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

In-situ bulk data analysis
by Raj kumar 10 Jan '17

10 Jan '17

Dear All, I am looking for an EXAFS software to handle bulk data and perform both linear combination and regular EXAFS fit. Regards, Raj

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Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 14
by Raj kumar 09 Jan '17

09 Jan '17

Hi Scott, Thanks for the detailed comments on parameter usage in fitting. I have started evaluating/checking the used model and other possible model for meaningful fit. Once i achieve that, i will get back to you. Regards, Raj On 8 January 2017 at 20:03, <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: Ifeffit Digest, Vol 167, Issue 11 (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 8 Jan 2017 13:03:44 -0600 > From: Scott Calvin <dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 11 > Message-ID: <00387E3A-5B7B-40C5-8C7D-F4053098816F(a)gmail.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Raj, > > The kind of thing I gather you did for #1 is almost always a bad idea. > Guessing parameters in one fit and then setting them to the results for > that fit in subsequent fits without further justification is asserting a > certainty about those parameters that you do not possess. Occasionally it > might be useful in an intermediate fit as a kind of diagnostic, but never > in fits from which you want to extract information.* Note that the fit in > which you set S02 is a different kind of constraint; rather than using the > result of a previous fit, you used an a priori plausible value. While that > can introduce its own biases, it at least is based on external information > (a ?reasonable" value for S02) rather than trying to do the fit in pieces > (I?ll run a fit, find values for guessed parameters, and then set those to > the first results for the next fit). > > Fundamentally, you just don?t have a good fit yet. Likely, something about > the system is a bit different than you envisioned it. But that?s part of > the point of using EXAFS, right? For fits to tell you that, and then you to > use your knowledge about the system to try out plausible modifications to > the model until you find something that works well, hopefully also > supporting it with other lines of evidence? > > That?s not something we?re going to be able to do for you on this list; > it?s the heart of the investigation you?re undertaking. > > Best, > > Scott Calvin > Lehman College of the City University of New York > > *I say ?never,? but I can think of one case where it might be justified, > and wouldn?t be surprised if there are others. If you were trying to decide > between a compound being 4-coordinated or 6-coordinated, and had some > reason for thinking it was purely one or the other, then a fitted > coordination number of, for example, 6.3 +/- 0.7 could reasonably be set to > 6 in future fits. But that?s not the kind of circumstance you have. > > > > On Jan 7, 2017, at 9:17 AM, Raj kumar <rajrk37(a)gmail.com> wrote: > > > > Hi Scott, > > > > Thanks for your comments. Please see below for my answers. > > > > 1. Initially, i have started the fitting using single Eo but couldn't > achieve satisfactory fit. Hence, moved to use two Eo's, one for first two > shells and another for rest other shells, for fitting the curve. With this > strategy, I have varied all parameters, including Eo's, mentioned in the > previous table. As a result, i have identified appropriate Eo's for > respective paths. Subsequently, evaluated all other parameters keeping both > Eo's fixed. The result remains almost same irrespective of varying or > fixing Eo's. > > > > 2. YbVO4 belongs to zircon structure. In this kind of structure, only > the position of oxygen varies and leaving both metal atoms unmoved. The > atomic config, I have used (YbVO4-Demeter: @ standard zircon position) for > modelling is attached along with the COD database file. Both files having > different oxygen positions and hence different splitting distances for > first oxygen shell. Further, i have compared first two oxygen paths, > obtained from COD file, with experimental signal. It seems, the second > oxygen distance might be exaggerated. Again, please see attachment for the > confirmation. > > <image.png> > > > > > > > > Regards, > > Raj > > > > On 7 January 2017 at 01:06, <ifeffit-request(a)millenia.cars.aps.anl.gov > <mailto:ifeffit-request@millenia.cars.aps.anl.gov>> wrote: > > Send Ifeffit mailing list submissions to > > ifeffit(a)millenia.cars.aps.anl.gov <mailto:ifeffit@millenia.cars. > aps.anl.gov> > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit < > 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 <mailto: > 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 <mailto:ifeffit-owner@ > 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: error when fitting in Artemis (George Sterbinsky) > > 2. Re: Problem with large so2: Updated (Scott Calvin) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Fri, 6 Jan 2017 16:32:45 -0600 > > From: George Sterbinsky <GeorgeSterbinsky(a)u.northwestern.edu <mailto: > GeorgeSterbinsky(a)u.northwestern.edu>> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov > <mailto:ifeffit@millenia.cars.aps.anl.gov>> > > Subject: Re: [Ifeffit] error when fitting in Artemis > > Message-ID: > > <CALoY8Yw=PYOKfKivpjFfeqmOALA95wJK++Yen+HAi70V3KH8_Q@mail. > gmail.com <mailto:PYOKfKivpjFfeqmOALA95wJK%2B%2BYen%2BHAi70V3KH8_Q@ > mail.gmail.com>> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Robert and Bruce, > > > > Thank you for your replies and, Robert, for providing a work-around. I > too > > apologize for taking so long to respond. I was hoping to investigate the > > problem a bit further as to provide a more actionable bug report before > > responding to Robert, but in light of Bruce's message that no longer > seems > > as necessary. I also do not see a "phase.bin" file on my computer, and I > do > > see "0_Warning.txt". I will try to figure out when, in the history of the > > file, it became damaged and report back to the list if that information > > will help others prevent the problem or indicates a fix. > > > > Thanks again, > > George > > > > > > > > On Wed, Jan 4, 2017 at 10:05 AM, Bruce Ravel <bravel(a)bnl.gov <mailto: > bravel(a)bnl.gov>> wrote: > > > > > On 12/22/2016 12:11 PM, George Sterbinsky wrote: > > > > > >> I have attached an Artemis project. Upon opening the project, and > > >> clicking the fit button the error in the attached log file is > generated > > >> and the fit is not run. Looking at the history, fits have been run > > >> previously without error. The error message indicates Feff may need to > > >> be run again, but upon opening the Atoms and Feff window and then > > >> clicking on the Feff tab, I see the Run Feff button is grey and cannot > > >> be clicked. What steps are necessary in order to run a fit? > > >> > > > > > > Hi George, > > > > > > Sorry it has taken so long to respond. Partly holidays, partly that I > > > have been doing a bunch of work on Demeter that needed to get finished. > > > > > > So, the problem here does not seem to be a problem with Artemis. It > seems > > > to be an issue with someone's antivirus software. > > > > > > The artemis.fpj is simply a zip file with a different file extension. > > > Opening it up, one finds a folder called "feff". In the case of your > > > project file, the relevant subfolder is "azxqc" (that's a randomly > > > generated 5-character string, which is how Demeter names most things > > > internally). In that folder, there should be a "phase.bin" file from > the > > > Feff run. It's absent. Instead, I see a file called "0_Warning.txt", > the > > > contents of which read: > > > > > > BLOCKED FILE ALERT > > > > > > A file has been blocked due to the 'Blocked for exchange' rule. > > > Context: 'phase.bin' > > > Disallowed due to > > > Ticket Number: '09e8-5852-0da2-0001' > > > See your system administrator for further information. Copyright > 1999-2013 > > > McAfee, Inc.All Rights Reserved.http://www.mcafee.com < > http://www.mcafee.com/> > > > > > > Now, I do not know if this happened when you mailed the project file to > > > the list or if it happened at some other time. While the error > message is > > > certainly misleading in this case, I think that it is Artemis' way of > > > complaining about the missing phase.bin file. > > > > > > Perhaps there is some other problem at play. I don't know. But I > cannot > > > possibly troubleshoot that other problem given that an anti-virus > package > > > has, at some point, irretrievably damaged this project file. > > > > > > I think that the only plausible work-around is Robert's suggestion. > > > Reimport the feff.inp file, rerun Feff, exclude the existing path, > > > drag-and-drop the replacement path, then push path parameter values > from > > > the old path to the new one. Awkward, but I don't know what else to > > > suggest. > > > > > > B > > > > > > PS: If anyone has any kind of working knowledge of McAfee or any other > AV > > > software, I would be open to a suggestion for how to fix this. Is it a > > > file /name/ problem -- should phase.bin be called something else? Is > there > > > something in the phase.bin file that triggered McAfee? Any wisdom > would be > > > welcome. > > > > > > > > > -- > > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > <mailto:bravel@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/ < > http://bruceravel.github.io/home/> > > > Software: https://github.com/bruceravel < > https://github.com/bruceravel> > > > Demeter: http://bruceravel.github.io/demeter/ < > http://bruceravel.github.io/demeter/> > > > > > > _______________________________________________ > > > Ifeffit mailing list > > > Ifeffit(a)millenia.cars.aps.anl.gov <mailto:Ifeffit@millenia.cars. > aps.anl.gov> > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit < > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> > > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > <http://millenia.cars.aps.anl.gov/mailman/options/ifeffit> > > > > >

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Fwd: about sigma2 for exafs fitting
by Scott Calvin 08 Jan '17

08 Jan '17

Shaofeng has given me permission to repost her question here on the ifeffit mailing list. It is quoted below my response. Dear Shaofeng, As Bruce and I said before, a sigma2 of 0.0007 A^2 is not impossible, although it indicates less disorder than is typically present. Your attached table does seem to show some improvement by using the model from the hydrogen-containing structure as compared to the arsenate. A more rigorous test for statistical improvement can be conducted using the Hamilton test (you mentioned you’ve consulted XAFS for Everyone; full details of the Hamilton test are given there). It’s also encouraging that the uncertainties on your sigma2 determinations using the hydrogen-containing model are quite small; it appears that the fit is not getting confused by correlations even though it’s fitting both coordination number and sigma2, as that would generally also cause high uncertainties in the correlated parameters. Is such a stiff sigma2 reasonable in this case? I have no idea. I just don’t know enough about this particular system; perhaps someone else on the list does. Oh, and one other question—was the data collected at room temperature? If it were collected at cryogenic temperatures, that would tend to reduce thermal disorder and thus lower sigma2’s. Even if no one on the list has insight in to this particular system, anyone have good published examples of room-temperature systems with sigma2’s < 0.001? It might help Shaofeng with her referee… Best, Scott Calvin Lehman College of the City University of New York P. S. I certainly hope no reviewer is using the “typical values” I provide for parameters in XAFS for Everyone as rigid criteria for rejecting results! It is most certainly not the way I use them in the book. Some systems actually are atypical! Begin forwarded message: From: Shaofeng Wang <wangshaofeng(a)iae.ac.cn<mailto:wangshaofeng@iae.ac.cn>> Subject: about sigma2 for exafs fitting Date: January 4, 2017 at 8:31:33 PM CST To: <scalvin(a)sarahlawrence.edu<mailto:scalvin@sarahlawrence.edu>> Reply-To: Shaofeng Wang <wangshaofeng(a)iae.ac.cn<mailto:wangshaofeng@iae.ac.cn>> Dear Dr. Calvin, I am a research from China. I know you are an expert on XAFS analysis. So I write this letter to you for some xafs analysisi problem. Recently, I am attempting to study the incorporation of arsenate into the barite structure. To investigate the species of arsenate in barite, I fitted the exafs data using Ba3(AsO4)2 and a dft optimized structure with HAsO4 incorporated in barite supercell (configuration C2), respectively and got some results. Please see the attached table. Smaller reduced chi2 and R-factor were obtained by using configuration C2 as the initial model. Does this mean the species of arsenate in barite is more likely to be HAsO42- instead of AsO43- ? We also have other evidences including XANES and vibrational spectroscopy to support this conclusion. However, using C2 as the initial model we obtained samll sigma2 (~0.0007). This seems too small and out of the normal range (0.002 每 0.03) as you mentioned in your publications (XAFS for everyone). So, my question is if our data are reasonable. If yes, could you provid some references to support? By the way, I asked simialr question on the ifeffit forum and you gave me some answer. However, the reviewer was not convinced and he insited on that sigma2 must be in the range of 0.002-0.03. How can I response this question? Any help is very appreciated. Best regards, Shaofeng -------------------------------------- Shaofeng Wang, Ph.D of Geochemistry Environmental Molecular Science Group Institute of Applied Ecology, Chinese Academy of Sciences Shenyang, 110016, China wangshaofeng(a)iae.ac.cn<mailto:wangshaofeng@iae.ac.cn> www.iae.cas.cn<http://www.iae.cas.cn/>

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Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 11
by Raj kumar 08 Jan '17

08 Jan '17

Hi Scott, Thanks for your comments. Please see below for my answers. 1. Initially, i have started the fitting using single Eo but couldn't achieve satisfactory fit. Hence, moved to use two Eo's, one for first two shells and another for rest other shells, for fitting the curve. With this strategy, I have varied all parameters, including Eo's, mentioned in the previous table. As a result, i have identified appropriate Eo's for respective paths. Subsequently, evaluated all other parameters keeping both Eo's fixed. The result remains almost same irrespective of varying or fixing Eo's. 2. YbVO4 belongs to zircon structure. In this kind of structure, only the position of oxygen varies and leaving both metal atoms unmoved. The atomic config, I have used (YbVO4-Demeter: *@ standard zircon position*) for modelling is attached along with the COD database file. Both files having different oxygen positions and hence different splitting distances for first oxygen shell. Further, i have compared first two oxygen paths, obtained from COD file, with experimental signal. It seems, the second oxygen distance might be exaggerated. Again, please see attachment for the confirmation. [image: Inline images 2] Regards, Raj On 7 January 2017 at 01:06, <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: error when fitting in Artemis (George Sterbinsky) > 2. Re: Problem with large so2: Updated (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 6 Jan 2017 16:32:45 -0600 > From: George Sterbinsky <GeorgeSterbinsky(a)u.northwestern.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] error when fitting in Artemis > Message-ID: > <CALoY8Yw=PYOKfKivpjFfeqmOALA95wJK++Yen+HAi70V3KH8_Q(a)mail.gm > ail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Robert and Bruce, > > Thank you for your replies and, Robert, for providing a work-around. I too > apologize for taking so long to respond. I was hoping to investigate the > problem a bit further as to provide a more actionable bug report before > responding to Robert, but in light of Bruce's message that no longer seems > as necessary. I also do not see a "phase.bin" file on my computer, and I do > see "0_Warning.txt". I will try to figure out when, in the history of the > file, it became damaged and report back to the list if that information > will help others prevent the problem or indicates a fix. > > Thanks again, > George > > > > On Wed, Jan 4, 2017 at 10:05 AM, Bruce Ravel <bravel(a)bnl.gov> wrote: > > > On 12/22/2016 12:11 PM, George Sterbinsky wrote: > > > >> I have attached an Artemis project. Upon opening the project, and > >> clicking the fit button the error in the attached log file is generated > >> and the fit is not run. Looking at the history, fits have been run > >> previously without error. The error message indicates Feff may need to > >> be run again, but upon opening the Atoms and Feff window and then > >> clicking on the Feff tab, I see the Run Feff button is grey and cannot > >> be clicked. What steps are necessary in order to run a fit? > >> > > > > Hi George, > > > > Sorry it has taken so long to respond. Partly holidays, partly that I > > have been doing a bunch of work on Demeter that needed to get finished. > > > > So, the problem here does not seem to be a problem with Artemis. It > seems > > to be an issue with someone's antivirus software. > > > > The artemis.fpj is simply a zip file with a different file extension. > > Opening it up, one finds a folder called "feff". In the case of your > > project file, the relevant subfolder is "azxqc" (that's a randomly > > generated 5-character string, which is how Demeter names most things > > internally). In that folder, there should be a "phase.bin" file from the > > Feff run. It's absent. Instead, I see a file called "0_Warning.txt", > the > > contents of which read: > > > > BLOCKED FILE ALERT > > > > A file has been blocked due to the 'Blocked for exchange' rule. > > Context: 'phase.bin' > > Disallowed due to > > Ticket Number: '09e8-5852-0da2-0001' > > See your system administrator for further information. Copyright > 1999-2013 > > McAfee, Inc.All Rights Reserved.http://www.mcafee.com > > > > Now, I do not know if this happened when you mailed the project file to > > the list or if it happened at some other time. While the error message > is > > certainly misleading in this case, I think that it is Artemis' way of > > complaining about the missing phase.bin file. > > > > Perhaps there is some other problem at play. I don't know. But I cannot > > possibly troubleshoot that other problem given that an anti-virus package > > has, at some point, irretrievably damaged this project file. > > > > I think that the only plausible work-around is Robert's suggestion. > > Reimport the feff.inp file, rerun Feff, exclude the existing path, > > drag-and-drop the replacement path, then push path parameter values from > > the old path to the new one. Awkward, but I don't know what else to > > suggest. > > > > B > > > > PS: If anyone has any kind of working knowledge of McAfee or any other AV > > software, I would be open to a suggestion for how to fix this. Is it a > > file /name/ problem -- should phase.bin be called something else? Is > there > > something in the phase.bin file that triggered McAfee? Any wisdom would > be > > welcome. > > > > > > -- > > 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/ > > > > _______________________________________________ > > 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 > > >

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Problem with large so2: Updated
by Raj kumar 06 Jan '17

06 Jan '17

Dear all, Earlier, I have posted few questions on large so2 value and got valuable suggestions from Scott and Bruce. Here i am presenting my summary of earlier emails and the present views. Could you please tell me whether am i going in right direction. I have been trying to fit EXAFS signal of YbVO4 both in bulk and nanoparticles form. Here, I would like to estimate so2 from bulk (reference) and subsequently use the number, as normalization parameter, to calculate the co-ordination number in all nanoparticles. Nanoparticles were synthesized by solution route. First, I have modelled my reference (bulk YbVO4) with two so2, N and R as free parameters. So2-1 is for first two shell and so2-2 is for rest other shells. If I use single so2, the value is obtained to be around 0.9 with unsatisfactory fit whereas second so2-2 incorporation leads to satisfied fit with large uncertainty on the obtained number i.e., (2.04 +/- 0.9). Using the same strategy, I could successfully fit the nanoparticles again with large so2-2 (1.79). From literature and IFEFFIT earlier discussion, i understood that so2 should be between 0.8-1.2 value. Further, so2-2 is found to well correlated with ss1 and delc (a parameter to define the movement of atoms in c direction). Among two, the former parameter (ss1) strongly correlate with so2 and take value of 0.8 and 1.9 for fixed and varying ss1, respectively, during the fit. This large value of so2 cannot be controlled with the used model. Also, I have tried to fit the curve with fixed so2 i.e., below 1 but leads to unsatisfactory fit. For your info, i have tabulated various strategy and the resultant parameters. After considering Scott suggestions *(and previous posts),* i have concluded the following: Since, so2 is used as a normalization parameter and with the estimated uncertainty, i would like to consider the obtained number as reasonable value to normalize the unknown to calculate the CN in other systems. Is this strategy good to calculate the CN in unknown? and later to describe the trend on obtained parameters? Regards, Raj

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error when fitting in Artemis
by George Sterbinsky 06 Jan '17

06 Jan '17

Hello, I have attached an Artemis project. Upon opening the project, and clicking the fit button the error in the attached log file is generated and the fit is not run. Looking at the history, fits have been run previously without error. The error message indicates Feff may need to be run again, but upon opening the Atoms and Feff window and then clicking on the Feff tab, I see the Run Feff button is grey and cannot be clicked. What steps are necessary in order to run a fit? Thank you, George

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Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 3
by Raj kumar 05 Jan '17

05 Jan '17

Hi Bruce, I agree with your comments. Side phase with less than 5% in total composition cannot be easily detected using regular XRD but comprehensively using EXAFS. Here, i have also recorded bulk sample, similar to nanoparticles composition, which is completely free from contamination. >From this data, i have ruled out the presence of heavy metals. Regards, Raj On 4 January 2017 at 12:38, <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: Ifeffit Digest, Vol 167, Issue 2 (Raj kumar) > 2. Re: Ifeffit Digest, Vol 167, Issue 2 (Bruce Ravel) > 3. Re: Ifeffit Digest, Vol 167, Issue 2 (Raj kumar) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 3 Jan 2017 21:32:51 +0100 > From: Raj kumar <rajrk37(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 2 > Message-ID: > <CACc-a9+uy+4i65LrZf8kiJRk6bdTD2cVSdeeGLp2r0x4fDBrSQ@mail. > gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Scott, > > Thank you very much for your prompt response. EXAFS measurement was done > after the XRD characterization. From XRD, it is confirmed that there is no > side phase formation and contamination. Hence, i guess the heavier element > role could be avoided here. > > Split distances could be the reason??. The following is the method, i have > opted for modelling the obtained curve. Since YbVO4 is zircon structure, i > have constrained distance in paths 3, 8 and 9 with the pre-structural info > and let other distances vary with regular mathematical expression > alpha*Reff. am i doing wrong here? Before this, I have tried alpha*Reff for > all paths but fit failed miserably for multi-shells. > > Regards, > Raj > > On 3 January 2017 at 19:00, <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: Problem with large so2 (Scott Calvin) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 3 Jan 2017 09:59:18 -0600 > > From: Scott Calvin <dr.scott.calvin(a)gmail.com> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Problem with large so2 > > Message-ID: <3EF5E209-7681-49C6-9713-4BBF34C619A5(a)gmail.edu> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Raj, > > > > I haven?t looked at your files, but the kinds of results you are > > describing often indicate the model you are using beyond the first shell > is > > incorrect. It may be that it has the wrong elements (e.g., heavier > elements > > are present than what you modelled) or that the model includes split > > distances when in reality the compound is more symmetric. > > > > In short, no, the high second S02 does not make sense (although it would > > be good to know the uncertainties). > > > > Best, > > Scott Calvin > > Lehman College of the City University of New York > > > > > On Jan 3, 2017, at 9:38 AM, Raj kumar <rajrk37(a)gmail.com> wrote: > > > > > > Dear All, > > > > > > > > > > > > I have been trying to fit EXAFS signal of YbVO4 both in bulk and > > nanoparticles form. Here, I would like to estimate so2 from bulk > > (reference) and subsequently use the number, as normalization parameter, > to > > calculate the co-ordination number in all nanoparticles. Nanoparticles > were > > synthesized by solution route. From our earlier understanding on the > > synthesis, in some cases, Yb may or may not completely involve in > reaction. > > Therefore, I except Yb in two environments, one surrounded by mere oxygen > > (in precise oxygen-Hydrogen; due to disorder one may expect a single > peak) > > and another one in YbVO4 environment. With this info and for reasonable > > fit, I have used two so2 as free parameters for N: one for first shell > > (oxygen at two distances) and another for rest other shells. If I use > > single so2, I obtain the value of around 0.92 with unsatisfactory fit > > whereas the fit seems plausible with two so2 i.e., 0.75 and 2.2, > > respectively. Using the same strategy, I could successfully fi! > > t the nanoparticles again with large second so2 (1.79). From literature > > and IFEFFIT earlier discussion, i understood that so2 should be between > > 0.8-1.2 value. Here, I would like to know, does this huge second so2 > value > > makes sense? is the obtained so2 value can be used to calculated > > coordination number for unknown? Further, i have attached my worked files > > with this message. > > > > > > > > > > > > Regards, > > > > > > Raj > > > > > > <YbVO4-bulk.fpj><YbVO4-nps.fpj>_____________________________ > > __________________ > > > 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 > > > >

1 1

Calculation of SPOIL value for the reconstruction of standard spectra
by Montarges-pelletier Emmanuelle 04 Jan '17

04 Jan '17

" <ifeffit(a)millenia.cars.aps.anl.gov> Content-Transfer-Encoding: quoted-printable Mime-Version: 1.0 (1.0) Dear all I have performed PCA on a set of 13 XAS spectra, and tried to validate the m= odel compounds or standards using the Target Transform function on ATHENA (d= emeter 09.22). I could get the TT coefficients for every standard. Is there a simple way to calculate the SPOIL value from the Target Transform= coefficients?=20 Indeed, although graphics can be used to demonstrate that such and such stan= dard are relevant to fit experimental data, SPOIL values are often reported .= Thanks in advance for your answer Best regards and Best wishes for 2017. =E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80= =A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2= =80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2= =E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80= =A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2=E2=80=A2 Emmanuelle Montarges-Pelletier CNRS universit=C3=A9 de lorraine 0631331030 Emmanuelle.montarges(a)univ-lorraine.fr=

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 167, Issue 2
by Raj kumar 04 Jan '17

04 Jan '17

Hi Scott, Thank you very much for your prompt response. EXAFS measurement was done after the XRD characterization. From XRD, it is confirmed that there is no side phase formation and contamination. Hence, i guess the heavier element role could be avoided here. Split distances could be the reason??. The following is the method, i have opted for modelling the obtained curve. Since YbVO4 is zircon structure, i have constrained distance in paths 3, 8 and 9 with the pre-structural info and let other distances vary with regular mathematical expression alpha*Reff. am i doing wrong here? Before this, I have tried alpha*Reff for all paths but fit failed miserably for multi-shells. Regards, Raj On 3 January 2017 at 19:00, <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: Problem with large so2 (Scott Calvin) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 3 Jan 2017 09:59:18 -0600 > From: Scott Calvin <dr.scott.calvin(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Problem with large so2 > Message-ID: <3EF5E209-7681-49C6-9713-4BBF34C619A5(a)gmail.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Raj, > > I haven?t looked at your files, but the kinds of results you are > describing often indicate the model you are using beyond the first shell is > incorrect. It may be that it has the wrong elements (e.g., heavier elements > are present than what you modelled) or that the model includes split > distances when in reality the compound is more symmetric. > > In short, no, the high second S02 does not make sense (although it would > be good to know the uncertainties). > > Best, > Scott Calvin > Lehman College of the City University of New York > > > On Jan 3, 2017, at 9:38 AM, Raj kumar <rajrk37(a)gmail.com> wrote: > > > > Dear All, > > > > > > > > I have been trying to fit EXAFS signal of YbVO4 both in bulk and > nanoparticles form. Here, I would like to estimate so2 from bulk > (reference) and subsequently use the number, as normalization parameter, to > calculate the co-ordination number in all nanoparticles. Nanoparticles were > synthesized by solution route. From our earlier understanding on the > synthesis, in some cases, Yb may or may not completely involve in reaction. > Therefore, I except Yb in two environments, one surrounded by mere oxygen > (in precise oxygen-Hydrogen; due to disorder one may expect a single peak) > and another one in YbVO4 environment. With this info and for reasonable > fit, I have used two so2 as free parameters for N: one for first shell > (oxygen at two distances) and another for rest other shells. If I use > single so2, I obtain the value of around 0.92 with unsatisfactory fit > whereas the fit seems plausible with two so2 i.e., 0.75 and 2.2, > respectively. Using the same strategy, I could successfully fi! > t the nanoparticles again with large second so2 (1.79). From literature > and IFEFFIT earlier discussion, i understood that so2 should be between > 0.8-1.2 value. Here, I would like to know, does this huge second so2 value > makes sense? is the obtained so2 value can be used to calculated > coordination number for unknown? Further, i have attached my worked files > with this message. > > > > > > > > Regards, > > > > Raj > > > > <YbVO4-bulk.fpj><YbVO4-nps.fpj>_____________________________ > __________________ > > 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 > >

2 2

Problem with large so2
by Raj kumar 03 Jan '17

03 Jan '17

Dear All, I have been trying to fit EXAFS signal of YbVO4 both in bulk and nanoparticles form. Here, I would like to estimate so2 from bulk (reference) and subsequently use the number, as normalization parameter, to calculate the co-ordination number in all nanoparticles. Nanoparticles were synthesized by solution route. From our earlier understanding on the synthesis, in some cases, Yb may or may not completely involve in reaction. Therefore, I except Yb in two environments, one surrounded by mere oxygen (in precise oxygen-Hydrogen; due to disorder one may expect a single peak) and another one in YbVO4 environment. With this info and for reasonable fit, I have used two so2 as free parameters for N: one for first shell (oxygen at two distances) and another for rest other shells. If I use single so2, I obtain the value of around 0.92 with unsatisfactory fit whereas the fit seems plausible with two so2 i.e., 0.75 and 2.2, respectively. Using the same strategy, I could successfully fit the nanoparticles again with large second so2 (1.79). From literature and IFEFFIT earlier discussion, i understood that so2 should be between 0.8-1.2 value. Here, I would like to know, does this huge second so2 value makes sense? is the obtained so2 value can be used to calculated coordination number for unknown? Further, i have attached my worked files with this message. Regards, Raj

2 1

Re: [Ifeffit] Ifeffit Digest, Vol 166, Issue 22
by Raj kumar 23 Dec '16

23 Dec '16

Hi Guanghui, Final particle size of these nanoparticles are about 30-40 nm. Regards, Raj On 23 December 2016 at 19:00, <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: First shell in nps taking small ss than bulk (Zhang, Guanghui) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sat, 24 Dec 2016 01:57:12 +0800 (GMT+08:00) > From: "Zhang, Guanghui" <brighton30(a)126.com> > To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> > Cc: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] First shell in nps taking small ss than bulk > Message-ID: <5ef8031e.595e.1592cd45fae.Coremail.brighton30(a)126.com> > Content-Type: text/plain; charset="utf-8" > > Raj, > I am wondering if you have TEM or other results suggesting the particle > size of you NPs samples. I looked at your data briefly, and the k-space > data of the bulk and the two NPs samples look identical to me. I suspect > you have big particles which seems "bulk" to EXAFS. > It is my understanding that EXAFS only works well for NPs smaller than > several nanometers if you want to compare N and ss carefully. > > > > Regards, > Guanghui > > > > > > > > > > > > > > On 12/23/2016 09:17? Raj kumar<rajrk37(a)gmail.com>wrote? > > Dear all, > > > I have characterized YbVO4 in bulk (pellet form: prepared through solid > state reaction) and nanoparticles (using continuous flow: prepared through > co-precipation process) forms. Surprisingly, i found out that First shell > Yb-O in nanoparticles takes small ss value (0.00298; YbVO4nps-1.fpj) than > bulk (0.00509; YVO4bulk.fpj), while rest other shells in nanoparticles > found to take large ss compared to bulk. One would expect later trend for > all shells than former one due to well ordered and compact nature of bulk > YbVO4 phase. Owing to this weird trend, i returned back to R-space for > qualitative inspection (YbVO4.prj), there i found, wider R-space signal for > (all shells) all YbVO4 nanoparticles compared to bulk. This behavior is > also well supporting to my rationalized understanding. Could someone please > help me in understanding the obtained result? or if i am missing some > important point, please warn me. For more clarification, i have attached > the athena and artemis files for the ! > same. > > > With regards, > Raj >

1 0

First shell in nps taking small ss than bulk
by Raj kumar 23 Dec '16

23 Dec '16

Dear all, I have characterized YbVO4 in bulk (*pellet form: *prepared through solid state reaction) and nanoparticles (*using continuous flow*: prepared through co-precipation process) forms. Surprisingly, i found out that First shell Yb-O in nanoparticles takes small ss value *(0.00298; YbVO4nps-1.fpj)* than bulk *(0.00509; YVO4bulk.fpj)*, while rest other shells in nanoparticles found to take large ss compared to bulk. One would expect later trend for all shells than former one due to well ordered and compact nature of bulk YbVO4 phase. Owing to this weird trend, i returned back to R-space for qualitative inspection *(YbVO4.prj)*, there i found, wider R-space signal for (all shells) all YbVO4 nanoparticles compared to bulk. This behavior is also well supporting to my rationalized understanding. Could someone please help me in understanding the obtained result? or if i am missing some important point, please warn me. For more clarification, i have attached the athena and artemis files for the same. With regards, Raj

2 1

Re: [Ifeffit] Ifeffit Digest, Vol 166, Issue 12
by Raj kumar 22 Dec '16

22 Dec '16

Hi Bruce, Thanks for the explanation. Yes, both files are generating the same kind of output but the positioning of atoms can mislead in the context of structure. That's why i have raised the question. Regards, Raj On 16 December 2016 at 16:48, <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. Web Atoms 1.8 vs Demeter 0.9.26: feff output are not same > (Raj kumar) > 2. Re: Web Atoms 1.8 vs Demeter 0.9.26: feff output are not same > (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 16 Dec 2016 16:34:32 +0100 > From: Raj kumar <rajrk37(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Web Atoms 1.8 vs Demeter 0.9.26: feff output are > not same > Message-ID: > <CAAW7+QO1uSwLVz2m8pRpAsZisFVpheU3=gD > bsGgJebSZbbewpQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear All, > > Recently, i found out that feff.inp generated by web atoms and Demeter > 0.9.26 are not the same. My main worry is in the position of atoms. For > evidence, i am attaching YbVO4 (*feff.inp*) files generated by both web > atoms and Demeter. With this kind of zircon type structure, one would > except V1_2 at position *x/2+c/4* (3.85250). In web atoms generated file, i > could see this relation clearly, while in Demeter generated file the > relation reads like *x/2+y/2+c/4* instead of earlier condition. > Furthermore, all atoms (except few) are represented with three coordinated > position for Demeter generated file instead of two coordinated position. > > I already posted this query in the ifeffit mailing domain but the message > was not get circulated. Hence, I writing this problem to you. > > With regards, > Raj >

4 11

open 2-year postdoc position in X-ray spectroscopy and environmental geochemistry
by Voegelin, Andreas 20 Dec '16

20 Dec '16

Dear all We are looking for a postdoctoral fellow for a 2-year collaboration project between the Paul Scherrer Institute (PSI) and the Swiss Federal Institute of Aquatic Science and Technology (Eawag) in the fields of X-ray spectroscopy and environmental geochemistry. The tasks of the postdoctoral researcher are: - Setting up a cryostat system at the microXAS beamline at the Swiss Light Source for microspectroscopic analyses of radiation- and redox-sensitive environmental samples. - Perform micro-XRF/XAS/XRD studies on the microscale distribution and speciation of thallium and its association with various host phases in environmental samples. For further information see https://www.psi.ch/pa/job-opportunities/1444 or attachment. Please feel free to forward this information to potential candidates. Best regards, Andreas °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° °°° Andreas Voegelin, PhD Eawag - Swiss Federal Institute of Aquatic Science and Technology Ueberlandstrasse 133, CH-8600 Duebendorf, Switzerland Tel: +41 58 765 54 70 Fax: +41 58 765 52 10 mailto:andreas.voegelin@eawag.ch http://www.eawag.ch/~voegelan

1 0

E0 problem
by Fuxiang Zhang 19 Dec '16

19 Dec '16

Hi, All I have a problem about E0. It seems that E0 has great effect on the R(x) and the fitting. Can anyone explain how Athena automatically find the E0 value from an EXAFS spectrum. Sometimes the value is not at the peak of derivative of u(E), shall it be corrected manually? Thanks Fuxiang Zhang

2 2

Web Atoms 1.8 vs Demeter 0.9.26: feff output are not same
by Raj kumar 16 Dec '16

16 Dec '16

Dear All, Recently, i found out that feff.inp generated by web atoms and Demeter 0.9.26 are not the same. My main worry is in the position of atoms. For evidence, i am attaching YbVO4 (*feff.inp*) files generated by both web atoms and Demeter. With this kind of zircon type structure, one would except V1_2 at position *x/2+c/4* (3.85250). In web atoms generated file, i could see this relation clearly, while in Demeter generated file the relation reads like *x/2+y/2+c/4* instead of earlier condition. Furthermore, all atoms (except few) are represented with three coordinated position for Demeter generated file instead of two coordinated position. I already posted this query in the ifeffit mailing domain but the message was not get circulated. Hence, I writing this problem to you. With regards, Raj

2 1

Problems with gnuplot graphics on Mac OS 10.12.1
by Paul Fons 09 Dec '16

09 Dec '16

Hi All, I just wanted to give an update to my earlier problems with the mysterious gnuplot errors. After editing the file Matt mentioned earlier, I decided to uninstall and install demeter to no avail. I then realized that I had been relying on the latest version of xquartz (the x11 system) and installed x11 using macports. After a bit of trouble with installation (I had to break the installation into pieces — but this is a typical macports problem), the x11 installation completed and athena worked fine. Thus my conclusion is that there was some sort of weird interference between x11 subsystems. In any case, all is well now.

2 1

Peakfitting CeO2 data in Athena
by Stephanie Laga 08 Dec '16

08 Dec '16

Dear all, I am trying to extract the % Ce(III) from some CeO2 nanoparticle XAS data. I have been using moved the peak fitting function in Athena to model the XANES with an arctan background function and a series of gaussians. Looking through the literature I haven't seen too many specifics to using this approach (rationale for choosing the widths of peaks or how to define the background function). Similarly, doesn't seem to be much rationale for choosing a 4 vs 5 peak fit for the XANES. My main question is then...1) Is there a rational for picking the background function, specifically the height and width (can I let the height vary or should I be keeping a constant arctan through all samples)? Any advice is greatly appreciated! Stephanie

4 8

error on installing demeter on MacOSX 10.11.6
by Valerio Scagnoli 07 Dec '16

07 Dec '16

Dear all, I was trying to install demeter on my Mac with mac port and the installation seemed to run smoothly (after following the advice on the installation page!). However, when I try to start Athena from the command line I get the following error message: bash-3.2$ athena IO::Compress::Base::Common version 2.069 required--this is only version 2.015 at /opt/local/lib/perl5/vendor_perl/5.24/Compress/Zlib.pm line 10, <DATA> line 1. BEGIN failed--compilation aborted at /opt/local/lib/perl5/vendor_perl/5.24/Compress/Zlib.pm line 10, <DATA> line 1. Compilation failed in require at /opt/local/lib/perl5/site_perl/5.24/darwin-thread-multi-2level/Demeter/Files.pm line 27, <DATA> line 1. BEGIN failed--compilation aborted at /opt/local/lib/perl5/site_perl/5.24/darwin-thread-multi-2level/Demeter/Files.pm line 27, <DATA> line 1. Compilation failed in require at /opt/local/lib/perl5/vendor_perl/5.24/Module/Runtime.pm line 317, <DATA> line 1. Compilation failed in require at /opt/local/lib/perl5/site_perl/5.24/darwin-thread-multi-2level/Demeter/UI/Athena.pm line 24, <DATA> line 1. BEGIN failed--compilation aborted at /opt/local/lib/perl5/site_perl/5.24/darwin-thread-multi-2level/Demeter/UI/Athena.pm line 24, <DATA> line 1. Compilation failed in require at /opt/local/bin/athena line 27, <DATA> line 1. BEGIN failed--compilation aborted at /opt/local/bin/athena line 27, <DATA> line 1. I tried to install the following zlib packages and uninstall/reinstall demeter, but the error still remains. bash-3.2$ port installed |grep zlib p5.24-compress-raw-zlib @2.69.0_0 (active) zlib @1.2.8_0+universal (active) I have the following perl package installed bash-3.2$ port installed |grep perl p5.24-libwww-perl @6.150.0_0+ssl (active) p5.24-perl-ostype @1.10.0_0 (active) p5.24-perlio-layers @0.11.0_0 (active) p5.24-perlio-utf8_strict @0.6.0_0 (active) perl5 @5.24.0_0+perl5_24 (active) perl5.24 @5.24.0_0+universal (active) Any help will be appreciated. Valerio Scagnoli

2 1

error install Demeter
by Maria Rosa BECCIA 07 Dec '16

07 Dec '16

Hello, I tried to install Demeter on my Macbook OS El Capitan (version 10.11.6), but when typing the "sudo port install xors-server demeter” line, it gives me an error. You can find the error lines in the attached file. Thank you in advance for your help. Kind regards, Maria Rosa Beccia Maria Rosa BECCIA Maître de conférences Institut de Chimie de Nice Université Côte d'Azur UMR 7272 28 Avenue Valrose 06108 Nice, France phone: +33 (0)4 92 07 63 71

4 3

problems installing athena et al under ubuntu 16.04 LTS
by Juan de la figuera 02 Dec '16

02 Dec '16

Dear all, I have been installing demeter from git under ubuntu 16.04 LTS, following the non-root instructions from: https://gist.github.com/waveform80/3959252 I also installed xraylarch from git. Xaylarch is only missing: #=== Warning: Some recommended Python Packages are missing: epics: needed for using the EPICS control system pyFAI: needed for xrd modules It seems to work, but when I try to open a file that can be open properly from Athena installed on Windows, I get: Trying Larch server: /home/juan/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Demeter/share/ini/larch_server.ini Trying Larch server: larch_server -p 4968 start larch_server port=4968: started gnuplot> set xrange [ 6900130000 : 7955610000 ] ^ line 0: warning: integer overflow; changing to floating point gnuplot> set xrange [ 6900130000 : 7955610000 ] ^ line 0: warning: integer overflow; changing to floating point and although it opens the data in a gnuplot window, the scale is off (7x10^9 instead of 7x10^3). I am assuming once it is confused about the scale, it makes a mess with the data. The output of probe -bv is: t/000_ifeffit.t ......... 1..6 ok 1 - show ok 2 - show arrays: ok 3 - get_scalar 1.2345 ok 4 - put scalar ok 5 - put/get_string: my.xmu ok 6 - put/get_array: ok t/001_base.t ............ 1..24 Trying Larch server: /home/juan/soft/demeter/blib/lib/Demeter/share/ini/larch_server.ini Trying Larch server: larch_server -p 4969 start larch_server port=4969: started ok 1 - new() works ok 2 - group is set: orihs ok 3 - unique group names: orihs & bcxkm ok 4 - installation location identified ok 5 - identity string ok 6 - generic object is not plottable ok 7 - generic object has no data ok 8 - Project role works ok 9 - demeter can do introspection ok 10 - ifeffit disposal mode flag: 1 ok 11 - handle unknown mode gracefully ok 12 - other disposal modes all false ok 13 - turn on screen disposal mode flag ok 14 - turn on file disposal mode flag ok 15 - turn on buffer disposal mode flag ok 16 - unknown window not recognized ok 17 - known element (Cu) is recognized ok 18 - unknown element (Ci) not recognized ok 19 - simple template works not ok 20 - simple disposal to Ifeffit: string # Failed test 'simple disposal to Ifeffit: string' # at t/001_base.t line 69. not ok 21 - simple disposal to Ifeffit: scalar # Failed test 'simple disposal to Ifeffit: scalar' # at t/001_base.t line 70. Use of uninitialized value in numeric eq (==) at t/001_base.t line 71. not ok 22 - simple disposal to Ifeffit: array # Failed test 'simple disposal to Ifeffit: array' # at t/001_base.t line 71. ok 23 - simple disposal wrapper works ok 24 - plot_with works # Looks like you failed 3 tests of 24. Any help would be appreciated. Juan

4 9

struggling to install demeter under ubuntu 16.04
by mfehse 02 Dec '16

02 Dec '16

Hi im trying to install demeter under ubuntu 16.04 following the protocol given by david hughes https://bruceravel.github.io/demeter/documents/SinglePage/demeter_nonroot.h… I have followed through all steps but I encountered a few errors when doing the /Build install and when i want to run the application by "dathena" i get the following: marquinhos@marquinhos-Lapi:~/demeter$ dathena No command 'dathena' found, did you mean: Command 'athena' from package 'horae' (multiverse) dathena: command not found I have attached the error file to this mail produced via "./Build test | tee ~/test_errors.txt" thanks in advance marcus

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Re: [Ifeffit] struggling to install demeter under ubuntu 16.04
by Bruce Ravel 30 Nov '16

30 Nov '16

Marcus, This is the last time I am going to respond to a personal email from you on this topic. It is important that you use the mailing list. The list gets archived, which means that the next fellow who has a similar problem might be able to find our conversation and, thus, find a solution to the problem. A private conversation precludes that possibility, so I will not continue to respond to these private emails -- even though I have been CCing them to the list. The problem seems to be that you are installing demeter into a place in your home directory without telling your shell where to look for the executables. Try putting something like export PATH=$PATH:/home/marquinhos/demeter/bin/ in your .bashrc file, which is found in your home directory. You will then need to reload your .bashrc file. This can be done by . ~/.bashrc (the dot is important, see http://stackoverflow.com/questions/2518127/how-do-i-reload-bashrc-without-l…!) As for the problem you mention below about './Build test' -- I just pushed a fix for that problem to github within the last few minutes. Update from github and try again. B On 11/30/2016 01:36 PM, mfehse wrote: > hi > > i have searched for dathena file and found it in the following Path > > /home/marquinhos/demeter/bin/dathena > /home/marquinhos/demeter/blib/script/dathena > > but when i go into the folders bin and script and and try $ dathena$ I > still get the same error message > "No command 'dathena' found, did you mean: >>> Command 'athena' from package 'horae' (multiverse) >>> dathena: command not found" > > so i still dont know whats going. Are there any essential packages > missing from what you > > when i do "./Build test" > i get the error message > "t/002_types.t ........... Can't exec "larch_server": No such file or > directory at /home/marquinhos/demeter/blib/lib/Larch.pm line 66." > > could this be the problem? > > many thanks > > marcus > > re is no On 30/11/2016 17:40, Bruce Ravel wrote: >> So, where did the dathena script get installed on your computer? >> >> B >> >> >> On 11/30/2016 10:49 AM, mfehse wrote: >>> thanks for the quick reply. I just registered with the mailing list >>> today, i didnt add any address. >>> >>> Concerning your remarks for my installation problem your two hints >>> resulted in this: >>> >>> marquinhos@marquinhos-Lapi:~/demeter$ echo $PATH". "./Build >>> /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin. >>> >>> ./Build >>> marquinhos@marquinhos-Lapi:~/demeter$ hash -r >>> marquinhos@marquinhos-Lapi:~/demeter$ dathena >>> No command 'dathena' found, did you mean: >>> Command 'athena' from package 'horae' (multiverse) >>> dathena: command not found >>> marquinhos@marquinhos-Lapi:~/demeter$ >>> >>> hash -r didnt do much im afraid and about the path im not sure what this >>> is supposed to tell me. >>> As you might have noticed im not a frequent terminal user and I think >>> this cpan/ perl/ demeter installation is probably the trickiest thing i >>> have ever done, so please excuse my lack of experience -- 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/

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Re: [Ifeffit] your mail to the ifeffit mailing list
by Bruce Ravel 30 Nov '16

30 Nov '16

So, where did the dathena script get installed on your computer? B On 11/30/2016 10:49 AM, mfehse wrote: > thanks for the quick reply. I just registered with the mailing list > today, i didnt add any address. > > Concerning your remarks for my installation problem your two hints > resulted in this: > > marquinhos@marquinhos-Lapi:~/demeter$ echo $PATH". "./Build > /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin. > ./Build > marquinhos@marquinhos-Lapi:~/demeter$ hash -r > marquinhos@marquinhos-Lapi:~/demeter$ dathena > No command 'dathena' found, did you mean: > Command 'athena' from package 'horae' (multiverse) > dathena: command not found > marquinhos@marquinhos-Lapi:~/demeter$ > > hash -r didnt do much im afraid and about the path im not sure what this > is supposed to tell me. > As you might have noticed im not a frequent terminal user and I think > this cpan/ perl/ demeter installation is probably the trickiest thing i > have ever done, so please excuse my lack of experience -- 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/

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Athena bug
by S.Rowe 29 Nov '16

29 Nov '16

Dear all, I have been experiencing a bug in Athena, this is occurring in the most recent version 0.9.25, as well as the older versions I have used. The big is occurring when using the difference spectra window to produce difference spectra for a set of data. When I use the 'Plot difference spectra for all marked groups' function it will produce the plot but if I change any parameters in the main window and want to check how this has changed the difference spectra it will only plot the original difference spectra. To see the new difference spectra after the changes have been made I need to close Athena down completely and open it up again. If I just close the project and load in new data and try to plot the difference spectra for this new set of data it will still only plot the difference spectra for the old data. I have attached an Athena project file, please let me know if there is something different I need to do to change the difference spectra plot. Kind regards, Sinead Rowe

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