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

Including MS paths with an aggregate feff calculation in Artemis
by Jamie Hart 15 Nov '19

15 Nov '19

Dear mailing list subscribers, Is it possible to perform an aggregate feff calculation in Artemis, and then perform a fit using multiple scattering paths? It appears that the aggregate feff calculation is able to successfully compute MS paths, but Artemis will not let me include these paths in a fit. I am only able to perform an (aggregate) fit using single scattering paths. Please let me know if there is anything I can do to perform an aggregate fit with MS paths. Thank you, Jamie

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Installation problems for Demeter on Ubuntu 16.04
by Jo Melville 14 Nov '19

14 Nov '19

Hello all, I am having some troubles successfully building Demeter from source on my Linux machine. All dependencies appeared to install correctly -- a few errors pop up upon running ./Build test (full error report attached), but as best I could discern, the errors produced were the same as those reported in this recent message <https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg06782.html> ( https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg06782.html ). Athena appear to install correctly and even start correctly, but upon attempting to import *any* data file into Athena, the following error message pops up (screenshot also attached): > 03:50:59 PM: Unknown warnings category 'experimental::script_run' at > /usr/share/perl/5.22/warnings.pm line 254. > warnings::Croaker("Unknown warnings category 'experimental::script_run'") > called at /usr/share/perl/5.22/warnings.pm line 332 > warnings::unimport("warnings", "experimental::script_run") called at (eval > 2455) line 1 > Pod::Simple::BlackBox::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > eval 'no warnings "experimental::script_run"; > qr/(*script_run: ^ .* $ )/x' called at > /usr/local/share/perl/5.22.1/Pod/Simple/BlackBox.pm line 74 > require Pod/Simple/BlackBox.pm called at > /usr/local/share/perl/5.22.1/Pod/Simple/LinkSection.pm line 7 > Pod::Simple::LinkSection::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Pod/Simple/LinkSection.pm called at > /usr/local/share/perl/5.22.1/Pod/Simple.pm line 9 > Pod::Simple::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Pod/Simple.pm called at /usr/share/perl/5.22/Pod/Text.pm line 34 > Pod::Text::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Pod/Text.pm called at > /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/PluginRegistry.pm > line 13 > Demeter::UI::Athena::PluginRegistry::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Demeter/UI/Athena/PluginRegistry.pm called at > /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm line 2114 > Demeter::UI::Athena::make_page(Demeter::UI::Athena=HASH(0x28f21b0), > "PluginRegistry") called at > /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/IO.pm line 260 > Demeter::UI::Athena::IO::test_plugins(Demeter::UI::Athena=HASH(0x28f21b0), > "/home/melville/Documents/XAFS/Sample Projects/Athena and Arte"...) called > at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/IO.pm line > 168 > Demeter::UI::Athena::IO::Import(Demeter::UI::Athena=HASH(0x28f21b0)) > called at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm > line 890 > Demeter::UI::Athena::OnMenuClick(Wx::Frame=HASH(0xab38570), > Wx::CommandEvent=SCALAR(0xdaee6e0), Demeter::UI::Athena=HASH(0x28f21b0)) > called at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm > line 808 > Demeter::UI::Athena::__ANON__(Wx::Frame=HASH(0xab38570), > Wx::CommandEvent=SCALAR(0xdaee6e0)) called at /usr/local/bin/dathena line 35 > eval {...} called at /usr/local/bin/dathena line 35 > > 03:50:59 PM: Unknown warnings category 'experimental::script_run' at > /usr/share/perl/5.22/warnings.pm line 254. > warnings::Croaker("Unknown warnings category 'experimental::script_run'") > called at /usr/share/perl/5.22/warnings.pm line 332 > warnings::unimport("warnings", "experimental::script_run") called at (eval > 2455) line 1 > Pod::Simple::BlackBox::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > eval 'no warnings "experimental::script_run"; > qr/(*script_run: ^ .* $ )/x' called at > /usr/local/share/perl/5.22.1/Pod/Simple/BlackBox.pm line 74 > require Pod/Simple/BlackBox.pm called at > /usr/local/share/perl/5.22.1/Pod/Simple/LinkSection.pm line 7 > Pod::Simple::LinkSection::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Pod/Simple/LinkSection.pm called at > /usr/local/share/perl/5.22.1/Pod/Simple.pm line 9 > Pod::Simple::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Pod/Simple.pm called at /usr/share/perl/5.22/Pod/Text.pm line 34 > Pod::Text::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Pod/Text.pm called at > /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/PluginRegistry.pm > line 13 > Demeter::UI::Athena::PluginRegistry::BEGIN() called at (eval 2455) line 1 > eval {...} called at (eval 2455) line 1 > require Demeter/UI/Athena/PluginRegistry.pm called at > /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm line 2114 > Demeter::UI::Athena::make_page(Demeter::UI::Athena=HASH(0x28f21b0), > "PluginRegistry") called at > /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/IO.pm line 260 > Demeter::UI::Athena::IO::test_plugins(Demeter::UI::Athena=HASH(0x28f21b0), > "/home/melville/Documents/XAFS/Sample Projects/Athena and Arte"...) called > at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena/IO.pm line > 168 > Demeter::UI::Athena::IO::Import(Demeter::UI::Athena=HASH(0x28f21b0)) > called at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm > line 890 > Demeter::UI::Athena::OnMenuClick(Wx::Frame=HASH(0xab38570), > Wx::CommandEvent=SCALAR(0xdaee6e0), Demeter::UI::Athena=HASH(0x28f21b0)) > called at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm > line 808 > Demeter::UI::Athena::__ANON__(Wx::Frame=HASH(0xab38570), > Wx::CommandEvent=SCALAR(0xdaee6e0)) called at /usr/local/bin/dathena line 35 > eval {...} called at /usr/local/bin/dathena line 35 > BEGIN failed--compilation aborted at (eval 2455) line 1. > Ignoring this message allows Athena to import data correctly at first, but clicking some buttons will consistently and immediately cause the program to close, without even an error message popping up. Actions that will induce a crash range from selecting any Energy value besides 1 in column selection to things as innocuous as clicking Help>Show Tip. As a result, though the program is (barely) usable, it is very unstable and prone to crashing without warning, causing frustrating data loss. I'm sure that this is due to some fault on my part during the installation process, and would welcome any guidance on how best to approach this issue. Thanks, Jo Melville -- Jonathan "Jo" Melville <https://stuff.mit.edu/~melville/> PhD Candidate, Surendranath Group <http://www.interphases.org/> (2016-) Contact: (620)-842-8756 *“People think of education as something they can finish.”* *--Isaac Asimov*

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Bug in Artemis
by Natasa Diklic 12 Nov '19

12 Nov '19

Greetings! I encounter an issue for which I find no explanation so far. When I try to export data and fit in k weight 2, the data gets exported in k weight 3 all the time. I can see that Artemis k weight is 2 but Artemis output k weight is 3. Everything was working properly until today. Does anyone knows how to change this Artemis output k weight? Thank you very much in advance! Natasa

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Problem with installation of demeter on MAC (Catalina v10.15)-Can't locate Demeter/Here.pm
by wei zhang 09 Nov '19

09 Nov '19

After installation of both xorg-server and demeter, when I launch Athena, the problem is as follows: Can't locate Demeter/Here.pm in @INC (you may need to install the Demeter::Here module) (@INC contains: /Library/Perl/5.18/darwin-thread-multi-2level /Library/Perl/5.18 /Network/Library/Perl/5.18/darwin-thread-multi-2level /Network/Library/Perl/5.18 /Library/Perl/Updates/5.18.4 /System/Library/Perl/5.18/darwin-thread-multi-2level /System/Library/Perl/5.18 /System/Library/Perl/Extras/5.18/darwin-thread-multi-2level /System/Library/Perl/Extras/5.18 .) at /opt/local/bin/athena line 7. So, what should I do to solve this problem? Thank you all! Wei Zhang

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Solved concatenation bug Arrays.pm line 115
by FonsPaul 06 Nov '19

06 Nov '19

I wanted to update the mailing list on my encounter with a concatenation bug. I discovered that the cause was having (Japanese) Chinese characters in the pathname. Moving the folder solved the problem. Paul Fons

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Athena problem on MacOS 10.15
by FonsPaul 05 Nov '19

05 Nov '19

Hi All, I am using demeter on Mac OS 10.15 (the latest release) and am encountering some problems that I was hoping could be cleared up, in particular with Athena. The Athena version is 0.9.25, the latest version from MacPorts. Athena starts and properly plots existing projects without trouble, but trying to open a new data set using the PFBL12C plug in. From the Perl error messages below, it appears that the underlying cause is not from the Plugin, but from some problem within Demeter, with an uninitialized values in particular at line 115 that starts with the “my $text” assignment. Any ideas on what could be going wrong or what other debugging information might be useful. Paul Fons Arrays.pm sub get_array { my ($self, $suffix, $part) = @_; $part ||= q{}; if (not $self->plottable) { my $class = ref $self; croak("Demeter: $class objects have no arrays associated with them and are not plottable"); }; my $group = $self->group; my $text = ($part =~ m{(?:bkg|fit|res|run)}) ? "${group}_$part.$suffix" : "$group.$suffix"; my @array = $self->fetch_array($text); return @array; }; Perl error messages: 16:07:51: Use of uninitialized value $suffix in concatenation (.) or string at /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/Demeter/Data/Arrays.pm line 115. 16:07:51: Use of uninitialized value in concatenation (.) or string at /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/Demeter/Data/Mu.pm line 231. 16:07:51: Use of uninitialized value in concatenation (.) or string at /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/Demeter/Data/Mu.pm line 232. 16:07:51: Use of uninitialized value in concatenation (.) or string at /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/Demeter/Data/Mu.pm line 233. 16:07:51: Use of uninitialized value in concatenation (.) or string at /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/Demeter/Data/Mu.pm line 233. 16:07:51: Use of uninitialized value in concatenation (.) or string at /opt/local/lib/perl5/site_perl/5.26/darwin-thread-multi-2level/Demeter/Data/Mu.pm line 234. Fragment of example data set causing trouble 9809 SPring-8 01b1 GeTe_reference 19.10.31 11:20 - 19.10.31 11:22 Te standard Ring : 8.0 GeV 99.5 mA - 99.5 mA Mono : SI(311) D= 1.63747 A Initial angle= 7.06039 deg 01b1 Transmission( 2) Repetition= 1 Points= 4798 Param file : angle axis (1) Block = 1 Block Init-ang final-ang Step/deg Time/s Num 1 7.00000 6.52000 -0.000100 0.03 4798 Ortec( 0) NDCH = 4 Angle(c) Angle(o) time/s 2 3 4 Mode 0 0 1 2 1 Offset 0 0 49961.200 49083.900 1124.500 6.99980 7.00417 0.025 121003 450174 6.99970 7.00407 0.025 120103 447134 6.99960 7.00398 0.025 120212 447353 6.99950 7.00388 0.025 120465 448618 6.99940 7.00379 0.025 121167 450721 6.99930 7.00370 0.025 120510 448136 6.99920 7.00361 0.025 120907 450140 6.99910 7.00352 0.025 120063 446166 6.99900 7.00343 0.025 120656 449360 6.99890 7.00335 0.025 120901 450062 6.99880 7.00326 0.025 120820 449932 6.99870 7.00317 0.025 120655 448835 6.99860 7.00308 0.025 120869 449502 6.99850 7.00299 0.025 120818 449723 6.99840 7.00290 0.025 121239 450978 6.99830 7.00280 0.025 120744 449404

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Postdoctoral position
by Anatoly Frenkel 31 Oct '19

31 Oct '19

Our group has an opening for a postdoctoral position in heterogeneous catalysis. Expert knowledge of X-ray absorption spectroscopy and in situ/operando characterization of catalysts are required. The postdoc will be stationed at Brookhaven National Laboratory. For inquires, please email me at my Stony Brook University address, with a subject line: Postdoc in heterogeneous catalysis. Thank you, Anatoly Frenkel Professor Department of Materials Science and Chemical Engineering Stony Brook University Stony Brook, NY 11794, Ph: 631-632-2751 Email: anatoly.frenkel(a)stonybrook.edu <https://mail.bnl.gov/OWA/redir.aspx?C=F6wCGt4adziN6IvpdRQ-rWdgy3Oaoif_x-0yb…> http://you.stonybrook.edu/frenkel Joint Appointment: Chemistry Department, Brookhaven National Laboratory Upton, NY 11973. Ph: 631-344-3013. Group: 631-344-3494 Email: frenkel(a)bnl.gov https://www.bnl.gov/chemistry/bio/FrenkelAnatoly.asp Spokesperson, Synchrotron Catalysis Consortium (SCC) at BNL http://you.stonybrook.edu/scc2 -------------------------------------------------------------------

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Fwd: 32 bit package for install
by Ravel, Bruce 28 Oct '19

28 Oct '19

http://bruceravel.github.io/demeter/#old -------- Forwarded Message -------- Subject: 32 bit package for install Date: Mon, 28 Oct 2019 20:30:40 +0200 From: Margaret Blazhynska <blazhynska(a)gmail.com> To: ifeffit-owner(a)millenia.cars.aps.anl.gov To whom it may concern, Could you please send me the 32-bit installer package of ifeffit? I am a student of a masters degree in Chemistry and I really need this pack to practice on XAS Thank you in advance -- Best regards, Margaret Blazhynska -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Lead Beamline Scientist, 6BM (BMM) Building 743, Room 114 Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Beamline: https://www.bnl.gov/ps/beamlines/beamline.php?r=6-BM Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Issue with the Athena software - Athena Warning: redundant argument in sprintf
by Clarissa Baldo 15 Oct '19

15 Oct '19

Good Afternoon, I am a new user of the Athena software. I am trying to fit my XANES spectra using the linear combination fitting tools in Athena. However, every time I run the fitting I receive the following warning message: [cid:image002.png@01D58286.ED191450] Would you please give me some advice to solve this problem? I am using the latest version of the Demeter system (version 0.9.26) for windows. I have attached a copy of the warning log and a screenshot of the error. Thanks, Clarissa

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trouble installing Demeter from source on Ubuntu 18.04
by Joseph Zsombor-Pindera 15 Oct '19

15 Oct '19

Dear mailing list members; I'm trying to build Demeter from source according to Bruce Ravel's guide (https://bruceravel.github.io/demeter/documents/SinglePage/installation.html) I have mostly been able to install the dependencies, but I had trouble with the libwxgtk packages, so I installed 3.1.0 according to these instructions: https://gist.github.com/abdulhalim-cu/f3ae4be0b45baabef5623ccdd20ca584. wx-config --version results in: 3.1.0, so I think it's installed correctly. libgif4 is no longer in the repository, so I installed libgif-dev and libgif7. WxPerl 0.9932 is installed. Iffeffit is installed, and gnuplot-x11 and pgplot5 are installed. I ran ./Build installdeps and it ran but eventually got stuck in a loop saying "please tell me where I can find your apache src", which I ignored. The script terminated with "/usr/bin/make install -- OK" and then I installed apache2 anyways. Now, if I rerun it, it outputs "all prerequisites satisfied". I ran perl Build.PL, which seemed to complete successfully, and then finally ./Build and ./Build test, however ./Build test fails one test: Test Summary Report------------------- t/003_config.t (Wstat: 512 Tests: 22 Failed: 2) Failed tests: 17, 22 Non-zero exit status: 2 Files=44, Tests=2671, 89 wallclock secs ( 0.34 usr 0.07 sys + 85.03 cusr 3.94 csys = 89.38 CPU) Result: FAIL Failed 1/44 test programs. 2/2671 subtests failed. corresponding to: # Failed test 'configuration system introspection works: groups 38 artemis' # at t/003_config.t line 66. # Failed test 'introspection after reading new group: groups' # at t/003_config.t line 80. # Looks like you failed 2 tests of 22. t/003_config.t .......... Dubious, test returned 2 (wstat 512, 0x200) Failed 2/22 subtests line 80 in demeter/t/003_config.t is: ok( ($#groups == $number_of_groups), 'introspection after reading new group: groups'); I'm not sure what's going wrong here. Does anyone know how to resolve this problem? any help would be much appreciated, Joseph -- *Joseph Zsombor-Pindera, BSc* PhD Student, UBC Chemistry Cell: 514.804.0798 6201 Cecil Green Park Road Vancouver BC, V6T 1Z1 C

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Geting Trouble in Fitting CuZr2 strucutr with Cu33Zr67 alloy using simulations
by Akash Deshmukh 12 Oct '19

12 Oct '19

I am trying to do EXAFS fitting using simulations for Cu33Zr67 (Cu33). After running lammps program, I have got.XYZ files for the Cu33. While running edamd command, I am not getting output files. However, the program is running continuously for more than 12 hours. I am considering CuZr2 crystal structure as an input file to fit with Cu33. Can anyone please help me to figure out this? _______________________________________________________________________________ With Best Regards, Akash A. Deshmukh, +91 9175477696

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XAS fitting
by Wang, Maoyu 11 Oct '19

11 Oct '19

Hi I am running an EXAFS fitting for spinel Co3O4. As we know, the Co3O4 will have two different two local coordinations. One is 6 Co-O coordinated octahedral site, and another one is 4 Co-O coordinated tetrahedral site. When we run the Feff calculation, we can only use one Co site to do the calculation once, and we can only get one site coordination by one calculation. However, the EXAFS will tell us the average local structure. How could we use these two different calculation paths to do the fitting? Sincerely, Maoyu Wang Chemical Engineering Oregon State University wangma(a)oregonstate.edu 541-602-1707

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software installation
by Shultz, Mary Jane 11 Oct '19

11 Oct '19

Has anyone had issues with software installation? I have installed it on a Windows machine (64 bit, 7 pro). It appears to install, but when I try to run it, it starts but immediately shuts down. Am I missing something? Thanks M Three colleagues are having the same issue.

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Larch install error
by Mangold, Stefan (IPS) 05 Oct '19

05 Oct '19

Dear Matt, I tried to install larch via Anaconda. Install of Anaconda and larch seems to work fine, but I couldn’t create the Links via larch -m [numexpr.utils] INFO : NumExpr defaulting to 8 threads. Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/larch Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/larch --wxgui Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/xas_viewer Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/gse_mapviewer Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/gse_dtcorrect Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/xrfdisplay Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/dioptas_larch Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/xrd2d_viewer Warning: could not create shortcut to /Users/myaccount/anaconda3/bin/xrd1d_viewer I have MacOS Sierra installed On a similar system I installed larch half a year ago without any issues. best regards Stefan Mangold

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Mac problems
by Enrico Tusini 04 Oct '19

04 Oct '19

Hey there, I have this problem with the installation of Athena package on Mac Mojave : Failed to build pgplot: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_macports_release_tarballs_ports_graphics_pgplot/pgplot/main.log for details. Error: Follow https://guide.macports.org/#project.tickets to report a bug. Error: Processing of port demeter failed I’ll be very thankful for any suggestion. Best regards Tusini Enrico

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Install for Mac error
by Wu Xiaohan 03 Oct '19

03 Oct '19

Hello everyone, I tried to install demeter on my Mac and run Athena. And get the error shown below: 16:59:44: Name "Demeter::Templates::DS" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 16:59:44: Name "Demeter::Templates::S" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 16:59:44: Name "Demeter::Templates::F" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 16:59:44: Name "Demeter::Templates::PT" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 16:59:44: Name "Demeter::Templates::T" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. 16:59:44: Name "Demeter::Templates::D" used only once: possible typo at /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm line 572, <DATA> line 236. I would like to ask help to correct this error. Thank you so much. Best regards Kelsey

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Re: [Ifeffit] Fluorescence sample thickness
by Wallick, Rachel 01 Oct '19

01 Oct '19

The complex is 13% by mass of the absorbing element (Copper K-edge). The solvent will be acetonitrile and by control the concentration, I mean that I can dictate how much of the sample may be put into the capillary. I won’t be able to control the amount of the absorbing element. Rachel Wallick Chemistry Graduate Student | van der Veen Group University of Illinois at Urbana-Champaign 3011 Materials Research Laboratory

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Fluorescence sample thickness
by Wallick, Rachel 01 Oct '19

01 Oct '19

I'm preparing for an XAS measurement in fluorescence of a solution-phase sample that will be measured in a capillary tube. I anticipate being able to control the concentration fairly easily, and I'm trying to figure out what the best capillary diameter would be. Is there a good way to figure this out? Rachel Wallick Chemistry Graduate Student Van der Veen Group University of Illinois at Urbana-Champaign 3011 Materials Research Laboratory

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About Athena
by Pankaj Singh Rawat 30 Sep '19

30 Sep '19

Hey There, Good Morning.I am using Athena to analyse O-k edge XAS data. After uploading the data to the Athena, Fourier transform parameters are not showing. attaching a screenshot of home page. I'll be thankful to you for any suggestion. Thank you. hoping to hear from you soon. -- Pankaj Singh Rawat PhD Research Scholar GBPUA&T Pantnagar

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Athena data uploading: Fourier transform parameters are not showing
by Pankaj Singh Rawat 30 Sep '19

30 Sep '19

Hey There, Do anyone have idea about following problem: I uploaded C-k edge on Athena but fourier transform parameters are not showing/open for modifications. Attaching the screenshot. Is this because of the data format of any software issue ? any suggestions? I'll be grateful to you for valuable suggestions. -- Pankaj Singh Rawat PhD Research Scholar GBPUA&T Pantnagar

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Larch single-file installers problem on Mac
by 朱宥銓 17 Sep '19

17 Sep '19

Hi everyone, I had a problem when I tried to launch XAS software “Larch” on Mac through single-file installers. After I followed the tutorial and installed it (double click the dmg file), when I typed the command “larch”, the terminal showed the followings: could not read history from /Users/willie/.larch/history.lar [Errno 13] Permission denied: '/Users/willie/.larch/init.lar' [Errno 13] Permission denied: '/Users/willie/.larch/history.lar' [Errno 13] Permission denied: '/Users/willie/.larch/history_larchgui.lar' [Errno 13] Permission denied: '/Users/willie/.larch/matplotlib/README' [Errno 13] Permission denied: '/Users/willie/.larch/dlls' [Errno 2] No such file or directory: '/Users/willie/.larch/dlls/README' [Errno 13] Permission denied: '/Users/willie/.larch/modules' [Errno 2] No such file or directory: '/Users/willie/.larch/modules/README' [Errno 13] Permission denied: '/Users/willie/.larch/plugins' [Errno 2] No such file or directory: '/Users/willie/.larch/plugins/README' Traceback (most recent call last): File "//anaconda3/bin/larch", line 11, in <module> load_entry_point('xraylarch==0.9.46rc1', 'console_scripts', 'larch')() File "//anaconda3/lib/python3.7/site-packages/larch/apps.py", line 230, in run_larch cli = shell(quiet=options.quiet, with_wx=with_wx) File "//anaconda3/lib/python3.7/site-packages/larch/shell.py", line 56, in __init__ maxhistory=maxhist) File "//anaconda3/lib/python3.7/site-packages/larch/interpreter.py", line 177, in __init__ for pname in sorted(os.listdir(plugins_dir)): FileNotFoundError: [Errno 2] No such file or directory: '/Users/willie/.larch/plugins’ Does anyone face this problem as well? How can I fix this problem? Thank you, Youchiuan

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Running FEFF 8 in Artemis
by Farideh Jalilehvand 16 Sep '19

16 Sep '19

Hi everyone, I am trying to do EXAFS data analysis using Artemis and FEFF 8. To do so, I have followed these steps: 1. Changed FEFF executable file path 2. Changed Process from Demeter to FEFF8 FEFF 8.10 runs, but it does not generate paths that I can pick for fitting. The console shows that paths have been found, but does not write it. When I run FEFF outside the Artemis program, it does write the paths as the PRINT card in FEFF.inp file is set at (PRINT 1 1 1 3). So, greatly appreciate if you can help me finding a solution for this problem. Kind regards, Farideh ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Farideh Jalilehvand, Ph.D. Associate Professor, and Associate Head (Undergraduate) Department of Chemistry, University of Calgary 2500 University Dr. NW, Calgary, AB T2N 1N4, Canada Tel: (403) 220-3855 / 220-5353│E-mail: faridehj(a)ucalgary.ca URL: http://www.chem.ucalgary.ca/research/groups/faridehj/

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Larch 0.9.46
by Matt Newville 14 Sep '19

14 Sep '19

Hi Folks, Larch 0.9.46 is now available, with installers for Windows, MacOS, and Linux at https://millenia.cars.aps.anl.gov/xraylarch/ It has been several months since I announced a release. For XAFS and XANES analysis, there have been several recent improvements: - add reading and visualizations tools for RIXS plane data (thanks, Mauro Rovezzi!). - better support for reading older Athena Project files. I think all Athena files are now supported, but if you run into trouble, please send me the file you are having problems with. - better support for reading and parsing data files from more XAFS beamlines, at least those in North America. If you have data files that are not being read correctly (or even "well", including figuring out how columns should be labeled), please send an example file and how you expect it to read. - several fixes to the XAS Viewer application. There is still a To-Do list for this, but if you have suggestions, problems, or irritations using this, please let me know. There have been steady improvements in using Larch as a Python library, especially from Jupyter consoles and Notebooks. Some improvement in the docs and examples have been made. These are still behind but will continue to be worked on over the next few months. If you having any questions or suggestions, please let us know. --Matt Newville

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Anyone use OCEAN?
by Matthew Marcus 12 Sep '19

12 Sep '19

OCEAN is the U. Washington program for doing XANES sims using ab-initio, Bethe-Salpeter methods (http://monalisa.phys.washington.edu/OCEAN/ocean-about.html) It seems to require a certain amount of experience and expertise to get it to produce any result, let alone correct results. I wonder if this might be a good forum for getting advice on solving problems with this code. Unlike ABINIT, which is one of the ab-inito engines OCEAN can use, OCEAN doesn't have a forum of its own. -- Sincerely, Matthew Marcus

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Occupation number error getorb
by Patridge, Christopher 12 Sep '19

12 Sep '19

Hello, I have searched back on the mailing list regarding the occupation number error and found bad counts with getorb. I have tried a number of settings as per the email thread, however nothing seems to correct the error. I trying to calculate a vanadium oxide K-edge but as the earlier email stated, it just hangs trying to iterate SCF. This email was quite a while ago and just wondered if anyone has had these issues come up again and were able to find conditions that worked for them? Attached is the feff.inp which triggers this error. Any guidance or suggestions beyond the thread would be greatly appreciated, Thanks, Chris ********************************************** Dr Christopher Patridge Associate Professor Dept of Chemistry SASE 315 716-829-8096 | patridgc(a)dyc.edu<mailto:patridgc@dyc.edu> www.dyc.edu<http://www.dyc.edu> Social: Twitter<http://www.twitter.com/drpatridgc> [cid:0edd417e-b4aa-4ba7-af9d-5051c7441a0a@namprd14.prod.outlook.com]

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