November 2014 - Ifeffit - millenia.cars.aps.anl.gov

Be EXAFS and publication
by Joshua Kas 08 Jul '15

08 Jul '15

Hi, This may be a long shot, but I was wondering if anyone is aware of EXAFS data on HCP Be. In particular we are looking for Debye-Waller Factors, so a publication would be great, but just data might work as well. Thanks, Josh Kas

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Re: [Ifeffit] Launching Athena on Mountain Lion (Mac OS 10.8)
by Kyler Carroll 05 Dec '14

05 Dec '14

Hello, I had posted a comment/question a few months back when I had initially installed Mountain Lion on my mac regarding iXAFS compatibility with XQuartz and the new OS not supporting X11 anymore. Since then I have received a few comments back and I found one solution to be the best. This was originally sent by Tsu-Chien Weng from SSRL (tsuchien(a)slac.stanford.edu) Please find the following solution below. Once you install XQuartz the rest will be done in the Terminal.app. This is a one time solution and I havent had any trouble thus far with the program. Hope this works as well for everyone else as it did for me. 1. Install XQuartz from <http://xquartz.macosforge.org/landing/> 2. open Terminal.app 3. cd /Applications/Utilities 4. sudo mkdir X11.app 5. cd X11.app 6. sudo ln -s ../XQuartz.app/Contents Thank you, Kyler J. Carroll, Ph.D. Assistant Project Scientist Department of NanoEngineering University of California, San Diego

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Fit a mixture
by kaziz sameh 03 Dec '14

03 Dec '14

Dear All,I look for advice or document that can help me to fit the FT EXAFS data of Pd2Au36(SR)24.The situation is as follows:In the sample there is 3 sites of the Pd ( in staples, in surface or in the core). the spectrum that I have presents a first bond of Pd_S and second bond of Pd_Au, so the palladium should be in the staples or in the surface because in core we cannot see Pd-S, but other results of the same sample confirm that the palladium is in core.I concluded that there is a mixture of some nano (x ) with Pd in staple and another nano(y) with Pd in core such y>x.Note that I fit the data with Pd2Au36(SR)24 structure in which I put the 2 palladium in the staple and I have got a good fit (attached) but I think that is not logical.If you can help me with an idea how to fit this mixture, I would be very grateful.Kaziz.

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S XANES question
by Matthew Marcus 26 Nov '14

26 Nov '14

A user on ALS 10.3.2 is taking S K-edge XANES and consistently finding a strong peak at 2484eV (calibration: gypsum white line = 2482.75eV). There's a shoulder at the nominal position of the sulfate peak. Now, peaks below sulfate I can understand, but since there's no such thing as heptavalent sulfur, what could give a peak *above* the sulfate white line? Anybody ever seen that? Yes, we checked calibration. mam

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experimental standard
by Yun Xu 18 Nov '14

18 Nov '14

Hi all I have a complex oxide BaTi8-xGaxO16. What standards I should run? Ga is the dopant. I guess I should run the sample without dopant BaTi8O16 as standard, or the simple oxide as BaO, TiO2 Ga2O3? or is the standard necessary? Also, I have colleage working on DFT, I assume the theoretical standard is the result from the DFT calculation, and by using the coordinates of the atoms, I can run FEFF and fit the data. Thanks Yun

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installing Demeter on Yosemite
by Katherine M. Davis 13 Nov '14

13 Nov '14

Dear all, I was wondering whether anyone had tried installing the software on the new Mac OS (10.10 Yosemite)? Everything seems to work fine initially. I installed Macports and checked it installed correctly. At least when I test various commands, it seems to work. The sudo port install xorg-server demeter-devel command ran for about 3 hours until it quit. I tried restarting, but whenever I run the command, the following error message appears: ---> Computing dependencies for xorg-server ---> Cleaning xorg-server ---> Computing dependencies for demeter-devel ---> Configuring demeter-devel Error: org.macports.configure for port demeter-devel returned: configure failure: command execution failed Please see the log file for port demeter-devel for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_demeter/demeter-devel/main.log To report a bug, follow the instructions in the guide: http://guide.macports.org/#project.tickets Error: Processing of port demeter-devel failed I will post the log file at the bottom of the email. The last 8 lines are as follows: portbuild::add_automatic_buildsystem_dependencies :debug:clean No need to upgrade! p5.16-term-twiddle 2.730.0_1 >= p5.16-term-twiddle 2.730.0_1 :debug:clean epoch: in tree: 0 installed: 0 :debug:clean p5.16-text-template 1.460.0_1 exists in the ports tree :debug:clean p5.16-text-template 1.460.0_1 is the latest installed :debug:clean p5.16-text-template 1.460.0_1 is active :debug:clean Merging existing variants '' int Would anyone be able to help me with this? Any advice would be useful. Thanks for your time. Best, Kate Davis

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Re: [Ifeffit] Fwd: Re: Re: problem about negative
by Bruce Ravel 12 Nov '14

12 Nov '14

On 11/11/2014 10:19 AM, Bruce Ravel wrote: > Rbkg>1.1 can avoid the first peak,but the remaining curve is somewhat > not smooth.How to distinguish whether a long wavelength oscillation > appear as a real peak or false one?I am confused about it. > I find when I avoid the first scattering peak after white > line(kmin=4.8 maybe too large),the first peak of R space > disappeared.Because usually the first scatering peak is related to the > first coordiantion shell,can I think the first peak in R space less 1A > is a real peak instead of noiseï¼ Zhanfei, As I said yesterday, I don't know anything about your sample, so it is hard for me to know what the "right" answer is to your problem. But I can make some observations and some suggestions. * Your data range is really short. As you seem to have noticed (judging from the very short k-range in your project file), your data has serious systematic problems starting at 9 or 10 inverse Angstroms. I cannot quite tell, but your data appear to be transmission data. Well it is possible that you have some instability or nonlinearity at the beamline, I would guess that your sample is not very homogeneous. It is possible that more disciplined sample preparation might help extend that range of the interpretable data. * You are right that slightly increasing the Rbkg value seems to make a positive difference in the extracted chi(k) data. Your data seem to be an example of the sort of data I was alluding to yesterday. The background subtraction is difficult because it is difficult to distinguish the Fourier components of the background function from the Fourier components of the data. I think that the background subtraction with Rbkg=1.1 looks much better than with Rbkg=1.0, but given how different they are, you have to be concerned about the correlations between the background and the parameters of the data. It is clear that your data are of the sort for which background subtraction is difficult. So how do you know what is an acceptable background subtraction? Well, using only Fourier methods, I think we have demonstrated that you cannot know the right answer without some kind of prior knowledge. So, how do you get that prior knowledge? Well, my advice is to first solve some simpler problems. Measure your standards. Measure the common forms of moly oxide and moly sulfide. Measure moly metal. Analyze all of them. The advantage of the standards is that you know what the answer should be. Do the data processing and data analysis. Make sure that, when you do the analysis, you get the right answers. Having done that exercise, you will then have a lot more knowledge about what the various forms of moly oxide look like and what the challenges are when doing the data processing and data analysis. Some questions: - Are there any forms of moly oxide for which the bond length is as short as 1.6? If so, do the conditions of formation exist in your system? Is your sample of a valence consistent with the valence of the Mo when it has such a short bond? - If you convince yourself that it is possible for moly to have an oxygen atom at 1.6 or 1.7, what did you have to do with your standard to get a sensible analysis of the EXAFS data? Hopefully, that will guide you to doing a sensible analysis of your unknown sample. - If none of your moly oxide standards have an O atom at 1.6 or 1.7, why do you think it is chemically reasonable for your unknown sample to have such a short bond? If, in fact, that short bond doesn't exist elsewhere in nature, why would your sample magically have such a short bond? - If you do not believe in such a short bond, then does your experience with the standards give you the confidence to increase Rbkg such that the low-R signal is removed by the background function? I completely understand that you have a compelling reason to understand your unknown sample and that I am suggesting that you spend a good chunk of time measuring and analyzing a bunch of standards that are not your actual research project. That might seem like time that takes you away from your real goal, but you have already demonstrated that you are stumped by your real goal. I am saying the only way to get over your current hurdle is to take a step back and gain a deeper understanding of the data, the physics of EXAFS, the methods of EXAFS analysis, and the intricacies of your current problem. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 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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too small bond length in R space
by ZHAN Fei 11 Nov '14

11 Nov '14

Dear all： I encounter a problem of exafs fit in an example of Mo which have Mo-O Mo-S Mo-Mo bond.The problem is that the Mo-O peak in R space has too small bond length (less than 1.4A(+0.5A for phase correction) ).Because when 1.2>rbkg>0.68 there is little change in spectrum of R and k space,and when I increase the value of rmin of forward Fourier transform the peak changes little,so I think it's not a noise.But when I try to fit it use the 1.35A path of Mo-O,I can't fit it well. Could you give me some advise about fit too small bond length,or recommend papers of similar situation? picture of R space is attached. Thanks Sincerely, zhanfei ihep of China

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Larch-0.9.24 with Python2
by Matthias Filez 05 Nov '14

05 Nov '14

Dear mailing list user, When running an example file of Larch-0.9.24 with Python2 on Ubuntu x86_64, the following error was reported. File "Py_usinglarch.py", line 32, in <module> autobk(xafsdat.energy, xafsdat.mu, rbkg=1.0, _larch=my_larch) File "/usr/local/lib/python2.7/dist-packages/larch/__init__.py", line 37, in wrapper return fcn(*args, **keywords) File "/usr/share/larch/plugins/xafs/autobk.py", line 187, in autobk fit.leastsq() File "/usr/local/lib/python2.7/dist-packages/larch/fitting/minimizer.py", line 395, in leastsq lsout = leastsq(self.__residual, self.vars, **lskws) File "/usr/local/lib/python2.7/dist-packages/larch/fitting/minimizer.py", line 222, in leastsq shape, dtype = _check_func('leastsq', 'func', func, x0, args, n) ValueError: need more than 1 value to unpack Is Larch-0.9.24 compatible with Python2 on Ubuntu x86_64? If not, what packages and dependencies could we install to make it work on Python2? Or is Larch-0.9.24 only compatible with Python3? Many thanks in advance, Matthias

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Reporting the fitting data (uncertainty associated with N)
by pushkar shejwalkar 05 Nov '14

05 Nov '14

Dear All, I have seen and also been told by few professors that when you report the fitting you must report the uncertainty associated with the measurement as evaluated by the program used for the fitting. Now, When I do the fitting I typically get the +/- values for E0, delR, ss and SO2. However, the N value we always put either 1,2 or such whole integers. Is there any way to find out the uncertainty associated with the coordination number (N used in XAFS equation)? If so how to find such uncertainty? can we see this in the log file generated after the fitting is over? Thank you very much for the help Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher,JSPS Fellow Hokkaido University, Sapporo, Japan

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