December 2016 - Ifeffit - millenia.cars.aps.anl.gov

error when fitting in Artemis
by George Sterbinsky 06 Jan '17

06 Jan '17

Hello, 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? Thank you, George

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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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Problems with gnuplot graphics on Mac OS 10.12.1
by Paul Fons 09 Dec '16

09 Dec '16

Hi All, I just wanted to give an update to my earlier problems with the mysterious gnuplot errors. After editing the file Matt mentioned earlier, I decided to uninstall and install demeter to no avail. I then realized that I had been relying on the latest version of xquartz (the x11 system) and installed x11 using macports. After a bit of trouble with installation (I had to break the installation into pieces — but this is a typical macports problem), the x11 installation completed and athena worked fine. Thus my conclusion is that there was some sort of weird interference between x11 subsystems. In any case, all is well now.

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Peakfitting CeO2 data in Athena
by Stephanie Laga 08 Dec '16

08 Dec '16

Dear all, I am trying to extract the % Ce(III) from some CeO2 nanoparticle XAS data. I have been using moved the peak fitting function in Athena to model the XANES with an arctan background function and a series of gaussians. Looking through the literature I haven't seen too many specifics to using this approach (rationale for choosing the widths of peaks or how to define the background function). Similarly, doesn't seem to be much rationale for choosing a 4 vs 5 peak fit for the XANES. My main question is then...1) Is there a rational for picking the background function, specifically the height and width (can I let the height vary or should I be keeping a constant arctan through all samples)? Any advice is greatly appreciated! Stephanie

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error on installing demeter on MacOSX 10.11.6
by Valerio Scagnoli 07 Dec '16

07 Dec '16

Dear all, I was trying to install demeter on my Mac with mac port and the installation seemed to run smoothly (after following the advice on the installation page!). However, when I try to start Athena from the command line I get the following error message: bash-3.2$ athena IO::Compress::Base::Common version 2.069 required--this is only version 2.015 at /opt/local/lib/perl5/vendor_perl/5.24/Compress/Zlib.pm line 10, <DATA> line 1. BEGIN failed--compilation aborted at /opt/local/lib/perl5/vendor_perl/5.24/Compress/Zlib.pm line 10, <DATA> line 1. Compilation failed in require at /opt/local/lib/perl5/site_perl/5.24/darwin-thread-multi-2level/Demeter/Files.pm line 27, <DATA> line 1. BEGIN failed--compilation aborted at /opt/local/lib/perl5/site_perl/5.24/darwin-thread-multi-2level/Demeter/Files.pm line 27, <DATA> line 1. Compilation failed in require at /opt/local/lib/perl5/vendor_perl/5.24/Module/Runtime.pm line 317, <DATA> line 1. Compilation failed in require at /opt/local/lib/perl5/site_perl/5.24/darwin-thread-multi-2level/Demeter/UI/Athena.pm line 24, <DATA> line 1. BEGIN failed--compilation aborted at /opt/local/lib/perl5/site_perl/5.24/darwin-thread-multi-2level/Demeter/UI/Athena.pm line 24, <DATA> line 1. Compilation failed in require at /opt/local/bin/athena line 27, <DATA> line 1. BEGIN failed--compilation aborted at /opt/local/bin/athena line 27, <DATA> line 1. I tried to install the following zlib packages and uninstall/reinstall demeter, but the error still remains. bash-3.2$ port installed |grep zlib p5.24-compress-raw-zlib @2.69.0_0 (active) zlib @1.2.8_0+universal (active) I have the following perl package installed bash-3.2$ port installed |grep perl p5.24-libwww-perl @6.150.0_0+ssl (active) p5.24-perl-ostype @1.10.0_0 (active) p5.24-perlio-layers @0.11.0_0 (active) p5.24-perlio-utf8_strict @0.6.0_0 (active) perl5 @5.24.0_0+perl5_24 (active) perl5.24 @5.24.0_0+universal (active) Any help will be appreciated. Valerio Scagnoli

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