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

EXAFS of wine
by Anatoly Frenkel 02 Nov '18

02 Nov '18

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

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Postdoc Opportunity in Catalysis Science at SSRL
by Bare, Simon R 01 Nov '18

01 Nov '18

Please see the attached postdoctoral positon available now at SSRL. It is also posted here: https://careers.slac.stanford.edu/sites/careers.slac.stanford.edu/files/Pos… Thanks! Simon R Bare Distinguished Staff Scientist SSRL, MS69 SLAC National Accelerator Lab 2575 Sand Hill Road Menlo Park CA 94025 simon.bare(a)slac.stanford.edu<mailto:simon.bare@slac.stanford.edu> Ph: 650-926-2629 [co_access_logo_text]

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Bump/oscillating pattern at high energies of EXAFS
by Raj kumar 01 Nov '18

01 Nov '18

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

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Problem with Athena
by Weronica Linpé 30 Oct '18

30 Oct '18

Hi, I have a problem when looking at the difference scan between two scans. When I move from the start up site to the differnece everything works fine and I get a differnece spectra. Here I can do some changes, but if I want to change which scans I'm using for the difference the program chrashes. Any ideas on why the program chrashes?

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ADDITION - Bug Report: incomplete data import in Athena when energy is given in keV
by Voegelin, Andreas 30 Oct '18

30 Oct '18

Dear Bruce & Ifeffit Mail-List We just found that the problem I described in my previous email for Demeter 0.9.26 does not occur with version 0.9.25. Thus, reinstalling the previous version seems the easiest work around for the moment. Best, Andreas

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Re: [Ifeffit] Bug Report: incomplete data import in Athena when energy is given in keV
by Kirill Lomachenko 26 Oct '18

26 Oct '18

Dear Bruce and dear all, I have the same problem with data import in Athena 0.9.26 that Andreas has just described and that, if I am not mistaken has already been mentioned in this mailing list before. Looking for the possible cause of the problem, in the list of changes made for Athena in the latest version of Demeter I found the following: "Fix a problem processing keV data when using Larch (Thanks to Juan de la Figuera) (See issue #42)" May it be that these modifications are responsible for the observed import bug? (just a guess) Thank you Kirill Dr. Kirill A. Lomachenko Scientist at BM23/ID24 beamlines European Synchrotron Radiation Facility (ESRF) 71 avenue des Martyrs CS 40220 38043 Grenoble Cedex 9, France Tel: +33 438 88 19 14 www.esrf.eu 25.10.2018 11:40, ifeffit-request(a)millenia.cars.aps.anl.gov пишет: > 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. Bug Report: incomplete data import in Athena when energy is > given in keV (Voegelin, Andreas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 25 Oct 2018 09:39:52 +0000 > From: "Voegelin, Andreas" <Andreas.Voegelin(a)eawag.ch> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Bug Report: incomplete data import in Athena when > energy is given in keV > Message-ID: > <D87798881B7774448873557DA6961A35F019A176(a)EE-MBX3.ee.emp-eaw.ch> > Content-Type: text/plain; charset="utf-8" > > Dear Bruce & Ifeffit Mail-List > > Working with Athena (executable Version 0.9.26 with Ifeffit 1.2.12 on Windows 10), I just noted a problem with data import when energy in the input file is given in keV. > > Attached an example of recently collected Ce L3 edge data (original_format.txt), with the energy in keV in the first column and the DT-corrected and normalized fluorescence signal in column 44. The file contains 2 header rows and 308 lines of data. When this spectrum is loaded into Athena, it consists of only 186 instead of 308 datapoints (see information on spectrum ?original_format,.txt? in Athena project file ?test_bug_data_import_in_keV.prj?). The problem also persisted when I reduced the input file to only two columns, energy and fluorescence data, and seemed not related to file size. The problem occurs on various computers all running with the latest version of Athena. > > Interestingly, the problem does not occur if the energy in the original file is given in eV instead of keV. From the original file, I created an input file ?test_energy_in_keV_eV.txt? in which columns 1 and 4 contain the energy in keV and columns 2 and 5 the energy in eV. When I import the spectrum using any of the columns with energy in eV, the spectrum is loaded correctly and consist of 308 datapoints. If I use any of the two columns with energy in keV, the imported spectrum again contains only 186 datapoints. > > Comparing the mue output files of the spectra read in eV and keV (mue files attached), one can see that incomplete data import starts at 5703 eV, i.e., where the step size in the scan was changed from 2 eV to 0.5 eV. Notably, if I select column 5 containing the energy in eV, but tell Athena that the energy is in keV and needs to be converted to eV, Athena loads all 308 datapoints (although with obviously wrong energy scale). This might suggest that the problem is related to the absolute difference in energy between datapoints rather than to the conversion from keV to eV. > > I tested also other data collected at the Mn K and Tl L3 edges and the problem is the same. > > For the moment, the easiest work-around may be to reprocess all input files by adding a column with energy in eV. If an easy fix could be found for correct data import in Athena, however, this would be helpful. > > 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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Bug Report: incomplete data import in Athena when energy is given in keV
by Voegelin, Andreas 25 Oct '18

25 Oct '18

Dear Bruce & Ifeffit Mail-List Working with Athena (executable Version 0.9.26 with Ifeffit 1.2.12 on Windows 10), I just noted a problem with data import when energy in the input file is given in keV. Attached an example of recently collected Ce L3 edge data (original_format.txt), with the energy in keV in the first column and the DT-corrected and normalized fluorescence signal in column 44. The file contains 2 header rows and 308 lines of data. When this spectrum is loaded into Athena, it consists of only 186 instead of 308 datapoints (see information on spectrum “original_format,.txt” in Athena project file “test_bug_data_import_in_keV.prj”). The problem also persisted when I reduced the input file to only two columns, energy and fluorescence data, and seemed not related to file size. The problem occurs on various computers all running with the latest version of Athena. Interestingly, the problem does not occur if the energy in the original file is given in eV instead of keV. From the original file, I created an input file “test_energy_in_keV_eV.txt” in which columns 1 and 4 contain the energy in keV and columns 2 and 5 the energy in eV. When I import the spectrum using any of the columns with energy in eV, the spectrum is loaded correctly and consist of 308 datapoints. If I use any of the two columns with energy in keV, the imported spectrum again contains only 186 datapoints. Comparing the mue output files of the spectra read in eV and keV (mue files attached), one can see that incomplete data import starts at 5703 eV, i.e., where the step size in the scan was changed from 2 eV to 0.5 eV. Notably, if I select column 5 containing the energy in eV, but tell Athena that the energy is in keV and needs to be converted to eV, Athena loads all 308 datapoints (although with obviously wrong energy scale). This might suggest that the problem is related to the absolute difference in energy between datapoints rather than to the conversion from keV to eV. I tested also other data collected at the Mn K and Tl L3 edges and the problem is the same. For the moment, the easiest work-around may be to reprocess all input files by adding a column with energy in eV. If an easy fix could be found for correct data import in Athena, however, this would be helpful. 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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the meaing of "beta=125.264" in path interpretation
by woschangqiang＠126.com 19 Oct '18

19 Oct '18

Dear, Firstly, i'm very grateful for the useful responses from Bruce Ravel and Matt Newville on my previous question. Now, I have another question about path. The screenshot below is the interpretation of a path in α-Fe. I was wondering what does "beta" means. Is that scattering angle? I tentatively construct a triangle according to the rleg values, and find that the three angles are consistent with the beta values. What does this mean? I searched the Artemis user guild and the mailing list, but could not find the answers. Do you have any ideas? Thanks in advance Qiang Chang Institute of Coal Chemistry, CAS Leyuan South II Street 1, Yanqi Development Zone Huairou District, Beijing, POB. 101407 P.R. China

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Re: [Ifeffit] Ifeffit Digest, Vol 188, Issue 14
by Joanna Kowalska 19 Oct '18

19 Oct '18

>From Ben I will send On 19 Oct 2018 16:25, <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. the meaing of "beta=125.264" in path interpretation (woschangqiang(a)126.com) ---------------------------------------------------------------------- Message: 1 Date: Fri, 19 Oct 2018 22:22:30 +0800 From: "woschangqiang(a)126.com" <woschangqiang(a)126.com> To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] the meaing of "beta=125.264" in path interpretation Message-ID: <201810192222293624981(a)126.com> Content-Type: text/plain; charset="gb2312" Dear, Firstly, i'm very grateful for the useful responses from Bruce Ravel and Matt Newville on my previous question. Now, I have another question about path. The screenshot below is the interpretation of a path in ?-Fe. I was wondering what does "beta" means. Is that scattering angle? I tentatively construct a triangle according to the rleg values, and find that the three angles are consistent with the beta values. What does this mean? I searched the Artemis user guild and the mailing list, but could not find the answers. Do you have any ideas? Thanks in advance Qiang Chang Institute of Coal Chemistry, CAS Leyuan South II Street 1, Yanqi Development Zone Huairou District, Beijing, POB. 101407 P.R. China

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Athena problem
by Elien Lemmens 18 Oct '18

18 Oct '18

Dear, I was trying to do some linear combination fitting using Athena software. Although the box "All weight between 0 and 1" is ticked I get negative weight results. I have read the online Athena's User's Guide, but I did not find what the issue can be. Do you have any ideas? Below you can find some print screens of my actions. I also get an "error" (print screen 2), which I don't understand. Thanks in advance Elien [cid:image001.jpg@01D46703.6DC31010] [cid:image002.png@01D46703.6DC31010] [cid:image003.png@01D46703.6DC31010]

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difference of feff interpretation generated by different version of artemis
by woschangqiang＠126.com 17 Oct '18

17 Oct '18

Hello, everyone. I recently ran into an issue in using Artemis software. I used two versions of Artemis (Artemis 0.8.012 and Demeter 0.9.25) to generate the paths from the same input file (FeS2.inp), but there is big difference between the two path results. e.g. 1, the path4 and path6 generated in Demeter 0.9.25 are not generated in Artemis 0.8.012, though they have a very low applitude. e.g. 2, the path7 in Demeter 0.9.25 is likely identical to path5 in Artemis 0.8.012 judging from the degenracy, reff, and amplitude, but their scattering name are different: (+)-S1-S2-(+) in Demeter 0.9.25 and (+)-S2-S1-(+) in Artemis 0.8.012. In my opinion, the scattring sequence of photoelectron in multiple scattering affect the paramters of paths. Why do these two paths have different scattering sequence? Thanks very much for your help. Qiang Chang Institute of Coal Chemistry, CAS Leyuan South II Street 1, Yanqi Development Zone Huairou District, Beijing, POB. 101407 P.R. China Email: woschangqiang(a)163.com

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restraints in larch
by Barbara Etschmann 12 Oct '18

12 Oct '18

Hello I'm trying to use larch to refine the coordination of Y in solution. I need to use 2xO paths to fit the first shell and would like to restrain the total coordination to be between 5.5 and 8. I can apply the constraint to each nO, but not the total, i.e. nO1 = param(7.0, min=5, max=7, vary=True), nO2 = param(1, vary=True), but ntot1 = param(expr='nO1+nO2', min=5.0, max=8.5) does not work. How can I restrain the total coordination? Also, having some problems with the gofs and errors - the chi square is rather small and often the errors are not reported and it is not clear why. Thanks Barb

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Better late than never
by Anatoly Frenkel 10 Oct '18

10 Oct '18

After 15 years or so of using Athena, I just accidentally learned that the vertical scale of the plot can be changed by simply turning the scroll wheel of the mouse! Anatoly

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Larch: GSE Mapviewer export error
by Naomi Intrator 06 Oct '18

06 Oct '18

Hello I made correlation plots in the GSE Mapviewer and am trying to export the data. When I click file, export data. I get an error that says 'Export Data to ASCII: Export Data not available" I have tried to do this on both a Mac and Windows. Has anyone else encountered this and know a way around it? Thank you, Naomi

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Re: [Ifeffit] Port p5.26-ifeffit not installing via MacPorts on Yosemite
by Fowler, Joseph W. (Assoc) 17 Sep '18

17 Sep '18

Dear Sergio, Thanks for the alert. I’m the official MacPorts maintainer of ifeffit, but I must make my usual warning: I am very experienced with Unix and Linux in general, but I know practically nothing about Perl and don’t really understand MacPorts. (If anyone reading this has the qualifications and the willingness to replace me as maintainer of ifeffit and demeter, we need to talk!) I have been trying for months—and failing—to get Demeter version 0.9.26 to build on my Mac, which gives you a sense of my competence for this job. Anyway, to the topic at hand. Thank you for including the log file. It looks clear to me that your linker is not finding a gfortran run-time library. You might lack the library on your system, or the library is simply not listed among the link options in your compile command. fowlerj@817jfmac:~$ port installed g95 The following ports are currently installed: g95 @0.93_5 (active) fowlerj@817jfmac:~$ port installed gcc7 The following ports are currently installed: gcc7 @7.3.0_3 (active) fowlerj@817jfmac:~$ port installed p5.26-ifeffit The following ports are currently installed: p5.26-ifeffit @1.2.13_0+gcc7 (active) fowlerj@817jfmac:~$ port installed ifeffit The following ports are currently installed: ifeffit @1.2.13_5+gcc7 (active) fowlerj@817jfmac:~$ port ech depof:ifeffit gcc7 libgcc libgcc7 libpng ncurses pgplot xorg-libX11 Do you have the package g95 (a FORTRAN compiler) installed? You can see (above) that I have it, but it’s not a listed dependency of ifeffit. Why don’t you try installing it (“sudo port install g95”) and then clean and install first the package ifeffit, then p5.26-ifeffit. If that works, then it means we should add g95 as a dependency for ifeffit (or p5.26-ifeffit). If it doesn’t work, then at least you might gather more clues. Best wishes, Joe Fowler On Sep 16, 2018, at 3:42 PM, ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov> wrote: Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov> To subscribe or unsubscribe via the World Wide Web, visit https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.ca… 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. Port p5.26-ifeffit not installing via MacPorts on Yosemite (Sergio Tatay) From: Sergio Tatay <sergio.tatay(a)uv.es> Subject: [Ifeffit] Port p5.26-ifeffit not installing via MacPorts on Yosemite Date: September 16, 2018 at 3:12:52 PM MDT To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Hi everybody, I’ve been trying to install Demeter package on MacOS using MacPorts. All the dependencies seem to install smoothly but for p5.26-iffefit. During port install I’ve got the following error: ---> Computing dependencies for demeter The following dependencies will be installed: p5.26-ifeffit Continue? [Y/n]: Y ---> Building p5.26-ifeffit Error: Failed to build p5.26-ifeffit: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/main.log for details. Error: Follow https://guide.macports.org/#project.tickets to report a bug. Error: Processing of port demeter failed I've pasted below an extract of the log file and attached the complete file to this mail. I’m completely newbie and I will be very grateful if someone could help me to get the problem solved. Thanks very much in advance, Sergio -LOG FILE- version:1 :debug:sysinfo OS X 10.10 (darwin/14.5.0) arch i386 :debug:sysinfo MacPorts 2.5.3 :debug:sysinfo Xcode 7.2.1 :debug:sysinfo SDK 10.10 :debug:sysinfo MACOSX_DEPLOYMENT_TARGET: 10.10 … …. :info:build /opt/local/lib/perl5/5.26/darwin-thread-multi-2level/CORE/libperl.dylib -L/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/work/ifeffit-1.2.final/wrappers/perl/../../src/lib -L/opt/local/lib -Wl,-headerpad_max_install_names -lifeffit -L/opt/local/lib -lpgplot -lpng -lX11 -L/opt/local/lib -lSystem -lm \ :info:build :info:build Undefined symbols for architecture x86_64: :info:build "__gfortran_compare_string", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _iffcmd_exec_ in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _ioflist_ in libifeffit.a(misc_arr.o) :info:build 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"__gfortran_stop_string", referenced from: :info:build _fstop_ in libifeffit.a(echo.o) :info:build "__gfortran_string_index", referenced from: :info:build _fixnam_ in libifeffit.a(misc_arr.o) :info:build _isvnam_ in libifeffit.a(misc_arr.o) :info:build _prenam_ in libifeffit.a(misc_arr.o) :info:build _glob_ in libifeffit.a(misc_arr.o) :info:build _iff_bkg_cl_ in libifeffit.a(iff_bkg_cl.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build _hexcol_ in libifeffit.a(iff_color.o) :info:build ... :info:build "__gfortran_string_len_trim", referenced from: :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _ioflist_ in libifeffit.a(misc_arr.o) :info:build _fixnam_ in libifeffit.a(misc_arr.o) :info:build _prenam_ in libifeffit.a(misc_arr.o) :info:build _fixarr_ in libifeffit.a(misc_arr.o) :info:build _iofarr_ in libifeffit.a(misc_arr.o) :info:build ... :info:build "__gfortran_transfer_character", referenced from: :info:build _iff_echo_ in libifeffit.a(iff_echo.o) :info:build _iread_ in libifeffit.a(iread.o) :info:build _rdffdt_ in libifeffit.a(rdffdt.o) :info:build _rdfb1_ in libifeffit.a(rdffdt.o) :info:build "__gfortran_transfer_character_write", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _chrdmp_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build _iff_color_ in libifeffit.a(iff_color.o) :info:build _iff_pstyle_ in libifeffit.a(iff_color.o) :info:build ... :info:build "__gfortran_transfer_integer_write", referenced from: :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _iff_color_ in libifeffit.a(iff_color.o) :info:build _iff_pstyle_ in libifeffit.a(iff_color.o) :info:build _iff_feffit_ in libifeffit.a(iff_feffit.o) :info:build _iff_getpath_ in libifeffit.a(iff_getpath.o) :info:build _iff_load_ in libifeffit.a(iff_load.o) :info:build _iff_macro_do_ in libifeffit.a(iff_macro.o) :info:build ... :info:build "__gfortran_transfer_real", referenced from: :info:build _str2dp_ in libifeffit.a(str.o) :info:build "__gfortran_transfer_real_write", referenced from: :info:build _iff_correl_s_.part.0 in libifeffit.a(iff_correl.o) :info:build _iff_cursor_ in libifeffit.a(iff_cursor.o) :info:build _iff_zoom_ in libifeffit.a(iff_cursor.o) :info:build _iff_feffit_ in libifeffit.a(iff_feffit.o) :info:build _iff_print_ in libifeffit.a(iff_print.o) :info:build _iff_save_ in libifeffit.a(iff_save.o) :info:build _ishsca_ in libifeffit.a(iff_show.o) :info:build ... :info:build ld: symbol(s) not found for architecture x86_64 :info:build clang: error: linker command failed with exit code 1 (use -v to see invocation) :info:build make: *** [blib/arch/auto/Ifeffit/Ifeffit.bundle] Error 1 :info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/work/ifeffit-1.2.final/wrappers/perl' :info:build Command failed: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/work/ifeffit-1.2.final/wrappers/perl" && /usr/bin/make -j4 -w all :info:build Exit code: 2 :error:build Failed to build p5.26-ifeffit: command execution failed :debug:build Error code: CHILDSTATUS 42934 2 :debug:build Backtrace: command execution failed :debug:build while executing :debug:build "system {*}$notty {*}$nice $fullcmdstring" :debug:build invoked from within :debug:build "command_exec build" :debug:build (procedure "portbuild::build_main" line 8) :debug:build invoked from within :debug:build "$procedure $targetname" :error:build See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/main.log for details. <main.log> _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.ca… Unsubscribe: https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmillenia.ca…

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Port p5.26-ifeffit not installing via MacPorts on Yosemite
by Sergio Tatay 16 Sep '18

16 Sep '18

Hi everybody, I’ve been trying to install Demeter package on MacOS using MacPorts. All the dependencies seem to install smoothly but for p5.26-iffefit. During port install I’ve got the following error: ---> Computing dependencies for demeter The following dependencies will be installed: p5.26-ifeffit Continue? [Y/n]: Y ---> Building p5.26-ifeffit Error: Failed to build p5.26-ifeffit: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/main.log for details. Error: Follow https://guide.macports.org/#project.tickets to report a bug. Error: Processing of port demeter failed I've pasted below an extract of the log file and attached the complete file to this mail. I’m completely newbie and I will be very grateful if someone could help me to get the problem solved. Thanks very much in advance, Sergio -LOG FILE- version:1 :debug:sysinfo OS X 10.10 (darwin/14.5.0) arch i386 :debug:sysinfo MacPorts 2.5.3 :debug:sysinfo Xcode 7.2.1 :debug:sysinfo SDK 10.10 :debug:sysinfo MACOSX_DEPLOYMENT_TARGET: 10.10 … …. :info:build /opt/local/lib/perl5/5.26/darwin-thread-multi-2level/CORE/libperl.dylib -L/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/work/ifeffit-1.2.final/wrappers/perl/../../src/lib -L/opt/local/lib -Wl,-headerpad_max_install_names -lifeffit -L/opt/local/lib -lpgplot -lpng -lX11 -L/opt/local/lib -lSystem -lm \ :info:build :info:build Undefined symbols for architecture x86_64: :info:build "__gfortran_compare_string", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _iffcmd_exec_ in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _ioflist_ in libifeffit.a(misc_arr.o) :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _glob_ in libifeffit.a(misc_arr.o) :info:build _settxt_ in libifeffit.a(misc_vars.o) :info:build ... :info:build "__gfortran_concat_string", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _fixnam_ in libifeffit.a(misc_arr.o) :info:build _prenam_ in libifeffit.a(misc_arr.o) :info:build _set_array_index_ in libifeffit.a(misc_arr.o) :info:build _getsca_ in libifeffit.a(misc_vars.o) :info:build _iff_bkg_cl_ in libifeffit.a(iff_bkg_cl.o) :info:build ... :info:build "__gfortran_getenv", referenced from: :info:build _iff_config_ in libifeffit.a(iff_config.o) :info:build "__gfortran_st_close", referenced from: :info:build _close_echofile_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _iff_history_ in libifeffit.a(iff_history.o) :info:build _iff_load_ in libifeffit.a(iff_load.o) :info:build _iff_log_ in libifeffit.a(iff_log.o) :info:build _iff_rddata_ in libifeffit.a(iff_rddata.o) :info:build _iff_save_ in libifeffit.a(iff_save.o) :info:build ... :info:build "__gfortran_st_inquire", referenced from: :info:build _iff_config_ in libifeffit.a(iff_config.o) :info:build _fefinp_ in libifeffit.a(fefinp.o) :info:build _openfl_ in libifeffit.a(misc_io.o) :info:build _newfil_ in libifeffit.a(misc_io.o) :info:build "__gfortran_st_open", referenced from: :info:build _rcldat_ in libifeffit.a(clcalc.o) :info:build _openfl_ in libifeffit.a(misc_io.o) :info:build "__gfortran_st_read", referenced from: :info:build _iff_echo_ in libifeffit.a(iff_echo.o) :info:build _str2dp_ in libifeffit.a(str.o) :info:build _iread_ in libifeffit.a(iread.o) :info:build _rdffdt_ in libifeffit.a(rdffdt.o) :info:build _rdfb1_ in libifeffit.a(rdffdt.o) :info:build "__gfortran_st_read_done", referenced from: :info:build _iff_echo_ in libifeffit.a(iff_echo.o) :info:build _str2dp_ in libifeffit.a(str.o) :info:build _iread_ in libifeffit.a(iread.o) :info:build _rdffdt_ in libifeffit.a(rdffdt.o) :info:build _rdfb1_ in libifeffit.a(rdffdt.o) :info:build "__gfortran_st_write", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _echo_.part.1 in libifeffit.a(echo.o) :info:build _chrdmp_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build ... :info:build "__gfortran_st_write_done", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _echo_.part.1 in libifeffit.a(echo.o) :info:build _chrdmp_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build ... :info:build "__gfortran_stop_string", referenced from: :info:build _fstop_ in libifeffit.a(echo.o) :info:build "__gfortran_string_index", referenced from: :info:build _fixnam_ in libifeffit.a(misc_arr.o) :info:build _isvnam_ in libifeffit.a(misc_arr.o) :info:build _prenam_ in libifeffit.a(misc_arr.o) :info:build _glob_ in libifeffit.a(misc_arr.o) :info:build _iff_bkg_cl_ in libifeffit.a(iff_bkg_cl.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build _hexcol_ in libifeffit.a(iff_color.o) :info:build ... :info:build "__gfortran_string_len_trim", referenced from: :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _ioflist_ in libifeffit.a(misc_arr.o) :info:build _fixnam_ in libifeffit.a(misc_arr.o) :info:build _prenam_ in libifeffit.a(misc_arr.o) :info:build _fixarr_ in libifeffit.a(misc_arr.o) :info:build _iofarr_ in libifeffit.a(misc_arr.o) :info:build ... :info:build "__gfortran_transfer_character", referenced from: :info:build _iff_echo_ in libifeffit.a(iff_echo.o) :info:build _iread_ in libifeffit.a(iread.o) :info:build _rdffdt_ in libifeffit.a(rdffdt.o) :info:build _rdfb1_ in libifeffit.a(rdffdt.o) :info:build "__gfortran_transfer_character_write", referenced from: :info:build _iffcmd_exec_.part.0 in libifeffit.a(ifeffit.o) :info:build _ifeffit_ in libifeffit.a(ifeffit.o) :info:build _chrdmp_ in libifeffit.a(echo.o) :info:build _fstop_ in libifeffit.a(echo.o) :info:build _iff_chieps_ in libifeffit.a(iff_chieps.o) :info:build _iff_color_ in libifeffit.a(iff_color.o) :info:build _iff_pstyle_ in libifeffit.a(iff_color.o) :info:build ... :info:build "__gfortran_transfer_integer_write", referenced from: :info:build _file_type_names_ in libifeffit.a(misc_arr.o) :info:build _iff_color_ in libifeffit.a(iff_color.o) :info:build _iff_pstyle_ in libifeffit.a(iff_color.o) :info:build _iff_feffit_ in libifeffit.a(iff_feffit.o) :info:build _iff_getpath_ in libifeffit.a(iff_getpath.o) :info:build _iff_load_ in libifeffit.a(iff_load.o) :info:build _iff_macro_do_ in libifeffit.a(iff_macro.o) :info:build ... :info:build "__gfortran_transfer_real", referenced from: :info:build _str2dp_ in libifeffit.a(str.o) :info:build "__gfortran_transfer_real_write", referenced from: :info:build _iff_correl_s_.part.0 in libifeffit.a(iff_correl.o) :info:build _iff_cursor_ in libifeffit.a(iff_cursor.o) :info:build _iff_zoom_ in libifeffit.a(iff_cursor.o) :info:build _iff_feffit_ in libifeffit.a(iff_feffit.o) :info:build _iff_print_ in libifeffit.a(iff_print.o) :info:build _iff_save_ in libifeffit.a(iff_save.o) :info:build _ishsca_ in libifeffit.a(iff_show.o) :info:build ... :info:build ld: symbol(s) not found for architecture x86_64 :info:build clang: error: linker command failed with exit code 1 (use -v to see invocation) :info:build make: *** [blib/arch/auto/Ifeffit/Ifeffit.bundle] Error 1 :info:build make: Leaving directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/work/ifeffit-1.2.final/wrappers/perl' :info:build Command failed: cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/work/ifeffit-1.2.final/wrappers/perl" && /usr/bin/make -j4 -w all :info:build Exit code: 2 :error:build Failed to build p5.26-ifeffit: command execution failed :debug:build Error code: CHILDSTATUS 42934 2 :debug:build Backtrace: command execution failed :debug:build while executing :debug:build "system {*}$notty {*}$nice $fullcmdstring" :debug:build invoked from within :debug:build "command_exec build" :debug:build (procedure "portbuild::build_main" line 8) :debug:build invoked from within :debug:build "$procedure $targetname" :error:build See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_perl_p5-ifeffit/p5.26-ifeffit/main.log for details.

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Data import issue on Ubuntu 18.04
by Joshua Wright 14 Sep '18

14 Sep '18

I am having some difficulty importing both .prj files and regular data files. I have included here two data files that open just fine on my Windows machine. When I try to import the raw data I get the following two popups: 1) Demeter::UI::Athena Warning Unquoted string "to" may clash with future reserved word at (eval 2479) line 1 2) Import warning Could not read "/path/to/file/Th_GWB.001" as either data or a project file. Do you need to enable a plugin? Selecting continue importing does nothing except close the dialogue box. When I import the project file the normal import window comes up, allowing me to select the data I want to import. Then a warning pops up: Warning! /path/to/file/ThoriumData.prj could not be read correctly. OK to continue importing data, cancel to quit importing data. Pressing OK just closes the dialogue box and nothing gets imported. Any ideas on what to do to fix this? Joshua

1 0

Job Posting
by Frejka, Jean M 12 Sep '18

12 Sep '18

Brookhaven National Laboratory currently has three post-doc positions in Material Characterizations available. Can you please post and/or upload the attached job postings? There are two pdf files per position: (1) short version for posting on a bulletin board and (2) a longer version to upload or email. If you have any questions, please contact me. Thank you for your assistance. Jeannie ************************************* Jean Marie Frejka Brookhaven National Laboratory Nuclear Science and Technology Department Building 817, 33 North Renaissance Road Upton, NY 11973 Phone: 631-344-2349 Fax: 631-344-2806 frejka(a)bnl.gov<mailto:frejka@bnl.gov>

1 0

XANES simulation
by Motta Meira, Debora 30 Aug '18

30 Aug '18

Good morning everyone, I'm trying to simulate XANES spectra for a material used for batteries. In the Figure, my experimental data are the blue (pristine material) and the red (charged state) curves. When I apply my EXAFS results to the original structure, to simulate using Feff, (I contracted the distances proportionally to what I found in the EXAFS fit) the XANES shifts accordantly, as you can see in the green and purple curves. However, the intensity is completely different. To fix this I changed S02 to 0.4. Additionally, I also correct the vr0 (found a value of -8.4) and I'm using Rpath = 5. The simulation using these parameters is the yellow curve. My problem is: using these parameters the simulation matches the experimental data, for the intensity and position, however, I'm missing the pre-edge and I also have a bump in the white line (yellow curve)... Does anyone know how to fix it, please? [cid:image003.jpg@01D44050.C0ECC210] Thank you, Debora

1 0

Constraining values in Artemis fit
by Thomas, Andrew (AGW) 23 Aug '18

23 Aug '18

Hello, Does anyone have any suggestions for breaking the correlation between the coordination number and sigma^2? Specifically, is there a way to set a maximum or minimum value for parameters in a fit? Andrew Thomas

4 3

32ビット版アプリケーションの申請
by 天田雄大 23 Aug '18

23 Aug '18

Ifeffit管理者様 32ビット版アプリケーションを使用したいので、 32ビット版のインストールアプリを添付していただけませんか？よろしくお願いします。

2 1

Accelerated Specotroscopy post-doc position at LBNL
by Santosh Suram 23 Aug '18

23 Aug '18

Hi everyone, I would like to bring to your attention an upcoming post-doc position on accelerated spectroscopy and analysis of XANES and EXAFS data. Please see the brief advertisement below and if interested please email your resume to jyano(a)lbl.gov and santosh.suram(a)tri.global -- best, Santosh -- Confidential or protected information may be contained in this email and/or attachment. Unless otherwise marked, all TRI email communications are considered "PROTECTED" and should not be shared or distributed. Thank you.

1 0

Fe K-edge EXAFS spectra for Fe-silicates
by Paul Francisco 22 Aug '18

22 Aug '18

Dear Everyone, Hello! I'm working on iron silicates and I'm wondering if anybody here would be willing to share some Fe K-edge EXAFS spectra (preferably ones that go up until k=14-15 A-1) for phyllosilicates (e.g. chlorite/saponite/serpentine); or if anybody can recommend some database or reference for these. Thanks in advance and I would really appreciate any help! Cheers, Paul

1 0

Modelling texture in Artemis
by Kirstine Dalgaard 20 Aug '18

20 Aug '18

Dear all How can texture in a powder sample be modeled in ARTEMIS? My samples are fine powders of a layered material, mixed with cellulose and pressed to pellets. The data were collected in fluorescence mode with a 45 degree tilt. PXRD data reveal that the samples are highly textured, including standards. I am new to XAFS, and I need some advise to deal with this issue. Best regards Kirstine Dalgaard

3 8

Re: [Ifeffit] using the mail list archive for mac install
by Matt Newville 17 Aug '18

17 Aug '18

Hi Joel, > I ran into the problem that some people seem to have with Demeter on mac while > upgrading to High Sierra. I found a fix on this mail list, but… Yeah, Demeter on MacOS is a continuing challenge. Even when it can be installed, parts of the GUI interaction are pretty buggy (I believe this must be due to wxPerl on Mac). MacPorts seems to need a fair amount of attention and expects the end user to know Unix command line tools well enough to be able to run updates and understand and react to error messages. For sure, it is a useful resource for developers, but it seems like it is not really designed for deploying end-user software. Still , I don't know of a better alternative for getting Demeter working on MacOS. I've tried many of the alternatives, and wxPerl seems to be a real stumbling block for all of them. > 1) I can’t download Template.pm from the archive (bin file that uncompresses to cpgz file > that uncompresses back to a bin file…) I think that the advice from Luke and Bruce back in April was to try to find and install version 1.47 of Text::Template. You might find this at https://metacpan.org/source/MSCHOUT/Text-Template-1.47/lib/Text and try unpacking and installing that. There may be a way to specify particular versions with the "cpan" program, but I do not know how to do it. I don't think we want "install old version of some library" to be a long term solution (this will break other things eventually), but it might work for you. > 2) Matt mentions that he installed 0.9.26 from macports, but I see only 0.9.25 (stable & develop). To clarify, in April I updated MacPorts to the latest versions, installed the packages for Demeter 0.9.25. Then I installed Demeter 0.9.26 from source code on top of that. That might also work , but it's probably more work than most folks would want to do. Cheers, --Matt

3 3