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

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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error install Demeter
by Maria Rosa BECCIA 07 Dec '16

07 Dec '16

Hello, I tried to install Demeter on my Macbook OS El Capitan (version 10.11.6), but when typing the "sudo port install xors-server demeter” line, it gives me an error. You can find the error lines in the attached file. Thank you in advance for your help. Kind regards, Maria Rosa Beccia Maria Rosa BECCIA Maître de conférences Institut de Chimie de Nice Université Côte d'Azur UMR 7272 28 Avenue Valrose 06108 Nice, France phone: +33 (0)4 92 07 63 71

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problems installing athena et al under ubuntu 16.04 LTS
by Juan de la figuera 02 Dec '16

02 Dec '16

Dear all, I have been installing demeter from git under ubuntu 16.04 LTS, following the non-root instructions from: https://gist.github.com/waveform80/3959252 I also installed xraylarch from git. Xaylarch is only missing: #=== Warning: Some recommended Python Packages are missing: epics: needed for using the EPICS control system pyFAI: needed for xrd modules It seems to work, but when I try to open a file that can be open properly from Athena installed on Windows, I get: Trying Larch server: /home/juan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/share/ini/larch_server.ini Trying Larch server: larch_server -p 4968 start larch_server port=4968: started gnuplot> set xrange [ 6900130000 : 7955610000 ] ^ line 0: warning: integer overflow; changing to floating point gnuplot> set xrange [ 6900130000 : 7955610000 ] ^ line 0: warning: integer overflow; changing to floating point and although it opens the data in a gnuplot window, the scale is off (7x10^9 instead of 7x10^3). I am assuming once it is confused about the scale, it makes a mess with the data. The output of probe -bv is: t/000_ifeffit.t ......... 1..6 ok 1 - show ok 2 - show arrays: ok 3 - get_scalar 1.2345 ok 4 - put scalar ok 5 - put/get_string: my.xmu ok 6 - put/get_array: ok t/001_base.t ............ 1..24 Trying Larch server: /home/juan/soft/demeter/blib/lib/Demeter/share/ini/larch_server.ini Trying Larch server: larch_server -p 4969 start larch_server port=4969: started ok 1 - new() works ok 2 - group is set: orihs ok 3 - unique group names: orihs & bcxkm ok 4 - installation location identified ok 5 - identity string ok 6 - generic object is not plottable ok 7 - generic object has no data ok 8 - Project role works ok 9 - demeter can do introspection ok 10 - ifeffit disposal mode flag: 1 ok 11 - handle unknown mode gracefully ok 12 - other disposal modes all false ok 13 - turn on screen disposal mode flag ok 14 - turn on file disposal mode flag ok 15 - turn on buffer disposal mode flag ok 16 - unknown window not recognized ok 17 - known element (Cu) is recognized ok 18 - unknown element (Ci) not recognized ok 19 - simple template works not ok 20 - simple disposal to Ifeffit: string # Failed test 'simple disposal to Ifeffit: string' # at t/001_base.t line 69. not ok 21 - simple disposal to Ifeffit: scalar # Failed test 'simple disposal to Ifeffit: scalar' # at t/001_base.t line 70. Use of uninitialized value in numeric eq (==) at t/001_base.t line 71. not ok 22 - simple disposal to Ifeffit: array # Failed test 'simple disposal to Ifeffit: array' # at t/001_base.t line 71. ok 23 - simple disposal wrapper works ok 24 - plot_with works # Looks like you failed 3 tests of 24. Any help would be appreciated. Juan

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