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

PGPLOT intallation error!
by Ernesto Ramos 26 May '16

26 May '16

Dear all, after running the PGPLOT_install script, I'm trying to continue the installation using ./configure, and sudo make, but in this step appears the following error message, collect2: error: ld returned 1 exit status make[3]: *** [libifeffit.so] Error 1 make[3]: Leaving directory `/home/ernesto/ifeffit-master/src/lib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/ernesto/ifeffit-master/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/ernesto/ifeffit-master' make: *** [all-recursive-am] Error 2 Could you help me to overcome this error? Thanks a lot! --------------------------------------------------------------------------- Ernesto Ramos Physical Engineer University of Brasilia, Campus Darcy Ribeiro 70910900 Brasilia DF, Brazil Tel. (+55) 61 30343370 Cel. (+55) 61 82317244 ---------------------------------------------------------------------------

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PGPLOT installation error!
by Ernesto 26 May '16

26 May '16

Dear all, after running the PGPLOT_install script, I'm trying to continue the installation using ./configure, and sudo make, but in this step appears the following error message, collect2: error: ld returned 1 exit status make[3]: *** [libifeffit.so] Error 1 make[3]: Leaving directory `/home/ernesto/ifeffit-master/src/lib' make[2]: *** [all-recursive] Error 1 make[2]: Leaving directory `/home/ernesto/ifeffit-master/src' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/home/ernesto/ifeffit-master' make: *** [all-recursive-am] Error 2 Could you help me to overcome this error? Thanks a lot!

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doubt on number of variables
by Jesús Eduardo Vega Castillo 26 May '16

26 May '16

Dear all, Perhaps this question is silly but I need to clarify a doubt I have: As far as I understand the number of variables refers to those parameters which have been "guessed" in the fit and it is limited by the number of independent points. If I have a group of variables but only set to guess a few of them while fixing the others, then fix some of the obtained values and guess other variables; I might include a large number of parameters in the resulting fit (even more than the independent points) without increasing the Number of variables of each individual fit. This also would keep reduced chi2 from increasing too much. Would this be cheating? The total number of parameters included is always restricted by the Number of independent points? or Can I include all the parameters I want as long as I set to guess no more that the number of independent points at the time? Thank you in advance as always, Yours Jesús esús

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Re: [Ifeffit] Question about H scattering
by Joshua Kas 24 May '16

24 May '16

Hi Riti, You can change the muffin-tin radius using the FOLP card, which is available in FEFF6 as well as later versions. For example, if the H atoms have the potential index 1, then use FOLP 1 0.8 to reduce the muffin tin radius of hydrogen. FOLP 1 1.0 will have touching muffin tin potentials. Josh On Tue, May 24, 2016 at 10:00 AM, <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: Question about H scattering (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 23 May 2016 15:44:20 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: Ritimukta Sarangi <ritimukta(a)gmail.com>, XAFS Analysis using > Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Question about H scattering > Message-ID: > <CA+7ESbofFBk26OR=8My-tbqkE1qhsj9nagcx5gT0Ho= > XPMmK9A(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Riti, > > > On Mon, May 23, 2016 at 1:50 PM, Ritimukta Sarangi <ritimukta(a)gmail.com> > wrote: > > > Hi Matt, > > I have a question about FEFF and I hope you can shed some light on it. > > Several references point to the high muffin tin radius of H (0.77) in > FEFF > > and say that it should be closer to 0.2. Is there a way of changing the > MT > > radius of H in FEFF? > > Thank you, > > -Riti > > > I'm CCing this to the Ifeffit mailing list, because there are probably many > people with more experience with this than me. > > I believe there is not a simple way to set the muffin tin radius for H or > other atoms. But, I think you can tweak this with the "FOLP" setting > (usually a number between 1 and 1.25 or so, representing the amount of > overlap between atoms). > > My understanding is that Feff 9 handles hydrogen better than earlier > versions, but I don't run very many calculations with H in the structures. > Hopefully someone who does will share some insight. > > --Matt >

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Re: [Ifeffit] Question about H scattering
by Matt Newville 23 May '16

23 May '16

Hi Riti, On Mon, May 23, 2016 at 1:50 PM, Ritimukta Sarangi <ritimukta(a)gmail.com> wrote: > Hi Matt, > I have a question about FEFF and I hope you can shed some light on it. > Several references point to the high muffin tin radius of H (0.77) in FEFF > and say that it should be closer to 0.2. Is there a way of changing the MT > radius of H in FEFF? > Thank you, > -Riti I'm CCing this to the Ifeffit mailing list, because there are probably many people with more experience with this than me. I believe there is not a simple way to set the muffin tin radius for H or other atoms. But, I think you can tweak this with the "FOLP" setting (usually a number between 1 and 1.25 or so, representing the amount of overlap between atoms). My understanding is that Feff 9 handles hydrogen better than earlier versions, but I don't run very many calculations with H in the structures. Hopefully someone who does will share some insight. --Matt

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N independent variables
by Jesús Eduardo Vega Castillo 23 May '16

23 May '16

Dear list, I made an EXAFS analysis in Artemis (in Demeter 0.9.22) using all the available variables. This is a fragment of the .log file I got: Independent points : 17.7666016 Number of variables : 17 Chi-square : 265.0947132 Reduced chi-square : 345.8050781 R-factor : 0.0026486 Number of data sets : 1 : k-range = 2.942 - 11.043 : dk = 1 : k-window = hanning : k-weight = 1,2,3 : R-range = 1.115 - 3.5 : dR = 0.0 : R-window = hanning : fitting space = r : background function = yes : phase correction = no : background removal = E0: 20002.215, Rbkg: 1.0, range: [2.25:17.4039986832903], clamps: 0/24, kw: 2 : epsilon_k by k-weight = 3.189e-004 : epsilon_r by k-weight = 2.339e-001 : R-factor by k-weight = 1 -> 0.00220, 2 -> 0.00224, 3 -> 0.00392 The problem is that when I use the Nyquist criterion Nind=2*deltak*deltar/pi + 1 for calculating the number of independent points the value I got is much lower and close to 13. I was not aware of this discrepancy and it caused a reviewer to think I made up the fit! Am I doing something wrong? Is there another way to calculate the Nind that might have been used by Artemis? I would really appreciate any help. Yours Jesús

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Consultation on Reduced Chi2
by Jesús Eduardo Vega Castillo 23 May '16

23 May '16

Dear list, I am back with a new consultation on EXAFS fitting within Artemis. I have made a fit and obtained a reduced Chi2 value of 391 and R-factor of 0.014 using 9 variables. Then I have added two more paths increasing the number of variables up to 12 and then I obtained a reduced Chi2 of 3039 and R-factor of 0.007. I am a little surprised by the huge increase of reduced Chi2 while R-factor decreases down to half. What could be the cause of this large increase? Does it mean that it is not worth to add these new paths? As always, thank you in advance Yours, Jesús

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Bug report ATHENA (Demeter 0.9.24)
by Patel, Sunil 16 May '16

16 May '16

Hello All, I am using the latest version of Demeter (0.9.24) in Windows 7 Enterprise (64-bit). In the process of doing LCF, the fit details (for ex. standards used for fitting, fitting range, phase fractions etc.) are not saved into the project file. This (very useful!) feature was available in the older version of ATHENA. Please find attached a project file. To reproduce the problem: 1. Open the project file in new ATHENA. 2. Do LCF for marked datasets (Data_1 to Data_6) using standards (Standard_1 and Standard_2), with LCF range= -20 to 40 eV and hitting the "Fit marked groups" tab. 3. Save the project file and close it. 4. Re-open the file and go to the LCF page. The details are not saved. We need to re-do the fits to get the values. 5. To check, open the ATHENA project file in older version of ATHENA and repeat the above steps. LCF details are shown on re-opening the file. A similar bug report was made last year for an earlier version of Demeter (0.9.21). (http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg05057.ht… ) Thanks & regards, Sunil Patel

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Bug report ATHENA (Demeter 0.9.24)
by Patel, Sunil 16 May '16

16 May '16

Hello All, I am using the latest version of Demeter (0.9.24) in Windows 7 Enterprise (64-bit). In the process of doing LCF, the fit details (for ex. standards used for fitting, fitting range, phase fractions etc.) are not saved into the project file. This (very useful!) feature was available in the older version of ATHENA. Please find attached a project file. To reproduce the problem: 1. Open the project file in new ATHENA. 2. Do LCF for marked datasets (Data_1 to Data_6) using standards (Standard_1 and Standard_2), with LCF range= -20 to 40 eV and hitting the "Fit marked groups" tab. 3. Save the project file and close it. 4. Re-open the file and go to the LCF page. The details are not saved. We need to re-do the fits to get the values. 5. To check, open the ATHENA project file in older version of ATHENA and repeat the above steps. LCF details are shown on re-opening the file. A similar bug report was made last year for an earlier version of Demeter (0.9.21). (http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg05057.ht… ) Thanks & regards, Sunil Patel

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Re: [Ifeffit] Ifeffit Digest, Vol 159, Issue 5
by Christopher Thomas Chantler 14 May '16

14 May '16

Hi All Most of them can be downloaded from either here https://www.researchgate.net/profile/Christopher_Chantler/ or here www.ph.unimelb.edu.au/~chantler/opticshome/papers.html ------------------------------------------------------------ Christopher Chantler, Professor, FAIP Editor-in-Chief, Radiation Physics and Chemistry Chair, International IUCr Commission on XAFS President, International Radiation Physics Society School of Physics, University of Melbourne Parkville Victoria 3010 Australia +61-3-83445437 FAX +61-3-93474783 chantler(a)unimelb.edu.au chantler(a)me.com http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html http://optics.ph.unimelb.edu.au/~chantler/home.html ________________________________________ From: Ifeffit [ifeffit-bounces(a)millenia.cars.aps.anl.gov] on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov [ifeffit-request(a)millenia.cars.aps.anl.gov] Sent: Sunday, 15 May 2016 9:20 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 159, Issue 5 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 159, Issue 4 (Matteo Busi) ---------------------------------------------------------------------- Message: 1 Date: Sun, 15 May 2016 01:20:03 +0200 From: Matteo Busi <basebush(a)gmail.com> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 159, Issue 4 Message-ID: <CAOyEiGgk5fqRzAoDAFTNibp_bctK=81Cp2+C4r-1T8v9+FyTbQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Dear Chris, I would be glad to at least read the papers you mentioned. If it possible you can send them here or at my email basebush(a)gmail.com when you have time. Regards, Matteo Den l?rdag 14. mai 2016 skrev <ifeffit-request(a)millenia.cars.aps.anl.gov> f?lgende: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov <javascript:;> > > 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 <javascript:;> > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov <javascript:;> > > 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 159, Issue 3 (Christopher Thomas Chantler) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 13 May 2016 21:43:34 +0000 > From: Christopher Thomas Chantler <chantler(a)unimelb.edu.au <javascript:;>> > To: "ifeffit(a)millenia.cars.aps.anl.gov <javascript:;>" > <ifeffit(a)millenia.cars.aps.anl.gov <javascript:;>> > Cc: Christopher Thomas Chantler <chantler(a)unimelb.edu.au <javascript:;>> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 159, Issue 3 > Message-ID: > < > 1C86B7F795364B44940B1EAAB9D774FADEE724BE(a)000s-ex-mbx-qs1.unimelb.edu.au > <javascript:;>> > > Content-Type: text/plain; charset="us-ascii" > > Dear All, Matteo > > It is difficult to do post facto, but if you have a well-defined solid, > foil or crystal then mapping the thickness, measuring the mass and hence > determining the mass per unit area, for the exact region illuminated by the > beam, provides accurate units. Usually you will need to make a measurement > of the average m/A from (i) total mass and (ii) total area, and then (iii) > map the whole sample with X-ray tomography and (iv) the region illuminated > by the X-ray beam. > > We have a series of papers which explain more than one methodology for > doing that within the XERT technique. If your sample is a solution it is a > bit more tricky, and I would refer you to recent JSR and JPCC papers for > our Hybrid technique. Both can work well but need a bit more care than a > normal XAFS measurement. > > Best wishes > Chris > ------------------------------------------------------------ > Christopher Chantler, Professor, FAIP > Editor-in-Chief, Radiation Physics and Chemistry > Chair, International IUCr Commission on XAFS > President, International Radiation Physics Society > School of Physics, University of Melbourne > Parkville Victoria 3010 Australia > +61-3-83445437 FAX +61-3-93474783 > chantler(a)unimelb.edu.au <javascript:;> chantler(a)me.com <javascript:;> > http://optics.ph.unimelb.edu.au/~chantler/xrayopt/xrayopt.html > http://optics.ph.unimelb.edu.au/~chantler/home.html > > > ________________________________________ > From: Ifeffit [ifeffit-bounces(a)millenia.cars.aps.anl.gov <javascript:;>] > on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <javascript:;> [ > ifeffit-request(a)millenia.cars.aps.anl.gov <javascript:;>] > Sent: Saturday, 14 May 2016 3:00 AM > To: ifeffit(a)millenia.cars.aps.anl.gov <javascript:;> > Subject: Ifeffit Digest, Vol 159, Issue 3 > > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov <javascript:;> > > 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 <javascript:;> > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov <javascript:;> > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. How to assign measure unit to XAFS data (Matteo Busi) > 2. Re: How to assign measure unit to XAFS data (Alexey Boubnov) > 3. Re: How to assign measure unit to XAFS data (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 13 May 2016 02:11:39 +0200 > From: Matteo Busi <basebush(a)gmail.com <javascript:;>> > To: ifeffit(a)millenia.cars.aps.anl.gov <javascript:;> > Subject: [Ifeffit] How to assign measure unit to XAFS data > Message-ID: > <CAOyEiGg1N7wL-tnzPXFBCrUYQD=6= > bvsRFnDNEe3ZaCeguFU5Q(a)mail.gmail.com <javascript:;>> > Content-Type: text/plain; charset="utf-8" > > Hi Bruce, Matt, and mailing list readers, > > I have one question regarding the XAFS data. I have collected absorption > coefficient in fluorescence regime of a CuSO4 penta hydrate sample(however > my question can be generalized to any compound). > Through Athena I then obtained the x\mu(eV) spectra as well as \chi(k) and > \chi(R). I am wondering how can I assign a unit to the x\mu values. I would > like to have it in the cm^-1 or cm^2 kg^-3 unit so than I can match it with > tabulated data for the Copper absorption coefficient and proceed with my > studies. > > In case a treatment is needed for the normalized \mu , that would also suit > my situation. > > My idea was to divide by the thickness of the sample but I don't find a > reasonable justificiation for this. > > I really hope I made the question clear to any reader this time, and if > that is not the case I apologyze in advance. > > Best Regards > Matteo >

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