September 2016 - Ifeffit - millenia.cars.aps.anl.gov

Smoothing aligned data in Athena
by Godfrey, Ian 29 Sep '16

29 Sep '16

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.godfrey(a)ucl.ac.uk<mailto:i.godfrey@ucl.ac.uk> i.godfrey(a)jaist.ac.jp<mailto:i.godfrey@jaist.ac.jp>

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Re: [Ifeffit] problem in data processing in athena (Arkaprava Das)
by Abhijeet Gaur 24 Sep '16

24 Sep '16

Dear Arkaprava, Can you tell us from which beamline at RRCAT you have recorded this data. As far as I know the EXAFS beamlines BL-8 and BL-9 at RRCAT does not have this strange format. As Matt says it is definitely from a solid state detector data. You should consult the beamline scientist for other details about the data acquisition. With best wishes Abhijeet On Sat, Sep 24, 2016 at 12:31 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. problem in data processing in athena (Arkaprava Das) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 24 Sep 2016 11:54:34 +0530 > From: Arkaprava Das <arkapravadas222(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] problem in data processing in athena > Message-ID: > <CAGJE4TqbXjnV3BN8M8BEL7kx61-yo9Vx0YuoyvjhF=hv-EAuTw@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Respected Sir, > I am a research scholar in Inter university accelerator centre, new Delhi, > India. I am facing one peculiar problem in athena data processing. I have > attached the .xls file in the mail for Zr k edge which has been generated > in the beam line at RRCAT. when I import this file in athena it always > shows a question mark in the place of Chai (?) at the y axis. I am not able > to sort out this issue that why that question mark is coming. I have > attached the snapshot of plot window also. > > I shalll be highly obliged if yo kindly help me in resolving the issue. > > Yours sincerely > > Arkaprava >

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problem in data processing in athena
by Arkaprava Das 24 Sep '16

24 Sep '16

Respected Sir, I am a research scholar in Inter university accelerator centre, new Delhi, India. I am facing one peculiar problem in athena data processing. I have attached the .xls file in the mail for Zr k edge which has been generated in the beam line at RRCAT. when I import this file in athena it always shows a question mark in the place of Chai (ϰ) at the y axis. I am not able to sort out this issue that why that question mark is coming. I have attached the snapshot of plot window also. I shalll be highly obliged if yo kindly help me in resolving the issue. Yours sincerely Arkaprava

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Re: [Ifeffit] problem in data processing in athena (Arkaprava Das)
by fred.mosselmans＠diamond.ac.uk 24 Sep '16

24 Sep '16

Dear Arkaprava, The beamline writes a bizarre no. of zeros in to the file. Also there are no headers on the columns which is pretty poor IMO. If you remove most of the zeroes (I just used replace in Wordpad) Athena understands the file fine, though I couldn't tell what the columns were so as there are no headers, so just guessed 5 might be the data. I don't think it is given the y scale but hopefully this shows how to do it. I think saving the file to an extension usually used for excel is a pretty odd thing to do also. So this is when Bruce might say ask the beamline staff not to output such strange data format and life would be easier for you. Thanks Fred J.F.W. Mosselmans Prinicipal Beamline Scientist I18 Diamond Light Source Ltd Diamodn House Harwell Campus Didcot OX11 0DE P + 44 1235 778568 M + 44 7785510211 E fred.mosselmans(a)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

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Ni(I), Ni(II), and Ni(III) Reference XAS required
by mazhar iqbal 20 Sep '16

20 Sep '16

Hello Can some please provide me the standard XAS of Ni(I), Ni(II), and Ni(III). Thanks in advance

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artemis doesn't read user's epsilon(k)
by Victor Streltsov 18 Sep '16

18 Sep '16

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

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Re: [Ifeffit] Ifeffit Digest, Vol 163, Issue 10
by Matteo Busi 13 Sep '16

13 Sep '16

Dear Bruce, Attached is an example of multiple data sets project, Please try to: 1. Load all the data sets of the project 2. Mark only the data set: "merge" 3. Save current group as: "____" 4. Save marked group as "____" 5. Open both files in a notepad 6. Notice the differences I hope this is detailed enough, ( I have attached my saved files as well) Best regards, Matteo 2016-09-12 19:00 GMT+02:00 <ifeffit-request(a)millenia.cars.aps.anl.gov>: > 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: Saving Bug (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 12 Sep 2016 09:34:52 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Saving Bug > Message-ID: <96f04ebb-4477-3911-d6e2-e5eef2973cdb(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > 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 ------------------------------------ bravel(a)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/ > > > ------------------------------ > > Subject: Digest Footer > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > ------------------------------ > > End of Ifeffit Digest, Vol 163, Issue 10 > **************************************** >

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Saving Bug
by Matteo Busi 12 Sep '16

12 Sep '16

Dear Bruce and all, I think I found a minor bug in the Athena package (0.9.25). 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) It is a minor bug but I think if it doesn't take much time it is worth correcting. Regards, Matteo Busi

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Re: [Ifeffit] Help in background removal with Athena
by fred.mosselmans＠diamond.ac.uk 07 Sep '16

07 Sep '16

-----Original Message----- From: Ifeffit [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: 06 September 2016 14:57 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 163, Issue 6 Dear Irina, Your efforts are probably sadly in vain. C K-edge NEXAFS or XANES is common, but the data range is rarely long enough for exafs analysis. You have ca 160 eV of data that is not enough for EXAFS analysis. Hence I don't think there is a way to get a good background and then FT for your data. Certainly looking at your data the noise level and thus uncertainty in which features are real and which may not be will probably prevent anything but a XANES analysis. There probably is an oscillation there but with the limited data range getting meaningful numbers from a fit is most unlikely. Best wishes Fred 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. Help in background removal with Athena (Irina Pi) ---------------------------------------------------------------------- Message: 1 Date: Tue, 6 Sep 2016 13:56:19 +0000 From: Irina Pi <Irina.Pi(a)icfo.eu> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Help in background removal with Athena Message-ID: <VI1PR0601MB22877AFA6B07BEE3CFDCEC798DF90(a)VI1PR0601MB2287.eurprd06.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Dear all, I am sorry to bother you with my tiny problems, but I have been struggling with it for a long time. The thing is I have XAS data from a graphite sample, and I don't know if I'm plotting the background correctly in it with Athena software, which determines a lot the response in the Fourier transform, and thus in our results. I'm attaching the data as data_exafs.txt, and also two different Athena projects of different backgrount fittings, graphite_exafs1.prj and graphite_exafs2.prj. Just in case projects cannot be seen, I'm also attaching screenshots (1-01deg.png and 2-01deg.png) of the different background fittings and the parameters used in Athena in only one set of data (01deg), because they are the same in the others (02deg and 35deg). Also, the final R-space plot in both fittings are sent (1-rspace.pdf and 2-rspace.pdf). What I wanted to ask is why it is so different the result according to the background removal. And are they correct the fittings I've done? I would like to have a background line similar to the other figure attached (0deg.pdf, but take into account that it is from different data), but I cannot get it. I guess this last fitting seems better, doesn't it? What could I do to have good results in the Fourier transform? Again, sorry but I don't have much experience and it seems to be so subjective that I fear doing it all wrong. Thank you very much, Best regards, Irina Pi Jauma.

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Re: [Ifeffit] Help in background removal with Athena
by fred.mosselmans＠diamond.ac.uk 06 Sep '16

06 Sep '16

Hi Irina, I guess in a normal situation you would want to FT at least 5 k(1/A) range to get some sort of shape to your FT peaks which would normally be a range of about 2 -7 k so maybe 190 eV above the edge. However added to that the data has to be good, I am not a C XAS expert but looking at your data I am unsure that all the oscillations are due the x-rays scattering , some might be experimental artefact which would then make the analysis even less trustworthy. WRT your data after the signal begins to die about 400 eV, i.e. you have ca 110 eV of data I might trust on a good day and even then I'd be more reassured if these were several scans added rather than just one. (I can't tell if this is the case). I doubt there is useful stuff that can be extracted past that point. Hence I think all that is probably there is the pre-edge changes in the XANES which I presume you are looking at as well. Thanks 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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