- Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 3
by Raj kumar 05 Jan '17

05 Jan '17

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-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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 <rajrk37(a)gmail.com> > To: ifeffit(a)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-request(a)millenia.cars.aps.anl.gov> > wrote: > > > Send Ifeffit mailing list submissions to > > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > > > You can reach the person managing the list at > > ifeffit-owner(a)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.calvin(a)gmail.com> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Problem with large so2 > > Message-ID: <3EF5E209-7681-49C6-9713-4BBF34C619A5(a)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 <rajrk37(a)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 > > > > > > <YbVO4-bulk.fpj><YbVO4-nps.fpj>_____________________________ > > __________________ > > > Ifeffit mailing list > > > Ifeffit(a)millenia.cars.aps.anl.gov > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > >

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Calculation of SPOIL value for the reconstruction of standard spectra
by Montarges-pelletier Emmanuelle 04 Jan '17

04 Jan '17

" <ifeffit(a)millenia.cars.aps.anl.gov> Content-Transfer-Encoding: quoted-printable Mime-Version: 1.0 (1.0) Dear all I have performed PCA on a set of 13 XAS spectra, and tried to validate the m= odel compounds or standards using the Target Transform function on ATHENA (d= emeter 09.22). I could get the TT coefficients for every standard. Is there a simple way to calculate the SPOIL value from the Target Transform= coefficients?=20 Indeed, although graphics can be used to demonstrate that such and such stan= dard are relevant to fit experimental data, SPOIL values are often reported .= Thanks in advance for your answer Best regards and Best wishes for 2017. =E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80= =A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2= =80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2= =E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80= =A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2 Emmanuelle Montarges-Pelletier CNRS universit=C3=A9 de lorraine 0631331030 Emmanuelle.montarges(a)univ-lorraine.fr=

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Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 2
by Raj kumar 04 Jan '17

04 Jan '17

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-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Problem with large so2 > Message-ID: <3EF5E209-7681-49C6-9713-4BBF34C619A5(a)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 <rajrk37(a)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 > > > > <YbVO4-bulk.fpj><YbVO4-nps.fpj>_____________________________ > __________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > >

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Problem with large so2
by Raj kumar 03 Jan '17

03 Jan '17

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 fit 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

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Re: [Ifeffit] Ifeffit Digest, Vol 166, Issue 22
by Raj kumar 23 Dec '16

23 Dec '16

Hi Guanghui, Final particle size of these nanoparticles are about 30-40 nm. Regards, Raj On 23 December 2016 at 19:00, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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" <brighton30(a)126.com> > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Cc: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] First shell in nps taking small ss than bulk > Message-ID: <5ef8031e.595e.1592cd45fae.Coremail.brighton30(a)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<rajrk37(a)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 >

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First shell in nps taking small ss than bulk
by Raj kumar 23 Dec '16

23 Dec '16

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

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Re: [Ifeffit] Ifeffit Digest, Vol 166, Issue 12
by Raj kumar 22 Dec '16

22 Dec '16

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-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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 <rajrk37(a)gmail.com> > To: ifeffit(a)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 > bsGgJebSZbbewpQ(a)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 >

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open 2-year postdoc position in X-ray spectroscopy and environmental geochemistry
by Voegelin, Andreas 20 Dec '16

20 Dec '16

Dear all We are looking for a postdoctoral fellow for a 2-year collaboration project between the Paul Scherrer Institute (PSI) and the Swiss Federal Institute of Aquatic Science and Technology (Eawag) in the fields of X-ray spectroscopy and environmental geochemistry. The tasks of the postdoctoral researcher are: - Setting up a cryostat system at the microXAS beamline at the Swiss Light Source for microspectroscopic analyses of radiation- and redox-sensitive environmental samples. - Perform micro-XRF/XAS/XRD studies on the microscale distribution and speciation of thallium and its association with various host phases in environmental samples. For further information see https://www.psi.ch/pa/job-opportunities/1444 or attachment. Please feel free to forward this information to potential candidates. Best regards, Andreas °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° Andreas Voegelin, PhD Eawag - Swiss Federal Institute of Aquatic Science and Technology Ueberlandstrasse 133, CH-8600 Duebendorf, Switzerland Tel: +41 58 765 54 70 Fax: +41 58 765 52 10 mailto:andreas.voegelin@eawag.ch http://www.eawag.ch/~voegelan

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E0 problem
by Fuxiang Zhang 19 Dec '16

19 Dec '16

Hi, All I have a problem about E0. It seems that E0 has great effect on the R(x) and the fitting. Can anyone explain how Athena automatically find the E0 value from an EXAFS spectrum. Sometimes the value is not at the peak of derivative of u(E), shall it be corrected manually? Thanks Fuxiang Zhang

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Web Atoms 1.8 vs Demeter 0.9.26: feff output are not same
by Raj kumar 16 Dec '16

16 Dec '16

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

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