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

Re: [Ifeffit] A small query on constricting mean square displacement in multi-edge EXAFS refinement
by Badari Rao 04 Dec '14

04 Dec '14

Dear Scott, Thank you for the answer. Date: Wed, 3 Dec 2014 08:03:56 -0500 > From: Scott Calvin <scalvin(a)sarahlawrence.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] A small query on constricting mean square > displacement in multi-edge EXAFS refinement > Message-ID: <A7199A7A-EA1B-4396-960B-301A94F68648(a)slc.edu> > Content-Type: text/plain; charset="utf-8" > > Yes. > > The only minor adjustment I can think of to that is something called the > ?McMaster correction,? which adjusts for an oversimplification in the usual > EXAFS method of normalization, and thus can be different for the two edges. > But that correction is generally quite small, and the difference in it > between two edges is even smaller. > > ?Scott Calvin > Sarah Lawrence College > > > On Dec 3, 2014, at 7:54 AM, Badari Rao <badari.rao(a)gmail.com> wrote: > > > > Dear All, > > > > Suppose I have a compound, say AB. I have the EXAFS data from both > A-edge as well as B-edge and I am simultaneously refining these data. > > Would it be correct to force the mean square displacement of the A-B > path in both the edges to be the same? > > > > -- Regards, > > Badari Narayana. A. R. > > Ph.D Student, Nanoscience and Nanotechnology, > > c/o Prof Rajeev Ranjan, > > Electroceramics Lab, > > Department of Materials Engineering, > > Indian Institute of Science. > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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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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A small query on constricting mean square displacement in multi-edge EXAFS refinement
by Badari Rao 03 Dec '14

03 Dec '14

Dear All, Suppose I have a compound, say AB. I have the EXAFS data from both A-edge as well as B-edge and I am simultaneously refining these data. Would it be correct to force the mean square displacement of the A-B path in both the edges to be the same? -- Regards, Badari Narayana. A. R. Ph.D Student, Nanoscience and Nanotechnology, c/o Prof Rajeev Ranjan, Electroceramics Lab, Department of Materials Engineering, Indian Institute of Science.

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open position at KIT
by Lichtenberg, Henning (IKFT) 02 Dec '14

02 Dec '14

Dear XAS community, we have an open position in the field of EXAFS and operando spectroscopy in our group. For further information see the attached job description. Please feel to contact us also if you are interested in a beamline scientist position or x-ray microscopy. with best regards, Henning Lichtenberg

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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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