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

Fitting EXAFS simulation to experimental
by Carl Brozek 29 May '14

29 May '14

Dear listhost, I'm using Artemis as a front end for ATOMS and FEFF and I would like to build a simulated EXAFS spectrum based on experimental data I have. I know how to generate a simulation based on a .cif or .xyz file, but is it possible to vary parameters in these input geometries to best match the experimental? Has someone implemented this in artemis or matlab? thanks, Carl -- PhD Candidate | Chemistry | MIT SB | 2010 | University of Chicago

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Re: [Ifeffit] Demeter on Ubuntu 14.04
by Denis Testemale 28 May '14

28 May '14

Thanks for your answer Bruce. Don't spoil your holidays/vacation for this! I had done the "perl Build.pl" or "./Build installdeps" steps. In fact I tried a clean install with all those steps. Right now, I tried the touch_wrapper you mentionned without success. I also tried an install as root for all the steps: no success either. I'm stuck and it might be something stupid I can't see. When you have some time to have a look, let me know, there's no rush right now. Cheers denis Le 22/05/2014 15:09, ifeffit-request(a)millenia.cars.aps.anl.gov a écrit : > 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. Re: Demeter on Ubuntu 14.04 (Ravel, Bruce) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 22 May 2014 13:09:14 +0000 > From: "Ravel, Bruce"<bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Demeter on Ubuntu 14.04 > Message-ID:<9ocjbe8obqgecedql4scmfu3.1400764153184(a)email.android.com> > Content-Type: text/plain; charset="us-ascii" > > I'm on vacation right now and only have my tablet, so typing a decent response is a challenge. > > >From what you included, it looks as though you pulled or cloned the latest from within, but did not do the "perl Build.pl" or "./Build installdeps" steps. If not starting from a clean install, it may help to also "./Build touch_wrapper". > > I'll be with email only sporadically for a while, unfortunately. > > B > > > On May 21, 2014, at 11:27AM, Denis TESTEMALE wrote: > > Dear members of the list, > > it's that time of the (Linux) Ubuntu life cycles where you do upgrades and break previously working programs... Upgrading to Ubuntu 14.04 made no exception for me. It also broke the old Hephaestus programs, but I think it is definitely time that I stop being lazy and switch to Demeter. So I'll focus on the Demeter problems. Sorry about the lengthy post full of pasted error messages. > > -------------------------------------------------------------------------------------------------------------- > Context: I'm running Ubuntu 64 bits 14.04. Demeter version 0.9.20. I followed Ubuntu specific instructions found here: > https://gist.github.com/3959252 > Demeter once worked but I cannot guarantee that it did just before the upgrade to 14.04. After the upgrade, both trying to run dathena or to rebuild the package ran into errors such as: > > denis@huchet4:~/demeter$ ./Build > Building Demeter > Perl API version v5.14.0 of DateTime does not match v5.18.0 at /usr/share/perl/5.18/XSLoader.pm line 92. > Compilation failed in require at lib/Xray/data/elam2st.PL line 405. > BEGIN failed--compilation aborted at lib/Xray/data/elam2st.PL line 405. > lib/Xray/data/elam2st.PL failed at /home/denis/perl5/lib/perl5/Module/Build/Base.pm line 2963. > > denis@huchet4:~/demeter$ dathena > Perl API version v5.14.0 of Wx does not match v5.18.0 at /usr/lib/perl/5.18/DynaLoader.pm line 207. > Compilation failed in require at /home/denis/perl5/bin/dathena line 11. > BEGIN failed--compilation aborted at /home/denis/perl5/bin/dathena line 11. > > ----------------------------------------------------------------------------------------------------------------------------------- > > So I erased the folders and reinstalled everything. The installation ran smoothly (except I had to install missing deps several times, but no error messages at the end). Now I can start the programs but run into problems: > > For Dephaestus: everything works, I can plot f' and f" (gnuplot is working) but when I try to plot some XANES references in the standards tab, it crashes with: > > Attribute (bkg_nc0) does not pass the type constraint because: Validation failed for 'LaxNum' with value 0,00000000000000 at /usr/local/lib/perl/5.18.2/Moose/Exception.pm line 37 > Moose::Exception::_build_trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x9a3fd18)') called at reader Moose::Exception::trace (defined at /usr/local/lib/perl/5.18.2/Moose/Exception.pm line 9) line 7 > Moose::Exception::trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x9a3fd18)') called at /usr/local/lib/perl/5.18.2/Moose/Exception.pm line 49 > Moose::Exception::BUILD('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x9a3fd18)', 'HASH(0xa3743c8)') called at /usr/local/lib/perl/5.18.2/Class/MOP/Method.pm line 128 > Class::MOP::Method::execute('Moose::Meta::Method=HASH(0xa44deb8)', 'Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x9a3fd18)', 'HASH(0xa3743c8)') called at /usr/local/lib/perl/5.18.2/Moose/Object.pm line 56 > Moose::Object::BUILDALL('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x9a3fd18)', 'HASH(0xa3743c8)') called at /usr/local/lib/perl/5.18.2/Moose/Meta/Class.pm line 282 > Moose::Meta::Class::new_object('Moose::Meta::Class=HASH(0x9a3f0d8)', 'HASH(0xa3743c8)') called at /usr/local/lib/perl/5.18.2/Moose/Object.pm line 27 > Moose::Object::new('Moose::Exception::ValidationFailedForInlineTypeConstraint', 'type_constraint_message', 'Validation failed for \'LaxNum\' with value 0,00000000000000', 'class_name', 'Demeter::Data', 'attribute_name', 'bkg_nc0', 'value', '0,00000000000000') called at /usr/local/lib/perl/5.18.2/Moose/Util.pm line 52 > Moose::Util::throw_exception('ValidationFailedForInlineTypeConstraint', 'type_constraint_message', 'Validation failed for \'LaxNum\' with value 0,00000000000000', 'class_name', 'Demeter::Data', 'attribute_name', 'bkg_nc0', 'value', '0,00000000000000') called at accessor Demeter::Data::bkg_nc0 (defined at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 309) line 4 > Demeter::Data::bkg_nc0('Demeter::Data=HASH(0xa372058)', '0,00000000000000') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Mu.pm line 323 > Demeter::Data::Mu::normalize('Demeter::Data=HASH(0xa372058)') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 674 > Demeter::Data::_update('Demeter::Data=HASH(0xa372058)', 'fft') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Plot.pm line 24 > Demeter::Data::Plot::plot('Demeter::Data=HASH(0xa372058)', 'E') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Standards.pm line 267 > Demeter::UI::Standards::plot('Demeter::UI::Standards=HASH(0x96b3d78)', 'Ferrihydrite', 'mu', 'plot') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Hephaestus/Standards.pm line 139 > Demeter::UI::Hephaestus::Standards::make_standards_plot('Demeter::UI::Hephaestus::Standards=HASH(0x9a2f018)', 'Wx::CommandEvent=SCALAR(0x9a2ee50)', 'Demeter::UI::Hephaestus::Standards=HASH(0x9a2f018)', 'mu') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Hephaestus/Standards.pm line 79 > Demeter::UI::Hephaestus::Standards::__ANON__('Demeter::UI::Hephaestus::Standards=HASH(0x9a2f018)', 'Wx::CommandEvent=SCALAR(0x9a2ee50)') called at /home/denis/perl5/bin/dhephaestus line 37 > eval {...} at /home/denis/perl5/bin/dhephaestus line 37 > > Similar story and message (at least the first line, since the rest is a bit obscure for me) for Dathena when I try to import a data file from an old Athena .prj project (i.e., as far as I understand and remember things, a file where there is no interactive import window to select columns, references, etc.). > > Attribute (bkg_nc0) does not pass the type constraint because: Validation failed for 'LaxNum' with value 68,42548963866604 at /usr/local/lib/perl/5.18.2/Moose/Exception.pm line 37 > Moose::Exception::_build_trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0xbd2adb0)') called at reader Moose::Exception::trace (defined at /usr/local/lib/perl/5.18.2/Moose/Exception.pm line 9) line 7 > Moose::Exception::trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0xbd2adb0)') called at /usr/local/lib/perl/5.18.2/Moose/Exception.pm line 49 > Moose::Exception::BUILD('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0xbd2adb0)', 'HASH(0xbd2e050)') called at /usr/local/lib/perl/5.18.2/Class/MOP/Method.pm line 128 > Class::MOP::Method::execute('Moose::Meta::Method=HASH(0xbd372b8)', 'Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0xbd2adb0)', 'HASH(0xbd2e050)') called at /usr/local/lib/perl/5.18.2/Moose/Object.pm line 56 > Moose::Object::BUILDALL('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0xbd2adb0)', 'HASH(0xbd2e050)') called at /usr/local/lib/perl/5.18.2/Moose/Meta/Class.pm line 282 > Moose::Meta::Class::new_object('Moose::Meta::Class=HASH(0xbd2d4c8)', 'HASH(0xbd2e050)') called at /usr/local/lib/perl/5.18.2/Moose/Object.pm line 27 > Moose::Object::new('Moose::Exception::ValidationFailedForInlineTypeConstraint', 'type_constraint_message', 'Validation failed for \'LaxNum\' with value 68,42548963866604', 'class_name', 'Demeter::Data', 'attribute_name', 'bkg_nc0', 'value', '68,42548963866604') called at /usr/local/lib/perl/5.18.2/Moose/Util.pm line 52 > Moose::Util::throw_exception('ValidationFailedForInlineTypeConstraint', 'type_constraint_message', 'Validation failed for \'LaxNum\' with value 68,42548963866604', 'class_name', 'Demeter::Data', 'attribute_name', 'bkg_nc0', 'value', '68,42548963866604') called at accessor Demeter::Data::bkg_nc0 (defined at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 309) line 4 > Demeter::Data::bkg_nc0('Demeter::Data=HASH(0xbd3ec78)', '68,42548963866604') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Mu.pm line 323 > Demeter::Data::Mu::normalize('Demeter::Data=HASH(0xbd3ec78)') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 674 > Demeter::Data::_update('Demeter::Data=HASH(0xbd3ec78)', 'fft') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Plot.pm line 24 > Demeter::Data::Plot::plot('Demeter::Data=HASH(0xbd3ec78)', 'E') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Artemis/Prj.pm line 209 > Demeter::UI::Artemis::Prj::do_plot('Demeter::UI::Artemis::Prj=HASH(0xbd2b4f8)', 'Demeter::Data::Prj=HASH(0xbd2a6a8)', 1) called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Artemis/Prj.pm line 162 > Demeter::UI::Artemis::Prj::plot_selection('Demeter::UI::Artemis::Prj=HASH(0xbd2b4f8)', 'Wx::CommandEvent=SCALAR(0xbd31420)', 'Demeter::Data::Prj=HASH(0xbd2a6a8)', 'ARRAY(0xbd2bc78)', 'ARRAY(0xbd30f00)') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Artemis/Prj.pm line 59 > Demeter::UI::Artemis::Prj::__ANON__('Demeter::UI::Artemis::Prj=HASH(0xbd2b4f8)', 'Wx::CommandEvent=SCALAR(0xbd31420)') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 769 > eval {...} at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 769 > Demeter::UI::Athena::IO::_prj('Demeter::UI::Athena=HASH(0xc7d498)', '/home/denis/Collaborations/C2RMF/Manip_FeCn/exafs_FeOH2.prj', '/home/denis/Collaborations/C2RMF/Manip_FeCn/exafs_FeOH2.prj', 1, '') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 165 > Demeter::UI::Athena::IO::Import('Demeter::UI::Athena=HASH(0xc7d498)', '/home/denis/Collaborations/C2RMF/Manip_FeCn/exafs_FeOH2.prj') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 793 > Demeter::UI::Athena::OnMenuClick('Wx::Frame=HASH(0xa2feb60)', 'Wx::CommandEvent=SCALAR(0xbd27218)', 'Demeter::UI::Athena=HASH(0xc7d498)') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 754 > Demeter::UI::Athena::__ANON__('Wx::Frame=HASH(0xa2feb60)', 'Wx::CommandEvent=SCALAR(0xbd27218)') called at /home/denis/perl5/bin/dathena line 39 > eval {...} at /home/denis/perl5/bin/dathena line 39 > > Finally, still Dathena when I try to import a new data file (i.e., a file where I expect an interactive import window to select the columns), there is no error message in the shell, but in the bottom line of the Dathena GUI window, it says that the file "cannot be read as data. (Do you need to enable a plugin?). > The thing is I never had to enable a plugin for such a data file (the data file is the cu10k.dat file that you provided in the Ifeffit CD some time ago, and you might still provide today). > > OK, enough. Let me know if I can try different things to help source the problem. > Regards. > Denis > >

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Demeter on Ubuntu 14.04
by Denis TESTEMALE 22 May '14

22 May '14

Dear members of the list, it's that time of the (Linux) Ubuntu life cycles where you do upgrades and break previously working programs... Upgrading to Ubuntu 14.04 made no exception for me. It also broke the old Hephaestus programs, but I think it is definitely time that I stop being lazy and switch to Demeter. So I'll focus on the Demeter problems. Sorry about the lengthy post full of pasted error messages. -------------------------------------------------------------------------------------------------------------- Context: I'm running Ubuntu 64 bits 14.04. Demeter version 0.9.20. I followed Ubuntu specific instructions found here: https://gist.github.com/3959252 Demeter once worked but I cannot guarantee that it did just before the upgrade to 14.04. After the upgrade, both trying to run dathena or to rebuild the package ran into errors such as: denis@huchet4:~/demeter$ ./Build Building Demeter Perl API version v5.14.0 of DateTime does not match v5.18.0 at /usr/share/perl/5.18/XSLoader.pm line 92. Compilation failed in require at lib/Xray/data/elam2st.PL line 405. BEGIN failed--compilation aborted at lib/Xray/data/elam2st.PL line 405. lib/Xray/data/elam2st.PL failed at /home/denis/perl5/lib/perl5/Module/Build/Base.pm line 2963. denis@huchet4:~/demeter$ dathena Perl API version v5.14.0 of Wx does not match v5.18.0 at /usr/lib/perl/5.18/DynaLoader.pm line 207. Compilation failed in require at /home/denis/perl5/bin/dathena line 11. BEGIN failed--compilation aborted at /home/denis/perl5/bin/dathena line 11. ----------------------------------------------------------------------------------------------------------------------------------- So I erased the folders and reinstalled everything. The installation ran smoothly (except I had to install missing deps several times, but no error messages at the end). Now I can start the programs but run into problems: For Dephaestus: everything works, I can plot f' and f" (gnuplot is working) but when I try to plot some XANES references in the standards tab, it crashes with: Attribute (bkg_nc0) does not pass the type constraint because: Validation failed for 'LaxNum' with value 0,00000000000000 at /usr/local/lib/perl/5.18.2/Moose/Exception.pm line 37 Moose::Exception::_build_trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x9a3fd18)') called at reader Moose::Exception::trace (defined at /usr/local/lib/perl/5.18.2/Moose/Exception.pm line 9) line 7 Moose::Exception::trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x9a3fd18)') called at /usr/local/lib/perl/5.18.2/Moose/Exception.pm line 49 Moose::Exception::BUILD('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x9a3fd18)', 'HASH(0xa3743c8)') called at /usr/local/lib/perl/5.18.2/Class/MOP/Method.pm line 128 Class::MOP::Method::execute('Moose::Meta::Method=HASH(0xa44deb8)', 'Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x9a3fd18)', 'HASH(0xa3743c8)') called at /usr/local/lib/perl/5.18.2/Moose/Object.pm line 56 Moose::Object::BUILDALL('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x9a3fd18)', 'HASH(0xa3743c8)') called at /usr/local/lib/perl/5.18.2/Moose/Meta/Class.pm line 282 Moose::Meta::Class::new_object('Moose::Meta::Class=HASH(0x9a3f0d8)', 'HASH(0xa3743c8)') called at /usr/local/lib/perl/5.18.2/Moose/Object.pm line 27 Moose::Object::new('Moose::Exception::ValidationFailedForInlineTypeConstraint', 'type_constraint_message', 'Validation failed for \'LaxNum\' with value 0,00000000000000', 'class_name', 'Demeter::Data', 'attribute_name', 'bkg_nc0', 'value', '0,00000000000000') called at /usr/local/lib/perl/5.18.2/Moose/Util.pm line 52 Moose::Util::throw_exception('ValidationFailedForInlineTypeConstraint', 'type_constraint_message', 'Validation failed for \'LaxNum\' with value 0,00000000000000', 'class_name', 'Demeter::Data', 'attribute_name', 'bkg_nc0', 'value', '0,00000000000000') called at accessor Demeter::Data::bkg_nc0 (defined at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 309) line 4 Demeter::Data::bkg_nc0('Demeter::Data=HASH(0xa372058)', '0,00000000000000') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Mu.pm line 323 Demeter::Data::Mu::normalize('Demeter::Data=HASH(0xa372058)') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 674 Demeter::Data::_update('Demeter::Data=HASH(0xa372058)', 'fft') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Plot.pm line 24 Demeter::Data::Plot::plot('Demeter::Data=HASH(0xa372058)', 'E') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Standards.pm line 267 Demeter::UI::Standards::plot('Demeter::UI::Standards=HASH(0x96b3d78)', 'Ferrihydrite', 'mu', 'plot') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Hephaestus/Standards.pm line 139 Demeter::UI::Hephaestus::Standards::make_standards_plot('Demeter::UI::Hephaestus::Standards=HASH(0x9a2f018)', 'Wx::CommandEvent=SCALAR(0x9a2ee50)', 'Demeter::UI::Hephaestus::Standards=HASH(0x9a2f018)', 'mu') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Hephaestus/Standards.pm line 79 Demeter::UI::Hephaestus::Standards::__ANON__('Demeter::UI::Hephaestus::Standards=HASH(0x9a2f018)', 'Wx::CommandEvent=SCALAR(0x9a2ee50)') called at /home/denis/perl5/bin/dhephaestus line 37 eval {...} at /home/denis/perl5/bin/dhephaestus line 37 Similar story and message (at least the first line, since the rest is a bit obscure for me) for Dathena when I try to import a data file from an old Athena .prj project (i.e., as far as I understand and remember things, a file where there is no interactive import window to select columns, references, etc.). Attribute (bkg_nc0) does not pass the type constraint because: Validation failed for 'LaxNum' with value 68,42548963866604 at /usr/local/lib/perl/5.18.2/Moose/Exception.pm line 37 Moose::Exception::_build_trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0xbd2adb0)') called at reader Moose::Exception::trace (defined at /usr/local/lib/perl/5.18.2/Moose/Exception.pm line 9) line 7 Moose::Exception::trace('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0xbd2adb0)') called at /usr/local/lib/perl/5.18.2/Moose/Exception.pm line 49 Moose::Exception::BUILD('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0xbd2adb0)', 'HASH(0xbd2e050)') called at /usr/local/lib/perl/5.18.2/Class/MOP/Method.pm line 128 Class::MOP::Method::execute('Moose::Meta::Method=HASH(0xbd372b8)', 'Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0xbd2adb0)', 'HASH(0xbd2e050)') called at /usr/local/lib/perl/5.18.2/Moose/Object.pm line 56 Moose::Object::BUILDALL('Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0xbd2adb0)', 'HASH(0xbd2e050)') called at /usr/local/lib/perl/5.18.2/Moose/Meta/Class.pm line 282 Moose::Meta::Class::new_object('Moose::Meta::Class=HASH(0xbd2d4c8)', 'HASH(0xbd2e050)') called at /usr/local/lib/perl/5.18.2/Moose/Object.pm line 27 Moose::Object::new('Moose::Exception::ValidationFailedForInlineTypeConstraint', 'type_constraint_message', 'Validation failed for \'LaxNum\' with value 68,42548963866604', 'class_name', 'Demeter::Data', 'attribute_name', 'bkg_nc0', 'value', '68,42548963866604') called at /usr/local/lib/perl/5.18.2/Moose/Util.pm line 52 Moose::Util::throw_exception('ValidationFailedForInlineTypeConstraint', 'type_constraint_message', 'Validation failed for \'LaxNum\' with value 68,42548963866604', 'class_name', 'Demeter::Data', 'attribute_name', 'bkg_nc0', 'value', '68,42548963866604') called at accessor Demeter::Data::bkg_nc0 (defined at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 309) line 4 Demeter::Data::bkg_nc0('Demeter::Data=HASH(0xbd3ec78)', '68,42548963866604') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Mu.pm line 323 Demeter::Data::Mu::normalize('Demeter::Data=HASH(0xbd3ec78)') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data.pm line 674 Demeter::Data::_update('Demeter::Data=HASH(0xbd3ec78)', 'fft') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/Data/Plot.pm line 24 Demeter::Data::Plot::plot('Demeter::Data=HASH(0xbd3ec78)', 'E') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Artemis/Prj.pm line 209 Demeter::UI::Artemis::Prj::do_plot('Demeter::UI::Artemis::Prj=HASH(0xbd2b4f8)', 'Demeter::Data::Prj=HASH(0xbd2a6a8)', 1) called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Artemis/Prj.pm line 162 Demeter::UI::Artemis::Prj::plot_selection('Demeter::UI::Artemis::Prj=HASH(0xbd2b4f8)', 'Wx::CommandEvent=SCALAR(0xbd31420)', 'Demeter::Data::Prj=HASH(0xbd2a6a8)', 'ARRAY(0xbd2bc78)', 'ARRAY(0xbd30f00)') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Artemis/Prj.pm line 59 Demeter::UI::Artemis::Prj::__ANON__('Demeter::UI::Artemis::Prj=HASH(0xbd2b4f8)', 'Wx::CommandEvent=SCALAR(0xbd31420)') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 769 eval {...} at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 769 Demeter::UI::Athena::IO::_prj('Demeter::UI::Athena=HASH(0xc7d498)', '/home/denis/Collaborations/C2RMF/Manip_FeCn/exafs_FeOH2.prj', '/home/denis/Collaborations/C2RMF/Manip_FeCn/exafs_FeOH2.prj', 1, '') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena/IO.pm line 165 Demeter::UI::Athena::IO::Import('Demeter::UI::Athena=HASH(0xc7d498)', '/home/denis/Collaborations/C2RMF/Manip_FeCn/exafs_FeOH2.prj') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 793 Demeter::UI::Athena::OnMenuClick('Wx::Frame=HASH(0xa2feb60)', 'Wx::CommandEvent=SCALAR(0xbd27218)', 'Demeter::UI::Athena=HASH(0xc7d498)') called at /home/denis/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/UI/Athena.pm line 754 Demeter::UI::Athena::__ANON__('Wx::Frame=HASH(0xa2feb60)', 'Wx::CommandEvent=SCALAR(0xbd27218)') called at /home/denis/perl5/bin/dathena line 39 eval {...} at /home/denis/perl5/bin/dathena line 39 Finally, still Dathena when I try to import a new data file (i.e., a file where I expect an interactive import window to select the columns), there is no error message in the shell, but in the bottom line of the Dathena GUI window, it says that the file "cannot be read as data. (Do you need to enable a plugin?). The thing is I never had to enable a plugin for such a data file (the data file is the cu10k.dat file that you provided in the Ifeffit CD some time ago, and you might still provide today). OK, enough. Let me know if I can try different things to help source the problem. Regards. Denis

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Problems in Energy calibration
by Lei Zhong 16 May '14

16 May '14

Dear all, we had beam line time in DESY (Hamburg) and ERSF (Grenoble) for NiMo sulfided supported samples. In DESY we got quite nice foil reference but in ERSF we failed since the third chamber showed problems. Therefore, we have critical issues to do the energy calibration for spectra collected from ERSF. We collected spectra for MoS2 crystals. So we are thinking about if it is reasonable to compare the spectra of MoS2 for the energy shift and further apply the energy calibration. Would you please give me suggestions? Thank you in advance. Q1. In two beam lines, for exactly the same MoS2 crystal, we got difference in XANES region. Spectrum from DESY has a weak preedge peak resolved in XANES while ERSF doesn't. And the derivative shape of the two spectra for MoS2 collected from two synchrotrons are not well overlapped. Is it acceptable? Q2. I tried to overlay the first derivative of the two spectra of MoS2. There is a energy shift at 2.5 eV from the different synchrotrons if we take the one from DESY as standard. Can I apply the energy shift at 2.5 eV for MoS2 from ERSF and then overlay the first derivative of the other NiMo samples with MoS2 to get the energy calibration? Or should I apply 2.5 eV for all the NiMo sulfided samples? Q3. Since we lost the signal for the foil reference in ERSF, we tried to put the foil in the sample position. The first derivatives of the foil spetra from time to time overlap quite well. Should we set the energy calibration at 0 according to the stable foil signal? Sorry for the long email. Thank you for the time reading it. Hopefully I made the questions understandable to you. Looking forward to your answer! Thanks. Regards, Lei Technical University of Munich

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atoms tab doesnt appear on d-artemis
by Kim, Sarah 13 May '14

13 May '14

Hello, I am currently using d-artemis (on 9.18.2) and when I import a feff.inp file, the run atoms button is unavailable and there are no paths under the paths tab. I have used this feff file before on the same program without this issue. I attached a screen shot of what I am looking at. I have already uninstalled/reinstalled the program. Ive also tried using different feff files and I have the same issue. Also, this feff file works fine on the old version of artemis. Thank you, Sarah Kim Washington State University

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XANES + EXAFS for light elements in diluted samples
by Marcelo Alves 11 May '14

11 May '14

Dear all, I am interested in running some measurements of XANES and EXAFS K-edge spectra of elements such as Ca and S sorbed onto commonly found oxisol minerals, i.e natural kaolinite, gibbsite, hematite, and goethite. Besides appropiate filters to attenuate the fluorescence signals that come from elements such as Al and Si, what would the other instrumental conditions (e.g detector type, photon flux, etc...) needed for getting usable spectra of those elements in diluted samples? Any suggestion on the more adequate beamline to carry out such measurements? Kind regards, Marcelo.

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Atoms and Feff for CuFe2O4 structure
by Qasim Imtiaz 04 May '14

04 May '14

Dear all, I am using Atoms to calculate a Feff input file for CuFe2O4 spinel. However running Atoms/Feff results in program crash owing to 'two atoms very close together'. I modified the .cif file before importing (owing to partial occupancy issue) as following: Deleted: Fe2 Fe3+ 8 d 0.5 0.25 0.125 . 0.5 0 Modified: Cu1 Cu2+ 8 d 0.5 0.25 0.125 . 0.5 0 to Cu1 Cu2+ 8 d 0.5 0.25 0.125 . 1 0 After importing the file in Atoms, I also used different shift vectors (e.g. -0.125 -0.125 -0.125) but the issue is not resolved. Can someone help me please to solve this problem? Thanks. Best Regards Qasim

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Possible bug in fitting
by Ditty Dixon 30 Apr '14

30 Apr '14

Hello IFEFFIT users, I am working on LiNi0.5Mn1.5O4 cathode materials, I am pretty sure that some of you already worked on it. On the first look, a multiple edge analysis on both Ni and Mn is interesting; however it’s not that straight forward due to multiple phase and oxidation states. I started doing multiple edge fit, but I gave up briefly. Then I did individual edge analysis and obtained some values. Looking at both edges my Ni fit looks good. So I thought of taking the Ni-Mn bond distance as well as DW factor value to Mn edge and set this value for my Mn-Ni paths. However it seems like this value is further evaluated in the fit and giving a new value. Can someone reproduce this, please see the project file and the Log file attached, Is it a possible bug or am I doing something wrong? Thank you, Ditty -- Ditty Dixon, Anorganische Chemie Karlsruhe Institute of Technology Kaiserstr 12 Karlsruhe, Germany Ph no: 004972160848093

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Re: [Ifeffit] Ifeffit Digest, Vol 134, Issue 20
by Ditty Dixon 30 Apr '14

30 Apr '14

Hello IFEFFIT users, Sorry, I used the wrong values I should have set the delta r value, Sorry again, Ditty On Wed, Apr 30, 2014 at 2:05 PM, <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. Possible bug in fitting (Ditty Dixon) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 30 Apr 2014 14:05:40 +0200 > From: Ditty Dixon <ditty.dixon(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Possible bug in fitting > Message-ID: > < > CABPBYUdrOG_atNjT9ef454J_ZhLXPmnTin8KXcNvi1ZVTCxOHg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello IFEFFIT users, > > > > I am working on LiNi0.5Mn1.5O4 cathode materials, I am pretty sure that > some of you already worked on it. On the first look, a multiple edge > analysis on both Ni and Mn is interesting; however it?s not that straight > forward due to multiple phase and oxidation states. I started doing > multiple edge fit, but I gave up briefly. Then I did individual edge > analysis and obtained some values. Looking at both edges my Ni fit looks > good. So I thought of taking the Ni-Mn bond distance as well as DW factor > value to Mn edge and set this value for my Mn-Ni paths. However it seems > like this value is further evaluated in the fit and giving a new value. Can > someone reproduce this, please see the project file and the Log file > attached, Is it a possible bug or am I doing something wrong? > > > > Thank you, > > > Ditty > > -- > Ditty Dixon, > Anorganische Chemie > Karlsruhe Institute of Technology > Kaiserstr 12 > Karlsruhe, Germany > Ph no: 004972160848093 >

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Rendering of windows in Artemis and transferring paths from feff calculation
by Alison Tebo 23 Apr '14

23 Apr '14

Hi All, I am running Demeter 0.9.18 installed on a Mac 10.6.8 via the (very helpful!) Macports port. I've had nearly no problems with processing my data, but Artemis appears very strange. Most of the button can't be seen and are black instead (I've attached a screenshot). The bigger problem is that once I run a Feff calculation, I can't seem to transfer the paths from the Feff Window into the Data Window (see second screenshot). The program seems to think it's doing it--there are no error messages in the log and it even makes the little graphic as it 'grabs' the path--but it never transfers it over to the Data Window. I have attached a project file where I get this error, the feff input file that I run the calculation on, and two screenshots of what Artemis looks like for me. I don't think the input and project file matter much since this happens for me even with examples from the various courses Bruce has given. Any advice would be greatly appreciated. Sincerely, Alison

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