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

larch xray plugin - incorrect chantler data at edges
by Dr. Johannes Zellner 14 Oct '15

14 Oct '15

Hi, the larch xraydb plugin doesn't provide correct numbers for chantler f1 data around edges. Apparently this is due to incorrect interpolation in xray/xraydb.py in line 274. Below is a plot of "delta" from xraydb_plugin.xray_delta_beta() for Silicon which is terrribly wrong. The more correct "delta" as from chantler is shown in the following plot: --> I'd recommend to replace (line 274 in plugin xray/xraydb.py): out = UnivariateSpline(te, ty, s=smoothing)(energy) by a simple linear interpolation out = np.interp(energy, te, ty) The latter yields linear segments between chantler's data, but this is still better than the totally unphysical spline interpolation. Best regards, -- Johannes

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a bug when installing demeter
by Zhenxing Feng 13 Oct '15

13 Oct '15

Hi, I am trying to install Demeter on my Mac OX X EI Capitan. After installing MacPorts properly, I run the command, “sudo port install xorg-server demeter”. However, it reports a bug when building libgcc, when the following errors: Error: org.macports.build for port libgcc returned: command execution failed Please see the log file for port libgcc for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/libgcc/main.log Error: Unable to upgrade port: 1 Error: Unable to execute port: upgrade ifeffit failed Could you help figure out how I can proceed further? Thanks, Zhenxing

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No plot window on Mac El Capitan
by Chloe Yi-Yi Wu 08 Oct '15

08 Oct '15

Hi Bruce, I just upgraded my mac from mountain lion to el capitan. I was using the old version, iXAFS, but I can't launch it on the new el capitan. I then installed Demeter with Macport by following the instructions. However, I'm not able to plot the data in athena and artemis. I read the thread about "no plot window on Yosemite", but still have no clue. I can plot gnuplot in aqua, x11 and wxt. It seems whenever I quit gnuplot to launch athena and enter gnuplot later again, it will always go back my default terminal, aqua, no matter how I set terminal. Is there a communication problem between Demeter and aqua? I'm not familiar with these commands, to be honest. If I did something wrong, please advise. Thanks, Chloe -- Yi-Yi (Chloe) Wu Kung Research Group Dept. of Chemical and Biological Engineering Northwestern University Evanston, IL USA

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Problems importing larch plugins to python
by Johan Nilsson 05 Oct '15

05 Oct '15

Hello everyone, I recently installed the latest development version of larch from github and now I'm having some problems importing larch plugins to my python scripts. I read in the documentation that there is a new method for doing this but that the old way should still work, this is what happens if I try to do it the way I've done it before: johan@johan-Latitude-E6430:~$ python Python 2.7.6 (default, Jun 22 2015, 17:58:13) [GCC 4.8.2] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from larch import use_plugin_path >>> use_plugin_path('xafs') >>> from pre_edge import pre_edge Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/johan/.larch/plugins/xafs/pre_edge.py", line 13, in <module> from larch_plugins.std import parse_group_args ImportError: No module named larch_plugins.std >>> I also tried the new method described in the docs: johan@johan-Latitude-E6430:~$ python Python 2.7.6 (default, Jun 22 2015, 17:58:13) [GCC 4.8.2] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import larch >>> from larch_plugins.xafs import autobk Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: No module named larch_plugins.xafs >>> I'm running ubuntu 14.04. Any ideas of what is going on here? Best regards, Johan

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problems with deglitching in D-Athena 0.9.22
by bajnoczi 03 Oct '15

03 Oct '15

Dear Ifeffit Staff, I have just installed the most recent version of Demeter on my computer both on Windows 8 64-bit as well as on a Virtual (WMware Player) Ubuntu 14.04.3 64-bit machine. I have exactly the same problem with both versions when I try to deglitch my data. When I go to the Deglitch and Truncate window, and choose the option "Choose a point" the plot appears with dots. So far it seems ok. Initially the orange crosshair is on the first data point. When I try to double-click on the point to be removed happens nothing at all. I can do whatever I want, the crosshair stays on the first measured data point, and stays there, so I only can remove this one. I've already consulted with the mailing list, but none of the proposed solutions worked for me. I have downloaded the DeglitchTruncate.pm from Github and upgraded my version, as well as set the energy shift to 0, but nothing helped. Do you have any idea what can be the solution for this problem? Thank you for your answer and help in advance. Regards: Éva Bajnóczi Hungary Hungarian Academy of Sciences, Wigner Research Centre for Physics

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problems with deglitching in D-Athena 0.9.22
by bajnoczi 03 Oct '15

03 Oct '15

Dear Ifeffit Staff, I have just installed the most recent version of Demeter on my computer both on Windows 8 64-bit as well as on a Virtual (WMware Player) Ubuntu 14.04.3 64-bit machine. I have exactly the same problem with both versions when I try to deglitch my data. When I go to the Deglitch and Truncate window, and choose the option "Choose a point" the plot appears with dots. So far it seems ok. Initially the orange crosshair is on the first data point. When I try to double-click on the point to be removed happens nothing at all. I can do whatever I want, the crosshair stays on the first measured data point, and stays there, so I only can remove this one. I've already consulted with the mailing list, but none of the proposed solutions worked for me. I have downloaded the DeglitchTruncate.pm from Github and upgraded my version, as well as set the energy shift to 0, but nothing helped. Do you have any idea what can be the solution for this problem? Thank you for your answer and help in advance. Regards: Éva Bajnóczi Hungary Hungarian Academy of Sciences, Wigner Research Centre for Physics

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changes to the Demeter Windows installer
by Bruce Ravel 01 Oct '15

01 Oct '15

Hi, Today, I posted a new windows installer which has a significant difference compared to previous versions: http://bruceravel.github.io/demeter/#windows It's the one called "pre-release trial #3". This version of the installer changes the default installation location and makes several other changes intended to make the Demeter package behave better on a wide variety of Windows environments. That said, the changes are not yet well tested and I am worried that they may behave very poorly for some people. In particular, I am concerned about how the new installer will behave for people with a space in their log-in name and for people with non-ASCII characters in their log-in name (e.g. a German eszett, a Cyrillic character, or any character from an Eastern language). If you are the sort who is willing to try the new version and report back to the mailing list with any problems, I would be very grateful for any feedback. If your log-in name meets one of my areas of concern, I would be doubly grateful for the feedback! Those who don't want to live near the edge should use 0.9.22 or 0.9.23_pre2 for now. Thanks! B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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mailing list / web page downtime
by Matt Newville 01 Oct '15

01 Oct '15

Hi Folks, The machine that hosts this mailing list, the ifeffit web pages, and xafs.org (millenia.cars.aps.anl.gov) is going to be replaced with a new machine today. I think everything should work, but there may be some outages over the next two days. If you have any troubles past that, let me know. --Matt

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Re: [Ifeffit] Problem with Hephaestus at Ca L-edges (Matthew Marcus)
by Jana Padeznik Gomilsek 29 Sep '15

29 Sep '15

It is very hard to measure or to calculate absolute absorption data, especially in the vicinity of the absorption edges and especially in the soft x-ray region. Therefore there are significant differences between the tables and I think nobody knows which are better. Chantler, for example, says the expected uncertainties of the tables in your region are 50 % to 100 % (http://physics.nist.gov/PhysRefData/FFast/Text2000/sec06.html#tab2) I would doubt the Chantler's L3+.1 number, all other numbers look ok - this is what you can get. jana padeznik gomilsek > Message: 3 > Date: Wed, 23 Sep 2015 18:02:08 -0700 > From: Matthew Marcus<mamarcus(a)lbl.gov> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Problem with Hephaestus at Ca L-edges > Message-ID:<56034B90.70405(a)lbl.gov> > Content-Type: text/plain; charset=utf-8; format=flowed > > I wanted to work out the edge-jump ratio between the L3 and L2 edges of Ca using Hephaestus. I ran into two problems: > > 1. The ratio implied by what it says for the unit-edge-step thickness does not agree with that derived by computing the absorption (cm^2/gm) above and below each edge and > dividing the difference (L3+ - L3-)/(L2+ - L2-). > > 2. The results differ wildly depending on which resource I use: > > L3-.1 L3+.1 L2-.1 L2+.1 (L1+ - L1-)/(L2+ - L2-) > Elam 4759.796 27837.796 27478.018 38434.277 2.106375908 > Chantler 4322.6 6547.121 32827.61 35436.543 0.852655473 > Cromer-Leiberman 4288.524 33471.375 32786.294 47072.991 2.042659055 > > The Henke table doesn't yield an L2 edge jump at all, while the Shaltout yields the same results as Cromer-Leiberman. Which one should I trust and why? > > This is old-style H. (V0.18), not Demeter. > mam > >

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Problems during copper (II) oxide data treatment
by Pedro F B D Martins 24 Sep '15

24 Sep '15

Hi everyone, I’m having problems during the data treatment. The two samples (please find the project attached with the as-obtained data only, not with the following treatment) are of CuO (copper (II) oxide) were measured in a row and both were measured together with a reference (Cu foil). I have some doubts: 1) The first thing that I did was to calibrate the Reference of the first measurement (peak at maximum of first derivative). Next, I aligned the second Reference keeping the first reference as standard. Did I do correctly until now? 2) I removed the glitches that appeared in the pre-edge (1 glitch) and the EXAFS region (3 glitches) in both measurements. 3) Next, I set the E0 for both samples in the background removal session to set the 0 (zero) point in chi(k). However, when I plot chi(k) the samples profile in high k values differ. I think that they should be at least very close considering that both are the same copper oxide standard and measured in sequence. Am I correct? 4) I've also noticed that the first measurement (Cu_o_2), when plot in chi(R) has a small (but significant) peak positioned at R = 1, which seems not be right, as bond distances are bigger (> 1.5, for example). Is there anything wrong or missing at background removal treatment? I know that it seems novice doubts but as I’m new to XAFS, it really intrigues me. Best regards, Pedro Martins

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