Raj kumar rajr...@gmail.com>> wrote: > > > > Dear All, > > > > I have monitored the growth process of YbVO4 nanoparticles using > EXAFS. Here, nanoparticles were synthesized in water medium. Both initial > and final products (EXAFS) of the synthesis were measured using the > continuous flow approach whereas the intermediate products were recorded, > in the glass capillary, using the stopped flow. In the attached figure, you > can find the same (all products). At high energies of EXAFS, both initial > and final measurements show smooth behavior whereas the oscillating > pattern/bump was observed for the intermediate states. > > > > Here, my question is: Is the oscillating pattern appearing in the > intermediate states due to the sedimentation/in-homogeneity of the product > in the capillary or it is the characteristic of
[Ifeffit] Bump/oscillating pattern at high energies of EXAFS
Dear All, I have monitored the growth process of YbVO4 nanoparticles using EXAFS. Here, nanoparticles were synthesized in water medium. Both initial and final products (EXAFS) of the synthesis were measured using the continuous flow approach whereas the intermediate products were recorded, in the glass capillary, using the stopped flow. In the attached figure, you can find the same (all products). At high energies of EXAFS, both initial and final measurements show smooth behavior whereas the oscillating pattern/bump was observed for the intermediate states. Here, my question is: Is the oscillating pattern appearing in the intermediate states due to the sedimentation/in-homogeneity of the product in the capillary or it is the characteristic of the synthesis? With regards, Raj ___ 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
[Ifeffit] In-situ bulk data analysis
Dear All, I am looking for an EXAFS software to handle bulk data and perform both linear combination and regular EXAFS fit. Regards, Raj ___ 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
Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 14
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 > confirmati
[Ifeffit] Problem with large so2: Updated
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 in 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 Description: MS-Word 2007 document ___ 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
Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 3
Hi Scott and Bruce, In continuation with earlier email, here, I am just briefing the observation on the analyzing systems. In my case, reference sample (bulk YbVO4) itself takes large second so2 with huge uncertainty(2.04 +/- 1.36) to get a satisfactory fit. Further, this parameter is found to correlate with ss1 and delc (a parameter to define the movement of atoms in c direction). Among two, the former parameter (ss1) strongly correlate with so2 and take value below 1 and large so2, for using ss1 as fixed and free parameter, respectively. 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. After considering your suggestion and closely look into second so2, i have concluded the following: Since, so2 is used as a normalization parameter and with the available uncertainty, i would consider the obtained number as reasonable value to normalize the unknown to calculate the CN in other systems. Is this good strategy to proceed to calculate the CN? and later to describe the trend on obtained parameters? Regards, Raj On 4 January 2017 at 12:38, <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 2 (Raj kumar) >2. Re: Ifeffit Digest, Vol 167, Issue 2 (Bruce Ravel) >3. Re: Ifeffit Digest, Vol 167, Issue 2 (Raj kumar) > > > ------ > > Message: 1 > Date: Tue, 3 Jan 2017 21:32:51 +0100 > From: Raj kumar <rajr...@gmail.com> > To: ifeffit@millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 2 > Message-ID: > <CACc-a9+uy+4i65LrZf8kiJRk6bdTD2cVSdeeGLp2r0x4fDBrSQ@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Scott, > > Thank you very much for your prompt response. EXAFS measurement was done > after the XRD characterization. From XRD, it is confirmed that there is no > side phase formation and contamination. Hence, i guess the heavier element > role could be avoided here. > > Split distances could be the reason??. The following is the method, i have > opted for modelling the obtained curve. Since YbVO4 is zircon structure, i > have constrained distance in paths 3, 8 and 9 with the pre-structural info > and let other distances vary with regular mathematical expression > alpha*Reff. am i doing wrong here? Before this, I have tried alpha*Reff for > all paths but fit failed miserably for multi-shells. > > Regards, > Raj > > On 3 January 2017 at 19:00, <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: Problem with large so2 (Scott Calvin) > > > > > > -- > > > > Message: 1 > > Date: Tue, 3 Jan 2017 09:59:18 -0600 > > From: Scott Calvin <dr.scott.cal...@gmail.com> > > To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Problem with large so2 > > Message-ID: <3ef5e209-7681-49c6-9713-4bbf34c61...@gmail.edu> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Raj, > > > > I haven?t looked at your files, but the kinds of results you are > > describing often indicate the model you are using beyond the first shell > is > > incorrect. It may be that it has the wrong elements (e.g., heavier > elements > > are
Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 3
Hi Bruce, I agree with your comments. Side phase with less than 5% in total composition cannot be easily detected using regular XRD but comprehensively using EXAFS. Here, i have also recorded bulk sample, similar to nanoparticles composition, which is completely free from contamination. >From this data, i have ruled out the presence of heavy metals. Regards, Raj On 4 January 2017 at 12:38, <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 2 (Raj kumar) >2. Re: Ifeffit Digest, Vol 167, Issue 2 (Bruce Ravel) >3. Re: Ifeffit Digest, Vol 167, Issue 2 (Raj kumar) > > > ------ > > Message: 1 > Date: Tue, 3 Jan 2017 21:32:51 +0100 > From: Raj kumar <rajr...@gmail.com> > To: ifeffit@millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 2 > Message-ID: > <CACc-a9+uy+4i65LrZf8kiJRk6bdTD2cVSdeeGLp2r0x4fDBrSQ@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Scott, > > Thank you very much for your prompt response. EXAFS measurement was done > after the XRD characterization. From XRD, it is confirmed that there is no > side phase formation and contamination. Hence, i guess the heavier element > role could be avoided here. > > Split distances could be the reason??. The following is the method, i have > opted for modelling the obtained curve. Since YbVO4 is zircon structure, i > have constrained distance in paths 3, 8 and 9 with the pre-structural info > and let other distances vary with regular mathematical expression > alpha*Reff. am i doing wrong here? Before this, I have tried alpha*Reff for > all paths but fit failed miserably for multi-shells. > > Regards, > Raj > > On 3 January 2017 at 19:00, <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: Problem with large so2 (Scott Calvin) > > > > > > -- > > > > Message: 1 > > Date: Tue, 3 Jan 2017 09:59:18 -0600 > > From: Scott Calvin <dr.scott.cal...@gmail.com> > > To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Problem with large so2 > > Message-ID: <3ef5e209-7681-49c6-9713-4bbf34c61...@gmail.edu> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Raj, > > > > I haven?t looked at your files, but the kinds of results you are > > describing often indicate the model you are using beyond the first shell > is > > incorrect. It may be that it has the wrong elements (e.g., heavier > elements > > are present than what you modelled) or that the model includes split > > distances when in reality the compound is more symmetric. > > > > In short, no, the high second S02 does not make sense (although it would > > be good to know the uncertainties). > > > > Best, > > Scott Calvin > > Lehman College of the City University of New York > > > > > On Jan 3, 2017, at 9:38 AM, Raj kumar <rajr...@gmail.com> wrote: > > > > > > Dear All, > > > > > > > > > > > > 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 nu
Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 2
Hi Scott, I would like to add an extra point to the previous message. Yes, i am getting a large uncertainty for the second so2 (2.04 +/- 1.36). Regards, Raj On 3 January 2017 at 21:32, Raj kumar <rajr...@gmail.com> wrote: > Hi Scott, > > Thank you very much for your prompt response. EXAFS measurement was done > after the XRD characterization. From XRD, it is confirmed that there is no > side phase formation and contamination. Hence, i guess the heavier element > role could be avoided here. > > Split distances could be the reason??. The following is the method, i have > opted for modelling the obtained curve. Since YbVO4 is zircon structure, i > have constrained distance in paths 3, 8 and 9 with the pre-structural info > and let other distances vary with regular mathematical expression > alpha*Reff. am i doing wrong here? Before this, I have tried alpha*Reff for > all paths but fit failed miserably for multi-shells. > > Regards, > Raj > > On 3 January 2017 at 19:00, <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: Problem with large so2 (Scott Calvin) >> >> >> -- >> >> Message: 1 >> Date: Tue, 3 Jan 2017 09:59:18 -0600 >> From: Scott Calvin <dr.scott.cal...@gmail.com> >> To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] Problem with large so2 >> Message-ID: <3ef5e209-7681-49c6-9713-4bbf34c61...@gmail.edu> >> Content-Type: text/plain; charset="utf-8" >> >> Hi Raj, >> >> I haven?t looked at your files, but the kinds of results you are >> describing often indicate the model you are using beyond the first shell is >> incorrect. It may be that it has the wrong elements (e.g., heavier elements >> are present than what you modelled) or that the model includes split >> distances when in reality the compound is more symmetric. >> >> In short, no, the high second S02 does not make sense (although it would >> be good to know the uncertainties). >> >> Best, >> Scott Calvin >> Lehman College of the City University of New York >> >> > On Jan 3, 2017, at 9:38 AM, Raj kumar <rajr...@gmail.com> wrote: >> > >> > Dear All, >> > >> > >> > >> > 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. From our earlier understanding on the >> synthesis, in some cases, Yb may or may not completely involve in reaction. >> Therefore, I except Yb in two environments, one surrounded by mere oxygen >> (in precise oxygen-Hydrogen; due to disorder one may expect a single peak) >> and another one in YbVO4 environment. With this info and for reasonable >> fit, I have used two so2 as free parameters for N: one for first shell >> (oxygen at two distances) and another for rest other shells. If I use >> single so2, I obtain the value of around 0.92 with unsatisfactory fit >> whereas the fit seems plausible with two so2 i.e., 0.75 and 2.2, >> respectively. Using the same strategy, I could successfully fi! >> t the nanoparticles again with large second so2 (1.79). From literature >> and IFEFFIT earlier discussion, i understood that so2 should be between >> 0.8-1.2 value. Here, I would like to know, does this huge second so2 value >> makes sense? is the obtained so2 value can be used to calculated >> coordination number for unknown? Further, i have attached my worked files >> with this message. >> > >> > >> > >> > Regards, >> > >> > Raj >> > >> > _ >> __ >> > Ifeffit ma
Re: [Ifeffit] Ifeffit Digest, Vol 166, Issue 22
Hi Guanghui, Final particle size of these nanoparticles are about 30-40 nm. Regards, Raj On 23 December 2016 at 19:00, <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: First shell in nps taking small ss than bulk (Zhang, Guanghui) > > > -- > > Message: 1 > Date: Sat, 24 Dec 2016 01:57:12 +0800 (GMT+08:00) > From: "Zhang, Guanghui" <brighto...@126.com> > To: "XAFS Analysis using Ifeffit" <ifeffit@millenia.cars.aps.anl.gov> > Cc: ifeffit <ifeffit@millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] First shell in nps taking small ss than bulk > Message-ID: <5ef8031e.595e.1592cd45fae.coremail.brighto...@126.com> > Content-Type: text/plain; charset="utf-8" > > Raj, > I am wondering if you have TEM or other results suggesting the particle > size of you NPs samples. I looked at your data briefly, and the k-space > data of the bulk and the two NPs samples look identical to me. I suspect > you have big particles which seems "bulk" to EXAFS. > It is my understanding that EXAFS only works well for NPs smaller than > several nanometers if you want to compare N and ss carefully. > > > > Regards, > Guanghui > > > > > > > > > > > > > > On 12/23/2016 09:17? Raj kumar<rajr...@gmail.com>wrote? > > Dear all, > > > I have characterized YbVO4 in bulk (pellet form: prepared through solid > state reaction) and nanoparticles (using continuous flow: prepared through > co-precipation process) forms. Surprisingly, i found out that First shell > Yb-O in nanoparticles takes small ss value (0.00298; YbVO4nps-1.fpj) than > bulk (0.00509; YVO4bulk.fpj), while rest other shells in nanoparticles > found to take large ss compared to bulk. One would expect later trend for > all shells than former one due to well ordered and compact nature of bulk > YbVO4 phase. Owing to this weird trend, i returned back to R-space for > qualitative inspection (YbVO4.prj), there i found, wider R-space signal for > (all shells) all YbVO4 nanoparticles compared to bulk. This behavior is > also well supporting to my rationalized understanding. Could someone please > help me in understanding the obtained result? or if i am missing some > important point, please warn me. For more clarification, i have attached > the athena and artemis files for the ! > same. > > > With regards, > Raj > -- next part -- > An HTML attachment was scrubbed... > URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/ > attachments/20161224/ced748b2/attachment-0001.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 166, Issue 22 > > ___ 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
Re: [Ifeffit] Ifeffit Digest, Vol 166, Issue 12
Hi Bruce, Thanks for the explanation. Yes, both files are generating the same kind of output but the positioning of atoms can mislead in the context of structure. That's why i have raised the question. Regards, Raj On 16 December 2016 at 16:48, <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. Web Atoms 1.8 vs Demeter 0.9.26: feff output are not same > (Raj kumar) >2. Re: Web Atoms 1.8 vs Demeter 0.9.26: feff output are not same > (Bruce Ravel) > > > ---------- > > Message: 1 > Date: Fri, 16 Dec 2016 16:34:32 +0100 > From: Raj kumar <rajr...@gmail.com> > To: ifeffit@millenia.cars.aps.anl.gov > Subject: [Ifeffit] Web Atoms 1.8 vs Demeter 0.9.26: feff output are > not same > Message-ID: > <CAAW7+QO1uSwLVz2m8pRpAsZisFVpheU3=gD > bsggjebszbbe...@mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear All, > > Recently, i found out that feff.inp generated by web atoms and Demeter > 0.9.26 are not the same. My main worry is in the position of atoms. For > evidence, i am attaching YbVO4 (*feff.inp*) files generated by both web > atoms and Demeter. With this kind of zircon type structure, one would > except V1_2 at position *x/2+c/4* (3.85250). In web atoms generated file, i > could see this relation clearly, while in Demeter generated file the > relation reads like *x/2+y/2+c/4* instead of earlier condition. > Furthermore, all atoms (except few) are represented with three coordinated > position for Demeter generated file instead of two coordinated position. > > I already posted this query in the ifeffit mailing domain but the message > was not get circulated. Hence, I writing this problem to you. > > With regards, > Raj > -- next part -- > An HTML attachment was scrubbed... > URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/ > attachments/20161216/6d9ca788/attachment-0001.html> > -- next part -- > A non-text attachment was scrubbed... > Name: YbVO4-Web atoms_1.8.inp > Type: application/octet-stream > Size: 7570 bytes > Desc: not available > URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/ > attachments/20161216/6d9ca788/attachment-0002.obj> > -- next part -- > A non-text attachment was scrubbed... > Name: YbVO4-Demeter.inp > Type: application/octet-stream > Size: 7415 bytes > Desc: not available > URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/ > attachments/20161216/6d9ca788/attachment-0003.obj> > > -- > > Message: 2 > Date: Fri, 16 Dec 2016 10:48:38 -0500 > From: Bruce Ravel <bra...@bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Web Atoms 1.8 vs Demeter 0.9.26: feff output > are not same > Message-ID: <584b756d-7c2b-8377-a2ff-5a023218f...@bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 12/16/2016 10:34 AM, Raj kumar wrote: > > Recently, i found out that feff.inp generated by web atoms and Demeter > > 0.9.26 are not the same. My main worry is in the position of atoms. For > > evidence, i am attaching YbVO4 (*feff.inp*) files generated by both web > > atoms and Demeter. With this kind of zircon type structure, one would > > except V1_2 at position *x/2+c/4* (3.85250). In web atoms generated > > file, i could see this relation clearly, while in Demeter generated file > > the relation reads like *x/2+y/2+c/4* instead of earlier condition. > > Furthermore, all atoms (except few) are represented with three > > coordinated position for Demeter generated file instead of two > > coordinated position. > > > > Hi Raj, > > I don't acknowledge that there is a problem. It is certainly true that > the two files have the atoms list rotated by 45 degrees relative to one > another, but all the distances are the same. Although I only > investigated at the level of running feff on each one and examining the > fi
[Ifeffit] Web Atoms 1.8 vs Demeter 0.9.26: feff output are not same
Dear All, Recently, i found out that feff.inp generated by web atoms and Demeter 0.9.26 are not the same. My main worry is in the position of atoms. For evidence, i am attaching YbVO4 (*feff.inp*) files generated by both web atoms and Demeter. With this kind of zircon type structure, one would except V1_2 at position *x/2+c/4* (3.85250). In web atoms generated file, i could see this relation clearly, while in Demeter generated file the relation reads like *x/2+y/2+c/4* instead of earlier condition. Furthermore, all atoms (except few) are represented with three coordinated position for Demeter generated file instead of two coordinated position. I already posted this query in the ifeffit mailing domain but the message was not get circulated. Hence, I writing this problem to you. With regards, Raj YbVO4-Web atoms_1.8.inp Description: Binary data YbVO4-Demeter.inp Description: Binary data ___ 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
[Ifeffit] Peak at short distance in FT - YbVO4 nanoparticles
Dear All, Recently, i have performed EXAFS for YbVO4 bulk (prepared through sintering process) and nanoparticles (at room temperature). Nanoparticles were synthesized by co-precipitation technique and their EXAFS was measured by passing the prepared solution using peristaltic pump. After all subtraction (background and solvent), nanoparticles XAS data were recovered and processed for the fitting. After Fourier transform, it was observed that both nanoparticles posses an additional short peak (or shoulder) at about 1.2 A from bulk. Since the peak appears much closer to 1 A, i suspect this may due to artifact or bad background subtraction. Hence, i would like to know the way to eliminate this peak at short distance. Regards, Raj YbVO4-29-5-15.prj Description: Binary data ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] Ifeffit Digest, Vol 147, Issue 20
Hi Bruce, The comments are very helpful to assure my data processing and for future experiments. Yes, all measurements were obtained in Dispersive EXAFS mode. As for i know (at least until my preparation time) the bulk sample (first one) doesn't contain the Hf impurities. However, i will double check that point. Regards, Raj On Fri, May 29, 2015 at 7:00 PM, 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: Peak at short distance in FT - YbVO4 nanoparticles (Bruce Ravel) -- Message: 1 Date: Fri, 29 May 2015 12:52:38 -0400 From: Bruce Ravel bra...@bnl.gov To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Peak at short distance in FT - YbVO4 nanoparticles Message-ID: 55689956.8040...@bnl.gov Content-Type: text/plain; charset=windows-1252; format=flowed On 05/29/2015 11:54 AM, Raj kumar wrote: Recently, i have performed EXAFS for YbVO4 bulk (prepared through sintering process) and nanoparticles (at room temperature). Nanoparticles were synthesized by co-precipitation technique and their EXAFS was measured by passing the prepared solution using peristaltic pump. After all subtraction (background and solvent), nanoparticles XAS data were recovered and processed for the fitting. After Fourier transform, it was observed that both nanoparticles posses an additional short peak (or shoulder) at about 1.2 A from bulk. Since the peak appears much closer to 1 A, i suspect this may due to artifact or bad background subtraction. Hence, i would like to know the way to eliminate this peak at short distance. Hi Raj, A few comments: 1. Your bulk sample (the first one in the list) may have a bit of Hf in it it. It's hard to tell, but the mu(E) seems to be trending upward right at the end of the data, which is the approximate edge energy of Hf L3. I got a slightly better background removal by changing the end of the spline range to 600. But this a minor detail. The real story seems to be that 2. You data are pretty noisy. If you plot chi(R) out to 10 Angstroms (which is, presumably, well beyond where you should expect to see good signal in your data), you get a sense of how the level of noise manifests itself in chi(R). To my eye, the peak/shoulder at about 1.2 that you are asking about is of about the same size as the level of noise in your data. You are asking how to get rid of a feature in the data that is aesthetically unpleasing. I don't think that's the right question. Your data are what they are. Your data are noisy and measured over a rather short energy range. That doesn't give you a lot of choices about how aesthetically appealing you can make the Fourier transform be. You seem to be operating Athena correctly and there aren't any magic buttons that will make your short, noisy data longer or less noisy. I don't see anything obviously wrong in how you are processing your data and -- short of using PhotoShop ;) -- I don't see any defensible way of making the feature at 1.2 go away. Am I correct in thinking that these data are measured in the dispersive geometry? If so, my suggestion is to reconsider how you make your samples. This kind of experiment is VERY sensitive to the homogeneity of the sample. You have to take extraordinary care to make your samples as homogeneous as possible. I suspect most of the glitchy little points in your data are indicative of sample inhomogeneity. You also should worry about purity of your source material. Granted, it canbe very difficult to obtain rare earth metal samples that are elementally pure. But if your data range is short because of other edges, then you need samples that are more pure. HTH, B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ -- ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest
[Ifeffit] (D)Artemis shutting down automatically
Dear All, Recently, i have faced automatic shutting down of artemis during the import of chi file. For more clarification, please see the first log file. Also, i observed emptying of .fpj files. This happens during the saving of old .apj to .fpj or/and during the frequent saving of .fpj files after .apj conversion. Please see the second log file for this problem. Regards, Raj dartemis.log Description: Binary data dartemis.log Description: Binary data ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
