- 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

1 0

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*

2 2

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

2 1

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

1 0

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

2 1

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

1 0

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 -------------------------------------------------------------------

1 0

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/

1 0

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

2 1

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

2 1