Re: [Ifeffit] XAFS detection limit
This is such a fantastic answer! Thank you for sharing your expertise.
On Sun, Feb 9, 2020, 9:50 AM Matt Newville
wrote:
> Hi Christian,
>
> On Thu, Feb 6, 2020, 8:40 PM Christian Wittee Lopes
> wrote:
>
>> Dear all,
>>
>> Recently I was questioned about the EXAFS detection limit when describing
>> different metal species in a bimetallic sample.
>>
>> By checking Pd and Cu K-edges, for example, I found Pd metal
>> nanoparticles and CuO clusters, respectively. But additional techniques
>> tell me I can have copper atoms in intimate contact with the Pd
>> nanoparticles. What would be the minimum amount of these "single atoms"
>> needed to be detected by EXAFS? is there a detection limit or it depends on
>> several parameters?
>>
>
> As Chris Chantler says, there are a lot of things that can influence this,
> so there really isn't one simple answer. Also, as Chris says, advances in
> analytic methods have been (mostly) been improving the situation.
>
> At my beamline, we often get asked questions about detection limits.
> We're typically working in a different context than
> nanoparticles/catalysts, but I think the basic ideas are about the same.
>
> A good starting rule-of-thumb for absolute detection limits is 1 ppm by
> atomic weight. You might be able to do better sometimes, but there are
> situations where XANES at 10 ppm is very hard. For sure, a matrix of
> light elements is much better than a matrix of heavy elements.
>
> For very dilute samples, one will be using fluorescence XAFS measurements
> with a solid-state detector or know very well why you are doing something
> different. These solid-state detectors and electronics are fundamentally
> limited to have energy resolutions of ~120 eV (often 250 eV) and maximum
> total count rates of 5 MHz (often 0.5 MHz). Many beamlines use "a
> handful" (2 to 16) parallel detectors, and some have up to 100 (but often
> with each having a lower individual maximum count rate, and perhaps
> less-than-ideal energy resolution).
> With a count rate of a few MHz total and a sample with 1ppm of "element of
> interest", the elastic and Compton scattering and/or fluorescence from
> other elements will dominate that total count rate and the energy
> resolution will give non-zero background in the fluorescence spectrum.
> That means that even seeing a peak from 1 ppm of an element in an X-ray
> fluorescence spectrum with a solid-state detector is challenging. Not
> impossible, but definitely not routine.
>
> For sure, adding more detectors or counting for a long time can help. But
> those are linear in time and the number of detectors (and no beamline has
> 1000 parallel detectors). Low Z matrices like water, biological material,
> carbon-rich materials are easier. Samples with nearby or overlapping
> fluorescence lines are much harder. That is 10 ppm Zn in water: yes, 1
> ppm Zn in water: maybe, 10 ppm Zn in CaCO3: maybe, 100 ppm Zn in Cu metal:
> no. For sure, XANES at 1ppm is sometimes possible. Getting interpretable
> XAFS would take a lot longer, perhaps days of counting.
>
> Using filters and/or Bent Laue Analyzers in front of a solid-state (or
> integrating) detector can sometimes help to eliminate the unwanted scatter
> signals before they get to the solid-state detector. Using crystal
> analyzers ("wavelength" vs "energy" dispersive fluorescence) can help -
> they have lower backgrounds and are not limited by the total scatter - but
> the solid angle for these tend to be small. Using crystal analyzer arrays
> are probably really needed to get the best detection limits. A few
> beamlines do regularly do HERFD analysis with arrays of crystal analyzers,
> and many of the rest of us are trying to catch up. Still, I believe that
> "1 ppm" is around the state of the art, if not "heroic".
>
> All of that is for the detection limit of an atomic species. If you are
> asking about detecting Cu in/on/with Pd nanoparticles with CuO also
> present, the answer is far worse. Cu XAS measurements will be an average
> of all Cu atoms in the illuminated volume -- you cannot avoid the CuO.
> Seeing that 1% of the Cu atoms are bound to Pd and not to oxygen would be
> very challenging.
>
> Hope that helps,
> --Matt
>
> ___
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
Re: [Ifeffit] Installation problems for Demeter on Ubuntu 16.04
Thank you for your advice, Bruce. After trying a few things that didn't
work (I already had Wx installed through apt, so that wasn't the culprit),
I attempted to remove Demeter entirely and reinstall it from scratch. This
proved to be a serious mistake, as I presumably failed to completely purge
my system, and now cannot even get any installed programs to run at all.
Running ./Build Test produces lines upon lines of Dubious, test returned 2
(wstat 512, 0x200), and attempting to run dathena outputs this garbage:
Can't locate PerlIO/utf8_strict.pm in @INC (you may need to install the
> PerlIO::utf8_strict module) (@INC contains:
> /home/melville/perl5/lib/perl5/5.22.1/x86_64-linux-gnu-thread-multi
> /home/melville/perl5/lib/perl5/5.22.1
> /home/melville/perl5/lib/perl5/x86_64-linux-gnu-thread-multi
> /home/melville/perl5/lib/perl5 /etc/perl
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1 /usr/local/share/perl/5.22.1
> /usr/lib/x86_64-linux-gnu/perl5/5.22 /usr/share/perl5
> /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22
> /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at
> /usr/local/share/perl/5.22.1/Mixin/Linewise/Readers.pm line 9.
> BEGIN failed--compilation aborted at
> /usr/local/share/perl/5.22.1/Mixin/Linewise/Readers.pm line 9.
> Compilation failed in require at
> /usr/local/share/perl/5.22.1/Config/INI/Reader.pm line 5.
> BEGIN failed--compilation aborted at
> /usr/local/share/perl/5.22.1/Config/INI/Reader.pm line 5.
> Compilation failed in require at /usr/share/perl/5.22/parent.pm line 20.
> BEGIN failed--compilation aborted at
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/IniReader.pm line 2.
> Compilation failed in require at
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/Config.pm line 31.
> BEGIN failed--compilation aborted at
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/Config.pm line 31.
> Compilation failed in require at
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter.pm line 191.
> BEGIN failed--compilation aborted at
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter.pm line 191.
> Compilation failed in require at
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm line 24.
> BEGIN failed--compilation aborted at
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Demeter/UI/Athena.pm line 24.
> Compilation failed in require at /usr/local/bin/dathena line 31.
> BEGIN failed--compilation aborted at /usr/local/bin/dathena line 31.
> Use of uninitialized value $Larch::larch_exe in concatenation (.) or
> string at /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Larch.pm line 288.
> Can't exec "-q": No such file or directory at
> /usr/local/lib/x86_64-linux-gnu/perl/5.22.1/Larch.pm line 288.
>
I've attached a full error log from the build test, but I'm hardly
optimistic I can clean up my mess at this point. My current plan is to
create a 19.10 partition just to run Demeter. Such is the life of a
mediocre Linux user.
Thanks,
Jo Melville
On Wed, Nov 13, 2019 at 4:12 PM Jo Melville wrote:
> 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 ca
[Ifeffit] Installation problems for Demeter on Ubuntu 16.04
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*
NOTE: Forcing use of Ifeffit in testing.
t/000_ifeffit.t . ok
t/001_base.t ok
t/002_types.t ... ok
t/003_config.t ..
Failed 2/22 subtests
t/004_data.t ok
t/005_plot.t ok
t/006_gds.t . ok
t/007_prj.t . ok
t/008_path.t ok
t/009_fit.t . ok
t/010_feff.t ok
t/011_sp.t .. ok
t/012_atoms.t ... ok
t/013_spacegroups.t . ok
t/014_vpath.t ... ok
t/015_sspath.t .. ok
t/016_fspath.t .. ok
t/017_structuralunit.t .. ok
t/018_multichannel.t ok
t/019_provenance.t .. ok
t/020_indicator.t ... ok
t/021_externalfeff.t ok
t/022_filetypes.t ... ok
t/023_files.t ... ok
t/024_graph.t ... ok
t/025_lcf.t . ok
t/026_xes.t . ok
t/028_fpath.t ... ok
t/029_threebody.t ... ok
t/030_xdi.t . ok
t/031_quench.t .. ok
t/032_miscellany.t .. ok
t/100_elam.t ok
t/101_mcmaster.t ok
t/102_chantler.t ok
t/103_henke.t ... ok
t/104_shaltout.t ok
t/105_fluo.t ok
t/500_checker.t . ok
t/501_dataBlock.t ... ok
t/502_dictionary.t .. ok
t/503_filter.t .. ok
t/504_parser.t .. ok
t/505_writer.t .. ok
Test Summary Report
---
t/003_config.t(Wstat: 0 Tests: 22 Failed: 2)
Failed tests: 17, 22
Files=44, Tests=2671, 95 wallclock secs ( 0.32 usr 0.10 sys + 89.79 cusr 5.32
csys = 95.53 CPU)
Result: FAIL
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
