Re: [Ifeffit] Constraining values in Artemis fit
On 08/23/2018 10:55 AM, Thomas, Andrew (AGW) wrote: Hello, Does anyone have any suggestions for breaking the correlation between the coordination number and sigma^2? Specifically, is there a way to set a maximum or minimum value for parameters in a fit? Matt is, of course, correct when he says that this correlation is inherent to EXAFS analysis and cannot be "broken". I would like to suggest a broader way of thinking about this sort of issue. When you have a very well behaved analysis problem -- that is, something like my teaching example of FeS2, something for which the structure is pretty well known -- then your EXAFS analysis will yield defensible values for CN and sigma^2 without too much effort. They will still be correlated, but sensible numbers will tend to just fall out. In a harder problem -- y'know something you are doing actual research on -- you often run into the situation where these correlations preclude a "fall right out" analysis. It is tempting to assert that the CN must be SOMETHING and the ss must be SOMETHING. That's true in a sense, but you have made a real measurement and are doing a real analysis with real measurement uncertainties. And you have to respect that. When you are running into trouble in your EXAFS analysis -- big uncertainties, indefensible values, that sort of thing -- that is usually the program trying to tell you something about your analysis. Usually, that would mean that you want to know something that the data do not support (or do not support beyond some level of precision or accuracy). Or it might mean that your fitting model is not realized in the data -- that is, your model is missing some important feature and the bad fit results are the result of missing that important feature. To summarize, I want to encourage you not to assert that you need to find a way to break the correlations. i want to encourage you think about what the wonky fit results are trying to tell you about your data or your fitting model. That was kind of rambling, I admit. Hopefully it was helpful nonetheless.... B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Lead Beamline Scientist, 06BM (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/ ___ 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] Ifeff calculation
more about your skepticism of the robustness of EXAFS LCF, Matt? To be fair, it suffers from many of the same drawbacks of XANES LCF, plus others. But I'm curious about your thoughts on it since yours seems to be what amounts to a "strong opinion" on the subject. I would not say that no one should ever do linear combination fitting for EXAFS. For sure, linear analysis of XANES is quite robust and verified many times to give good results, at least at level of a few percent. Linear analysis of EXAFS suffers more data processing challenges and conceptual problems that limit its robustness. For sure, there are cases for which it can work well. Longer answer: Any linear analysis (LCF, PCA, MCR-ALS, etc) of XANES works reasonably well (typically to a few percent) because: a) the processing needed is minimal. Data need to have a common energy calibration better than the intrinsic energy resolution -- typically energy calibration of 0.25 eV or better will be OK. Data need to have a consistent normalization of mu(E), typically to a few percent. Variations in these processing steps will have a direct and negative effect on the results. b) conceptually, the assumption is that there exists a nearly 1 to 1 correspondence between "local chemical configuration" and "measured XANES", and that the "local chemical configurations" that are being investigated are discrete and well-defined (ie "iron carbonate") and not continuous. That is, if you determine that your Fe XANES spectra is "50% iron carbonate and 50% iron sulfate" then implicit conclusion is that 50% of the iron atoms are iron carbonate and 50 percent are iron sulfate, not that all irons are 50% carbonate and 50% sulfate. To be clear, linear analysis of XANES does not work well to ppm levels, partly due to the poor experimental contrast (that is, mu(E) tend to all look alike and features are intrinsically broadened to the ~eV level), but also conceptually, because at the ppm level, local chemical configurations are not always limited to 3 to 10 discrete states. Linear Combination EXAFS is more challenging from both the processing and conceptual point of view. For Processing, EXAFS requires more data processing than XANES. The selection of E0 and the background mu0(E) will have an effect on linear analysis of EXAFS if not done consistently. It is not really obvious how E0 or mu0(E) can be selected consistently for very different spectra. Conceptually, EXAFS is much more sensitive to disorder and subtle variations in the bond lengths (thermal or static disorder) and can have significant variation in its sensitivity to second and further neighbors. In that sense, EXAFS is much less discrete and much more continuous in its variability across different kinds of local structures. Again, this is not to say that linear analysis of EXAFS cannot ever work, just that is probably more limited in applicability and absolute accuracy than linear analysis of XANES. Of course, for EXAFS you can also do an actual fit of structural parameters. The information content is somewhat limited so that refining multiple overlapping components may not always be possible, and linear combinations of end-member spectra may look attractive Hopefully, anyone who has other insights or experiences will be able to correct any of my misunderstandings. --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 ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Lead Beamline Scientist, 06BM (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/ ___ 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] Demeter on ubuntu 14.04
Is larch up to date? Or even installed? It would seem that $larch_exe is not being evaluated properly and is undefined when you get to line 288 in Larch.pm. B On 08/08/2018 10:07 AM, Edmund Welter wrote: Dear all, I am hitting a wall trying to install the latest Demeter version on my ubuntu laptop. System: Ubuntu 14.04 Demeter: 0.9.26 perl: 5.18.2 pdl and pdl::stats from repositories. (I tried a newer versions from cpan, but ot no avail) moose: initially from repositories, than vs. 2.2011 from cpan I did follow the installation instructions on https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.html and tried to install demeter in ~/perl5 and also the instructions in: https://bruceravel.github.io/demeter/documents/SinglePage/installation.html to install Demeter as sudo Both attempts ended with the same result when I start dathena in a terminal the image of the goddess appears briefly and I get the following error messages in the terminal: - Invalid version format (non-numeric data) at /usr/local/lib/perl/5.18.2/Moose/Exporter.pm line 11, line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Moose/Exporter.pm line 11, line 90. Compilation failed in require at /usr/local/lib/perl/5.18.2/Moose.pm line 15, line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Moose.pm line 15, line 90. Compilation failed in require at /usr/local/lib/perl/5.18.2/Demeter.pm line 123, line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Demeter.pm line 123, line 90. Compilation failed in require at /usr/local/lib/perl/5.18.2/Demeter/UI/Athena.pm line 24, line 90. BEGIN failed--compilation aborted at /usr/local/lib/perl/5.18.2/Demeter/UI/Athena.pm line 24, line 90. Compilation failed in require at /usr/local/bin/dathena line 31, line 90. BEGIN failed--compilation aborted at /usr/local/bin/dathena line 31, line 90. Use of uninitialized value $Larch::larch_exe in concatenation (.) or string at /usr/local/lib/perl/5.18.2/Larch.pm line 288, line 90. Can't exec "-q": No such file or directory at /usr/local/lib/perl/5.18.2/Larch.pm line 288, line 90. When i try to start denv to create the nice overview of installed components I only get the following errors: [PDL->Version: 10 PDL_CORE_VERSION: 8 XS_VERSION: ] PDL::Stats::Distr needs to be recompiled against the newly installed PDL at /usr/lib/perl/5.18/DynaLoader.pm line 207. Compilation failed in require at (eval 1130) line 5. BEGIN failed--compilation aborted at (eval 1130) line 5. BEGIN failed--compilation aborted at /usr/local/bin/denv line 24. Use of uninitialized value $Larch::larch_exe in concatenation (.) or string at /usr/local/lib/perl/5.18.2/Larch.pm line 288. Can't exec "-q": No such file or directory at /usr/local/lib/perl/5.18.2/Larch.pm line 288. -- This is insofar interesting as I got the same error about PDL when I tried to start dathena before I installed the pdl::stats module from cpan, that means when both, pdl and pdl::stats were installed from repositories. Any hint would be welcome, upgrading ubuntu to a newer LTS version might be useful (It is absolutely possible that something is weird with this installation after a lot of playing around) but I am currently reluctant to do so, because it will for sure break other things... Best regards, Edmund ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Lead Beamline Scientist, 06BM (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/ ___ 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] Basic questions about the preliminary data processing in Athena
On 07/27/2018 01:32 PM, Haifeng Li wrote: What is the real difference between calibration and alignment? Do they have specific meaning? In Athena, calibration means to determine a value for e0 shift such that a particular point in the data is specified to be a particular energy. Then the value for E0 is set to that particular energy. Thus, calibration changes both e0 and e0 shift for the group being calibrated. For example, set the E0 shift such that the first inflection point in copper is made to be 8979 eV. Then set the value for E0 in the background removal to 8979. In Athena alignment is the process by which one data group is given an e0 shift value such that it lines up with another data group. This is to compensate for some scan-to-scan variability in the behavior of the monochromator. Often, but not always, alignment is done using a zero-valent (or some other) reference which is measured simultaneously with the actual sample. In Athena, the alignment tool DOES NOT change the value of e0, but certainly does change the value of e0 shift for the group being aligned. The alignment tool does not change either e0 or e0 shift for the alignment standard. Whether you want to do one, the other, both, or neither depends upon the beamline and the type of data ensemble you have measured. This /is/ explained in the user manual. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Lead Beamline Scientist, 06BM (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/ ___ 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] window 10
One of the values of a mailing list is that past posts are archived and can be searched. This particular problem has -- I think -- been discussed many times in recent months. https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg06031.html You should go to the preferences and make sure the settings for the feff6 and gnuplot executables are set correctly for your new machine. I am sorry this continues to be a problem. I am not with a lot of time for software development these days. Also, an email that simply says "the program crashed" is not at all helpful. There is no way that you can expect me to understand the nature of the problem with such an insubstantial bug report. As I have asked many times, please consult this page for hints on how to write an actionable bug report. http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html B On 07/11/2018 10:12 AM, dien...@srnl.doe.gov wrote: Hi, Bruce and Matt We just transitioned to Window 10 yesterday. I just found that as I ran Artemis for EXAFS data fitting, it constantly crashed (stopped running) my computer, I am using Demeter 9:24 I believe, is it possible I need a new version, where is the link for latest version? Thanks. Dien Li Savannah River National Laboratory ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Lead Beamline Scientist, 06BM (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/ ___ 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] copper fluoride
Hi all, I wonder if anyone has a spectrum of copper fluoride, CuF2, that they are willing to share. This would be a big help for my undergraduate student's summer research project. Thanks! B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Lead Beamline Scientist, 06BM (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/ ___ 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] Artemis Error
Hi Chính, First off, I have to apologize for the very slow response. For the last month, I have been busy with the first few user groups to visit our newly commissioned beamline here at NSLS-II. I haven't had much time to manage software issues. I haven't forgotten about your post to the mailing list, though, and I would like to look into the problem. The picture you posted with your bug report is useful, but not quite sufficient. It would be helpful to me to see both the project file that triggered the problem and the log file (http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html#capturing-error-messages) that gets written when Artemis crashes. B On 03/29/2018 12:36 AM, Lê Ngọc Chính wrote: Dear Demeter developer I have some trouble when using artemis. I have used artemis normally on windows 10, but recently I can't use it anymore. The error message appears after I click "FIT" button. I also have tried re-install the software, but nothing happened. Please provide me the way to fix it. Thank you so much -- Chính ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II 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/ ___ 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] install for mac error
On 04/03/2018 01:47 PM, Luke Higgins wrote: I see this error too. This is a bit of a bodge job, but if you replace: /opt/local/lib/perl5/vendor_perl/5.26/Text/Template.pm With the attached template.pm from p5.24, it seems to work fine. I’d just rename the old Template.pm in the same directory, rather than deleting it – since another program may end up needing the most recent one. Luke, It's better than a bodge. It seems to be a good idea. It seems there was a big change in Text::Template at version 1.48. Your attachment was version 1.47 -- i.e. before this significant change. This confuses me. I've read the relevant code and I don't understand why it's a problem. Even more, I don't understand how it can be a problem only on the Mac and not everywhere. Weird. Anyway, I think replacing Text::Template as Luke suggests is a good idea for anyone seeing this problem on the Mac. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II 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/ ___ 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] install for mac error
On 04/03/2018 12:52 PM, Matt Newville wrote: I see the same problem with athena from demeter 0.9.25. I think the warnings about "Demeter::Templates::F" and so forth are meant to be warnings only -- I think they may not be related to the crash of athena. For me, hephaestus gives the same sort of warnings, but runs fine. Those are only warnings and should not be related to whatever is causing Athena to crash. I am confused why those warnings get reported. I am using the same version of perl as Chris (5.26), so presumably the same version of Text::Template. I don't see those warnings and don't understand why they would show up on a different system. That said, I can think of a couple ways to suppress those warnings, but it is something someone would have to volunteer to test for me. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II 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/ ___ 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] Problem building latest demeter on Debian 32bit Stretch
On 03/30/2018 01:47 PM, Matthew Newville wrote: Hi Al, Bruce, Is there a need to run analysis codes running 32-bit Linux? I haven't seen one of those in a long time, and don't plan on testing or supporting any codes on that platform. I'm not even excited about supporting 32-bit Windows. Well... neither am I, but that's what the question was B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II 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/ ___ 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] Problem building latest demeter on Debian 32bit Stretch
Still puzzling. I sort of understand what you are seeing, but it makes little sense, isn't consistent with my understanding of how package loading in perl works, and certainly is not something I have seen before. Try putting use Graphics::GnuplotIF; somewhere near the top of lib/Demeter/Plot/Gnuplot.pm. Doesn't much matter where. After line 57 would be fine. If that works -- great! Both of my suggestions do no harm, so I'll just commit them to github B On 03/30/2018 12:49 PM, Al Kwiatkowski wrote: Hm, we're getting somewhere. Putting the 'use Carp;' line now has dathena come up, but delivering this error: Use of uninitialized value in subroutine entry at /usr/local/lib/i386-linux-gnu/perl/5.24.1/Demeter/Plot/Gnuplot.pm line 29. and when you exit, it pops up a dialogue box with this error: Use of uninitialized value in stat at /usr/local/lib/i386-linux-gnu/perl/5.24.1/Demeter/Plot/Gnuplot.pm line 270. The program seems to behave ok otherwise, but I don't know what operations would have problems with an uninitialized gnuplot module variable or subroutine. Why would it have issues initializing in the first place (or not finding the Carp module)? Thanks for the help so far! -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II 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/ ___ 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] Problem building latest demeter on Debian 32bit Stretch
Well ... the beam just dumped, so let's see if I can figure this out
Demeter does not use Carp::Clan, so the version number of
libcarp-clan-perl is irrelevant.
This is a puzzler for me. I have never seen this problem over many,
many versions of perl. So there is something I don't understand about
your system. I cannot reproduce this problem, so it's going to be
difficult to resolve.
Try this:
Put
use Carp;
just after line 257 of lib/Demeter/Plot/Gnuplot.pm. Line 257 is the one
that says
{ no warnings 'redefine';
No guarantees, but maybe that'll help Let me know.
B
On 03/30/2018 10:19 AM, Al Kwiatkowski wrote:
Hello -
We're trying to install demeter on a 32-bit system running Debian 9.2
Stretch. The 'perl Build.PL' and 'Build' run into no issues, but when
we try running 'Build test' we get the following error messages:
t/001_base.t String found where operator expected at
/home/kwiatal/sources/demeter-master/blib/lib/Demeter/Plot/Gnuplot.pm line
273, near "croak "Couldn't unlink $self->{__error_log}: $!""
(Do you need to predeclare croak?)
syntax error at
/home/kwiatal/sources/demeter-master/blib/lib/Demeter/Plot/Gnuplot.pm line
273, near "croak "Couldn't unlink $self->{__error_log}: $!""
Compilation failed in require at
/home/kwiatal/sources/demeter-master/blib/lib/Demeter.pm line 244.
Compilation failed in require at t/001_base.t line 22.
BEGIN failed--compilation aborted at t/001_base.t line 22.
# Looks like your test exited with 255 before it could output anything.
t/001_base.t Failed 24/24 subtests
t/002_types.t ... String found where operator expected at
/home/kwiatal/sources/demeter-master/blib/lib/Demeter/Plot/Gnuplot.pm line
273, near "croak "Couldn't unlink $self->{__error_log}: $!""
(Do you need to predeclare croak?)
syntax error at
/home/kwiatal/sources/demeter-master/blib/lib/Demeter/Plot/Gnuplot.pm line
273, near "croak "Couldn't unlink $self->{__error_log}: $!""
Compilation failed in require at
/home/kwiatal/sources/demeter-master/blib/lib/Demeter.pm line 244.
The "croak" command not getting found appears to come from the "Carp"
perl module - we have version 6.06-1 of the 'libcarp-clan-perl' package
installed. Any suggestions as to what's causing this error? Again, the
'perl Build.PL' command shows no issues with the installed modules, but
since most of them were installed from the Debian repository, maybe
there's a discrepancy with the modules installed when we run './Build
installdeps'?
Thanks for any assistance -
Al Kwiatkowski
kwia...@phys.iit.edu
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--
Bruce Ravel bra...@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
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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Re: [Ifeffit] Athena crashes on windows10
Thanks, Lisa, I have been seeing a similar problem this week at the beamline. Some tests on my own computer make it clear that LCF is not working correctly in the current release. I will work on this as soon as possible, however, I am with users for a while B On 03/28/2018 01:56 PM, Lisa Bovenkamp-Langlois wrote: Hello. Me and other people running windows 10 have problems with Athena (demeter version 0.9.26). when switching to the LCF window the program crashes. I tested that indeed sometimes this happens when the list of data sets is long. However, it recently happened with only 3 data sets in the list. In one case Athena crashes at this same spot repeatedly. In other cases if works after restarting Athena or the PC. Is there a fix in sight or do I have to go back to windows7? Thanks, Lisa Lisa Bovenkamp-Langlois, PhD CAMD/LSU 6980 Jefferson Hwy Baton Rouge, LA 70806 Email: lbovenk...@lsu.edu <mailto:lbovenk...@lsu.edu> website: http://www.camd.lsu.edu/ ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II 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/ ___ 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] Report a bug
Once again, the fine manual is your friend: http://bruceravel.github.io/demeter/documents/Athena/import/columns.html#data-types-and-energy-units B On 03/19/2018 12:17 PM, Matt Noerpel wrote: Hello Zhengrui, It looks like you may be importing the data as XANES instead of u(E). There's a pulldown menu about halfway down the import screen labelled "Data type" where you can change that. Or you can hold down alt+ctrl and left click on the blue text near the top of the home screen that says "Datatype:XANES" to change it to "Datatype: xmu". I was able to plot it in k once the datatype was changed. I hope that helps, Matt On Mon, Mar 19, 2018 at 11:59 AM, Zhengrui Xu <z...@vt.edu <mailto:z...@vt.edu>> wrote: To whom it may concern, I found a bug when I am dealing with my data. I am using Windows system, and the software version is 0.9.26. I can plot my data in E, however, not in k, R and q. This problem happen to all of my data. My other three group members also have this problem. My raw data is attached for your review. We really appreciate your help. Best, Zhengrui Xu First-year PhD student Department of Chemistry Virginia Tech ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov <mailto:Ifeffit@millenia.cars.aps.anl.gov> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit <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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II 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/ ___ 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] Error in Atoms output
On 02/19/2018 06:23 AM, Kaustubh Priolkar wrote: We are trying to fit low temperature V K edge EXAFS data in V2O3. As per the cif files available (attached herewith – V2O3_10K data.cif) the structure is described by I2/a space group. When this file is read by ATOMS it gives an erroneous output ( attached herewith - feff.inp). In particular the values of V-O and V-V bond distances are not correct and do not match with bond distances reported in literature (Phys. Rev. B 2 (1970) 3771). Could anyone tell me where am I making a mistake. I am aware that I2/a is a non standard space group but I am not sure if I need to take any precaution while reading the cif file in ATOMS. Thanks and regards, Hi Kaustubh, Thanks for this bug report. This uncovered not one but two bugs in how Atoms handles monoclinic space groups. How economical! I will be pushing a fix to github soon and I will try to find some time to make a new windows installer. I should point out that, even with the bug fix, the distances using the CIF file you attached will not match Phys. Rev. B 2 (1970) 3771. The CIF file that you supplied is from doi:10.1016/S0022-4596(03)00295-0, which reports slightly different numbers for the undoped V2O3 compared to the 1970 paper. I have attached a feff.inp file that I think is correct. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II 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/ V2O3_feff.inp Description: chemical/gamess-input ___ 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] Artemis having trouble
On 02/04/2018 12:50 PM, Sheraz Gul wrote: Thank you for the suggestions. I have other project files in the same folder and they open fine. Anyways, I upgraded to Demeter version 0.9.26 pre 2 and somehow every project file opens fine now. Although, in the ini file, I had to correct the paths corresponding to exe files for gunplot and feff; otherwise, Athena/Artemis will crash before opening. Yesterday, I posted a new version of the Windows installer that should address the exe paths problem. I am pretty sure it is done correctly in the new installer. I was able to reproduce that problem on our beamline windows computer and I was able to verify that the new installer works (at least on that one computer). This installer also addresses a number of other issues that have come up in the last year. Details are in the change log on the Demeter website. I also made a new tag and new release on Demeter's github page. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II 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/ ___ 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] How to use Artemis with feff85L
Jose, I am unclear what you are sad about. The version of Feff has little to do with the quality of the analysis. See our recent paper: https://doi.org/10.1107/S1600577517011651 It is true that feff8l would simplify and streamline the code, making it easier to write and maintain. That's a bit incentive /for/ /me/ to do that work. But I think you are overstating the impact on the analysis you and others do with Artemis. B On 01/12/2018 07:15 AM, José Carlos Conesa wrote: OK Bruce, I understand. (Sigh) Good luck in your actual job. JC El 12/01/2018 a las 12:35, Bruce Ravel escribió: Yes. But I am pretty busy these with my new beamline. "Beamline scientist" is my actual job. "Software guy" is a side project. So the software work gets done when it gets done. B On 01/12/2018 05:25 AM, José Carlos Conesa wrote: Dear Bruce, Do you foresee that (in a not far future) Artemis may be adapted so that it can use the results of feff8.5L? All the best, El 12/09/2017 a las 19:11, Bruce Ravel escribió: Feff8L is not properly integrated into Artemis yet. Sorry. I have a new beamline these days. It's hard to find time to work on the software. This is on my to do list, but it's going to take a while. B On 09/12/2017 12:54 PM, José Carlos Conesa wrote: Hi, I should like to use feff85L within Artemis (from Demeter 0.9.25), just to check in my system whether selfconsistency has a role in unifying E0 values (with feff 6, allowing different E0 for each scatterer leads to E0 differences >10 eV, which seems too much to me). I find that after loading the EXAFS data (from Athena) and a model (a .cif file containing Cu, Ce and O atoms), if I click Run Atoms and then Run Feff with feff6 as executable I get the usual set of paths that allow me doing a fit of the data, but if I try to use the feff85L.exe that comes with the Demeter software (by changing the feff executable in the File/Edit preferences menu), after clicking the Run Feff button (without including the SCF card) a bit of computation happens and after finishing it the path list is empty. ¿Any idea of the possible reason why I get no path list? Thanks in advance -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II 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/ ___ 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] How to use Artemis with feff85L
Yes. But I am pretty busy these with my new beamline. "Beamline scientist" is my actual job. "Software guy" is a side project. So the software work gets done when it gets done. B On 01/12/2018 05:25 AM, José Carlos Conesa wrote: Dear Bruce, Do you foresee that (in a not far future) Artemis may be adapted so that it can use the results of feff8.5L? All the best, El 12/09/2017 a las 19:11, Bruce Ravel escribió: Feff8L is not properly integrated into Artemis yet. Sorry. I have a new beamline these days. It's hard to find time to work on the software. This is on my to do list, but it's going to take a while. B On 09/12/2017 12:54 PM, José Carlos Conesa wrote: Hi, I should like to use feff85L within Artemis (from Demeter 0.9.25), just to check in my system whether selfconsistency has a role in unifying E0 values (with feff 6, allowing different E0 for each scatterer leads to E0 differences >10 eV, which seems too much to me). I find that after loading the EXAFS data (from Athena) and a model (a .cif file containing Cu, Ce and O atoms), if I click Run Atoms and then Run Feff with feff6 as executable I get the usual set of paths that allow me doing a fit of the data, but if I try to use the feff85L.exe that comes with the Demeter software (by changing the feff executable in the File/Edit preferences menu), after clicking the Run Feff button (without including the SCF card) a bit of computation happens and after finishing it the path list is empty. ¿Any idea of the possible reason why I get no path list? Thanks in advance -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II 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/ ___ 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] data table for larch data group
On 12/22/2017 04:53 PM, Matthew Newville wrote: > > At the moment, No. But that should be easy and a very good idea to separate reading headers plus the data table from naming of the 1d arrays... Like, I often run into cases where I want to rename arrays after reading the file. I'll work on that. Cool. I was working on it this morning, but didn't like my solution. Hence the question. > I'd also like to be able to sensibly handle columns of non numeric data. Maybe that's too separate a topic Not this topic but a very good idea nonetheless. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II 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/ ___ 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] data table for larch data group
Matt, If I read an ascii file with read_ascii() like so: a = read_ascii(file) The "a" group has a data attribute which contains the entire data table as a 2D array. It also has 1D arrays for each column from the data table. Those 1D arrays have attribute names taken from the column labels. If I do something to change the data table, is there a function that I can call that repopulates the 1D arrays with the columns of the altered data table? For example: a = read_ascii(file) a.data is, say,
Re: [Ifeffit] current-amp recommendation
Hi Matthew, At NSLS-II, we use a solution developed here at BNL for quad BPMs and other current-measurement operations. (I am using it for ion chambers at my beam line.) It is a box developed in the Instrumentation Division with a current amplifier, an A2D converter, and a microprocessor all inside a box that's about the size of a box of Pop Tarts. It has 4 SMA input channels and a single gain for all four channels. SMA to BNC cables are readily available from all the standard vendors. The output is an ethernet cable. The microprocessor runs a small debian system and starts an EPICS IOC and a DHCP client on boot. the 4 current get exposed as 4 PVs and the IOC does a lot of useful statistics on the fly. Seems to work pretty well. You could contact Pete Siddons. (Search for Siddons at the BNL website. When I tried it, the second hit was his staff page.) B On 11/14/2017 03:16 PM, Matthew Marcus wrote: I've gotten involved with a project in which stabilization of the position of a monochromatic, soft X-ray beam is needed. The offending frequencies seem to be vibration frequencies like 57 and 116Hz. We have in mind to use a thin Au film with a gap in the middle, measuring the drain current from the films, much as people normally use the jaws of slits. Now, I'd like to find a couple of current amplifiers which are small enough so that they can be connected with very short cables to the BNC connectors on the air-side of this detector, and which would have decent frequency response and low noise with inputs of the order of 0.1-1nA. Although this topic is outside the realm of XAFS analysis with IFEFFIT, I figure that people on this group might have some good experience. mam ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II 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/ ___ 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] Hephaestus: Absorption Data Source
On 11/13/2017 11:15 AM, Daniel Przyrembel wrote: Still I can't see any reference to 'Keski-Rahkonen and Krause' in http://bruceravel.github.io/demeter/documents/Athena/hephaestus.html#absorption Here is the relevant bit from Feff: https://github.com/xraypy/feff85exafs/blob/master/src/COMMON/setgam.f Note that that bit in Feff is less sophisticated than you might think. My memory (Matt or John might remember better) is that Steve Zabinski (main author of Feff6) "interpolated" those values from the plots in the K paper. This was done with a ruler back in the days before we had software tools for such chores. I am not saying that the values in setgam.f are wrong -- just not as precise as you might imagine. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II 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/ ___ 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] How to use Artemis with feff85L
On 09/13/2017 09:35 PM, Matt Newville wrote: Then again, maybe Demeter does come with a working feff8l, and I just wasn't aware of it. Not yet. :( B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Ifeffit Digest, Vol 174, Issue 8
On 08/17/2017 05:16 PM, Bruce Ravel wrote: That's a thumbs-up from me, Hiroyuki. Carmelo set out to use Larch specifically to address the problem of processing many MANY files. I think Athena and PrestoPronto could both have a good place in anyone's toolbox. Although I was thrilled to hear that you got Larch+Demeter+Windows working, Hiroyuki. It is very gratifying that a third party -- not me, not Matt -- was able to do so. Whew! B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Ifeffit Digest, Vol 174, Issue 8
That's a thumbs-up from me, Hiroyuki. Carmelo set out to use Larch specifically to address the problem of processing many MANY files. I think Athena and PrestoPronto could both have a good place in anyone's toolbox. B On 08/17/2017 04:29 PM, Carmelo Prestipino wrote: Hi Hiroyuki, I done a small interface to Larch to work with a lot of files http://soonready.github.io/PrestoPronto/ It is not nice as Athena and it has not all its possibility but if you are used to Athena you should not get lost (the name of parameter is the same). It is not fast how it should be but give a try, maybe could be useful Carmelo On Thu, Aug 17, 2017 at 7:00 PM, <ifeffit-requ...@millenia.cars.aps.anl.gov <mailto:ifeffit-requ...@millenia.cars.aps.anl.gov>> wrote: Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov <mailto:ifeffit@millenia.cars.aps.anl.gov> To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> or, via email, send a message with subject or body 'help' to ifeffit-requ...@millenia.cars.aps.anl.gov <mailto:ifeffit-requ...@millenia.cars.aps.anl.gov> You can reach the person managing the list at ifeffit-ow...@millenia.cars.aps.anl.gov <mailto:ifeffit-ow...@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: How to use Larch as backend for Athena and Artemis on Windows (Bruce Ravel) 2. Re: How to use Larch as backend for Athena and Artemis on Windows (ASAKURA, Hiroyuki) -- Message: 1 Date: Wed, 16 Aug 2017 13:17:13 -0400 From: Bruce Ravel <bra...@bnl.gov <mailto:bra...@bnl.gov>> To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov <mailto:ifeffit@millenia.cars.aps.anl.gov>> Subject: Re: [Ifeffit] How to use Larch as backend for Athena and Artemis on Windows Message-ID: <1956f39f-85f4-7a92-a989-24a5436df...@bnl.gov <mailto:1956f39f-85f4-7a92-a989-24a5436df...@bnl.gov>> Content-Type: text/plain; charset=utf-8; format=flowed Hi Hiroyuki, Sorry I didn't respond yesterday. Yesterday was a bit of crazy day... I suppose that this is still a work in progress. I believe that Demeter works with Larch on Windows, but it is certainly not as easy or convenient yet as it should be. In the place where Demeter got installed on your computer, there is a folder called \perl\site\bin -- you can look at the properties of the Athena desktop icon to see where that is. In that folder is the "dathena.bat" file which the Athena desktop icon points at. You should also find a file called "lathena.bat". Try running that or pointing your desktop icon at it instead. The difference between "lathena.bat" and "dathena.bat" is line 25 that sets an environment variable that Demeter uses to decide which of ifeffit or larch to use. Obviously, there are number of other ways to get this environment variable set. The bottom line is, yes, there is a switch. The switch is the DEMETER_BACKEND environment variable. Unfortunately, that switch cannot be in the configuration files, although what you tired in item 2 of your email was a sensible guess. It turns out that the choice of larch/ifeffit has to made long before the configuration files are read. Do let me know how you get on. While Demeter + larch should work, there are still almost certainly problems. I need to get a new version of the Demeter installer out soon, so it would be nice to get some feedback in this area. As for using Demeter + larch + 100s of file -- it should work after a fashion. But I worry that Athena's performance might not be what you are hoping for. Athena does a lot of things that are more user-friendly than performance-friendly Cheers, B On 08/15/2017 06:10 AM, ASAKURA, Hiroyuki wrote: > Dear all, > > I would like to use the latest Larch as backend for Athena and Artemis > on Windows to handle hundreds of XAS data (, hopefully). > But, I'm stuck. I would appreciate any comments and suggestions. > > Matt announced it is now possible on this list, but I still cannot do it > on Windows. > > [Ifeffit] Larch 0.9.33 > http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2017-April/009091.html <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2017-April/009091.html> > >> The "serve
Re: [Ifeffit] How to use Larch as backend for Athena and Artemis on Windows
Hi Hiroyuki, Sorry I didn't respond yesterday. Yesterday was a bit of crazy day... I suppose that this is still a work in progress. I believe that Demeter works with Larch on Windows, but it is certainly not as easy or convenient yet as it should be. In the place where Demeter got installed on your computer, there is a folder called \perl\site\bin -- you can look at the properties of the Athena desktop icon to see where that is. In that folder is the "dathena.bat" file which the Athena desktop icon points at. You should also find a file called "lathena.bat". Try running that or pointing your desktop icon at it instead. The difference between "lathena.bat" and "dathena.bat" is line 25 that sets an environment variable that Demeter uses to decide which of ifeffit or larch to use. Obviously, there are number of other ways to get this environment variable set. The bottom line is, yes, there is a switch. The switch is the DEMETER_BACKEND environment variable. Unfortunately, that switch cannot be in the configuration files, although what you tired in item 2 of your email was a sensible guess. It turns out that the choice of larch/ifeffit has to made long before the configuration files are read. Do let me know how you get on. While Demeter + larch should work, there are still almost certainly problems. I need to get a new version of the Demeter installer out soon, so it would be nice to get some feedback in this area. As for using Demeter + larch + 100s of file -- it should work after a fashion. But I worry that Athena's performance might not be what you are hoping for. Athena does a lot of things that are more user-friendly than performance-friendly Cheers, B On 08/15/2017 06:10 AM, ASAKURA, Hiroyuki wrote: Dear all, I would like to use the latest Larch as backend for Athena and Artemis on Windows to handle hundreds of XAS data (, hopefully). But, I'm stuck. I would appreciate any comments and suggestions. Matt announced it is now possible on this list, but I still cannot do it on Windows. [Ifeffit] Larch 0.9.33 http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2017-April/009091.html The "server mode" for Athena and Artemis now works on all platforms and I strongly encourage everyone to use this over the ifeffit back end. Here is what I did. Environment: Windows 10 Pro (Japanese) Demeter 0.9.25 (via official website) Python 3.6 (official distribution) 1. Installation of the latest Larch git clone https://github.com/xraypy/xraylarch.git (sha1: 5a372cfe1368a8ac10c2ebfc5bef4e9a9a325f6d) cd xraylarch python setup.py install # Some dependency related to XRD is not fulfilled. 2. Start Larch server cd %LOCALAPPDATA%\Programs\Python\Python36\Scripts python larch_server start larch_server port=4966: started I found a parameter of peakfit backend in demeter.ini and changed to larch, but did not work (as expected). In the dathena.log, Athena still uses ifeffit as backend. perl version: v5.18.2 backend: ifeffit Should I compile Demeter package by myself to use the Larch backend? Or, is there any "switch" to use Larch? Thanks in advance, ASAKURA, Hiroyuki -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Demeter on Windows with Inkscape (and possibly other programs)
Windows users: I got an interesting bug report today from a fellow who develops a popular open source program for vector graphics editing (Inkscape). Apparently, there is a problem in Demeter's installer that has an impact on the ability of that program (and possibly others) in accessing system font files. The issue with Inkscape is described here: https://github.com/bruceravel/demeter/issues/51 I mention this here on the mailing list in an effort to help the folks who maintain Inkscape. If you use Demeter and Inkscape on your Windows machine, there is a problem and it is my fault :( The simplest solution is to uninstall Demeter, then continue using Inkscape. If that's not true or if someone needs a better solution right now, post here and I will help you work out a solution. I think the real fix to the problem is simple and I will work on a new installer this month. Cheers, B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Exporting Curves (as Data rather than Images)
On 06/26/2017 09:08 AM, Zhang, Guanghui wrote: Felix, After you finish the fitting, you can go to the "Data" window, data-> save data and fits as. There are also other save options you can try. relevant document page: http://bruceravel.github.io/demeter/documents/Artemis/data.html#the-data-menu Also relevant to this thread: http://bruceravel.github.io/demeter/documents/Athena/plot/other.html#single-file-output That single-file output option is available in both A & A. B -- Regards, Guanghui At 2017-06-26 02:36:16, "Felix E. Feiten" <fei...@cat.hokudai.ac.jp> wrote: Dear all, I think the title is almost enough explanation. I would like to export the data corresponding to fits, chi(k), fourier-transform and back-transform to plot them with a different software. I couldn't figure out how, can someone please help me? With kind regards Felix ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] FEFF8/FEFF9 in Demeter
My standard response to the feff9 question: http://bruceravel.github.io/SCFtests/scf.html B On 06/15/2017 02:55 AM, 이국승(에너지환경소재연구팀) wrote: Dear Ifeffit users, I remember that one of you have posted the method how we can use FEFF8/FEFF9 in Demeter program. But I cannot find the posting in the archives. Could you please kindly let me know how can I find it or directly write again? Best, Kug-Seung Lee Kug-Seung Lee, Ph.D. Staff Scientist Manager, 8C Nano Probe XAFS Beamline Pohang Accelerator Laboratory Pohang 790-784, Republic of Korea Office: +82-54-279-1522 Fax: +82-54-279-1599 C. P.: +82-10-6419-7801 Researcher ID: http://www.researcherid.com/rid/D-7088-2011 ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] nonsensical negative values / restrictions
Felix, When you fit your EXAFS data using Artemis + Ifeffit or Larch, you are using a Levenberg-Marquardt non-llinear, steepest descent algorithm. The fit does kn ow anything /at all/ about what you are trying to do. It doesn't know what a sensible value for sigma^2 or any other parameter is. All it knows is that you have data and a model that you are throwing at the data. Armed with data and model, the algorithm optimizes the parameters that you have flagged as the variables. It changes those values until it makes the sum of the paths look as much like the data as possible. It's goal is to make the red line look like the blue line. That's it. That's all it does. That's how sigma^2 can come out as a negative number. A negative sigma^2 or any other nonsensical parameter doesn't represent a failure of Artemis. It is information that is useful to you, the person doing the fit. A nonsense parameter is trying to tell you about a way that the model you have proposed does not represent the data that you have measured. And it is a hint about what changes you need to explore in your model to more properly represent the data. An example: suppose you have an unknown oxide phase and you have reason to believe it is some sort of highly disordered phase. Just to pull an example out of the air, you might think that your sample is filled with FeO(OH) when in fact it is filled with FeO. FeO(OH) is pretty disordered, whereas FeO is rocksalt. If you run Feff on Feo(OH), you will get a spread of paths at several distances for the first shell. When you make the fit with the FeO(OH) model, the structural contribution to the disorder is MUCH higher than in the actual sample. The fit is likely to use a negative sigma^2 to counteract that effect. That's a simple and contrived "explaining example", but it makes the point (I hope). Artemis didn't fail. The fit is trying to tell you that you assumptions were not realized in the data. In short, I agree that your results make no sense, but I suggest that the problem is that you are making a poor assumption in your fitting model. It also might be the case that there is a problem with the measurement of your data that introduces a systematic error that the fit compensates for by applying a weird parameter value. Or maybe you have a sulfide instead of the oxide you were expecting. Or maybe you ran Feff for the Pt K edge rather than the Pt L3 edge. (Oops! I actually do that with embarrassing frequency) Or something else I haven't thought of HTH, B On 06/16/2017 02:09 AM, Felix E. Feiten wrote: Dear all, I have the following problem: In some fits using Artemis (Demeter 0.9.25) I will get negative values for parameters where it makes no sense at all. For example, when trying to fit two first shell paths, Pt-Pt and Pt-O, for a Pt nanoparticle, sigma^2 for the Pt-O path becomes negative. Obviously, sigma^2 has to be a positive number. My questions: 1. Why does the fit algorithm do this? 2. What can I do to avoid this? I know that there are most likely significant problems with my fit if this behaviour occurs. As far as I know it's possible to impose restrictions in Artemis and if anyone could point me towards a tutorial explaining how to implement restrictions that might be a first step in the right direction. Currently, the chapter "Constraints and restraints" in the Artemis documentation is "Coming soon..". With kind regards, Felix ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Calculating Ce oxidation state at the L3 edge
On 05/16/2017 01:31 PM, Stephanie Laga wrote: I have a (hopefully) quick question about calculating oxidation state of CeO2 at the L3 edge. When calculating ox state by taking the ratio of peak areas, is the pre-edge feature for Ce included in this calculation? This point isn't clear to me from looking at various papers. I've attached an image from Bernardi 2015, which shows that the %Ce III calculation doesn't include the fitted pre-edge feature A. I'm not sure why this would not be included? Is this because we only consider 2p > 5d transitions and the pre-edge is 2p > 4f (forbidden) transition? I am not sufficiently knowledgeable about CeO2 specifically to answer your question specifically. However, there are some general principles that apply. The concept here is to come up with a set of peak shapes that describe the shapes of the end member spectra. Those two sets of peaks, taken together, represent the contribution to the spectra from each end member. Sum the areas of each set of peaks, that represents the contribution. You then fit all of both sets of peaks to an unknown spectrum and sum up each set. You now have enough information to quantify the amount of each end member. So, in general, yes, you would include the fitted peak A because that is part of your quantification metric. So, I disagree with the formula in the figure you attached. But peak A is small, so neglecting it has scant impact on the result. Some caveats: 1. You must be very careful about normalization. If you do not normalize consistently, then you will introduce systematic error in the phase quantification. 2. You must use the same step-like function for both end members and for the unknowns. If the step function changes, then the areas under the peaks will change, introducing systematic error. It would be interesting to compare this to linear combination analysis to see if you get the same answers HTH, B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Error importing data into Athena
Sharon, It's pretty important to ask questions in a way that aids and encourages answers. In this case, it's basically impossible to help given that you shared neither the error message nor an example of the data that triggered the error. /Good/ questions get good answers. B On 05/01/2017 02:18 PM, Bone, Sharon Elizabeth wrote: Hi, I’m running the current version of Athena on a windows 10 machine. It had been working fine, but now I get an error whenever I try to import new data (.dat file from SSRL). The error tells me the program can’t read the file and asks whether I need a plugin. Do I need a plugin? How do I uninstall and reinstall the program? I’m guessing this might be the best fix? Thanks! Sharon ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Silent Oxygen
On 04/18/2017 11:10 AM, Fuxiang Zhang wrote: Hi, all, I am in studying the EXAFS of perovskite and clearly see the split of the first peak after ion irradiation. It should come from a symmetry change, so I use a tetragonal model (instead the original cubic) which contains two independent O sites. However, after running Atoms and Feff, all paths are contributed by only one O atom and nothing related to another Oxygen atoms (see attached file). As a result it may be difficult to get a good fit of the first split Ta-O peaks. I am not sure if it is true or something wrong. Thank you very much A fairly common question here on the mailing list. This is a *feature* of Artemis, not a bug. http://bruceravel.github.io/demeter/documents/Artemis/extended/fuzzy.html If you want to /model/ a split in distance, you can drag that path into the path list twice and adjust the delta R and amplitude parameters accordingly. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Information content from Athena for Hamilton test?
On 04/09/2017 11:59 PM, Will Bennett wrote: How is this value of "Information Content" determined in Athena? This is not explained well in the manual. The number Athena reports is the fitting range of the data divided by the core-hole lifetime of the edge measured. I am not certain that is especially well-justified, but it seems like a reasonable approximation. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Conflicting FEFF calculation
On 04/04/2017 11:58 AM, Robert Gordon wrote: Seems to be looking for gnuplot in the wrong location. Gnuplot was installed to: C:\Users\ragordon\AppData\Roaming\DemeterPerl\c\bin\gnuplot not C:\Strawberry... Drat! I thought I had that working correctly. You can manually fix that in the preferences. Change Gnuplot-->program the the fully resolved path where it is installed. also, log has this: C:/Users/ragordon/AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Artemis.pm line 26 Which has the slashes in the wrong direction for windows...just something from the log writing or a linux-typo in the program somewhere? Don't know. Was there any context? B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Conflicting FEFF calculation
On 04/04/2017 01:42 PM, Ashis Biswas wrote: In the new pre-release version of Artemis I am getting similar paths for TAA regardless of the order of import. Therefore, the problem does not exist anymore. Thank you very much for your time and help. Whew! I was getting worried about that one! B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Conflicting FEFF calculation
On 03/27/2017 11:02 AM, Ashis Biswas wrote: Thank you very much for your reply. Here I am attaching two Artemis projects files (TAA_TPA and TPA_TAA), named according to their order of import. In my computer the paths for *TAA* are different in two project files. For example, i) in TAA_TPA project the Reff for three single scattering paths of O (@O1.1; @O3.1, and @O5.1) are different to that in TPA_TAA project, ii) the single scattering path @C5.1 (path number 6) at Reff of 2.682 A0 in TAA_TPA project is missing in TPA_TAA project, and so on. I am also attaching the papers from where the coordinates for TAA and TPA are obtained: TAA (Kamenar et al., 1993: tables 1 & 2; Fig. 1) and TPA (Pappalardo et al., 1983: Table 1; Fig. 1). I agree that the TPA_TAA.fpj project file that you sent me has incorrect data in the Feff tab for TAA. I have not, however, been able to reproduce that here. And not for want of trying -- I spent the last half hour trying to find a way to replicate what you are showing in the TPA_TAA file. Regardless of the order in which I import the two structures and regardless of whether I have discarded and reimported Feff calculations, when I click the "Run Atoms" button on the TAA cif file, I /always/ get the structure from Table 4 in the Kamenar paper. I cannot reproduce the Feff tab that you show in your TPA_TAA project file. I have no idea how you got into the state you show in the TPA_TAA project. It is clear that something went awry, but I don't know if it is an error of the program or of the user. I can't fix a problem I can't observe. I understand that this is not the answer you were looking for. I am simply not seeing the problem you are reporting. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Multiple data set fit limit
Victor, I now believe that you are seeing the problem you claim to be seeing, but it's going to take a lot of work for me to understand how you got there. When I import the Artemis project files you sent, I see that you have 24 copies of the FeS2 data in the project and you seem to be including 3 of them in the fit. I suspect the central problem here is that Demeter is making an ifeffit group for each copy of the data, even the ones you are excluding from the fit. This exceeds the normal compiled-in limit of 16. From a user interface perspective, I suspect that the sin is that Demeter blithely does this without warning you about Ifeffit's limit of 16 data sets. It is going to take me a long time to really track down all the things you have done to push at the boundaries of what Artemis + Ifeffit can do. I have not done much testing beyond a handful of data sets (neighborhood of 6). It's possible I have done no testing in double digits and I have clearly not done much testing up against Ifeffit's compiled-in limitation on number of data sets. Some suggestions: 1. Don't exceed 16 data sets, even if you are planning on clicking off the "include" button for some of them. In earlier email, when I said I do not see what you are observing, what I really meant was that if I do a fit with a handful of data sets, all of which are included in the fit, I see no such problem. 2. Try using Larch. Larch, not being a Fortran program, does not have Ifeffit's compiled in limits. That is not to say that Artemis+Larch will certainly work correctly with a large number of data sets (some of which are excluded from the fit) -- there most certainly could still be bugs in this untested regime. In any case, there are things that could be done to make it easier to identify the exact problem you are uncovering. I can see from examining your project files that you added a large number of copies of the data then hit the Fit button a couple dozen times before finally saving and sending me the project file. From my perspective as developer and bug-squisher, it is always better to see an example that is as minimal as possible. The more data you add after seeing a problem, the more times you hit the fit button after seeing a problem, the harder it is for me to track down the actual proximate cause of problems. I acknowledge that this was likely not the answer you were hoping for. I guess I am saying, take small steps as you build up a big, complex fitting model. It is true that a program written by a competent programmer should be able to take whatever you throw at it. Alas, Artemis was written by a dilettante. B On 03/18/2017 10:59 PM, Victor Streltsov wrote: Hi Bruce, Sorry for delayed reply. I didn't want to take up too much of your time and I have attempted to run more tests to reproduce the problem with other data and models. First, I thought that you were able to reproduce the problem (maybe partially) since you wrote: On 03/08/2017 10:53 AM, Bruce Ravel wrote: Well . a multiple data set fit using larch runs to completion and reports sensible values for parameters, but does not manage the data sets correctly. One obvious sign that something has gone wrong is the after-fit plot attached. Yikes! Similar behaviour I observed in my refinement using Ubuntu version of Demeter/Artemis/Ifeffit. Windows version works fine. (Switching to Linux version is related to my previous bug report about user input of epsilon which is still not available under Windows (until next release), but fixed in the latest Linux version(s)) The task I was running included 3 data sets and a model with 55 paths. However, the "Monitor/Debug options/Show mode status" in Demeter/Artemis shows content with 330 paths instead of expected 3x55= 165, if I understand correctly this option. It seems that it counts all added and previous replaced/removed data sets (extra 3 datasets which were not included and even removed). It doesn't effect Windows based run, however, creates the problem I mentioned before using the same project file under Linux. Is number of paths a compiled-in limit (less than ~300 or so) in Linux/Ifeffit? To avoid any possible problems caused by my model and data I used available for Artemis example FeS2 data for test runs. I have simply added many the same FeS2 data sets in the Artemis but included only 3 data sets to actual fit. Extra unused data sets did not affect at all the fit of 3 data sets under Windows, however, the problem reproduced using Linux version. I have attached (zip) project files, log files and contents file (mode status) for both runs under Windows and Linux. I hope it is more helpful. Victor -Original Message- From: Ifeffit [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Bruce Ravel Sent: Saturday, 11 March 2017 1:17 AM To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.a
Re: [Ifeffit] Conflicting FEFF calculation
On 03/21/2017 09:10 AM, Ashis Biswas wrote: I have a problem of conflicting FEFF calculation for tris(acetate-O)arsenic [As(OCOCH3)3] (TAA) and tris(phenyl thio)arsenic [As(SC6H5)3] (TPA); respective cif and atom input files are attached. In Artemis, when I import TAA after TPA, the paths obtained for TAA from FEFF calculation are different compared to the scenario when I import and calculate the path for TAA at first. The problem is similar in both computers with Windows 7 home premium 64 bit operating system and 0.9.24 version of Demeter and Windows 7 professional 32 bit operating system and 0.9.25 version of Demeter. I have even tried a scenario, where I discarded both FEFF objects after getting inconsistent results for TAA and then imported TAA at first without restarting Artemis and I got wrong paths again, indicating software can remember from last calculation. Any explanation for this problem will be deeply appreciated. I don't observe this using the input data you supplied and the recipes you describe. I have no idea what TAA is supposed to look like, but the atoms list and the path list are identical regardless of the order in which I import your two files. You will need to find a way to demonstrate to me better how to see what you are seeing. Perhaps if you saved Artemis project files that I could then open on my own computer B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] [Question about XANES] Hello I'm a graduate student in Korea
Doyoub's question is a common enough one that I added a section to the Athena user manual: http://bruceravel.github.io/demeter/documents/Athena/bkg/short.html My answer to Doyoub's question is much the same as Matt's. B On 03/17/2017 09:18 AM, Matt Newville wrote: Dear Doyoub, On Thu, Mar 16, 2017 at 10:59 PM, 김도엽(신소재공학과) <mdyk...@postech.ac.kr <mailto:mdyk...@postech.ac.kr>> wrote: Hello I'm a graduate student at POSTECH in Korea. Currently, I obtained XANES spectra over a narrow energy range and looked through the Athena manual But, I'm kind of lost as to how exactly I'm supposed to normalize raw data which only has XANES spectra. It would be very generous of you if you help me figure this out It's hard for us to answer questions that are so vague. Generally, it is recommended to collect XANES spectra out to at least 100 eV (and better 300 eV) above the edge in order to get a decent normalization. Well, for "normal" hard X-ray spectra: for edges below about 3000 eV, you can often get by with less energy range. If you don't have that, it is sometimes OK to pick an energy as far above the edge as possible and pick an edge step so that all the spectra is 1.0 at that energy. That is definitely prone to systematic biases in normalization. Furthermore, if your data is particularly noisy, it can add a lot of variation in the normalization to use just a single energy. Which just brings me back to the original point: it's hard to say in general how to best handle XANES with a short energy range. --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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Ifeffit Digest, Vol 169, Issue 9
On 03/14/2017 06:15 AM, Abhinav Prabhakar wrote: Attached is the CIF file in question. The crystal is Tobermorite 14A, taken from COD website. Abhinav, I don't understand the contents of the CIF file in the context of the copy of the International Tables that I have in front of me. The list of equivalent positions given in the CIF file just doesn't seem to be right for space group 9. The CIF file is clearly using the C axis as the unique axis since the z coordinate is the negated coordinate. But the list of positions does not correspond to any of the three cell choices. While this could be a problem in Artemis, I am inclined to think that the authors of the paper cited in the CIF file made some kind of non-standard choice for the setting of their crystal. As I said before, Artemis does what the International Tables tell it to do. If the author of a crystallography paper makes some non-standard choice, Artemis won't know how to deal with it. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Data export and coordination number
On 03/13/2017 09:48 AM, Abhinav Prabhakar wrote: i) Is it possible to extract the normalized/background corrected data from Athena (in E-,k- and R- space) and export it as numbers (to Excel perhaps)? This is explained in the manual. ii) Using Artemis, how can coordination numbers (N) be expressed as 'guess' parameters (Artemis allows only numerical values for N)? This has been discussed many times on this mailing list. You cn find that by searching the archives. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Space group type in Artemis
On 03/11/2017 05:56 AM, Abhinav Prabhakar wrote: Hello, I have a question about the working of Artemis as a new user. Artemis does not recognize the space group B11b. When importing a cif file of a crystal with this symmetry, it sends a prompt message that the space group symbol cannot be recognized. As a result, I changed it to P11b and it works. But would this change any crystal information (for eg. Degen, Reff values) significantly? I am not a crystallography expert in any sense. When I wrote Artemis, I meticulously followed what I found in the fourth edition of the International Tables for Crystallography, Volume A. Every symbol defined in there is recognized by Artemis. (Well, I guess I should say that every symbol is /supposed to be/ recognized by Artemis. If one is missing, that's a bug and should be reported.) "B11b" is not a symbol that I found in my copy of ITC volume A. As Robert suggested, there may be a way to rotate group 9 so that "B11b" is an interpretable symbol in the abstract. But Artemis does not know how to do that. (Nor do I.) "P11b" is a setting for space group #7. If, as Robert suggests, your CIF file is for space group #9, then the answer to your last question is yes. It is plainly obvious that using a different space group will change the degeneracies and distances. Of course, you did not bother to include a copy of the CIF file in question to your original email, so it is not actually possible for Robert or I or anyone else to actually help you effectively. At the risk of sounding like an annoyingly broken record, everyone should take the time to ask a good question or write an actionable bug report: http://bruceravel.github.io/demeter/documents/SinglePage/help.html http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Multiple data set fit limit
On 03/09/2017 05:15 AM, Victor Streltsov wrote: 3 data set refined to completion with sensible refined parameter, however, R-factor for 3^rd data set is 1. (overall R for 3 data set is huge too) and after-fit plot for 3^rd data set is missing, only experimental one shown. I am using latest versions of programs. Again, I don't see this behavior on my own computer. It is always better to /show/ something to me than to /explain/ something to me. If you are unwilling or unable to make an actionable bug report, then there isn't anything that I am going to be able to do for you. It is not my intent to be difficult. You are telling me about things that I cannot reproduce on my own computer. Despite my explicit request for a more useful bug report, you are not showing me how to see what you are seeing. If you cannot do something to make this conversation more productive, then I am just going to stop responding. http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Multiple data set fit limit
On 03/08/2017 10:53 AM, Bruce Ravel wrote: Well . a multiple data set fit using larch runs to completion and reports sensible values for parameters, but does not manage the data sets correctly. One obvious sign that something has gone wrong is the after-fit plot attached. Yikes! This turned out to be a few Larch syntax problems. I just checked a fix into github. As far as I know, the head of github has an Artemis that works for single and multiple data set fits with Larch or Ifeffit. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Multiple data set fit limit
On 03/08/2017 09:37 AM, Bruce Ravel wrote: On 03/08/2017 09:31 AM, Matt Newville wrote: Can Artemis use Larch? Yes. B Well . a multiple data set fit using larch runs to completion and reports sensible values for parameters, but does not manage the data sets correctly. One obvious sign that something has gone wrong is the after-fit plot attached. Yikes! Shouldn't be too hard to fix. A single data set fit with larch or any fit with ifeffit works as I expect. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Multiple data set fit limit
On 03/08/2017 09:31 AM, Matt Newville wrote: Can Artemis use Larch? Yes. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Multiple data set fit limit
On 03/08/2017 03:46 AM, Victor Streltsov wrote: The Linux latest version of Artemis limits multiple data set fit to 2 data sets. The input takes any number of data sets but 2 sets is used in the fit only. I’ve tried latest available windows version it uses more than 2 in fit (e.g. I used 3). That does not seem to be true. I just ran a three-data-set fit on my Ubuntu 16.04 machine. If you need to me to do something, you will need to submit a more informative bug report. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] downloading Demeter
To those who have noticed that Demeter has not been available for download in the last day or so: I use Amazon's S3 service to distribute the large installer files. You may have seen the news in the last 12 hours about a massive outage of that service, or you may have noticed that other internet resources that you use are unresponsive. There is nothing I can do to resolve this problem. Eventually Amazon S3 will come back on line and you will again be able to download Demeter. Please be patient and try again later. Regards, B Example news article: https://techcrunch.com/2017/02/28/amazon-aws-s3-outage-is-breaking-things-for-a-lot-of-websites-and-apps/ -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Limitations of maximum number of points in a data file in Athena
On 02/28/2017 08:17 PM, Harishchandra Singh wrote: Hi All, I have a query regarding limitation of maximum number of data points (or maximum size) of data file in to be imported in Athena. It would be great to hear form you all. It would be helpful to tell us what you are trying to do. Your questions, as asked, is vague and open-ended. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Units for various parameters of ‘feffNNNN.dat’ file
On 02/28/2017 11:09 AM, Samy Ould-Chikh wrote: I am a bit surprised about φc and φeff. I was expecting radian unit... Sorry, as Matt said, phase is intended to be interpreted as radians. I suppose that was stated unclearly. Phi is added to 2*k*R. k*R is [Ang^-1]*[Ang], which is unitless and interpreted as radians. And I forgot about that page in the Larch manual. It's great that Matt captured that in the modern documentation. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Units for various parameters of ‘feffNNNN.dat’ file
On 02/28/2017 10:10 AM, Samy Ould-Chikh wrote: Dear Ifeffit mailing list, I have a question which concern units and I can’t find the answer in the Feff manual. In a FeffNNN.dat output file, what are the unit of the numbers (if any) corresponding to φc, |Feff|, φeff, the reduction factor, λ, Re(p) Samy, This is a peculiar reference, but I think the clearest written explanation of this is in the manual for the ancient "feffit" program. Here is a copy of its manual: http://cars.uchicago.edu/~newville/feffit/feffit.pdf You will want to look at page 22. While the rest of the manual is not so useful anymore (in the sense that there are very few users of the old feffit remaining), it's explanation of how the feff.dat files are used is excellent. Eq. 6.1 should clarify how each term is used and what the units are. Column 1 is, of course, inverse Angstroms. Columns 2, 3, and 4 are unitless. The two phase terms go into the argument of the sine, thus must be unitless. The amplitude term is multiplied by N and S02, thus is also unitless. The reduction factor, as well, is unitless -- it is used in the computation of the amplitude term in equation 6.1. Lambda has units of angstroms, the real part of p (which is the complex wavenumber used in the Feff calculation) has units of inverse Angstrom. I am pretty certain I got all that right. I think it would be a good idea to capture all of this information as well as eq. 6.1 in the Artemis manual. HTH, B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] command buffer input
I still don't really understand the problem. You are describing something I haven't seen before but you're not giving me any way to visualize or reproduce the problem. Are you telling me that the command buffer window does not look like this on certain Windows computers? http://bruceravel.github.io/demeter/documents/Artemis/monitor.html#the-command-buffer Does it help to resize the window? B On 02/21/2017 03:03 PM, Karl-Michael Schindler wrote: Am 21.02.2017 um 20:17 schrieb Bruce Ravel <bra...@bnl.gov>: OK you didn't tell us exactly what you tried to do, you didn't tell us what you expected to happen, and you didn't tell us what actually happened. I don't know if this a bug report or a question or something else? B OK, I try again. In Artemis I select the menu Monitor → Show command buffer and the corresponding panel Ifeffit & Plot Buffer opens. In this panel i use the command prompt to enter commands like write_data or others. The problems is that unter Windows Server I do not get an active cursor in the text filed of the command prompt and i cannot enter any character, what ever i try and yesterday it also happened under Mac OS X → VirtualBox → Windows XP. Today the latter works again, but the trouble with the Windows Server is permanent. So, what could be the reason, why I cannot use the command prompt and how can i fix it? My main use of this is to export data for further processing in IgorPro. My current workaround is to check the files in the folder Stash and load the data from there. Michael. ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] command buffer input
OK you didn't tell us exactly what you tried to do, you didn't tell us what you expected to happen, and you didn't tell us what actually happened. I don't know if this a bug report or a question or something else? B On 02/20/2017 07:22 AM, Schindler Karl-Michael wrote: Hi. I used to issue some commands in the command field of the command buffer panel, mainly to export arrays with data with write_data. At least i thought so. However, now i cannot enter commands any longer. Can someone give me a hint? Michael. ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Calculation of metal concentration (and hence density) from Edge Jump
This might help: https://doi.org/10.1107/S1600577514001283 Note that we measured a sequence of standards of known thickness and concentration /prior/ to the rest of the experiment, so the methodology in that paper might not be useful after the fact in the absence of that prep work. B On 02/20/2017 10:19 PM, pushkar shejwalkar wrote: Dear All, First of all, is it possible to calculate the concentration of metal (loading, therefore) from just the edge jump? Is there a simpler equation like knowing the Flux values or some basic instrumental information we can calculate the concentration term using Io and It values of beamline (the simplest form of Beer-lambert law)? if so what formula should we use. I searched in the mailing list archive and have found one such archive but it discusses how to use calculation to find out how much sample would be needed to get the edge jump. I am rather interested in the reverse way. I have an experimental edge jump and want to calculate (if possible with as much accuracy as possible) the concentration of metal. I know with only edge jump it will be difficult and XRF will be a better and more reliable way. But for better understanding and cross checking between different samples, I wish to do such calculations. Can anyone guide me to the right direction and equations to do such calculations? Thank you all in advance Warmest regards Pushkar -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Tokyo-to Japan ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Trigonometric Function in GDS
I've never seen that before. You have provided no context. Without some context, I cannot be expected to provide an answer. http://bruceravel.github.io/demeter/documents/SinglePage/help.html B On 02/06/2017 10:36 AM, Mikhail Solovyev wrote: Hello to all. I am encountering an issue when trying to input a trigonometric function in my GDS window. When trying to fit the data, i get what appears to be an error GDS: 'FeN0' function_2 And it applies to every GDS that has the trig function in it. What exactly does the function_2 mean? Thank you. ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] XEAFS fitting problems
On 01/30/2017 04:31 PM, Fuxiang Zhang wrote: Dear all, I am new for XAS analysis and now working on solid solution alloys with EXAFS measurements. Here are some general questions about EXAFS fitting that may need your help. 1. In NiCoCr alloys, I always get obvious smaller ss for the pairs of Ni-Cr or Co-Cr than Ni-Co (0.002 vs 0.008-0.011), when measuring the K-edge of Ni and Co, does it suggest that Cr is favorably bonded with Ni and Co? Possibly, but I'd be skeptical. That sort of alloy is not one of the strengths of XAFS. The backscattering amplitudes of elements close in Z number are pretty similar, making it difficult in a numerical sense to distinguish them. Z-numbers that differ by only 3 or 4 are very hard to distinguish in XAFS. As a result, I would expect uncertainties on your sigma2 values to be rather large. I would also expect correlations between the various amplitude and sigma2 parameters to be high. As a result, I think you would have trouble making a strong and defensible argument. I would certainly be a skeptical reviewer of a manuscript claiming this unless it had a very compelling argument backed up by strong data from another measurement or from theory. 2. In order to get the bond length of different pairs in binary AB system, can I use formula alpha1*Reff and alpha2*Reff to refine the length of pairs of A-A, A-B (simple cubic symmetry)? The "alpha*reff" thing is a way of expressing all the DeltaR parameters of a purely cubic crystals using a single parameter. That is the only situation in which that formula is, strictly speaking, applicable. https://speakerdeck.com/bruceravel/discussion-of-the-fes2-exafs-analysis-example?slide=9 It is a mistake to think that there are magical formulas that can be memorized to make EXAFS analysis easy. No such things exist. Every way of parameterizing the terms in your EXAFS analysis in Artemis must be defensible in the context of the model you are using to try to understand your data. What I mean by defensible is that you can explain to the reviewer of a paper or to a member of your thesis defense jury why the fitting model is reasonable, why you chose to use that parameterization, and how that model helps to answer the scientific question without introducing an unsupportable approximation or some other form of systematic uncertainty. So, the answer to your specific question is "Maybe". 3. The selection of k range in Fourier transformation Parameters seems to have some effect on the fitting results, how to select the range in order to get reasonable results. This has been discussed plenty in recent months on this mailing list and Scott discussed it at some length in his book. Executive summary: include /data/ in the FT range, not noise. If the measurement is dominated by statistical or systematic uncertainty after some value of k, don't use that part of the measurement. HTH, B Many thanks Fuxiang Zhang ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] GNU plot crashes
Marcus, Without a reproducible recipe, I cannot observe this problem in action. So I don't know how I can help. A bit of googling quickly turned up a situation involving a conflict between libgtk versions. Since you didn't offer any information about the environment in which you are running the software, there is, again, nothing I can do to help. B On 01/31/2017 06:07 AM, mfehse wrote: Hi everyone while working in athena project gnu plot sometimes crashes and gives the following error: Gdk:ERROR:/build/gtk+2.0-KsZKkB/gtk+2.0-2.24.30/gdk/gdkregion-generic.c:337:miSetExtents: assertion failed: (pExtents->y1 < pExtents->y2) Aborted (core dumped) Its a bit strange because I have not observed this error when working with other athena projects before and it also does not happen every time I want to plot something, only sometimes. It seems quite random to me. I have attached the athena project file so you can try yourself many thanks marcus ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] delR and sigma2 models for multiple Scattering Paths
On 01/18/2017 01:27 PM, Mikhail Solovyev wrote: I'm currently trying to Artemis fit a molecule that is highly symmetric with multiple scattering paths playing a large role. delR and sigma2 have been handled rather well for all of the single paths. I am, however, confused as to how to handle it for multiple scattering paths. Reff for them seems to be close to the value of the furthest atom, but is always ~5-10% off. (which would be my second question, how is Reff determined for multiple scattering paths) I've looked at the presentation and examples, such as FeS2. I am trying to incorporate all of the same variables used in single scattering paths for multiple scattering paths the best i can. Mikhail, The definition of Reff is /always/ "half-path-length". For a single scattering path, this is trivial. It's simply the inter-atomic distance. For a multiple scattering path, you add up the length of each leg, then divide by 2. For the case of strictly collinear multiple scattering path, Reff is the distance between the two atoms farthest apart. However, if there are scattering angle that are something other than 0 or 180 degrees, Reff will be related to interatomic distances via some kind of trigonometric relationship that has to do with scattering angles. You are wise to try to build constraints between SS and MS paths in your fit. For DeltaR parameters, trigonometry helps, but may only be an approximation. Possibly a good approximation, but an approximation nonetheless. Scott discusses how to parameterize sigma^2 in his book: https://www.amazon.com/XAFS-Everyone-Scott-Calvin/dp/1439878633 There are some situations (see https://doi.org/10.1103/PhysRevB.54.156) where MS sigma^2 can be related exactly to SS. In general, though, MS sigma^2s usually can only be approximated by constraint with the SS sigma^2s. https://speakerdeck.com/bruceravel/discussion-of-the-fes2-exafs-analysis-example?slide=6 HTH, B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] error when fitting in Artemis
On 12/22/2016 12:11 PM, George Sterbinsky wrote: I have attached an Artemis project. Upon opening the project, and clicking the fit button the error in the attached log file is generated and the fit is not run. Looking at the history, fits have been run previously without error. The error message indicates Feff may need to be run again, but upon opening the Atoms and Feff window and then clicking on the Feff tab, I see the Run Feff button is grey and cannot be clicked. What steps are necessary in order to run a fit? Hi George, Sorry it has taken so long to respond. Partly holidays, partly that I have been doing a bunch of work on Demeter that needed to get finished. So, the problem here does not seem to be a problem with Artemis. It seems to be an issue with someone's antivirus software. The artemis.fpj is simply a zip file with a different file extension. Opening it up, one finds a folder called "feff". In the case of your project file, the relevant subfolder is "azxqc" (that's a randomly generated 5-character string, which is how Demeter names most things internally). In that folder, there should be a "phase.bin" file from the Feff run. It's absent. Instead, I see a file called "0_Warning.txt", the contents of which read: BLOCKED FILE ALERT A file has been blocked due to the 'Blocked for exchange' rule. Context: 'phase.bin' Disallowed due to Ticket Number: '09e8-5852-0da2-0001' See your system administrator for further information. Copyright 1999-2013 McAfee, Inc.All Rights Reserved.http://www.mcafee.com Now, I do not know if this happened when you mailed the project file to the list or if it happened at some other time. While the error message is certainly misleading in this case, I think that it is Artemis' way of complaining about the missing phase.bin file. Perhaps there is some other problem at play. I don't know. But I cannot possibly troubleshoot that other problem given that an anti-virus package has, at some point, irretrievably damaged this project file. I think that the only plausible work-around is Robert's suggestion. Reimport the feff.inp file, rerun Feff, exclude the existing path, drag-and-drop the replacement path, then push path parameter values from the old path to the new one. Awkward, but I don't know what else to suggest. B PS: If anyone has any kind of working knowledge of McAfee or any other AV software, I would be open to a suggestion for how to fix this. Is it a file /name/ problem -- should phase.bin be called something else? Is there something in the phase.bin file that triggered McAfee? Any wisdom would be welcome. -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Ifeffit Digest, Vol 167, Issue 2
On 01/03/2017 03:32 PM, Raj kumar wrote: From XRD, it is confirmed that there is no side phase formation and contamination. Hence, i guess the heavier element role could be avoided here. Raj, While this might be true for your sample, in general, a statement like this always concerns me. From XRD, you can say is that there is no /crystalline/ side phase formation and that there is no contamination in the /diffracting/ /portion/ of the sample. It is very common when preparing nanoparticulate matter for there to be non- or poorly-diffracting content in the sample. If that content contains the absorbing element, then it will have an impact on the XAS data. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Ifeffit Digest, Vol 166, Issue 12
Robert,
It seems you are sort of cherry picking through the code.
When I first wrote Xray::Crystal, I spent a lot of time pouring over
chapter 5 of ITC volume A. I am mostly confident that the various
transformations are applied correctly in response to space group symbol
choices. Demeter does that by applying a transformation to place the
positions under the alternate symbol onto the setting of the standard
symbol (*) then transforms back after applying symmetry operations.
Again, my goal was to build the cluster correctly but without concern
for alignment to a particular set of axes.
None of this is to say that I do not welcome actionable bug reports, but
emphasis is on the "actionable".
B
(*) "Standard" means "has an entry in chapter 7 of ITC Volume A", as
opposed to being tabulated in Chapter 4. Atoms tried to recognize all
the symbols in Chapter 4, but it transforms coordinates to the standard
settings before applying symmetry operations.
Obviously, a program like Atoms need not work that way. It could simply
apply symmetries encoded in any symbol from Chapter 4. But Atoms does
what I described.
On 12/21/2016 08:22 PM, Robert Gordon wrote:
Hi Bruce,
I looked at Site.pm and Cell.pm as well (and I don't program in perl, so
please forgive
any naivete).
In Site.pm, lines 188 - 191, it says:
#-- rotate from F or C settings to P or I
if ($is_tetr) {
($x, $y) = ($x-$y, $x+$y);
};
and this looks like a 45 degree rotation to me, and I can understand why if
someone specified a cell that was "c-centred tetragonal" which is really P
or face-centred tetragonal being I, but is it being applied to all
tetragonal systems?
In Cell.pm, lines 516 - 521, it says:
## rotate a tetragonal group to the standard setting
if (($crystal_class eq "tetragonal" ) and ($setting ne 'positions')) {
my ($a, $b) = $self->get(qw(a b));
$self->a($a/sqrt(2));
$self->b($b/sqrt(2));
};
but I see a re-scaling, not a rotation.
Possibly related: When I look at Site.pm on my linux box, from line 134
on, it is almost all
purple. z and utag are highlighted in red, as is $self on line 138. The
file looks normal
on github, but if I copy it, these colour changes manifest. I normally
associate
blue with comments, purple with text strings, green for $self...
thanks,
-R.
On 12/21/2016 12:58 PM, Bruce Ravel wrote:
On 12/21/2016 02:50 PM, Robert Gordon wrote:
So, for all but tetragonal, the orientation of the cluster can be
identified with the
orientation of the crystal axes. Does it not seem more logical to
preserve the
apparent orientation with respect to the crystal axes so that, when
using POLARIZATION
(issues in FEFF6 aside), confusion is less-likely?
Hmm ... I think I understand your point.
I think you may be ascribing too much agency and intelligence to the
the Atoms algorithm. The way Atoms works these days is to use this
tabulation of chapter 7 of volume A of the International Tables:
https://github.com/bruceravel/demeter/blob/master/lib/Xray/Crystal/share/space_groups.db.PL
It selects the symmetry operations appropriate to the specified space
group and applies them to the list of unique coordinates. In the case
of a space group with multiple settings, it uses some heuristics to
try to guess the correct setting. (That's what things like "b_unique"
and so on are all about. Those heuristics often fail.) It expands
out a unit cell and weeds through the unit cell to identify duplicates
(i.e. high symmetry positions that repeatedly generate the same
location when the symmetry operations are applied). It then stacks up
enough unit cells to contain the cluster, then translates fractional
coordinates to Cartesian coordinates.
At no point in that operation does the program make any decisions on
the basis of the definitions of the Cartesian axes.
None of this is a value judgment on what you have said or on Raj's
original question -- I'm simply explaining how the program works.
There just isn't an obvious mechanism in the code to let the user
orient the cluster in a certain way. That's an interesting idea, but
not something available at this time.
To use Feff's polarization, you have to choose a polarization vector
appropriate to the cluster as written. Or, I suppose, write your own
tool to rotate the cluster to a more convenient orientation.
B
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Synchrotron Science Group at NSLS-II
Building 743, Room 114
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Homepage:http://bruceravel.github.io/home/
Software:https://gi
Re: [Ifeffit] Ifeffit Digest, Vol 166, Issue 12
On 12/21/2016 02:50 PM, Robert Gordon wrote: So, for all but tetragonal, the orientation of the cluster can be identified with the orientation of the crystal axes. Does it not seem more logical to preserve the apparent orientation with respect to the crystal axes so that, when using POLARIZATION (issues in FEFF6 aside), confusion is less-likely? Hmm ... I think I understand your point. I think you may be ascribing too much agency and intelligence to the the Atoms algorithm. The way Atoms works these days is to use this tabulation of chapter 7 of volume A of the International Tables: https://github.com/bruceravel/demeter/blob/master/lib/Xray/Crystal/share/space_groups.db.PL It selects the symmetry operations appropriate to the specified space group and applies them to the list of unique coordinates. In the case of a space group with multiple settings, it uses some heuristics to try to guess the correct setting. (That's what things like "b_unique" and so on are all about. Those heuristics often fail.) It expands out a unit cell and weeds through the unit cell to identify duplicates (i.e. high symmetry positions that repeatedly generate the same location when the symmetry operations are applied). It then stacks up enough unit cells to contain the cluster, then translates fractional coordinates to Cartesian coordinates. At no point in that operation does the program make any decisions on the basis of the definitions of the Cartesian axes. None of this is a value judgment on what you have said or on Raj's original question -- I'm simply explaining how the program works. There just isn't an obvious mechanism in the code to let the user orient the cluster in a certain way. That's an interesting idea, but not something available at this time. To use Feff's polarization, you have to choose a polarization vector appropriate to the cluster as written. Or, I suppose, write your own tool to rotate the cluster to a more convenient orientation. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Ifeffit Digest, Vol 166, Issue 12
Robert, You have me confused. You seem to be saying that using the correct space group symbol is important. I couldn't possibly disagree. Raj's original question had to do with the fact that two different versions of atoms, which used different algorithms for interpreting the crystal data, resulted in clusters that were rotated relative to one another. My answer, appropriate (I think) in that case, was to shrug. You seem to be commenting on something unrelated to the original question, but I'm not understanding the point. B On 12/21/2016 01:13 PM, Robert Gordon wrote: Hi Bruce, The atoms.inp file attached is for bct Fe. In symmetry I4/mmm, the resulting feff input has the coordinates rotated, while in Immm the resulting coordinates are not rotated relative to the crystal axes (i.e. in Immm the 2nd near neighbour is obvious as a lattice constant away in each direction). So, with no polarization, the results for scattering paths are the same (using CRITERIA default), as expected Path # Degen Reff Scattering Path Type Rank I4/mmm Rank Immm 1 8 2.48 fe1 ss 100 100 2 4 2.835 fe2 ss 37.56 37.56 3 2 2.92 fe3 ss 17.59 17.59 4 16 3.897 fe1-fe1 ms 3.42 3.42 5 32 3.897 fe1-fe2 ms 12.83 12.83 7 16 3.94 fe1-fe3 ms 6.37 6.37 Now consider with POLARIZATION 1 0 0 (and 1 1 0 for I4/mmm) # Degen Reff Scatt. Path Type I4 1 0 0 I4 1 1 0 Im 1 0 0 4 2.48 fe1 ss 100 4 2.48 fe1 ss 7.89 8 2.48 fe1 ss 100 100 4 2.835 fe2 ss 55.45 2 2.835 fe2 ss 62.05 62.05 16 3.897 fe1-fe1 ms 4.41 9.90 15.43 16 3.897 fe1- fe2 ms 19.03 21.58 21.59 For that first multiple scattering path, the scattering angles are 36.1/90 for I4(1 0 0), 55.1/55.1 for I4(110) and for Im(100) they are 55.1/124.9. The ranking of this path is not the same, and the plots for this path differ as well - in shape as well as amplitude. Conceptually, the Immm model calculation has the atoms aligned with the crystal lattice and the I4/mmm has the atoms rotated. FEFF sees a difference, and I would take the Immm result as the correct one based on the positions of the atoms in the cluster relative to the axes. -R. On 12/21/2016 6:49 AM, Bruce Ravel wrote: On 12/19/2016 11:01 PM, Robert Gordon wrote: What if one were to do this FEFF calculation using the POLARIZATION card? 1 0 0 means something different if the atom positions have been rotated by 45 degrees relative to the crystal axes along which the polarization is defined. Well ... you could rotate the polarization vector by 45 degrees ... I guess I have always considered FEFF's polarization card to be an a posteriori addition to the feff.inp file -- i.e. a decision that the user makes after using Atoms to convert crystal data to a cluster in feff.inp. B ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Ifeffit Digest, Vol 166, Issue 12
On 12/19/2016 11:01 PM, Robert Gordon wrote: What if one were to do this FEFF calculation using the POLARIZATION card? 1 0 0 means something different if the atom positions have been rotated by 45 degrees relative to the crystal axes along which the polarization is defined. Well ... you could rotate the polarization vector by 45 degrees ... I guess I have always considered FEFF's polarization card to be an a posteriori addition to the feff.inp file -- i.e. a decision that the user makes after using Atoms to convert crystal data to a cluster in feff.inp. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Web Atoms 1.8 vs Demeter 0.9.26: feff output are not same
On 12/16/2016 10:34 AM, Raj kumar wrote: Recently, i found out that feff.inp generated by web atoms and Demeter 0.9.26 are not the same. My main worry is in the position of atoms. For evidence, i am attaching YbVO4 (*feff.inp*) files generated by both web atoms and Demeter. With this kind of zircon type structure, one would except V1_2 at position *x/2+c/4* (3.85250). In web atoms generated file, i could see this relation clearly, while in Demeter generated file the relation reads like *x/2+y/2+c/4* instead of earlier condition. Furthermore, all atoms (except few) are represented with three coordinated position for Demeter generated file instead of two coordinated position. Hi Raj, I don't acknowledge that there is a problem. It is certainly true that the two files have the atoms list rotated by 45 degrees relative to one another, but all the distances are the same. Although I only investigated at the level of running feff on each one and examining the first few dozen items in the path list, it seems these two feff input files yield identical results. So ... what's the problem? B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Problems with gnuplot graphics on Mac OS 10.12.1
On 12/08/2016 10:19 PM, Paul Fons wrote: Hi All, I just wanted to give an update to my earlier problems with the mysterious gnuplot errors. After editing the file Matt mentioned earlier, I decided to uninstall and install demeter to no avail. I then realized that I had been relying on the latest version of xquartz (the x11 system) and installed x11 using macports. After a bit of trouble with installation (I had to break the installation into pieces — but this is a typical macports problem), the x11 installation completed and athena worked fine. Thus my conclusion is that there was some sort of weird interference between x11 subsystems. In any case, all is well now. Hi Paul, Glad it worked out. I don't quite understand what happened. If you have any suggestions for what I can add to the Mac installation instructions to help the next poor soul, that would be great. http://bruceravel.github.io/demeter/documents/SinglePage/macinstallation.html B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] error message when trying to reopen Artemis file
On 12/02/2016 09:01 AM, Bruce Ravel wrote: Your cif file triggered a very specific bug in my software that has nothing to do with your recent difficulties. Had you picked almost any other cif file for any other material, you would have been fine. I am guessing you chose this one: http://www.crystallography.net/cod/cod/cif/7/20/60/7206075.cif or something very similar. Demeter makes a mistake parsing the space group symbol in that file. Try this: http://cars9.uchicago.edu/atomsdb/TiO2-ana.inp It seems to work correctly without triggering the specific problem that the cif file triggers which, again, has to do with the specific symbol used and how Demeter parses it. Thanks for reporting this. I'll work on it. I just pushed a fix for this to github. The project file you sent me is not fixable (well ... not easily). The best thing to do is to discard it and start again. Thanks again for uncovering a fairly obscure bug! B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] error message when trying to reopen Artemis file
Marcus,
Your cif file triggered a very specific bug in my software that has
nothing to do with your recent difficulties.
Had you picked almost any other cif file for any other material, you
would have been fine.
I am guessing you chose this one:
http://www.crystallography.net/cod/cod/cif/7/20/60/7206075.cif
or something very similar. Demeter makes a mistake parsing the space
group symbol in that file.
Try this:
http://cars9.uchicago.edu/atomsdb/TiO2-ana.inp
It seems to work correctly without triggering the specific problem that
the cif file triggers which, again, has to do with the specific symbol
used and how Demeter parses it.
Thanks for reporting this. I'll work on it.
B
On 12/02/2016 06:07 AM, mfehse wrote:
Hi
so i have created a little Artemis project to practice. Its tio2 data
file with anatase cif file, i just included teh first path but havent
done any fitting yet. When i close artemis and want to reopen it I get
the following error:
"You must define a method name at
/usr/lib/i386-linux-gnu/perl5/5.22/Class/MOP/Mixin/HasMethods.pm line 96
Class::MOP::Mixin::HasMethods::has_method('Class::MOP::Class::Immutable::Moose::Meta::Class::__ANON__::SERIAL::1=HASH(0xe06c454)',
'') called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm
line 442
Demeter::Atoms::parse_line('Demeter::Atoms=HASH(0x106b5394)', ' :')
called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm
line 465
Demeter::Atoms::parse_line('Demeter::Atoms=HASH(0x106b5394)', 'space
= I 41/a m d :1') called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm
line 390
Demeter::Atoms::read_inp('Demeter::Atoms=HASH(0x106b5394)') called
at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm
line 200
Demeter::Atoms::__ANON__('Demeter::Atoms=HASH(0x106b5394)',
'/home/marquinhos/.horae/stash/_dem_djyzliqy/feff/gflkw/atoms.inp', '')
called at accessor Demeter::Atoms::file (defined at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm
line 204) line 10
Demeter::Atoms::file('Demeter::Atoms=HASH(0x106b5394)',
'/home/marquinhos/.horae/stash/_dem_djyzliqy/feff/gflkw/atoms.inp')
called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Atoms/Xtal.pm
line 667
Demeter::UI::Atoms::Xtal::open_file('Demeter::UI::Atoms::Xtal=HASH(0x1312b8e0)',
'/home/marquinhos/.horae/stash/_dem_djyzliqy/feff/gflkw/atoms.inp')
called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis.pm
line 1388
Demeter::UI::Artemis::make_feff_frame('Wx::Frame=HASH(0x127f5b3c)',
'/home/marquinhos/.horae/stash/_dem_djyzliqy/feff/gflkw/atoms.inp',
1010942) called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis/Project.pm
line 351
Demeter::UI::Artemis::Project::read_project('HASH(0x102e8084)',
'/home/marquinhos/Desktop/TIO2_tryout.fpj') called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis.pm
line 1026
Demeter::UI::Artemis::OnMenuClick('Wx::Frame=HASH(0x127f5b3c)',
'Wx::CommandEvent=SCALAR(0x12ab14cc)') called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis.pm
line 440
Demeter::UI::Artemis::__ANON__('Wx::Frame=HASH(0x127f5b3c)',
'Wx::CommandEvent=SCALAR(0x12ab14cc)') called at demeter/bin/dartemis
line 31
eval {...} at demeter/bin/dartemis line 31
"
i have attached the project so you can try if you can open it on your
artemis
many thanks
marcus
On 01/12/2016 19:26, Bruce Ravel wrote:
On 12/01/2016 01:20 PM, mfehse wrote:
and am now able to launch the athena and it seems to work, however i
still get the error message:
"Could not find Larch Server -- falling back to Ifeffit"
is this something i should care about?
Nope.
It's a message that will eventually go away. Right now, Matt and I
are working on migrating to Larch. This week we have been figuring
out how to make Athena's interaction with Larch work reliably. That
message is there so that I know what is going on while I am working on
the code. In this case, it is Demeter telling you that it is
gracefully recognizing that you do not have Larch installed.
If you don't want to be looking at the head of the main branch, then
you could download the zip file for the most recently tagged release:
https://github.com/bruceravel/demeter/tree/0.9.25
B
--
Bruce Ravel bra...@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 743, Room 114
Upton NY, 11973
Homepage:http://bruceravel.github.io/home/
Software:https://github.com/bruceravel
Demeter: http://bruceravel.github.io/demeter/
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Re: [Ifeffit] problems installing athena et al under ubuntu 16.04 LTS
I just checked a fix into github that addresses the problem Juan identified. Matt's assessment at https://github.com/bruceravel/demeter/issues/42 was exactly right. I adopted his second solution. Thanks to all of you for this discussion. B On 11/25/2016 05:23 AM, Juan de la figuera wrote: Hi, I send one of the data files we are currently acquiring (SPLINE beamline at ESRF). I have checked that my compiled 0.9.24 version works with the examples cu10k.dat file, but it is true, as Robert confirmed, that strange things happen if you mark ev instead of kev. With our data files like the one enclosed, dathena chokes on the scale. Actually it opens the window but it has x10^9 scale. On the other hand, the 0.9.24 for Windows opens the files ok. Now, the files are MSDOS-ended files, I tried converting them to Linux-ending, but same result. I also tried putting a # comment on the first line. I stress that Athena 0.8.061 (included in the horae package in ubuntu) opens the file like a charm. One additional detail (just in case), I have Ubuntu 16.04 LTS 64-bit. Best, Juan ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] struggling to install demeter under ubuntu 16.04
On 12/01/2016 01:20 PM, mfehse wrote: and am now able to launch the athena and it seems to work, however i still get the error message: "Could not find Larch Server -- falling back to Ifeffit" is this something i should care about? Nope. It's a message that will eventually go away. Right now, Matt and I are working on migrating to Larch. This week we have been figuring out how to make Athena's interaction with Larch work reliably. That message is there so that I know what is going on while I am working on the code. In this case, it is Demeter telling you that it is gracefully recognizing that you do not have Larch installed. If you don't want to be looking at the head of the main branch, then you could download the zip file for the most recently tagged release: https://github.com/bruceravel/demeter/tree/0.9.25 B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] struggling to install demeter under ubuntu 16.04
Sorry. That wasn't quite right. At the command line: DEMETER_FORCE_IFEFFIT=1 dathena to force the use of Ifeffit in that instance of Athena. Or, export DEMETER_FORCE_IFEFFIT=1 later, dathena That forces the use of Ifeffit in that instance of the shell so that, later, when you fire up Athena, it uses Ifeffit. Or put the "export" line in your .bashrc to make it persist the next time you log in. B On 12/01/2016 01:18 PM, Bruce Ravel wrote: On 12/01/2016 12:57 PM, Juan de la figuera wrote: Is there a switch in demeter to select the backend? Or in other words, to go back to ifeffit, should I delete the larch binaries? At the command line: export DEMETER_FORCE_IFEFFIT=1 dathena or put export DEMETER_FORCE_IFEFFIT=1 in your ~/.bashrc file B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] struggling to install demeter under ubuntu 16.04
On 12/01/2016 12:57 PM, Juan de la figuera wrote: Is there a switch in demeter to select the backend? Or in other words, to go back to ifeffit, should I delete the larch binaries? At the command line: export DEMETER_FORCE_IFEFFIT=1 dathena or put export DEMETER_FORCE_IFEFFIT=1 in your ~/.bashrc file B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] struggling to install demeter under ubuntu 16.04
On 12/01/2016 09:12 AM, mfehse wrote: In my struggle to install demeter under ubuntu 16.04 I'm slowly advancing. I think some of the packages that were supposed to be installed following the first line of the protocol were incomplete. I have redone this and have now managed to build the dathena and other files, but when I want to start it I get the following error message: "marquinhos@marquinhos-Lapi:~/demeter$ bin/dathena Could not find Larch Server -- falling back to Ifeffit Can't locate object method "new" via package "Graphics::GnuplotIF" at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter.pm line 239. Compilation failed in require at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Athena.pm line 24. BEGIN failed--compilation aborted at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Athena.pm line 24. Compilation failed in require at bin/dathena line 27. BEGIN failed--compilation aborted at bin/dathena line 27. Can't exec "-p": No such file or directory at /home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Larch.pm line 270. " any ideas what might be the problem? That seems to be saying that Graphics::GnuplotIF is not installed. It should have been installed when you did the "./Build installdeps" step. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] your mail to the ifeffit mailing list
So, where did the dathena script get installed on your computer? B On 11/30/2016 10:49 AM, mfehse wrote: thanks for the quick reply. I just registered with the mailing list today, i didnt add any address. Concerning your remarks for my installation problem your two hints resulted in this: marquinhos@marquinhos-Lapi:~/demeter$ echo $PATH". "./Build /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin. ./Build marquinhos@marquinhos-Lapi:~/demeter$ hash -r marquinhos@marquinhos-Lapi:~/demeter$ dathena No command 'dathena' found, did you mean: Command 'athena' from package 'horae' (multiverse) dathena: command not found marquinhos@marquinhos-Lapi:~/demeter$ hash -r didnt do much im afraid and about the path im not sure what this is supposed to tell me. As you might have noticed im not a frequent terminal user and I think this cpan/ perl/ demeter installation is probably the trickiest thing i have ever done, so please excuse my lack of experience -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Athena bug
On 11/29/2016 08:11 AM, S.Rowe wrote: I have been experiencing a bug in Athena, this is occurring in the most recent version 0.9.25, as well as the older versions I have used. The big is occurring when using the difference spectra window to produce difference spectra for a set of data. When I use the 'Plot difference spectra for all marked groups' function it will produce the plot but if I change any parameters in the main window and want to check how this has changed the difference spectra it will only plot the original difference spectra. To see the new difference spectra after the changes have been made I need to close Athena down completely and open it up again. If I just close the project and load in new data and try to plot the difference spectra for this new set of data it will still only plot the difference spectra for the old data. I have attached an Athena project file, please let me know if there is something different I need to do to change the difference spectra plot. Kind regards, Sinead Rowe Sinead, I am having trouble reproducing this problem, but I am suspicious that Athena might be getting confused if the Standard is also one of the marked spectra. Athena should exclude the Standard from the list of marked groups, but clearly is not doing so. When you observe this behavior, what group from the file is selected as the Standard? Is it "BiFeO3_410C"? Does the problem get better if you unmark that group (i.e. unclick its checkbutton in the groups list)? Since I am having trouble reproducing the problem, it would help if you could give me a click-by-click recipe for reproducing the problem. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Athena bug
Hi Sinead, I have a long list of chores waiting for me after the holiday that just finished here in the States, but I will get to your difference spectrum issue just as soon as I can. B On 11/29/2016 08:11 AM, S.Rowe wrote: Dear all, I have been experiencing a bug in Athena, this is occurring in the most recent version 0.9.25, as well as the older versions I have used. The big is occurring when using the difference spectra window to produce difference spectra for a set of data. When I use the 'Plot difference spectra for all marked groups' function it will produce the plot but if I change any parameters in the main window and want to check how this has changed the difference spectra it will only plot the original difference spectra. To see the new difference spectra after the changes have been made I need to close Athena down completely and open it up again. If I just close the project and load in new data and try to plot the difference spectra for this new set of data it will still only plot the difference spectra for the old data. I have attached an Athena project file, please let me know if there is something different I need to do to change the difference spectra plot. Kind regards, Sinead Rowe ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Problems with gnuplot graphics on Mac OS 10.12.1
Hi Paul,
I have a hard time understanding how that happens, but I have a couple
ideas. Let's look into the simpler one first.
In the installation location of Demeter, there is a file called
lib/Demeter/templates/plot/gnuplot/marker.tmpl
It should look exactly like this:
https://github.com/bruceravel/demeter/blob/master/lib/Demeter/templates/plot/gnuplot/marker.tmpl
Could you check to verify that that file has not been altered in any way?
If that file is ok, then we'll dig deeper.
B
On 11/28/2016 02:35 PM, Paul Fons wrote:
Hi All,
I have installed demeter using Macports on 10.12.1 and while
hephaestus seems to run normally, athena has some trouble with graphics.
The usual athena perl based panel shows up just fine, but upon loading
some data, there is always an error when gnuplot is invoked to plot
graphics (as reproduced below). It would seem that the command “set” is
missing the first letter. Does anyone have a suggestion as to what to
check to fix this?
Axion:perl5.24 $ use_macports.sh athena
gnuplot> et label '{/Symbol \305}' at 400.7,853.0387 center front
textcolor ls 12
^
line 0: invalid command
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--
Bruce Ravel bra...@bnl.gov
National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 743, Room 114
Upton NY, 11973
Homepage:http://bruceravel.github.io/home/
Software:https://github.com/bruceravel
Demeter: http://bruceravel.github.io/demeter/
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Re: [Ifeffit] error on installing demeter on MacOSX 10.9.5
Y'know, this mailing list isn't only a place where you can ask questions. It is also a place where you can search and /find/ answers. From less than three weeks ago: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2016-November/008866.html B On 11/23/2016 11:54 AM, christophe den auwer wrote: Dear all, I am trying to install Demeter on OS 10.9.5 and I am stuck! I installed Xcode 6.2 fine with the licence agreement and everything. Then I installed MacPort 2.3.5 fine as well. I also checked updated version and everything worked fine. Then I tried to install Demeter and got stuck with the following lines : Error: org.macports.archivefetch for port libcxx returned: archivefetch failed for libcxx @3.9.0_0+universalError: Failed to install libcxx Please see the log file for port libcxx for details: Error: Processing of port demeter failed I attached to my message, if of any use, the full procedure and feedback from terminal window. If someone could help that would be really great!!! Thanks a lot Christophe - Christophe Den Auwer Professeur Institut de Chimie de Nice Université de Nice Sophia Antipolis 06108 Nice, France 0492076362 christophe.denau...@unice.fr <mailto:christophe.denau...@unice.fr> -- -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Athena crashing with "Larch_Server not found"
On 11/14/2016 03:29 PM, Frederik Eistrup wrote: Now, followed again the instructions and ran into new problems. Can't get over the "./Build test" (terminal output: screen_message_Frederik_test.txt) and "./Build install" gives error (terminal output: screen_message_Frederik_install.txt). What is the problem now? Im very sorry for not being able to solve it myself! Frederik, Not sure. At the command line, in the directory where you are running "./Build test" could you do the following command instead: prove -bv and capture /all/ the screen output. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Athena crashing with "Larch_Server not found"
rederik/perl5/bin/dathena line 31/ So, where is the problem? Can anyone helo with this? Made sure larch was installed through sudo apt-get install, but all stays the same. Thanks for any help! Frederik David Hughes' guide to Demeter Installation on Ubuntu ... <https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.html> bruceravel.github.io David Hughes' guide to Demeter Installation on Ubuntu¶ These instructions cover a non-root manual build of Bruce Ravel's Demeter package under Ubuntu 12.04. Found out that Athena ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] athena LCF issue
Thanks Fred. Simple enough to fix. As you said, it is mostly a bit of a nuisance message. In any case, it will be fixed in the next release (whenever that is...). B On 10/28/2016 12:16 PM, fred.mosselm...@diamond.ac.uk wrote: Dear Bruce, I realise you may be travelling soon , This is not a very serious bug as I have work rounds. I was demonstrating linear combination fitting in Athena using the gold thiobacteria example this week. I am using 9.25 on a windows 7 computer. I read in all the data from the cynaobacteria project file I mark 5 or 6 standards In the LCF tab I use marked groups, untick the sum weights to 1 option leaving just the all weights between 0 and 1 option selected. I pick a sample spectrum eg 4.73 I select fit all combinations It rolls through them and reports the apparently correct results but an error message is reported: Redundant argument in sprint at C:/… /AppData/Roaming/DemeterPerl/perl/site/lib/Demeter/UI/Athena/LCF.prm line 780, line 122 Clicking any of the answers in the combinatorics tab brings up this error again. If I do a fit of lot of spectra using the same set of standards, I get a similar error message except this time it is line 906 and some of the combined spectra don’t plot properly until you refit them as a single spectra in the standards tab I attach a log file but not a project as I assume you can find that on github! Regards Fred J.F.W. Mosselmans Prinicipal Beamline Scientist I18 Diamond Light Source Ltd Diamond House Harwell Campus Didcot OX11 0DE P + 44 1235 778568 M + 44 7785510211 E fred.mosselm...@diamond.ac.uk -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Athena and "norm" file groups
Read these: http://bruceravel.github.io/demeter/documents/SinglePage/bugs.html http://bruceravel.github.io/demeter/documents/SinglePage/help.html You "question" isn't one that I can realistically answer. I have no idea what the problem is and you have not provided enough information to replicate your problem on my own computer. I can only give a good answer when asked a good question. B On 10/15/2016 04:06 PM, Mike Massey wrote: Hi everyone, Apologies if this has been covered before, I'm just getting around to upgrading to Demeter. I have a bunch of old project files with a mishmash of data from different sources, and I'm having trouble getting them to work fully with the new software. Any group with a data type of "xmu" (energy space) seems to work as expected, but any group with a data type of "norm" (normalized data) doesn't seem to work properly when it comes to spline or post-edge background subtraction (which is handy if I want to do LCF, for example). Is this a bug or a feature? Has anybody yet developed a workaround? Any thoughts or advice would be greatly appreciated. The ultimate workaround is to use different data, but I'd like to use existing projects if possible (saves a lot of time and brain damage). Cheers, and thanks! Mike ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] General question
On 10/13/2016 05:17 PM, Dimitar Popmintchev wrote: I would like to ask, after a fit (in Artemis) which column in the output file gives the uncertainty for peaks position dR (R+/-dR i.e. 3+/-0.02 Angstroms) ? Error bars are not propagated in Artemis currently. That's something you, the user, has to do using the math expression that relates your variable(s) to the delta R in question. The simplest common case is one where you have guess delr = 0 then later, for some path, reff = 3.0 deltaR = delr In that case, delr is varied and the path length is 3.0 + delr. Propagating the uncertainty in this case is trivial: delta( 3.0 + delr) = delta(3.0) + delta(delr) 3.0 is a constant, so the error bar in the path length is the same as the error bar in the variable. HTH, B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Artemis crash on import
ata 2016-10-13 14:52:35.148 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:38.016 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data 2016-10-13 14:52:38.017 perl5.24[20180:991862] CFPasteboardRef CFPasteboardCreate(CFAllocatorRef, CFStringRef) : failed to create global data Oct 13 14:52:38 perl5.24[20180] : Window Server is not available. Oct 13 14:52:38 perl5.24[20180] : Window Server is not available. Segmentation fault: 11 ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Smoothing aligned data in Athena
Hi Ian, Thank you for a very clear and well articulated bug report. It is much appreciated. This was a simple one to fix. When I implemented the boxcar filter in Athena, I neglected to copy the energy shift value from the noisy group to the smoothed group. Oops! I just pushed a fix to github which will be included in the next windows installer. If you would like to mend the copy of Athena on your computer, it's a small edit, as shown here: https://github.com/bruceravel/demeter/commit/a84e5fb605cef26dd4be42bba46924264d941900 Thanks, B On 09/28/2016 11:33 AM, Godfrey, Ian wrote: Dear All, I have a bug to report when using the Athena data smoothing feature with aligned data. Exemplar project and log files are attached, along with a screenshot. I am running Windows 10 x64 with Athena 0.9.25 x64. Summary: When using the data smoothing feature in Athena with data that has previously been aligned using the alignment feature, the smoothing is performed on the non-aligned data, and the resulting, processed dataset is shifted in E. Recipe: Open Athena Import a dataset that has a reference channel Import a second dataset with reference Import a standard dataset, with a slightly off alignment wrt to the first two datasets (I imported all three from Athena projects, rather than raw datafiles) Use the alignment tool to align the reference channel of one of the datasets to the standard (I used the automatic alignment) Go to the smoothing tool. You can immediately see that the smoothed curve is in the wrong place for the aligned dataset. The dataset that wasn't aligned will appear correctly Many thanks, Ian Ian Godfrey PhD Student, UCL/JAIST Programme Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London and School of Materials Science, Japan Advanced Institute of Science and Technology i.godf...@ucl.ac.uk <mailto:i.godf...@ucl.ac.uk> i.godf...@jaist.ac.jp <mailto:i.godf...@jaist.ac.jp> ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Ni(I), Ni(II), and Ni(III) Reference XAS required
On 09/19/2016 02:49 AM, mazhar iqbal wrote: Hello Can some please provide me the standard XAS of Ni(I), Ni(II), and Ni(III). Mazhar, You probably need to be more specific about what you want. There are /lots/ of Ni compounds. No one here knows what you work on, so no one here can possibly know which standards you are looking for. As always, vague, open ended questions are unlikely to get a response. Clear, concise questions usually do. Please read: http://bruceravel.github.io/demeter/documents/SinglePage/help.html B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] artemis doesn't read user's epsilon(k)
This has been fixed and pushed to the head of the GitHub repository. The fix will be included in the next Windows installer. B On 08/29/2016 09:55 AM, Bruce Ravel wrote: Victor, You are correct. That is shockingly broken. I'll let you know when and how it gets fixed. B On 08/28/2016 04:20 AM, Victor Streltsov wrote: Hi Bruce, Epsilon(k) input “A user specified values for measurement uncertainty” in Artemis does not change the default value determined by Ifeffit. It assumes that input is a value of 0. I’ve tried the latest Artemis versions for Windows and Linus and they both behave the same. Best regards, Victor Streltsov ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Saving Bug
On 09/10/2016 07:03 PM, Matteo Busi wrote: It occurs when I try to save groups to files, it seems that the saving option change the output while it shouldn't. When I save using the "Save current group as ..." option I get the full log with many columns, whereas when I save using the "Save marked group as ..." option I only get 2 columns. (I saved only as xmu and norm but I guess it is occuring for every extension) I do not see this behavior. It's not that I don't believe you, it is that you have not provided enough information for me to see the problem on my own computer. I need to know things about the state of Athena that should be contained in the project file. Specifically, I want to know that you have actually marked groups before trying to "Save marked groups as ..." So, post a project file that displays this behavior AND provide an explicit recipe of mouse clicks so I can reproduce it on my computer. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Help in background removal with Athena
On 09/06/2016 10:55 AM, Irina Pi wrote: Thank you for the quick answer. Which range should I have for the EXAFS analysis to be meaningful? Like 200eV above the edge? I am always uncomfortable when newcomers ask for "rules". Having a rule without understanding when and why it might apply seems counter-productive. Firstly, lets discuss the relation ship between "energy above the edge" and photoelectron wave number. The conversion constant between energy and wavenumber is k = sqrt( ETOK * (E-E0) ) where ETOK is the appropriate combination of fundamental constants (2m_e / hbar^2, where m_e is the mass of the electron and hbar is Planck's constant) about equal to 1 / 3.81. So, 10 inverse Angstroms is about 381 volts above the edge. The extent of the signal in k determines how well you can interpret an EXAFS signal in a quantitative sense. See this page in the Athena manual: http://bruceravel.github.io/demeter/documents/Athena/plot/krange.html Scott Calvin discusses this in his book. There is more information about EXAFS data reduction among the tutorials at http://xafs.org/Tutorials. As Fred and Robert have said, you need "enough" data range to make a useful interpretation of the EXAFS. 200 eV is not a lot -- that will leave you with only a small handful of independent measurements in your data, possibly not even enough to reliably determine a first shell bond length. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Phase correction not working in Athena
On 08/31/2016 09:05 AM, Sebastian George wrote: I hope that I am writing this in the correct place, and if I am not, I apologize. The problem I'm having is pretty much summed up in the Subject line. I'm analyzing some experimental EXAFS data in Athena, and it seems that ticking the "phase correction" box has no effect on my Forward Fourier transform. Has anybody run into this problem, and if so, were you able to fix it? The material I'm studying is amorphous SmCo. Could it be that having multiple backscattering species or a lack of crystalline structure causing problems for the phase correction? You didn't think to say so, but I am assuming you are using a Windows computer. The phase correction has been broken for a while in the Windows installer. I noticed that last week. Happily, I noticed it in time for the recently posted 0.9.25 release of the Windows installer. If you got to the Demeter homepage and grab the latest, you should find that phase correction now works. If any of my assumptions were wrong (understandable given that you provided little information), let me know and I will continue to look into the problem. More generally, I'm wondering how exactly this phase correction is determined anyway. If used, is it the sort of thing that can put the first peak in my FT fairly close to the true nearest neighbor distance? In Athena, nothing is known about the scatterers, so the phase correction is only for the central atom part of the phase shift in the EXAFS equation. The central atom phase shift data used by Athena is simply a static tabulation computed using Feff6. Perhaps a better phrased question is: when can the phase transformation be expected to give a quantitatively accurate radial distribution (in terms of peak positions), Basically never. In rare situations, it might be possible that the first peak of a phase-corrected FT might approximate an RDF for the first neighbor in some sense. But I caution you against thinking about it that way. You are more likely to be wrong than right. Here's a dose of wisdom from Shelly from many moons ago: http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg00171.html and when is it more likely to only be qualitatively useful? Always. The Fourier transform of chi(k) is not a radial distribution function. I am going to say that again all caps because this point is so important that I want to yell it at you. THE FOURIER TRANSFORM OF CHI(K) IS NOT A RADIAL DISTRIBUTION FUNCTION. * chi(k) includes multiple scattering * chi(k) includes a complex scattering factor * For heavy elements, the magnitude of the complex scattering factor has a lot of structure, resulting in a sort of Ramsauer-Townsend effect -- see https://speakerdeck.com/bruceravel/the-ramsauer-townsend-effect-in-x-ray-absorption-spectroscopy * chi(k) can have scattering atoms at very close distances and the contributions from those scatterers can overlap in surprising ways * chi(k) has a sigma^2 term * chi(k) has a mean-free-path term For all of these reasons, the FT of chi(k) is just chi(R). It is not a radial distribution function. That said, when we analyze chi(R) in Artemis, we extract information from the fit that can be used to reconstruct partial pair distribution functions. Also, I would have assumed that a backscattering species would need to be given in order to calculate the phase shift, but I haven't found anywhere to do that. Have I missed something? Nope. But in Athena, nothing is yet known about the scatterers. Correcting the FT for the full phase shift is a chore that cannot be done until something is known about them. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] artemis doesn't read user's epsilon(k)
Victor, You are correct. That is shockingly broken. I'll let you know when and how it gets fixed. B On 08/28/2016 04:20 AM, Victor Streltsov wrote: Hi Bruce, Epsilon(k) input “A user specified values for measurement uncertainty” in Artemis does not change the default value determined by Ifeffit. It assumes that input is a value of 0. I’ve tried the latest Artemis versions for Windows and Linus and they both behave the same. Best regards, Victor Streltsov ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] pgplot and ifeffit installation on current linux systems
Hi Anselm, Things change over time and there are a lot of slightly different linux distributions out there. If you get to a point where you can build correctly on Arch and would like to contribute an how to or some modifications to build scripts, that would be great. I would be more than happy to see that your contributions get used or linked to as appropriate. B On 08/26/2016 07:33 AM, Loges, Anselm G wrote: Dear all, I hope this is the right platform for my question. If not, sorry to bother anyone. The question: Has anyone successfully installed pgplot and ifeffit on a recent Arch Linux system and could provide a quick how-to guide (also for the Demeter website maybe)? Although I have not yet tested it, my problem may also be relevant for current Debian/Ubuntu systems. Here's the situation: I am trying to install ifeffit on a current Arch Linux machine and therefore need to install pgplot first. The PGPLOT_install script on the respective GitHub page (as linked by a tutorial on the Demeter page, see links below) does not work because it relies on several outdated paths to dependencies. The one culprit I was able to isolate and fix was the path to the X11 libraries, which the script looks for here: /usr/X11or /usr/X11R6 but in current Arch Linux (at least in mine, which is Manjaro to be precise, link below) is here: /usr/share/X11 This alone does not fix all problems, there are several dependencies missing in the X11 directory and I could not find out what the actual relevant package names are in Arch (Debian/Ubuntu names cannot be found). Also the config files of pgplot seem to have a bunch of similar problems that (at least partially) seem to stem from use of an old fortran-to-c translator (f2c) instead of the gcc fortran frontend and missing dependencies for that. If I am not mistaken, the latest Ubuntu LTS (16.04.) also has the /usr/share/X11 path, so the script should not work there either. I'd be happy to provide an updated installation script if I ever get it running but I thought I'd ask if someone has done that already or has solved the related problems so as not to invent the wheel anew. Links: <https://bruceravel.github.io/demeter/documents/SinglePage/installation.html>https://bruceravel.github.io/demeter/documents/SinglePage/installation.html https://github.com/newville/ifeffit <https://manjaro.github.io/>https://manjaro.github.io/ Best regards, Anselm ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Demeter Installation issues
So, there is not really enough information to go on in this email. I don't know what system you are one, although I'd guess it is some kind of linux. I don't really know what is meant by "so I installed pgplot separately". Installed from source? From the package manager? I don't know why ifeffit's PGPLOT_install script failed for you. It has always worked just fine for me. Anyway, when I did not find a file called "libgcc_path.sh" on my own computer, I turned to good ol' Google. As near as I can tell, cpg/libgcc_path.sh is a script that compiles a simple C program, then probes the result to figure out what libraries it is compiled against. In short, it seems to be a way to figure out how to put the right collection of default -L command line directives into the compilation command so that program compiled against the pgplot library isn't missing anything. Or some such. I don't know how to resolve this problem either and it seems beyond the scope of what I can reasonably support given that went off-script to get pgplot installed on your computer. Doing that sort of thing presumes a certain level of independent spirit In the absence of other information, I would recommend that you figure out where libgcc_path.sh got installed on your machine then figure out how to make sure that it gets resolved at Build time. One fragile way to do that would be to "sudo mkdir /cpg" if it doesn't exist. Then make a symlink in /cpg to wherever your copy of libgcc_path.sh resides. Make sure it is accessible and executable by a normal user. B On 08/19/2016 01:26 PM, Gaurab Rimal wrote: Hello, I have been trying to install demeter in my archlinux machine but have issues in the build process. I had issues installing pgplot from ifeffit git source so I installed pgplot separately (as outlined in the original pgplot instructions). After installing ifeffit and after all dependencies were met, I ran ./Build and got an error about 'cpg/libgcc_path.sh'. Below is the full output from ./Build. I am unsure of this error because it seems to be related to ifeffit and pgplot and do not know how to resolve this. $ ./Build Ifeffit's installations directory is /usr/local/share/ifeffit (found by capturing `ifeffit -i`) Compilation flags (from /usr/local/share/ifeffit/config/Config.mak): -L/usr/local/lib -lifeffit -L/usr/local/pgplot/ -lpgplot -lX11 `/cpg/libgcc_path.sh` -lgcc -lm -lc -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1 -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1/../../.. -lgfortran -lm -lgcc_s -lquadmath cc -I/usr/lib/perl5/core_perl/CORE -fPIC -L/usr/local/lib -lifeffit -L/usr/local/pgplot/ -lpgplot -lX11 `/cpg/libgcc_path.sh` -lgcc -lm -lc -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1 -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1/../../../../lib -L/lib/../lib -L/usr/lib/../lib -L/usr/lib/gcc/x86_64-pc-linux-gnu/6.1.1/../../.. -lgfortran -lm -lgcc_s -lquadmath -c -D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -march=x86-64 -mtune=generic -O2 -pipe -fstack-protector-strong -o src/ifeffit_wrap.o src/ifeffit_wrap.c cc: error: `/cpg/libgcc_path.sh`: No such file or directory error building src/ifeffit_wrap.o from 'src/ifeffit_wrap.c' at /usr/share/perl5/core_perl/ExtUtils/CBuilder/Base.pm line 174, line 11. Gaurab ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Athena interpolation when removing mono glitches
mbers of the Ifeffit list, I recently collected some EXAFS data with some significant monochromator glitches that I am looking to remove. I have used a python script graciously written by the beamline scientist to remove the offending regions, but when I import the data into Athena, Athena does some funny business in an attempt to join together the regions outside of the data gap. (See the bending away in the dataset and/or attached image.) I have confirmed by plotting with other software that the strange step-like behaviour in the mu(E) is present only after importing into Athena (the raw data is fine). I have looked through the mailing list archives and also the user manual, but can't seem to find anything that explains it, or other people who have experienced this problem in the past. From what I can determine, Athena joins together the segments to obtain a linear interpolation in the norm(E)? This leads to a warping in the mu(E). ==How does Athena try to treat this data?== I was wondering if other people have had similar issues, and what steps can be taken to remedy the problem. For example, replacing removed data points with artificial points along a linear interpolation would be possible, but the act of adding artificial points that don't exist is concerning to me. ==What is the best way to treat data with mono glitches to reduce spurious features not intrinsic to the sample?== If you are interested, I have included links to .prj datasets and images to highlight these problems below. With thanks for your time, Michael -- .prj file with 4 ways of working up the same data: http://bit.ly/2bnfNZ5 1) raw data 2) mono glitches removed 3) rebinned data 4) rebinned and manually removed points (This leads to some strange-looking features in k-space, and this would be less than desireable on the many datasets we have collected) images to highlight these problems: a) mu(E) http://bit.ly/2aYaJIf b) norm(E) http://bit.ly/2aYaX27 c) k http://bit.ly/2baWh0h ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Statistical errors in linear combination fits
On 08/11/2016 04:31 PM, Joshua Kas wrote: I was wondering if it is possible to pass a value for the uncertainty in the data to Athena when doing linear combination fits. We have calculated chi^2 values using a simple estimate of the statistical uncertainty, and find that our values differ by several factors of 10 when compared to the reported values from Athena. I assume that this has to do with value of the uncertainty that Athena is using, but I certainly could be mistaken. In any case, the reduced chi^2 reported by Athena is much smaller than 1, while the fit is off by fairly large amounts compared to any reasonable estimate of the statistical error. Not so easy with Ifeffit, quite easier with larch. It's on my to do list, but has not yet been implemented in Athena. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Converting PDF files to CIF files for usage in Artemis
On 08/09/2016 01:50 PM, Matthew Marcus wrote: This actually results in a bit of inconvenience - if you want to use ATOMS, you have to load some data into Artemis and pretend you want to analyze it. There is a "Stand-alone Atoms" item in the frickin' Start Menu. How does that constitute an inconvenience? If that's too many clicks for you, drag and drop a shortcut to the desktop. You can use atoms from the command line to read an input or CIF file and write to a file or to standard output. You can use atoms from the command line with the "--wx" switch to fire up the stand-alone GUI app. I acknowledge that the web app that died last January was widely used and that I am an unredeemable lay-about for not recreating it. But your criticism is a bit unfair, Matthew. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Converting PDF files to CIF files for usage in Artemis
Have you read the Colinet & Pasturel paper? Skimming through it, it seems like section III.b along with Fig 1 gives enough information to fill in the Atoms window (http://bruceravel.github.io/demeter/documents/Artemis/feff/index.html) by hand. B On 08/08/2016 05:02 PM, Ed Han wrote: Dear All, In the upcoming fall, my research group plans on performing XAS studies observing the Hf L3-edge for various Hf-Al intermetallic samples. In preparation for the experiments, I am looking for CIF files of the various Hf-Al intermetallic systems, including HfAl3, HfAl2, Hf4Al3, etc. Upon scavenging through a multitude of crystallographic databases, I was not able to find any CIF files of Hf-Al intermetallics. However, I have acquired powder diffraction files (PDF) for said intermetallics. Seeing as how PDFs cannot be used in Artemis for EXAFS data analysis (to my knowledge), is there a way to convert PDFs into CIFs? I have attached one of the PDF files to demonstrate what information it contains. I would really appreciate your help! Regards, Edmund Han ___ 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 -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Amorphous
On 08/08/2016 11:19 AM, Carlos Triana Estupinan wrote: I want to know if it is possible to obtain a 3D structure (.cif file) of an amorphous material from the EXAFS fitting carried out from artemis. I mean, there is a way to extract a .cif file with the structural data obtained from the refined spectra. No. EXAFS is basically a one-dimensional measurement. You measure R. Multiple scattering gives you limited information about the 3D arrangement of atoms, but mostly EXAFS is just R. Unless I am misunderstanding the question, I don't think you can do what you are asking even for a well-ordered crystal, much less an amorphous material. Also, in amorphous materials there must be a distribution of interatomic bond distances and coordination, and so, how can I address such a structural distribitions. Well, sure. There is a while literature on the use X-ray or neutron scattering along with EXAFS and molecular dynamics and monte carlo methods to study amorphous materials. It seems that the most successful approaches involve forward modeling -- i.e. testing structures against the EXAFS data. There simply isn't enough information in EXAFS to invert the EXAFS and extract a 3d configuration. Artemis does not even try to do that. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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] Questions about fitting of EXAFS
On 08/03/2016 05:36 PM, Fuxiang Zhang wrote: Hi, Everyone, I have several detailed questions about EXAFS processing and fitting 1. Are there any physical meaning for DeltaE0 in the paths, why it should be less than 10eV This paper is a good explanation of why Delta E0 should be reasonably sized: https://doi.org/10.1107/S0909049598002970 2. The cutting range of Kmax (FT transform parameters) has great effect on FTs of EXAFS, how do I know to use the best value of Kmax; If you have measured data with signal well above the level of noise, why would you choose to use less data? Similarly, if, at some point in your data, the signal becomes dominated by noise -- either statistical or systematic -- why would you include it in the analysis? 3. How to make refinement equation for multi-scattering paths? Such as in NiFe alloys (simple fcc structure), the path [Ni-FM-3m] Fe1.1 Ni1.4 Fe1.1., I use 0.67*Efe+0.33*Eni for DeltaE0, and 0.67*ssFe1+0.33*ssNi4 for sigma2, is that right? Many thanks Have you been reading the messages posted on this mailing list? If so, you have certainly noticed that I often answer questions like this one in terms of whether or not a fitting result is "defensible". For example: http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg05551.html http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04067.html http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg00396.html and many others. Make use of the resources at http://bruceravel.github.io/XAS-Education/ http://bruceravel.github.io/demeter/ http://xafs.org/Tutorials and elsewhere. Check out Scott's book, https://www.crcpress.com/XAFS-for-Everyone/Calvin/p/book/9781439878637 or Grant's book http://www.cambridge.org/us/academic/subjects/physics/condensed-matter-physics-nanoscience-and-mesoscopic-physics/introduction-xafs-practical-guide-x-ray-absorption-fine-structure-spectroscopy?format=HB The library at your university may have either or both of those. B -- Bruce Ravel bra...@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 743, Room 114 Upton NY, 11973 Homepage:http://bruceravel.github.io/home/ Software:https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ___ 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
