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

about WebAoms
by Park Gyuchul 20 Nov '19

20 Nov '19

Hi All, I am trying to simulate the EXAFS spectrum of pure molybdenum through FEFF9 software. I got the atomic configurations of molybdenum from molecular dynamics simulations, and I'd like to import it into FEFF 9. In order to do that, I converted lammps file into cif file, and I am trying to convert cif file into feff.inp. I am using Webatoms to convert cif file into feff.inp. The default value of cluster size and longest path is 8 and 5, respectively (in angs). However, when I try to increase the cluster size and the longest path to 10, it stops working, and I got the internal error. I am working with 1024 atoms (8x8x8 cells, bcc crystal structure). Are 1024 atoms too many to deal with in webatoms? or is there other ways to convert cif file into feff.inp? I don't have any problems when I use the ideal cif file (not from molecular dynamics simulations). Sincerely, Gyuchul Park

3 4

Re: [Ifeffit] webatoms for large cluster
by Gentle, Cecilia M 20 Nov '19

20 Nov '19

Hi Gyuchul, Have you tried using Stand Alone Atoms (it comes with the demeter package) instead of webatoms? In my experience, stand alone atoms should not have a problem with 10 angstrom cluster. Hope this helps, Cecilia -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Wednesday, November 20, 2019 12:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 201, Issue 11 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. about WebAoms (Park Gyuchul) ---------------------------------------------------------------------- Message: 1 Date: Wed, 20 Nov 2019 02:27:27 +0000 From: Park Gyuchul <park855(a)purdue.edu> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] about WebAoms Message-ID: <MN2PR22MB209315A18585A0B381D2FEB9934F0(a)MN2PR22MB2093.namprd22.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Hi All, I am trying to simulate the EXAFS spectrum of pure molybdenum through FEFF9 software. I got the atomic configurations of molybdenum from molecular dynamics simulations, and I'd like to import it into FEFF 9. In order to do that, I converted lammps file into cif file, and I am trying to convert cif file into feff.inp. I am using Webatoms to convert cif file into feff.inp. The default value of cluster size and longest path is 8 and 5, respectively (in angs). However, when I try to increase the cluster size and the longest path to 10, it stops working, and I got the internal error. I am working with 1024 atoms (8x8x8 cells, bcc crystal structure). Are 1024 atoms too many to deal with in webatoms? or is there other ways to convert cif file into feff.inp? I don't have any problems when I use the ideal cif file (not from molecular dynamics simulations). Sincerely, Gyuchul Park

1 0

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 13 Nov '19

13 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 08 Nov '19

08 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