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

How to identify Mn Mn Corner edge paths in Artemis
by Sathish Mayanna 07 Jan '14

07 Jan '14

Dear all I am sorry for disturbing you all again, since I am self learning to fit multiple scattering for biogenic Mn oxides in Artemis, I am quite lost in understanding the basics of Mn Mn corner sharing path. All reports are included Mn-Mn Corner at ~ 3.4 A, which I cannot find in my Feff calcuation for Phyllomanganate layer (Na-Birnessite) model. Below are the crystallographic information of Na birnessite I used (*also available in the attachment*), Na is excluded. A = 5.174 B = 2.850 C = 7.336 and angles 90, 103.18 and 90 for alpha, beta, gamma respectively Parameters X Y Z Mn 0 0 0 O1 0.37600 0 0.1330 I have two questions 1) How to identify the Mn Mn corner paths from the Paths result. 2) Where can I find the Coordination Number for Mn Mn Corner, If i see in eg. Webb et al., 2005 ( http://www.intl-ammin.geoscienceworld.org/content/90/8-9/1342.short) the CN numbers for Mn-Mn Corner is 0.6(1.0) or 0.8(8), what does the number represent in the brackets? It will be looking forward for your help. Regards -- Sathish

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Re: [Ifeffit] Standard Mn(III) oxides for LCF fitting? problem in
by fred.mosselmans＠diamond.ac.uk 03 Jan '14

03 Jan '14

Dear Sathish, You are right to be dubious about your Mn2O3 spectra, it looks to have much too small a white line compared to literature data and thus probably suffers from Some sort of thickness effects. You can find some MnOxide spectra in Matt's data base http://cars9.uchicago.edu/cgi-bin/newville/Model-Search.cgi however the resolution may be different to wherever you collected your data, but the spectra should be better. Assuming all your data was collected at the same time the edge position of your sample suggests by inspection that it is mainly Mn(IV), In the recess of my mind i know people have published nicely correlated pictures of oxo-Mn compounds edge positions against oxidation states to get a nice linear plot. I am sure you can find this if you search for it in google scholar or the like. However there are several different isomorphs of MnO2 and they have different XANES/EXAFS , thus LCF will only work if you have spectra of all of them (or at least all the types in your sample) Thus unless you are sure that delta is the only type in your sample (by XRD?) , LCF is not likely to get you very far. Given the edge position ab initio fitting might work OK. Otherwise you need to track down absorption spectra of the other isomorphs and try again. For LCF to work well (or at all) you need to have a basis set of all the components in your sample not just one for each possible oxidation state. HTH Regards Fred -- 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

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Standard Mn(III) oxides for LCF fitting? problem in fitting
by Sathish Mayanna 03 Jan '14

03 Jan '14

Dear all Wish you a very happy new year! I was trying to apply LCF for XANES or EXAFS for biogenic Mn oxides (layer type Mn oxides). Using the standards (Mn2O3, Aqueous Mn2+ and dMnO2) I cannot fit the LCF for my XANES or EXAFS data *(attachment)*. I am not really sure what are the problems with the standards (as I expect mainly Mn(III) or Mn(IV) in my samples). It would be really great, if anyone could provide me the Mn(III) oxide standard or have a look at the data and please let me know, if I have done any thing wrong. Best regards Sathish

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Athena deglitch problem
by Sathish Mayanna 03 Jan '14

03 Jan '14

Dear Matt After installing Demeter to other than C drive there is no problem with deglitching. For me its easier to rebin the data points and then deglitch the terrible glitch in my data. If I don't rebin I need hours to deglitch a single spectra since the data contains a big glitch. I believe the major problem is solved for now, thanks a lot for your help. Regards Sathish On Tue, Dec 17, 2013 at 7:00 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov>wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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: Athena deglitch problem (Sathish Mayanna) > 2. Re: Athena deglitch problem (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 16 Dec 2013 19:42:25 +0100 > From: Sathish Mayanna <satty334(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Athena deglitch problem > Message-ID: > <CABVfawm9mL4XhhvBJoPX2= > ZZ-MNek5YCkRcTHUP6S1UL6+xcaQ(a)mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > *Dear Matt* > > > > > > Now it seems working well except some minor things, I can remove the > > points > > > from the data, the random point selection by software works better for > > > rebinned data. I think the only problem I have now is I still cannot > move > > > the cursor after double click (I can only remove the points which the > > > software decides - at least now it choose the points where I double > > click). > > > When i move my mouse cursor on the plot, it shows the correct > > coordinates. > > > > I'm still a bit confused about whether this actually working for you. > > The data you sent has fairly large arrays (>2400 points), but all the > > data was well-ordered in energy... I think that should "just work", > > without needing re-binning. And it does for me, and I don't see how > > re-binning would affect this. > > > * If I don't rebin the data, Athena will not choose the point which I am > intend to remove (I think i have some minor issues here). If I rebin the > data from ~ 2400 to 350 points, Athena will work correctly.* > > > > > > > I think it's always been the case that you double-click near the point > > to be removed, and hope that Athena does select the one you intended. > > > > *This works perfect for rebinned data. * > > > > > > I have one clarifications, when u choose the option to deglitch the > data > > > (rebinned or non rebinned data), does the x(E) data plot looks like in > > the > > > attached file (line) or it looks like sets of blue round points same > > size as > > > cursor. > > > > For me, it looks very much like the image you attached. I do not see > > a series of dots. > > > > > I think, the issue is solved except that I cannot move the randomly > > chosen > > > point. > > > > Why can't you remove the point chosen? That seems like it's not > > working to me. Wasn't that the problem you were having? > > > > *I mentioned "MOVE" in my above sentence, (Just to be more specific, when I > double click on the plot to choose a point, sometimes Athena select its own > random points away from the point where I clicked, when I try to drag that > randomly chosen cursor to the point of my interest, it will not work), IS > THIS NORMAL? * > > *I will try to figure out all the possible ways for non-rebinned data, if > it does not work at least for now rebinned data works.* > > *Regards* > *Sathish* > > > > > > Again, it may be that I'm not understanding. Cheers, > > > > --Matt > > > > > > ------------------------------ > > > > Message: 2 > > Date: Mon, 16 Dec 2013 08:30:39 -0500 > > From: Bruce Ravel <bravel(a)bnl.gov> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Handling time resolved data > > Message-ID: <52AF007F.4050600(a)bnl.gov> > > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > > On 12/13/2013 09:00 AM, Ditty Dixon wrote: > > > Dear Bruce, > > > > > > Recenetly we did some time resolved measurements, QEXAFS mode. While > > > the old Athena arranged the file as we want i.e file 1, 2, 3 etc, the > > > new did it bit different 1, 11 12 and again 2, 21 etc. Screenshot > > > attached. Why is it doing diffrently for the two version? Can it be > > > fixed some how. > > > > You haven't explained exactly where these data come from, so I am > > assuming that each scan was written to its own file and these files were > > imported into Athena. > > > > In Athena, data are imported in "ascii-betical" order, that is, sorted > > in order of characters in the ASCII chart: > > > > http://en.wikipedia.org/wiki/ASCII#ASCII_printable_characters > > > > In that sense, Athena sorted your data as expected. As Chris pointed > > out, if you want things like > > > > nr_1.spec > > nr_2.spec > > ... > > nr_10.spec > > > > to sort numerically by the number between the _ and the .spec, you need > > to format the them so that numerical and ascii-ordered sorting come out > > the same. This is done as > > > > nr_01.spec > > nr_02.spec > > ... > > nr_10.spec > > > > For a quick exafs experiment, two digits is probably not enough, so > > you'd want something like > > > > nr_00001.spec > > nr_00002.spec > > ... > > nr_00010.spec > > > > > > I don't recall quite how the sorting worked in the old version of Athena > > (it has been over 5 years since I stopped working on it), but my vague > > memory is that, on Windows, they were imported in the order that they > > were clicked upon the file selection dialog. The way it is currently > > done is much better in that it is reproducible. > > > > > > > > > > > > -- > > 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://xafs.org/BruceRavel > > Software: https://github.com/bruceravel > > > > > > ------------------------------ > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > End of Ifeffit Digest, Vol 130, Issue 22 > > **************************************** > > > > > > -- > Satty >

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