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

Small larch bug
by Johan Nilsson 27 May '16

27 May '16

Hello, I've found a small "bug" in larch when I tried to run the pre_edge function for some spectra. It seems that find_e0 will not accept a 2d 1-column array as input for energy or mu, and it gives a traceback which is quite difficult to decipher. Other functions like plot accepts these arrays without any problems, which made it a bit difficult to figure out what the problem was. Maybe there can be some some sort of warning if arrays have unexpected shapes, or an internal reshape if that works. I've attached a script that should give a minimum working example, my output is: larch> run('cu.lar') (612,) 8977.58 (612, 1) File "/usr/local/lib/python2.7/dist-packages/larch/__init__.py", line 37, in wrapper return fcn(*args, **keywords) File "/usr/share/larch/plugins/xafs/pre_edge.py", line 51, in find_e0 dmu = np.gradient(mu)/np.gradient(energy) File "/usr/lib/python2.7/dist-packages/numpy/lib/function_base.py", line 918, in gradient out[slice1] = (f[slice2] - f[slice3])file cu.lar, line 14 IndexError: index 1 is out of bounds for axis 1 with size 1 find_e0(e,cu.mu,group=cu) find_e0(e,cu.mu,group=cu) file cu.lar, line 14 larch> Best wishes, Johan

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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

1 0

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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Re: [Ifeffit] Ifeffit Digest, Vol 159, Issue 4
by Matteo Busi 14 May '16

14 May '16

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 lørdag 14. mai 2016 skrev <ifeffit-request(a)millenia.cars.aps.anl.gov> følgende: > 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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Re: [Ifeffit] Ifeffit Digest, Vol 159, Issue 3
by Christopher Thomas Chantler 13 May '16

13 May '16

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 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: Saturday, 14 May 2016 3:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 159, Issue 3 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. 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> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] How to assign measure unit to XAFS data Message-ID: <CAOyEiGg1N7wL-tnzPXFBCrUYQD=6=bvsRFnDNEe3ZaCeguFU5Q(a)mail.gmail.com> 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

1 0

How to assign measure unit to XAFS data
by Matteo Busi 13 May '16

13 May '16

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

3 2

Artemis/FEFF question
by Dimitar Popmintchev 03 May '16

03 May '16

Dear All, The database at http://cars9.uchicago.edu/~newville/adb/search.html is down and I am trying to create an input file (for feff calculation) for pure scandium ( http://www.periodni.com/sc.html ). The problem is when the 'atoms', and 'feff' in Artemis calculate the scattering paths, they shows distances smaller than the expected 3.256A nearest neighbor distance. What is the error in the input file attached below ? Thank you. Dimitar ATOMS * this list contains 117 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Sc1 0.00000 0.00000 0.00000 2.63650 1 Sc1.1 2.63650 0.00000 0.00000 -2.63650 1 Sc1.1 2.63650 2.86568 1.65450 0.00000 1 Sc1.2 3.30900 -2.86568 1.65450 0.00000 1 Sc1.2 3.30900 Input file for scandium ## This Atoms file was generated by Demeter 0.9.22 ## Demeter written by and copyright (c) Bruce Ravel, 2006-2015 title = name: scandium title = formula: Sc title = sites: Sc1 title = refer1: Kittel, ISSP title = refer2: title = schoen: title = notes1: metal, hcp space = P63/mmc a = 3.30900 c = 5.27300000 rmax = 9.00000 core = Sc1 atoms # el. x y z tag Sc 0.00000 0.00000 0.00000 Sc1

2 2

Postdoctoral position
by Anatoly I Frenkel 03 May '16

03 May '16

Dear IFEFFIT subscribers: A postdoctoral position in my group will be available on July 1, 2016. The postdoc will be employed by Yeshiva University in New York City. She or he will be stationed in Brookhaven National Laboratory on Long Island and utilize XAFS and XRD/PDF techniques for studying mechanisms of electrostriction in novel electromechanical materials. Prior experience with these methods, including high energy resolution XAS, is required. This position is part of international collaboration, and will involve occasional travel to research sites outside of the US. For all inquiries please contact me. Anatoly Frenkel, Ph.D. Professor and Chair, Department of Physics, Yeshiva University 245 Lexington Avenue, New York, NY 10016 https://yu.edu/faculty-bios/frenkel/ Spokesperson, Synchrotron Catalysis Consortium http://yu.edu/scc Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.frenkel(a)yu.edu

1 0

XASLIB (was Re: data availability)
by Matt Newville 27 Apr '16

27 Apr '16

Hi Nino, Thanks for bringing this up and for the kind words. I agree that not only is access to measured XAFS spectra a problem now, it's been a problem for a long time, as evidenced by the Farrel Lytle database. In fact, it has long been a topic of discussion in the XAFS community of how to provide such databases, and developments over the past few years on data formats have been driven at least partly by the desire to have better spectral databases. For everyone: please try out XASLIB at http://cars.uchicago.edu/xaslib and let us know if you have any questions, comments, or suggestions for improving this database. Right now, there is not a lot of data here, but it is enough to give you an idea of how it works. Comments can either come here or as github Issues at the source repository for this code: https://github.com/XraySpectroscopy/XASDataLibrary There is a bit of documentation and wiki pages at https://github.com/XraySpectroscopy/XASDataLibrary/wiki A longer explanation: The standard XDI format for XAFS data (largely the work of Bruce) was presented at an IXAS workshop (Q2XAFS) in Tsukuba, Japan in 2011. At the most recent Q2XAFS meeting in Hamburg last August (as a satellite meeting of the XAFS conference), I presented an initial version of an on-line database based on this format, and intended for general use in the community. With feedback from that meeting, the version linked above is now ready for beta testing and comments. The plan is to move this to the IXAS Portal http://www.ixasportal.net/ixas/, but we'd like to get community suggestions and features and testing before we make that move. The database uses proper relational database to store the actual data, and tries to use modern web technologies for the interface. Some of the main features of this database are: - spectra can be uploaded from XDI files through the web interface. - multiple spectra can be tagged as belonging to the same Suite. - individual spectra or Suites can be rated and/or commented on by anyone, giving "Amazon-like" reviews. - in order to upload or comment, one has to log in by email address. The ratings and reviews are meant to provide some mechanism for data quality assurance, but to avoid having one person "police" the data before it can be added. This is trying to recognize that no one person can actually curate all the spectra, that truly bad data can be best identified by experts on that system, and also that there is actually some value to imperfect data. The requirements for data to be uploaded are fairly minimal except that the data must be in XDI format (basically so that metadata can be parsed easily and the columns are well-labeled), and that the monochromator lattice constant must be provided (so that energy re-calibration can be done if needed). We can help translate existing data into XDI so it can be uploaded into this database. There are several features to add or improve including: - adding some information about energy resolution. - being able to export a Suite of spectra as a single zip file or Athena project. - better web page interface to setting citation information. - better web page interface to setting sample information. But suggestions from anyone would be greatly appreciated. Finally, although the database is meant to provide a public, on-line databases useful to anyone, and uses modern relational database engines as the backend, the software can actually run on an individual machine to provide a local, private database of XAS spectra, with the same web-based interface. This is not very well documented at the moment, but if anyone is interested in trying to set such a database at their home institution, let me know. --Matt Newville

1 0

Farrel Lytle IXAS XAFS database data energy calibration
by bajnoczi 26 Apr '16

26 Apr '16

Dear List Members, I need some nickel reference spectra, and I thought to use the Farrel Lytle IXAS XAFS database. I have found some proper ones, e.g.: http://ixs.csrri.iit.edu/data/Farrel_Lytle_data/RAW/Ni/nifl.090 and http://ixs.csrri.iit.edu/data/Farrel_Lytle_data/RAW/Ni/nicl.047 , but it is not clear from the files how these spectra are energy calibrated. Can somebody help and give some detailed information about it for me? Thank you for your help in advance. Best Regards, Eva Bajnoczi

4 3

data availability
by pereira 26 Apr '16

26 Apr '16

New to this mailing list, so excuse my innocence: Today I see two questions about standards. Some time ago I was looking for what I think is similar, and was pointed to the XAS data base http://cars.uchicago.edu/xaslib/about/. If I understand the questions properly, this database may be of great help. It was to me. I thank the people organizing it, Matt Newville and Bruce Ravel, for their great service to the community in volunteering to make seemingly reliable data available in a convenient way. Nino

1 0

Request for CuCl and CuSO4 XAFS/ XANES standard data
by Halder, Avik 26 Apr '16

26 Apr '16

I was trying to find the bulk standards for CuCl and CuSO4. If you would have this data could you please share with me. Best regards, Avik Halder

1 0

how to use the data in the XAN library to estimate the transmission of an x-ray filter
by pereira 13 Apr '16

13 Apr '16

Hi All, new to this list and to the field, so please be patient and kind and helpful in any response you may have. So far everyone I've reached on this topic has been extraordinary good. I still have to learn the lore though. I'd like to compute the x-ray transmission as function of the x-ray energy, for a particular mass per unit area of a substance, say Zn. In the XAS data base I find Zn foil at room temperature, recently measured and even more recently put into the data base just in time for my purpose. Thank you! The question is: is there a ready-made program to use those data? I see that your community has a whole slew of programs that do the opposite, go from the attenuation and/or fluorescence measured on a beam line to the attenuation coefficient, apparently without having to know the mass per unit area of the filter. I see Demeter, Athena, Larch, and various others but they all seem to go the wrong way for (and much further than) what I need. Instead, I'd like to pick up the data you guys measured on the synchrotron, and convert those into the X-ray transmission of a filter for which I select the mass per unit area. In trying to figure out how to do this I look at the graphs in the database, and the numbers behind Zn foil.xdi. The graph on the top left side gives the "Raw XAFS" (y, say) as function of energy. I interpret that as y = - ln (itrans/i0), where i0 and itrans are in Zn foil.xdi as the intensity of the incoming x-ray beam, and the beam behind the particular filter. Far from the edge, at 9600 eV, I see i0=93769.049842 and itrans=56429.849906, so that y=0.508. I can't tell from the graph whether this is indeed the case, so I go to the NIST tables. They give 35.05 cm^2/g on the low side of the edge. Then, the mass per unit area of this particular foil must have been 14.5 mg/cm^2. At 10000 eV the same thing gives y=3.603. This is pretty close to what I see in the graph, so I'm tempted to think that guessing "Raw XAFS"= ln(i0/itrans). However, for (mu/rho) NIST gives 233.1 cm^2/g, so I get for the foil's mass per unit area 16 mg/cm^2. Not quite right. Any comments on what I might have done wrong? It seems to me that by measuring the transmission of a particular filter on some X-ray source we might have available would then in effect measure the mass per unit area, so that this can be taken into account by simply exponentiating itrans/i0 with the right exponent ( = multiplying the logs with the right factor). Is something like this already implemented in one of your programs? If so, which one? Thank you, Nino

2 1

SSRL XAS Summer School 2016 - update
by Ritimukta Sarangi 12 Apr '16

12 Apr '16

Hello Everyone, The agenda and application pages are online for the XAS summer school at SSRL in July. Please note that there are two hands-on tracks and you can choose to attend one of either XAS-imaging or EXAFS sessions. The lecture part is the same for both the sessions and both sessions will benefit from the XANES and advanced spectroscopy lectures on the final day of the summer school. Note that the deadline for application is May10th. Accepted participants will be emailed before the 20th of May. http://ssrl.slac.stanford.edu/conferences/workshops/exafs2016/index.html <http://ssrl.slac.stanford.edu/conferences/workshops/exafs2016/index.html> Best Wishes, -Riti Sarangi Staff Scientist SSRL, SLAC > On Apr 4, 2016, at 12:32 PM, Ritimukta Sarangi <ritimukta(a)gmail.com> wrote: > > Hello Everyone, > This is an announcement for the XAS summer school to be held at SSRL between July 18-22, 2016. We will cover XAS, EXAFS and Imaging beamlines with hands on data collection sessions at beamlines, followed by in-depth data analysis in a classroom setting. You can find more information at :http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2016/index.html <http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2016/index.html>. The agenda and application pages will be finalized within a week and I will post an update once it is up and running. But I wanted interested users and participants to get a heads up. > > > > >

1 0

Importing chi(k) data
by Matteo Busi 12 Apr '16

12 Apr '16

Hi, I am experiencing several bugs when trying to import data as chi(k). I have the data as a .dat ascii files with k the second column and the relevant chi(k) and corrected chi(k) as the 4th and 5th columns. This data was previously exported as .xmu from athena, the k grid column was obtained as k ~= sqrt(0.262468*(E-E0)). When I try to import this new data back in athena, I get something totally different from expectations! However sometimes by clicking repeatedly in the importing menu I get the expected result. This looks like a bug to me! You can find the file as attachment. Regards

2 1

Bug report
by Lorenzo Stievano 11 Apr '16

11 Apr '16

Hi, I have to report a bug on a computer where Demeter 0.9.24 is installed. Athena worked fine until a few days ago, but from a certain point it started to crash when I try to import a simple text data file (which worked well before). I have tried reinstalling Demeter (I actually did it twice) but the problem persist. The computer works under WIndows 7 Professional, SP1, 64 bits. Can you help me? Thank you in advance, Lorenzo PS: The athena log after the crash is attached.

3 14

(no subject)
by Matteo Busi 08 Apr '16

08 Apr '16

Hi Matt. Thanks for the hints, they are very useful. What would you suggest to use if not the bkg? Regarding the xmu(E) I have been using exactly the values exported through the .xmu ascii file. I have been reading though the Athena's user guide and I didn't find any hint about which unit I could assign to them. Anyway I would like to get them with the cm^-1 units which would suit with the correction expression I want to perform. How can this be done? My idea was to divide the xmu data by the penetration depth in the sample (i.e. the radius of the capillar sample). Is this correct? Can this be applied to the bkg data aswell? Moreover the data I have is not scanned through the Cu fluorescence energy you have mentioned (8046 eV). Would you recommend to use data from Chantler or Cromer-Liberman? And how can I merge it with my other measured data to make it unit meaningful? Thanks and regards, Matteo I report our previous conversation for reference: > What I am trying to do is to perform a new developed self-absorption > correction using collected fluorescence absorption coefficient data on a > CuSO4 (pentahydrate) capillar (cylinder) and spherical sample with Cu as > absorber, having different values of molarity and penetration depth. > The correction expression requires these measured quantity: > ?X(E) : the absorption coefficient due to a given core excitation of the > absorbing atom > - I used the background function for this ( bkg(E)) Wouldn't using bkg(E) suppress the fine-structure you are trying to recover? Anyway what are the units, are you normalizing bkg(E) to something meaningful? I would suggest using data from Chantler or Cromer-Liberman here. Or perhaps match mu(E) or bkg(E) to these. > ?o = ?(E) : photoelectric total linear absorption coefficient of the > sample at incident energy E > - I used the xmu(E) for this > Again, be mindful of what the units are. > ?h = ?(E) :photoelectric total linear absorption coefficient of the sample > at fluorescence emission Ef > - I used the xmu(Ef) with Ef the K absorption edge of > Cu ( 8.9789 eV) > I am pretty sure that this is not what you want. You probably want mu(E) at the Cu fluorescence energy (8.046 keV). This can make a significant difference.

1 0

Fuzzy degeneracy
by Panagiotis Mougkogiannis 07 Apr '16

07 Apr '16

Dear Bruce, Hello I am quite new in the field and I was reading your paper : ''Path degeneracy and EXAFS analysis of disordered materials, Journal of Synchrotron Radiation,volume 21, issue 6, pages 1269-1274,year 2014''. A simple question, Where can I find the Ti K-edge data of CaZrTi2O7 in order to manipulate EXAFS data analysis by myself? and something more How do you plot in the same figure the paths of strict and fuzzy degeneracy -Figure1a-? What I managed to do is in the attached picture ( 4 figures with the strict and fuzzy degeneracy)... Many Thanks Yours Faithfully Panagiotis

2 1

frequently asked questions
by Bruce Ravel 06 Apr '16

06 Apr '16

Hi all, I am making a new stab at creating a list of frequently asked questions about the software and other topics on this mailing list. Here's my first draft: http://bruceravel.github.io/demeter/documents/SinglePage/faq.html I want to solicit suggestions for good questions and answers. If there is a topic that you think would make a good question for the FAQ, please open an issue at Demeter's GitHub page: https://github.com/bruceravel/demeter/issues There is a "FAQ question" label that can be used as a tag. If you would like to edit the FAQ directly and submit a diff file or make a pull request, here is the source file: https://github.com/bruceravel/demeter/blob/master/documentation/SinglePage/… You'll get a copy when you clone the demeter repository or you can click the "raw" button to get the source for the faq page. Thanks in advance! Bruce -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

1 0

SSRL XAS Summer School 2016
by Ritimukta Sarangi 04 Apr '16

04 Apr '16

Hello Everyone, This is an announcement for the XAS summer school to be held at SSRL between July 18-22, 2016. We will cover XAS, EXAFS and Imaging beamlines with hands on data collection sessions at beamlines, followed by in-depth data analysis in a classroom setting. You can find more information at :http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2016/index.html <http://www-ssrl.slac.stanford.edu/conferences/workshops/exafs2016/index.html>. The agenda and application pages will be finalized within a week and I will post an update once it is up and running. But I wanted interested users and participants to get a heads up. Best Wishes, Ritimukta Sarangi SSRL

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 158, Issue 3
by Matteo Busi 04 Apr '16

04 Apr '16

Hi Bruce, Thanks for your help, it's really appreciated. I was trying to keep it simple but it seems I'm just messing around. What I am trying to do is to perform a new developed self-absorption correction using collected fluorescence absorption coefficient data on a CuSO4 (pentahydrate) capillar (cylinder) and spherical sample with Cu as absorber, having different values of molarity and penetration depth. The correction expression requires these measured quantity: μX(E) : the absorption coefficient due to a given core excitation of the absorbing atom - I used the background function for this ( bkg(E)) μo = μ(E) : photoelectric total linear absorption coefficient of the sample at incident energy E - I used the xmu(E) for this μh = μ(E) :photoelectric total linear absorption coefficient of the sample at fluorescence emission Ef - I used the xmu(Ef) with Ef the K absorption edge of Cu ( 8.9789 eV) χ: and here I used the chi(E) values of the exported ascii .xmu file Hope it's clear now. Matteo 2016-04-02 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: Ifeffit Digest, Vol 158, Issue 1 (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 1 Apr 2016 15:56:29 -0500 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 158, Issue 1 > Message-ID: > <CA+7ESbrsbsFQGMGLwGNPJmVO= > fGzksbv1SezR3M5pRkXanNyDg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Matteo, > > > On Fri, Apr 1, 2016 at 8:35 AM, Matteo Busi <basebush(a)gmail.com> wrote: > > > Hi Bruce, > > Now this is clear. > > In my case the correction I have to perform requires these > > measured/evaluated parameters: chi, mu (not sure if it's better to work > > with normmu here) and the background function. > > Is it physically meaningless to have the mu(k) and bkg(k) data? If that > is > > not the case I would like to have these two columns exported in the ascii > > chi(k) file. > > So then I can perform the correction and re-import the new corrected > > chi(k) and make comparison with the uncorrected. > > > > Kind regards, > > Matteo > > > > > It would certainly help (and by that I mean "help you get the answers > you're looking for") if you gave us more details about what you're trying > to do rather than ask for how to what you think you want to do. > > Just to be clear: Converting from E to k does not involve a Fourier > transform, just > k = sqrt((2m*e/hbar**2)*(E-E0)) > > for k in Ang^-1 and E in eV, that's k ~= sqrt(0.262468*(E-E0)) > > I'm not sure what you're trying, but I would image you want to use > normalized mu(E) or at least pre-edge subtracted mu(E). That is, what we > call mu(E) is typically really -ln(I/I0) > where I and I0 are not the actual intensities before and after the sample, > but counts or counts per time in some detector that samples the flux. > These values include more or less arbitrary scale factors (amplifier gains, > etc) included. That means that (unless you very careful) mu(E) does not > have meaningful units, certainly not cm^-1 or cm^2/gram. > > Normalized mu(E) doesn't have such units either, but it's an easier place > to start. > > --Matt >

4 5

Self-absorption xmu units
by Matteo Busi 04 Apr '16

04 Apr '16

Hi Matt. Thanks for the hints, they are very useful. What would you suggest to use if not the bkg? Regarding the xmu(E) I have been using exactly the values exported through the .xmu ascii file. I have been reading though the Athena's user guide and I didn't find any hint about which unit I could assign to them. Anyway I would like to get them with the cm^-1 units which would suit with the correction expression I want to perform. How can this be done? My idea was to divide the xmu data by the penetration depth in the sample (i.e. the radius of the capillar sample). Is this correct? Can this be applied to the bkg data aswell? Moreover the data I have is not scanned through the Cu fluorescence energy you have mentioned (8046 eV). Would you recommend to use data from Chantler or Cromer-Liberman? And how can I merge it with my other measured data to make it unit meaningful? Thanks and regards, Matteo I report our previous conversation for reference: > What I am trying to do is to perform a new developed self-absorption > correction using collected fluorescence absorption coefficient data on a > CuSO4 (pentahydrate) capillar (cylinder) and spherical sample with Cu as > absorber, having different values of molarity and penetration depth. > The correction expression requires these measured quantity: > ?X(E) : the absorption coefficient due to a given core excitation of the > absorbing atom > - I used the background function for this ( bkg(E)) Wouldn't using bkg(E) suppress the fine-structure you are trying to recover? Anyway what are the units, are you normalizing bkg(E) to something meaningful? I would suggest using data from Chantler or Cromer-Liberman here. Or perhaps match mu(E) or bkg(E) to these. > ?o = ?(E) : photoelectric total linear absorption coefficient of the > sample at incident energy E > - I used the xmu(E) for this > Again, be mindful of what the units are. > ?h = ?(E) :photoelectric total linear absorption coefficient of the sample > at fluorescence emission Ef > - I used the xmu(Ef) with Ef the K absorption edge of > Cu ( 8.9789 eV) > I am pretty sure that this is not what you want. You probably want mu(E) at the Cu fluorescence energy (8.046 keV). This can make a significant difference.

1 0

Re: [Ifeffit] Ifeffit Digest, Vol 158, Issue 1
by Matteo Busi 01 Apr '16

01 Apr '16

Hi Bruce, Now this is clear. In my case the correction I have to perform requires these measured/evaluated parameters: chi, mu (not sure if it's better to work with normmu here) and the background function. Is it physically meaningless to have the mu(k) and bkg(k) data? If that is not the case I would like to have these two columns exported in the ascii chi(k) file. So then I can perform the correction and re-import the new corrected chi(k) and make comparison with the uncorrected. Kind regards, Matteo 2016-04-01 15:06 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. Chi(E) data export and import (Matteo Busi) > 2. Re: Chi(E) data export and import (Bruce Ravel) > 3. Re: Question about Io during data collection (Luxton, Todd) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 1 Apr 2016 13:58:23 +0200 > From: Matteo Busi <basebush(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Chi(E) data export and import > Message-ID: > < > CAOyEiGhFhPbQ5Xn1is+R4MPVDQ4mxS4wXCcWM-j2qBcO5117-g(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Bruce, > this message il linked to the previous solutions you find for me. > > For the reference, I asked to have a column of the chi(E) in the exported > mu(E) data. > This has worked correctly so far. > > Now for my master thesis, I'm performing a correction to chi(E) in the E > space regarding to some geometrical properties of the sample. > I have also tried to re-import the corrected data as a chi(k), having > reproduced the right k grid column, but it looks totally wrong. > The thing I'm not sure about is if the chi(E) needs to be fourier > trasnformed into chi(k) or not. > That's because I would have liked to make comparison in the Athena software > between the two chis, but if that's not possible I will keep it to the > external software (mathematic) with which the correction is performed. > Or if you can share me the fourier transform routine performed I can > include it to my correction script. > > Hope the message is clear, > Kind Regards, > > Matteo >

2 1

Question about Io during data collection
by Luxton, Todd 01 Apr '16

01 Apr '16

All: Recently our group was at the APS collecting Pb L(III) spectra on an ID line using quick XAFS. Data was collected from -200 to +800 eV for Pb L(III) at 0.2 eV steps with a count rate of 0.025 seconds. Each scan took about 2.5 minutes to complete. During our measurements we began noting issues with the linearity of scans collected in the extended region of the same sample. After poking around in the data we noticed that Io was not linear throughout the measurement for a portion of the scans. This was not always the true (see Athena project attached to the email, and images attache to the email). I was always under the impression that Io should ideally remain linear throughout the energy region scanned, or at least remain unchanged between replicate scans. We worked with the beamline scientists to try alleviate/fix the issue, but it kept persisting. I realize this is not an IFEFFIT issue, but I was hoping someone might be able to help me understand what was going on and why this was happening? If I have not included enough information for the question please let me know. [cid:image001.jpg@01D18B37.F66BD820] [cid:image002.jpg@01D18B37.F66BD820] All the Best, todd All the Best, Todd Luxton, Ph.D. Office of Research and Development National Risk Management Research Laboratory Land Remediation and Pollution Control Division Waste Management Branch Mailing Address: 5995 Center Hill Ave Cincinnati, OH 45243 Phone: Office: (513) 569-7210 Cell: (513) 319-5104 Fax: (513) 569-7879 Email: Luxton.todd(a)epa.gov<mailto:Luxton.todd@epa.gov> "A nation that destroys its soils destroys itself" Franklin D. Rosevelt

3 3

Chi(E) data export and import
by Matteo Busi 01 Apr '16

01 Apr '16

Hi Bruce, this message il linked to the previous solutions you find for me. For the reference, I asked to have a column of the chi(E) in the exported mu(E) data. This has worked correctly so far. Now for my master thesis, I'm performing a correction to chi(E) in the E space regarding to some geometrical properties of the sample. I have also tried to re-import the corrected data as a chi(k), having reproduced the right k grid column, but it looks totally wrong. The thing I'm not sure about is if the chi(E) needs to be fourier trasnformed into chi(k) or not. That's because I would have liked to make comparison in the Athena software between the two chis, but if that's not possible I will keep it to the external software (mathematic) with which the correction is performed. Or if you can share me the fourier transform routine performed I can include it to my correction script. Hope the message is clear, Kind Regards, Matteo

2 1

Questions to Bruce
by Dien.Li＠srs.gov 24 Mar '16

24 Mar '16

HI, Bruce and Matt I have two questions for you, please help me. 1. I collected U EXAFS data on APS 10-ID, while I input a single data file with reference data in Athena, it was OK, however, when I input multiple data files (scans) also with reference data, it was crushed. I could input multiple data files without reference data, which Matt helped me trouble shoot. The Demeter 8.24 version is used on my computer, I believe. Matt suggested me to update to the current version. I do not know if other users have this problem. 2. I have a U EXAFS data file which was collected at SSRL, however, I could not input this data file using Athena, how to fix this? format? See the attachment. thanks you so much. Dien Li, Ph.D. Environmental Sciences and Biotechnology Savannah River National Laboratory Aiken, South Carolina, 29808 Tel: 803-725-7520

4 3

Running Examples for larch
by Panagiotis Mougkogiannis 19 Mar '16

19 Mar '16

Hello Dear all, I am struggling to run the larch-0.9.27 examples. >From previous email messages in IFEFFIT info page I managed to install larch and the icons appeared in my desktop (see attached picture larch_1) but when I am trying to run the example http://cars.uchicago.edu/xraylarch/xafs/autobk.html#examples I received this message (see attached picture larch_2) what is happened? what is the working directory of larch? Is it like something python ? If you use the commands import os print os.getcwd() you 'll find your working directory and after you can run your modules? Many thanks Regards Panagiotis

2 1

where can I acquire quantitative date on the attenuation at the low-energy end of Zn and some of its compounds
by Nino Pereira 18 Mar '16

18 Mar '16

Dear All, I'm not part of your community, but I've been at the APS synchrotron enough to know that you might have the information I'm looking for, and willing to share it. My question is in the subject line. The reason for this question is an upcoming measurement of the ionization energy shift in a hot plasma. We have chosen Ta, because its Lbeta-2 line happens to be slightly lower in energy than the nominal energy of the Zn K-edge. Hence, a small increase, perhaps as low as 1 eV, should produce a substantial change in the attenuation of a sufficiently thick K-edge filter. Crystal spectrometers of the type we use rarely have a resolution that exceeds 2000, so that for a 10 keV l-line we could as best see a 5 eV energy change. With the same approach we could measure a ~10 eV shift on the ~63,000 eV Kalpha_2 line of Ir, with a K-edge filter of Lu. It so happens that their nominal energies are 27 eV apart (according to the x-ray data booklet, not according to Deslattes et al, 2001), so that the line and the K-ege overlap. Both are life time broadened by about 40 eV, so as the energy of the line increases, the transmission of a filter decreases. We first separate the two Kalpha lines (which are 1.3 keV apart), and then measured the decrease in the intensity behind the filter. The idea is to preferentially absorb the high-energy side of the Ir Kalpha_2 line, so that an increase in the line center becomes a decrease in line intensity behind the filter. I appreciate any comment you may have on this matter. Thank you, Nino

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Re: [Ifeffit] Ifeffit Digest, Vol 157, Issue 9
by Matteo Busi 14 Mar '16

14 Mar '16

Hi Bruce, Sorry if I insisted, didn't mean to be rude. By the way the solution you proposed is exactly what I meant and I thank you. Anyways if you're going to implement this in the new release, personally I would prefer to have the mu(E) data in the .chi saved file as it simplifies my work. Don't know if it is the same to everybody. Thank you very much and have a good Easter Matteo Busi, UiS 2016-03-11 19:00 GMT+01:00 <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: Exporting Athena projects data (Bruce Ravel) > 2. Re: Exporting Athena projects data (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 11 Mar 2016 08:57:50 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Exporting Athena projects data > Message-ID: <56E2CEDE.3040803(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 03/11/2016 06:52 AM, Matteo Busi wrote: > > Hi Bruce I'm sending this again, probably the latest message was lost in > > the confusion. > > Or ... perhaps ... I've been really busy lately. > > I understand what you are looking for and will have a solution for you > soon, once I get some other, more pressing things done. > > B > > > I would like to have an output file containing chi(E) and mu(E) using the > > same energy (E) grid. > > If I export them separately ( the only available way I think right now) > > they have > > different energy grid. > > > > The previous messaging was: > >> Hi Mateo, > > > >> I'm not quite clear on what you are asking for. Do you want an ascii > >> output file that has a column containing chi(E) using the energy grid of > >> the original data? > > > >> If so, would it suffice to add a column to the mu(E) ascii output file? > >> That seems to me like a natural solution. > > > >>Cheers, > >>B > > > > Thanks and Regards > > Matteo, UiS > > > > > > > > > > _______________________________________________ > > 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 > > > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 2 > Date: Fri, 11 Mar 2016 11:56:22 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Exporting Athena projects data > Message-ID: <56E2F8B6.7060508(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > > Matteo, > > A fully correct solution to this will have to wait until the next > release, but I can offer a partial solution which you can implement > immediately. > > Locate the file > "perl\site\lib\Demeter\templates\process\ifeffit\save_xmu.tmpl" in > whatever location Demeter was installed on your computer. > > Grab this: > > > https://raw.githubusercontent.com/bruceravel/demeter/master/lib/Demeter/tem… > > and replace the previous "save_xmu.tmpl". When you download the > replacement, be sure that its filename is "save_xmu.tmpl" and that > your browser does not "helpfully" add a .txt extension. > > When you next save current group as mu(E), there will be an additional > column which contains the chi(E) on the grid of the original data. > That column will be 0 below the lower bound of the spline range and > above the upper bound of the spline range (i.e. in the energy range > over which chi is not defined). It is un-k-weighted. If you want to > look at k-weighted chi(E), /you/ will have to apply the k-weighting > /yourself/. > > I think that addresses your request. Let me know what you think. > > B > > > On 03/11/2016 06:52 AM, Matteo Busi wrote: > > Hi Bruce I'm sending this again, probably the latest message was lost in > > the confusion. > > > > I would like to have an output file containing chi(E) and mu(E) using the > > same energy (E) grid. > > If I export them separately ( the only available way I think right now) > > they have > > different energy grid. > > > > The previous messaging was: > >> Hi Mateo, > > > >> I'm not quite clear on what you are asking for. Do you want an ascii > >> output file that has a column containing chi(E) using the energy grid of > >> the original data? > > > >> If so, would it suffice to add a column to the mu(E) ascii output file? > >> That seems to me like a natural solution. > > > >>Cheers, > >>B > > > > Thanks and Regards > > Matteo, UiS > > > > > > > > > > _______________________________________________ > > 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 > > > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > 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 157, Issue 9 > *************************************** >

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Exporting Athena projects data
by Matteo Busi 11 Mar '16

11 Mar '16

Hi Bruce I'm sending this again, probably the latest message was lost in the confusion. I would like to have an output file containing chi(E) and mu(E) using the same energy (E) grid. If I export them separately ( the only available way I think right now) they have different energy grid. The previous messaging was: > Hi Mateo, > I'm not quite clear on what you are asking for. Do you want an ascii > output file that has a column containing chi(E) using the energy grid of > the original data? > If so, would it suffice to add a column to the mu(E) ascii output file? > That seems to me like a natural solution. >Cheers, >B Thanks and Regards Matteo, UiS

2 2

Absorption length
by 이국승(에너지환경소재연구팀) 11 Mar '16

11 Mar '16

Dear members, I have seen many times the absorption length in materials for introduction of XAFS. The absorption length equals 1/mu, which is the thickness that I0 is attenuated to 1/e. But I do not understand why the absorption length is important. More importantly, I do not understand why the particle size in samples should be smaller than the absorption length. Could any one explain the absorption length including the question above and the relation between the absorption length and edge step calculations? Thanks in advance. Kug-Seung Lee Kug-Seung Lee, Ph.D. Staff Scientist Manager, 8C Nano Probe XAFS Beamline Pohang Accelerator Laboratory Pohang 790-784, Republic of Korea Office: +82-54-279-1522 Fax: +82-54-279-1599 C. P.: +82-10-6419-7801 Researcher ID: http://www.researcherid.com/rid/D-7088-2011

2 2

Error in N (Number of Scatterers)
by Carolyn Carr 09 Mar '16

09 Mar '16

Hello Mailing List, I have read papers describing that EXAFS has an error regarding N the number of scatters of +/- 20%. The only original reference I can see to support this is "The effect of statistical noise on structural parameters in EXAFS data analysis" by L. Incoccia, S. Mobilio (1984, Il Nuovo Cimento D). However, in the more recent D. C. Koningsberger review "XAFS spectroscopy; fundamental principles and data analysis" (2000, Topics in Catalysis) he cites an error of 5% for N (although the paper cites slightly varying error for different absorber-scatterer pairs). Several months ago, I wrote to the mailing list regarding the difference of fitting in R- and k-space in Artemis and received several responses revealing that some comments made in the Koningsberger review are no longer valid in Artemis. In my literature search, I did not find additional papers describing the error inherent in N when fitting in Artemis. Since the paper cited by Koningsberger (X-ray-absorption fine-structure standards: A comparison of experiment and theory, G. G. Li, F. Bridges, and C. H. Booth, Physical Review B, 1995) utilized Feff6 for their theoretical standards and so does Artemis, is the error in N still the same? I was wondering if there is some literature that I have missed, or if the developers of the Demeter package can shed some light on this issue. Thank You, Carolyn Carr

2 1

Path Missing Using Artemis
by lijuncha＠msu.edu 08 Mar '16

08 Mar '16

Hi all, During my use of Artemis, I found out that the FEEF paths finder had some problem with my atom, which is Cu12Sb4S13 in the attachment. I firstly ran atom on Cu12e, then ran the FEFF calculation. Then I found that the S24g.1 path was missing. Since S24g is near the core atom Cu12e and the path should exist, I was confused to send the message and hopefully get your response. Thanks, Junchao

2 1

Any XAFS schools in North America this year?
by Robert Gordon 07 Mar '16

07 Mar '16

Hi All, I have a couple of students who are novices. I was hoping that one could go to a school to learn and perhaps get some hands-on experience before they get into the meat of their thesis work. I haven't seen any notices yet about schools taking place in the late spring or summer and was wondering if there are any plans to hold such. I am aware of the 1/2-day workshop planned for the DXC. Are there other options? Thanks, Robert

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Re: [Ifeffit] Ifeffit Digest, Vol 157, Issue 1
by Matteo Busi 07 Mar '16

07 Mar '16

> Hi Mateo, > I'm not quite clear on what you are asking for. Do you want an ascii > output file that has a column containing chi(E) using the energy grid of > the original data? > If so, would it suffice to add a column to the mu(E) ascii output file? > That seems to me like a natural solution. >Cheers, >B Hi Bruce I would like to have an output file containing chi(E) and mu(E) using the same energy (E) grid. If I export them separately ( the only available thing right now) they have different energy grid. Thanks and Regards 2016-03-04 15:18 GMT+01:00 <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. Exporting Athena projects data (Matteo Busi) > 2. Collected k-space and fitting range (Taehoon Kim) > 3. Re: Collected k-space and fitting range (Scott Calvin) > 4. Re: Exporting Athena projects data (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 3 Mar 2016 23:53:54 +0100 > From: Matteo Busi <basebush(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Exporting Athena projects data > Message-ID: > <CAOyEiGi7jNury5oTAostBixxinOF+Vxcg2= > 8Sf8VeM9rywEmrg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Bruce, hi mailing list readers. > With the project I'm working with, it came out that would be really useful > for me to export groups in both .xmu and .chi . > More in details I have to deal with a function that depends on both the chi > and xmu data. I tried to look at all the chances and through the guide but > I didn't find any function to do that. I was thinking of exporting > separately the .chi and .xmu data, but they have different point of the > Energy(eV) and that makes hard the programming of my evaluating scripts. > Should I use the spline function to estimate the .xmu data and use it > combined to the .chi data? > > Hope it's all clear. Thanks > Best Regards, > Matteo, UiS >

1 0

Collected k-space and fitting range
by Taehoon Kim 04 Mar '16

04 Mar '16

Hello, I am a bit confused about the range of k-space, which may affect the quality of EXAFS fitting. I would like to understand whether there is a difference between the fitting using an identical fitting range of k-space obtained from different range of k-space collected. For example, is there a notable difference between a fitting of k = 2.3-11 which was deduced from a spectra data collected up to k=12 and a spectra data collected up to k=13 ? Kind regardsTerry

3 2

Exporting Athena projects data
by Matteo Busi 04 Mar '16

04 Mar '16

Hi Bruce, hi mailing list readers. With the project I'm working with, it came out that would be really useful for me to export groups in both .xmu and .chi . More in details I have to deal with a function that depends on both the chi and xmu data. I tried to look at all the chances and through the guide but I didn't find any function to do that. I was thinking of exporting separately the .chi and .xmu data, but they have different point of the Energy(eV) and that makes hard the programming of my evaluating scripts. Should I use the spline function to estimate the .xmu data and use it combined to the .chi data? Hope it's all clear. Thanks Best Regards, Matteo, UiS

2 1

Re: [Ifeffit] fluo_corr() script
by Matt Newville 26 Feb '16

26 Feb '16

Hi Gerome, (I'm CCing this to the Ifeffit mailing list) On Thu, Feb 25, 2016 at 9:30 PM, Gerome Melaet <gmelaet(a)lbl.gov> wrote: > Dear Dr. Newville, > I have tried to use the flu_corr() function to correct some of my recent > x-ray data on the cobalt K-edge. > Unfortunately, after multiple tryout I am unable to get it to work > properly. > I have received this error message a couple of time. > > > *File > "/Volumes/Python/anaconda/lib/python2.7/site-packages/larch/__init__.py", > line 37, in wrapper* > * return fcn(*args, **keywords)* > * File "/Volumes/Python/anaconda/share/larch/plugins/xafs/fluo.py", line > 57, in fluo_corr* > * muvals = material_mu(formula, energies, density=1, _larch=_larch)* > * File > "/Volumes/Python/anaconda/lib/python2.7/site-packages/larch/__init__.py", > line 37, in wrapper* > * return fcn(*args, **keywords)* > * File "/Volumes/Python/anaconda/share/larch/plugins/xray/materials.py", > line 68, in material_mu* > * mater = _materials.get(name.lower(), None)file <stdin>, line 0* > *AttributeError: ‘int' object has no attribute 'lower'* > > I have a .dat file two column with energy and normalized mu (I have done > most of the energy corrections during my shift at the synchrotron). > I am able to load both energy and mu, yet I am not sure I handle the > different args correctly in the fluo_corr() function. > > Here is how I tried: > > fluo_corr(dat.energy, dat.mu, formula=None, elem=‘Co’, edge=‘K’) > > Thanks in advance for your help, > > Best, > Gerome > Yes, you need to pass a valid (even if approximate) formula for the chemical composition of the material. See http://xraypy.github.io/xraylarch/xray/index.html#x-ray-properties-of-mater… for some further details. You might want to do something like fluo_corr(dat.energy, dat.mu, formula='Co0.5Fe0.5S04', elem=‘Co’, edge=‘K’) Perhaps obviously, getting the composition of light elements perfect is not critical. It's often noticed that one has to lower the concentration of the absorbing element some (perhaps even by half) to avoid over-correcting. As with many things, it's always good to practice on a system where you're pretty confident what the right answer should be. --Matt

1 0

Re: [Ifeffit] problem with transfer of prj fils
by fred.mosselmans＠diamond.ac.uk 22 Feb '16

22 Feb '16

Hi Thomas Are you sure both the users have the same version of Athena. I have seen this behaviour when discussing analysis with my users and they are not using the latest version of Demeter and I am. Then the prj crashes Athena for the person with the old version. 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

2 1

Problem with transfer of prj files
by Huthwelker Thomas (PSI) 22 Feb '16

22 Feb '16

Dear All, I find this Problem with the transfer of Athena project files: An Athenae project file is created on a one computer and saves on a harddisk. This file is then transferred to another person working on another computer. When opening the *.prj file on the new PC, Athena crashes. This happens if Athena is opened first and one tries to import the prj file into an open Athena, or if one just double clicks the *.prj file to start Athena. Operating system: Windows 7 Thanks for information, Thomas

2 1

problem with Artemis crashing on mac
by Katherine M. Davis 16 Feb '16

16 Feb '16

Hello all, I was wondering whether anyone had experienced this problem or had some advice for what I can try. I have Demeter installed successfully on my mac (Yosemite 10.10.5). Athena works just fine. However, when I try running Artemis, it begins to open fine and all the GUI windows look good, but then a popup that says 'Restore from an autosave file' with buttons for 'Cancel' or 'OK' appears. I'm not able to click on anything and the program does not progress from this point. I don't remember this happening when I first installed. Is there an easy way to go in and trash some potential autosave file I have that is causing problems? If so, where would that be located? I dug around a bit, but couldn't find anything obvious. It's a little odd, because I've not really used the program. I simply tested it when I first installed to ensure it worked and that was it. Any thoughts or comments would be useful. If additional information would help in diagnosing the issue, I'm happy to provide it. Thanks, Kate

2 1

Re: [Ifeffit] Ifeffit Digest, Vol 156, Issue 6
by Adi Shivprasad 10 Feb '16

10 Feb '16

Dear Riti, Thanks for the response. It was very helpful in better understanding my system. Adi On Wed, Feb 10, 2016 at 1:00 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Feature near edge of Ni XANES spectrum (Aditya Shivprasad) > 2. Re: Feature near edge of Ni XANES spectrum (Ritimukta Sarangi) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 9 Feb 2016 21:19:21 -0500 > From: Aditya Shivprasad <aps202(a)psu.edu> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] Feature near edge of Ni XANES spectrum > Message-ID: > <CAFbAhodYDnzzK1keVptQVfhS4OJMR-VgB-vR= > wFL8TKVCfEBHw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear list, > > I have obtained nickel XANES spectra (attached) from metallic Zircaloy-2 > nuclear fuel cladding (Zr, 1.5% Sn, 0.15% Fe, 0.1% Cr, 0.05% Ni). > > In the spectrum, I identify the edge as being approximately 8331-8332 eV > (based on maximum of first derivative), as it is for pure Ni. However, I > also identify a sharp feature at less than 1 eV past the edge. If anyone on > the list could help me to understand the origin of this feature, that would > be very helpful. > > Thanks > -- > Aditya Shivprasad > > aps202(a)psu.edu > Ph.D Candidate > Nuclear Engineering Department > Pennsylvania State University >

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Feature near edge of Ni XANES spectrum
by Aditya Shivprasad 09 Feb '16

09 Feb '16

Dear list, I have obtained nickel XANES spectra (attached) from metallic Zircaloy-2 nuclear fuel cladding (Zr, 1.5% Sn, 0.15% Fe, 0.1% Cr, 0.05% Ni). In the spectrum, I identify the edge as being approximately 8331-8332 eV (based on maximum of first derivative), as it is for pure Ni. However, I also identify a sharp feature at less than 1 eV past the edge. If anyone on the list could help me to understand the origin of this feature, that would be very helpful. Thanks -- Aditya Shivprasad aps202(a)psu.edu Ph.D Candidate Nuclear Engineering Department Pennsylvania State University

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Re: [Ifeffit] Ifeffit Digest, Vol 156, Issue 4
by Pierre Lecante 09 Feb '16

09 Feb '16

Hi Pinit, here is what you can expect from a SDD: "At X-ray energies greater than silicon K absorption edge, which we have measured for crystalline silicon to be 1839 eV, the response function of the device shows two distinct peaks in addition to the primary one. One of them at energy /E/_/f/ = 1739 eV is due to the silicon fluorescent photons that have escaped far enough from the original site of interaction to be detected as a separate event. The other peak centered at energy /E/_/e/ = /E/_0 - /E/_/f/ , where /E/_0 is energy of the incident photon, is called an escape peak." So, indeed this shouldn't be a concern if you had a perfect rejection of harmonics on your beamline; if not, inelastic scattering of harmonic by the sample, even rejected by energy analysis, should likely induce internal fluorescence and escape peaks not observed in TM. Just an hypothesis, but easy to check: presence or not of harmonic in your scattering. Pierre Le 02/02/2016 23:41, ifeffit-request(a)millenia.cars.aps.anl.gov a écrit : > 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: Could you please give me some information? (Bruce Ravel) > 2. Re: Athena with IOS "El Capitan" (Manuel Cossio Kohler) > 3. Re: Athena with IOS "El Capitan" (Bruce Ravel) > 4. Re: Athena with IOS "El Capitan" (Manuel Cossio Kohler) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 2 Feb 2016 15:30:45 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: pinit <pinit(a)slri.or.th> > Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Could you please give me some information? > Message-ID: <56B111F5.7050108(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 02/01/2016 11:58 PM, pinit wrote: >> Dear Bruce, >> >> I am Pinit from SLRI, Thailand. I have some questions concerning the >> Si-drift detector. >> >> Could you give me some suggestions if Si-detector can detect the >> corrected Si K-edge or not? This is because I have seen a significant >> EXAFS signal (higher in amplitude in FT) measured by Si-drift detector >> differs from Lytle detector or ionization chambers (TM mode). > Hi Pinit, > > Nice to hear from you. I am CCing my answer to the Ifeffit Mailing > List. Someone else may have more insight into your question than I > do. You should CC the list in your response. > > I'd probably need to know more about the sample and the nature of the > measurement you made to understand why you are seeing a different > signal with the Si drift detector. > > Normally one would expect that he EXAFS would be /attenuated/ either > due to self-absorption or due to the energy dependence of the I0 > detector. That you are seeing a larger EXAFS signal with the Si-drift > seems surprising. > > One thing that occurs to me is that the Compton and elastic peaks > probably overlap the Si K alpha ROI quite a bit, even extending into > the EXAFS region. I would have thought that, too, would serve to > attenuate the EXAFS (but maybe I am thinking about that wrongly). > > Perhaps it would help to show us some of the data...? > > B > > > > -- Groupe MC2 CEMES-CNRS, 29 rue Jeanne Marvig, 31055 Toulouse Cedex 4, France Tel: +33 (0)5 62 25 78 51, Fax: +33 (0)5 62 25 79 99 Email: lecante(a)cemes.fr http://www.cemes.fr/MC2 Full list of publications: http://www.researcherid.com/rid/A-8745-2011

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Re: [Ifeffit] Could you please give me some information?
by Pierre Lecante 09 Feb '16

09 Feb '16

Hi Pinit, here is what you can expect from a SDD: "At X-ray energies greater than silicon K absorption edge, which we have measured for crystalline silicon to be 1839 eV, the response function of the device shows two distinct peaks in addition to the primary one. One of them at energy /E/_/f/ = 1739 eV is due to the silicon fluorescent photons that have escaped far enough from the original site of interaction to be detected as a separate event. The other peak centered at energy /E/_/e/ = /E/_0 - /E/_/f/ , where /E/_0 is energy of the incident photon, is called an escape peak." So, indeed this shouldn't be a concern if you had a perfect rejection of harmonics on your beamline; if not, inelastic scattering of harmonic by the sample, even rejected by energy analysis, should likely induce internal fluorescence and escape peaks not observed in TM. Just an hypothesis, but easy to check: presence or not of harmonic in your scattering. Pierre Le 02/02/2016 23:41, ifeffit-request(a)millenia.cars.aps.anl.gov a écrit : > 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: Could you please give me some information? (Bruce Ravel) > 2. Re: Athena with IOS "El Capitan" (Manuel Cossio Kohler) > 3. Re: Athena with IOS "El Capitan" (Bruce Ravel) > 4. Re: Athena with IOS "El Capitan" (Manuel Cossio Kohler) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 2 Feb 2016 15:30:45 -0500 > From: Bruce Ravel <bravel(a)bnl.gov> > To: pinit <pinit(a)slri.or.th> > Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Could you please give me some information? > Message-ID: <56B111F5.7050108(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 02/01/2016 11:58 PM, pinit wrote: >> Dear Bruce, >> >> I am Pinit from SLRI, Thailand. I have some questions concerning the >> Si-drift detector. >> >> Could you give me some suggestions if Si-detector can detect the >> corrected Si K-edge or not? This is because I have seen a significant >> EXAFS signal (higher in amplitude in FT) measured by Si-drift detector >> differs from Lytle detector or ionization chambers (TM mode). > Hi Pinit, > > Nice to hear from you. I am CCing my answer to the Ifeffit Mailing > List. Someone else may have more insight into your question than I > do. You should CC the list in your response. > > I'd probably need to know more about the sample and the nature of the > measurement you made to understand why you are seeing a different > signal with the Si drift detector. > > Normally one would expect that he EXAFS would be /attenuated/ either > due to self-absorption or due to the energy dependence of the I0 > detector. That you are seeing a larger EXAFS signal with the Si-drift > seems surprising. > > One thing that occurs to me is that the Compton and elastic peaks > probably overlap the Si K alpha ROI quite a bit, even extending into > the EXAFS region. I would have thought that, too, would serve to > attenuate the EXAFS (but maybe I am thinking about that wrongly). > > Perhaps it would help to show us some of the data...? > > B > > > > -- Groupe MC2 CEMES-CNRS, 29 rue Jeanne Marvig, 31055 Toulouse Cedex 4, France Tel: +33 (0)5 62 25 78 51, Fax: +33 (0)5 62 25 79 99 Email: lecante(a)cemes.fr http://www.cemes.fr/MC2 Full list of publications: http://www.researcherid.com/rid/A-8745-2011

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Athena with IOS "El Capitan"
by Manuel Cossio Kohler 02 Feb '16

02 Feb '16

Hello, I am having some issues with the Athena software. After upgrading the OS of the macbook pro to "El Capitan" Version 10.11.3, Athena stopped working properly. Once the iXAFS icon was clicked nothing happened. I decided to do a bit of research and installed the latest verion of XQuartz version 2.7.8. I was able to launch athena by executting "athena" from the terminal. Up to that point, I figured that everything was running smoothly until I realized that I could prompt any plots. Something in the software or operating system was not allowing Athena to display plots. I would be really grateful if you could provide me with a solution to this problem (if there is any) or any advice that would allow me to process XAS data again. Thank you Regards, Manuel Cossio

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Re: [Ifeffit] Could you please give me some information?
by Bruce Ravel 02 Feb '16

02 Feb '16

On 02/01/2016 11:58 PM, pinit wrote: > Dear Bruce, > > I am Pinit from SLRI, Thailand. I have some questions concerning the > Si-drift detector. > > Could you give me some suggestions if Si-detector can detect the > corrected Si K-edge or not? This is because I have seen a significant > EXAFS signal (higher in amplitude in FT) measured by Si-drift detector > differs from Lytle detector or ionization chambers (TM mode). Hi Pinit, Nice to hear from you. I am CCing my answer to the Ifeffit Mailing List. Someone else may have more insight into your question than I do. You should CC the list in your response. I'd probably need to know more about the sample and the nature of the measurement you made to understand why you are seeing a different signal with the Si drift detector. Normally one would expect that he EXAFS would be /attenuated/ either due to self-absorption or due to the energy dependence of the I0 detector. That you are seeing a larger EXAFS signal with the Si-drift seems surprising. One thing that occurs to me is that the Compton and elastic peaks probably overlap the Si K alpha ROI quite a bit, even extending into the EXAFS region. I would have thought that, too, would serve to attenuate the EXAFS (but maybe I am thinking about that wrongly). Perhaps it would help to show us some of the data...? B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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pi/2deltak
by Ritimukta Sarangi 01 Feb '16

01 Feb '16

Hello, I was recently asked about the accuracy of this formulation for obtaining EXAFS resolution and I did not have a good answer. Can someone point to a reference or explain here? Thank you for your time, Best, -Riti

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FW: Data summation - missing groups
by Godfrey, Ian 01 Feb '16

01 Feb '16

Sorry, I've just seen that this has already been reported. Ian From: Godfrey, Ian Sent: 27 January 2016 11:21 To: 'XAFS Analysis using Ifeffit' <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Data summation - missing groups Dear All, When using the data summation tool in Athena (0.9.24 x64 on Win10 Pro) the first group in the group list seems to be missing from the dropdown showing the potential components of a summation (see attached screenshot). To reproduce: 1) Open attached project file and import with "select all" on the import dialogue box 2) Change to data summation window 3) Try and add the first data group (234) to the summation from the dropdown menus. (In the screenshot I've changed the default normmu(E) to mu(E), but the same behaviour is displayed in both cases.) On a related note, I'm not sure I fully understand how the data summation is different from the merge? Clearly data summation allows you more control (arbitrary weighting of groups etc.) and is intended for XANES analysis, but is it a fundamentally different procedure or just a different interface for the same thing? 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 Advaned 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> 02076 794864

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Re: [Ifeffit] pi/2deltak
by Avakyan L.A. 31 Jan '16

31 Jan '16

Hello Riti, the criterion of R-resolution of pi/2deltak can be drawn from the Nyquist theorem. The amount of information in the spectra is limited by Nidp = 2 deltak deltaR / pi. Then, in assumption of equal distribution of information over the R-interval, the minimal interval can be estimated as deltaR / Nidp = pi/2deltak. The problem is that exact formula for Nidp is not known. Sometimes it has addition of +1 or +2 to represent the fact that single point (deltak=0) still contains information. Moreover, information is not equally distributed: some k-regions are more rich, other are less... And when energy interval is very short (glass, liquid) this question becomes vital. Sometimes, this resolution limit can even be overcome as it is shown in [http://dx.doi.org/10.1103/PhysRevB.82.064204] Best regards, Leon Leon Avakyan PhDr, Physics Faculty, Southern Federal University laavakyan(a)sfedu.ru On 31.01.2016 21:00, ifeffit-request(a)millenia.cars.aps.anl.gov wrote: > Message: 2 > Date: Sat, 30 Jan 2016 17:35:04 -0800 > From: Ritimukta Sarangi<ritimukta(a)gmail.com> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] pi/2deltak > Message-ID: > <CAMWiF7ymrKEDSZw31pcgwCzZH5tsFvFk+151gxfjRz9jUARH4w(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello, > > I was recently asked about the accuracy of this formulation for obtaining > EXAFS resolution and I did not have a good answer. Can someone point to a > reference or explain here? > Thank you for your time, > Best, > -Riti

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Re: [Ifeffit] Ifeffit Digest, Vol 155, Issue 16
by Christopher Thomas Chantler 30 Jan '16

30 Jan '16

Dear Jason Good topic We have published a few papers discussing analysis with thickness distributions and roughness. Normally the XERT method will address this especially for small samples. Particularly see J. L. Glover, C. T. Chantler, M. D. de Jonge, ‘Nano-roughness in gold revealed from X-ray signature,’ Physics Letters A373 (2009) 1177-1180. The general topic of thickness effects is of course wider, and partially addressed in a couple of other papers. Hope this helps 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 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, 31 January 2016 5:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 155, Issue 16 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: Effect of gradual thickness variation in beam (Jason Gaudet) ---------------------------------------------------------------------- Message: 1 Date: Fri, 29 Jan 2016 14:32:43 -0500 From: Jason Gaudet <jason.r.gaudet(a)gmail.com> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Effect of gradual thickness variation in beam Message-ID: <CANMcWtOLubiomegk-GM6SMS6CSpw0B0Hg21rMe9-hV8uQEkxhw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Anatoly, Sorry, I meant to write 1000 um inner diameter. Energies will be V and Fe, 5465 & 7112 eV. Samples are roughly 1 absorption length thick for the metal (V, Fe) and about 2-2.5 absorption lengths for the entire sample. Bruce, I may just flip over the sample holder and have the sample tubes in plane with the storage ring to take advantage of the greater horizontal spread, rather than focusing on the vertical. Cutting the vertical slits down to 100-300 um while keeping the horizontal around 500 um ought to get me the most beam at the least variation in mu(E), especially if I go with 1500 um ID tubes. The samples are nice and concentrated so I can afford to give up a lot of photon flux. Bar-napkin calculations tell me with a 1500 um ID tube and 200 um V 750 um H slits I'll lose an acceptable amount of photon flux and have a <1% thickness variation. I'm fairly confident I've made pressed pellets with as much or more variation from one spot to another, without noticeable mu(E) changes from spot to spot, in the vicinity of this energy range. I'll go ahead and take your advice, and amend my setup procedure with some measurements of Io intensity and mu(E) reproducibility as a function of slit width. While a bit of a bother, it's still worth it to keep our sample prep simple and inexpensive. Thanks, Jason On Thu, Jan 28, 2016 at 9:12 AM, Bruce Ravel <bravel(a)bnl.gov> wrote: > On 01/27/2016 07:05 PM, Jason Gaudet wrote: > >> I'm planning on some transmission-mode XAS with smaller than usual >> sample tubes. I'm realizing I might be in danger of creating excessive >> non-uniformity in my samples by having the beam size on the same order >> of magnitude as the sample tube radius. >> >> For example, let's say I want to measure liquid in a sample tube with a >> 1000 micron outer diameter, with a beam 500 microns wide and centered on >> the sample tube. If the tube is orthogonal to the ring plane, the entire >> vertical portion of the beam will pass through the same length of >> liquid. But in the horizontal plane, the center of the beam will pass >> through 1000 microns of sample while the edges of the beam will pass >> through 866 microns of sample, due to the curvature of the sample cell >> across the horizontal plane. >> >> Most of what I know about the statistics of thickness effects are about >> leakage and pinholes - nonlinearity caused by a few spots having very >> low or negligible sample thickness. But I don't know how significant a >> "mild" thickness distribution might be. If this sort of thickness >> distribution is going to be an issue it would be great to know that >> beforehand and either go with larger samples, smaller beam size, or more >> creative orientation. >> > > > Jason, > > There may be some distortion to the data due to the varying thickness. > On the plus side, liquids tend to be very homogeneous. > > Probably the best solution to this situation, if it's available at the > beamline, is to focus the beam in the vertical, for example, using a > flat mirror on a bender. Focusing to a spot would also address the > thickness situation, but you need to be mindful that the intense beam > could generate radicals from the liquid, causing sample damage. > > If the sample is sufficiently concentrated, then you could simply slit > the beam down to 100 or 200 microns and still have enough for a > transmission measurement. In fact, that would be the way to decide if > you are seeing a big problem from the shape of the tube. Compare the > mu(E) with the slits at 500 to mu(E) with the slits at 100 (carefully > aligning the sample both times, of course). If they are the same, > then, then you're golden. > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > 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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Effect of gradual thickness variation in beam
by Jason Gaudet 29 Jan '16

29 Jan '16

Sample cell Hi all, I'm planning on some transmission-mode XAS with smaller than usual sample tubes. I'm realizing I might be in danger of creating excessive non-uniformity in my samples by having the beam size on the same order of magnitude as the sample tube radius. For example, let's say I want to measure liquid in a sample tube with a 1000 micron outer diameter, with a beam 500 microns wide and centered on the sample tube. If the tube is orthogonal to the ring plane, the entire vertical portion of the beam will pass through the same length of liquid. But in the horizontal plane, the center of the beam will pass through 1000 microns of sample while the edges of the beam will pass through 866 microns of sample, due to the curvature of the sample cell across the horizontal plane. Most of what I know about the statistics of thickness effects are about leakage and pinholes - nonlinearity caused by a few spots having very low or negligible sample thickness. But I don't know how significant a "mild" thickness distribution might be. If this sort of thickness distribution is going to be an issue it would be great to know that beforehand and either go with larger samples, smaller beam size, or more creative orientation. Thanks, Jason

3 3

Data summation - missing groups
by Godfrey, Ian 27 Jan '16

27 Jan '16

Dear All, When using the data summation tool in Athena (0.9.24 x64 on Win10 Pro) the first group in the group list seems to be missing from the dropdown showing the potential components of a summation (see attached screenshot). To reproduce: 1) Open attached project file and import with "select all" on the import dialogue box 2) Change to data summation window 3) Try and add the first data group (234) to the summation from the dropdown menus. (In the screenshot I've changed the default normmu(E) to mu(E), but the same behaviour is displayed in both cases.) On a related note, I'm not sure I fully understand how the data summation is different from the merge? Clearly data summation allows you more control (arbitrary weighting of groups etc.) and is intended for XANES analysis, but is it a fundamentally different procedure or just a different interface for the same thing? 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 Advaned 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> 02076 794864

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Re: [Ifeffit] Ifeffit Digest, Vol 155, Issue 9
by Adi Shivprasad 25 Jan '16

25 Jan '16

Dear all, Thanks for the quick and informative responses! When I mentioned consistency, I should have clarified that, since I am in the Nuclear Engineering field, the audience for my paper may not have any prior experience with XAS, so I wanted to understand how to explain spectrum features in a way that is accurate and easy to understand from their point of view. To that end, I wanted to make sure I had a better understanding before writing anything incorrect. Thanks, Aditya On Mon, Jan 25, 2016 at 10:14 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: XANES pre-edge vs. edge features (Scott Calvin) > 2. Re: XANES pre-edge vs. edge features (Guanghui Zhang) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 25 Jan 2016 10:06:17 -0500 > From: Scott Calvin <scalvin(a)sarahlawrence.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] XANES pre-edge vs. edge features > Message-ID: <9A201B66-AE18-4F10-A367-7E9A7851F705(a)slc.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Aditya, > > Matt gave a good explanation of what?s responsible for the various > features, which was part of your question. Another aspect of your question > has to do with the way we use terminology. > > (Bruce?s answer, and your response, came in while I was writing this. So > it may be somewhat superfluous, but since it?s already mostly written, I > figure I?ll pass it along.) > > As Matt said, ?edge? is a poorly defined term. One meaning of it is that > it?s the big rise in absorption that occurs at the start of a XAFS > spectrum. That, for example, is the meaning that?s in use when we try to > quantify an ?edge step? or an ?edge jump? so that we can normalize the > data. In that sense, if a feature occurs before most of that rise, it can > be called ?pre-edge.? > > But another use of the word ?edge? is as a synonym for ?E0,? which is > itself a concept that is not unambiguously defined. One definition of E0 > would be ?the energy origin needed to make the EXAFS equation accurate.? > But the EXAFS equation is itself an approximation which is only useful at > energies starting many eV above E0. So there?s no theoretical reason that > the E0 used in EXAFS has to correspond to an energy with a simple > theoretical meaning or to any particular feature in the spectrum. The best > we can say is that it should be within, or sometimes a bit above, the > rising portion of the absorption spectrum. > > But when we?re trying to align and process data we need some working > definition of E0, both for XANES analysis and to get a preliminary chi(k) > for EXAFS analysis. So we come up with other definitions, such as ?the > maximum of the first significant peak in the first derivative spectrum.? As > Bruce said, the exact definition used is not important, but it is important > that the same definition be used with all spectra being compared. > > Depending on the definition chosen, the preliminary value of E0 may very > well be chosen well below the bulk of the rise in the spectrum. If we call > the energy of E0 the ?edge,? but also call features that come before the > big rise "pre-edge features,? we end up with the confusing terminology that > the edge energy may well be below some of the pre-edge features! > > That terminology is unfortunate for people new to the field, but rarely > causes any actual ambiguity. > > ?Scott Calvin > Sarah Lawrence College > > > On Jan 25, 2016, at 9:40 AM, Matt Newville <newville(a)cars.uchicago.edu > <mailto:newville@cars.uchicago.edu>> wrote: > > Aditya, > > The distinction between "edge" and "pre-edge" is not very clear, either > when looking at a single spectrum or even conceptually. > > In broad terms, the main edge is at the energy where the unoccupied > electron levels start - the Fermi energy. For 1s levels, the transition > is to p levels (and for Fe K edge, the 4p level). So, the main edge is at > the energy of the empty 4p levels. This the transition as being to an > atomic level. In a solid (or liquid), the energy levels above the Fermi > level are highly delocalized and spread over many (if not all) atoms in the > systems. Once you get much above the main edge, it's not very easy to > assign transitions to identifiable atomic transitions, or even assign a > good quantum number to them. > > Pre-edge features are generally considered to be unoccupied atomic levels > (that is, still assignable to a particular atom, or at least almost so) > below the main edge. For the transition metal K edges (such as Fe), the > main edge is 1s -> 4p. But Fe has many unoccupied 3d levels. For a K > edge to get to transition to these levels, either you need a quadrupole > transition (unlikely, but not impossible), or (more likely) for > bonding/anti-bonding with ligands (typically oxygen) to mix their > p-orbitals with the metal d-orbitals. This hybridization is often called > a ligand field or crystal field. It often gives very identifiable (and > at very predictable energies) peaks below the main edge. Two and > sometimes even three peaks can be seen and assigned with ligand field > terminology. There's sort of a whole industry built up around these > peaks for transition metal oxides. > > These peaks can "leak" into the main edge, and in some cases (say, Cu1+) > the classification of "sharp features at the edge" is not very clear. For > Fe metal, it's pretty clear that the main edge (derivative at 7110.75 eV, a > small peak on the main edge around 7112.5 eV) is the 4p level, and the rest > of the features are actually explainable as EXAFS. > > Hopefully, someone will correct anything I got wrong! > > --Matt > > > > On Mon, Jan 25, 2016 at 8:13 AM, Aditya Shivprasad <aps202(a)psu.edu<mailto: > aps202(a)psu.edu>> wrote: > Dear list, > > I was looking at the XANES standard for Fe foil from Hephaestus and I > noticed that there was a small, curved feature at the edge (7112 eV), > another inflection point at 7116.4 eV, and then the edge step at around > 7131 eV. My question is: why is the feature at 7112 eV considered as the > edge and not as a pre-edge feature? Are they due to fundamentally different > phenomena? I would like to understand where this type of feature comes from > so as to be consistent in the current paper that I am writing. I have > attached the standard, just in case. > > Thanks > -- > Aditya Shivprasad > > aps202(a)psu.edu<mailto:aps202@psu.edu> > Ph.D Candidate > Nuclear Engineering Department > Pennsylvania State University > > _______________________________________________ > 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 > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > > _______________________________________________ > 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 > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > >

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XANES pre-edge vs. edge features
by Aditya Shivprasad 25 Jan '16

25 Jan '16

Dear list, I was looking at the XANES standard for Fe foil from Hephaestus and I noticed that there was a small, curved feature at the edge (7112 eV), another inflection point at 7116.4 eV, and then the edge step at around 7131 eV. My question is: why is the feature at 7112 eV considered as the edge and not as a pre-edge feature? Are they due to fundamentally different phenomena? I would like to understand where this type of feature comes from so as to be consistent in the current paper that I am writing. I have attached the standard, just in case. Thanks -- Aditya Shivprasad aps202(a)psu.edu Ph.D Candidate Nuclear Engineering Department Pennsylvania State University

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Regarding calculations for scattering amplitude
by pushkar shejwalkar 24 Jan '16

24 Jan '16

Dear All, I sent a related question in the month of Dec but it seems that the question did not appeared on list because of mailbox being full, as we all have received an email. Since mailing list is started again I am sending this question once more. My question is actually regarding finding out the nanoparticle size. In this respect, I am referring to Harris's work in which by using a simple equation we can roughly estimate the nanoparticle size J. Appl. Phys., Vol. 94, No. 1, 1 July 2003 Now the question is that in this paper and another paper I found online as well, it refers to Nnano and Nbulk. I am guessing that this is basically coordination number of nanoparticle and bulk. But my first question is how do I calculate it?? e.g. I am working on Pd K-edge. So should I fit Pd foil with Pd crystal data and get the CN? but that would be 12 anyways. So would Nbulk be 12 in that case? and what will be Nnano then? In another context, CN is proportional to amplitude, so in that case is it directly proportional? as in, can I simply replaced in formula, Nbulk/Nnano with Amplitudebluk/amplitudenano? Third thing is that, if above is true then how should/can I calculated the amplitude? isnt that amplitude is always calculated by Feff? if so could someone help me with the procedure to do so? How will I know amplitude for nanoparticles, because I cannot have FEFF for nanoparticles, right? I went through lot of material, however, so far my calculations give me a solution that is vaguely correlated to TEM images. The TEM value is about 2nm (rouhgly 20 angstrom). my current values I am getting by solving the equation by my current understanding is only 2Ao. about 10 times less. What I am doing is simply plotting the crude data in athena to get x(R) Vs radial distance graph, calculate A-3 for nanoparticles and bulk and using this as amplitudes. It is possible that I may be doing something totally irrelevant, so please help me in this aspect. Thank you Sincerely Pushkar -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Tokyo-to Japan

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Re: [Ifeffit] Fwd: Citing XANES standards
by Bruce Ravel 21 Jan '16

21 Jan '16

On 01/21/2016 12:14 PM, Aditya Shivprasad wrote: > Hi Dr. Ravel, > > I am a graduate student in Nuclear Engineering at Penn State. I study > corrosion of Zr-based alloys using microbeam XANES at the APS. For my > linear combination fitting of iron XANES spectra I have used your iron > foil standard that is available through the Hephaestus program. I was > wondering if there was a paper or work I could cite to reference this > standard. Aditya, I am CCing my answer to the Ifeffit mailing list. This seems like a general enough question that it should go onto the list. The advice I have given others who have asked this question is to state that the standard is distributed with the Demeter software package and to use the standard citation for the software. Cheers, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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DAFS calculation
by JeongEunSuk 21 Jan '16

21 Jan '16

Hello I've heard that Atoms 3.0 code is available to calculate DAFS. I would like to calculate it. Do you have any example for it? I don't know how to use keywords in Atoms 3.0 such as dafs, emin, emax and others. Best regards Eun-Suk Jeong

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Ifeffit Mailing List
by Matt Newville 15 Jan '16

15 Jan '16

Hi Folks, As some of you no doubt noticed, the server (millenia.cars.aps.anl.gov) running this mailing list as well as the ifeffit web pages and xafs.org has been down for much of the past month. There was a hard-disk failure that brought this server down on Dec 21. I was out of town at the time, and didn't return until this week. FWIW, I know that Bruce Ravel was also away and unable to answer questions. It's possible the hard disk was telling us we all needed a break over the holidays. If you're getting this message, the mailing list is back up, and should be working now. Any messages you may have posted since Dec 21 are probably lost, and you may want to re-ask them. The ifeffit web site and xafs.org are also back up now. The Atoms web page is not yet functioning, but I'm working on that. If you notice any problems or have any questions, feel free to send me an email either on this list or in private. --Matt Newville <newville at cars.uchicago.edu>

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Solution to running Demeter on an ORNL computer
by Mullins, David R. 17 Dec '15

17 Dec '15

After having run Athena and Artemis for years on my office computer in Oak Ridge they suddenly stopped working. The command prompt window and "credits window" appeared briefly and then shut down. I tried upgrading from v 9.21 to v 9.24. This didn't help. The problem appears to be similar to what was reported in October 2015 by Matt Noerpel on EPA computers. The problem is related to the restricted Administrator privileges imposed by ORNL IT. To install new software we temporarily obtain Administrator privileges. When we do this it changes our User Directory from our standard User Directory to Admin. Demeter's default is to install in the current User Directory which is now the Admin directory and apparently programs installed there won't run when Administrator privileges are gone. To solve the problem I changed the installation directory from Admin to my User Directory name in the long line "Install Demeter in ...". Note that I just substituted my User Directory name for Admin and didn't change any of the other directory specifications. Hope this helps. I suspect that as time goes by many other national labs and companies will institute similarly restrictive Admin privileges. Dave ********************** David R. Mullins Oak Ridge National Laboratory PO Box 2008, MS 6201 Oak Ridge, TN 37831-6201 PH: 865-574-2796 FAX: 865-241-5152 E-MAIL: mullinsdr(a)ornl.gov<mailto:mullinsdr@ornl.gov> WWW:http://www.ornl.gov/sci/csd/Research_areas/SCC_group.html

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Measurment of size of nanoparticles using one measurement of sample
by pushkar shejwalkar 17 Dec '15

17 Dec '15

Dear All, I am currently trying to find out the size of my Pd nanoparticles using EXAFS analysis. But I am totally new to this field and I have no physics background as well. With this I started digging into the email archives as to if it is possible to speculate the size of the nanoparticles that I have. My preliminary information from SEM lets me start from the point where the nanoparticles are around 2-3 nm in size and about spherical in nature. I started with the following thread from archive http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2013-October/011474.html and it was pretty useful as well. I read the documents and other threads involved in it. and then I realized that with the knowledge of amplitude of known (lets say in this case Pd foil) and my sample I can find out the extent to which the Pd atoms are present at the farthest distance. by doing so I can find out what the nanoparticles size. To be specific I am talking about this particular paper. http://scitation.aip.org/docserver/fulltext/aip/journal/jap/94/1/1.1581344.… (http://dx.doi.org/10.1063/1.1581344) I am using this paper since it works with spherical nanoparticles and hence my assumptions can best be supported by this model. I am open to other references as well and I would cite them all if they are useful. Now my question is, in order to make up to the reduced amplitude, it is recommended that for spherical nanoparticles only two variables in fitting parameteres are needed 1) Radius 2) amplitude reduction factor (SO2) I think I have understood the basic concept as to why the amplitude is reduced and somehow we need to increase the number N of number of paths/number of atoms in the cluster so that the amplittude will now increase so much so that it would match the theory. BUT what I have not understood is how to do so? e,g do we do that during fitting? in artemis? in which case the amplitude is by default adjusted to get the fit and now there is no difference in the absolute value of x(R) (A-3Ao) Y-axis. OR have I misunderstood something? Could someone shine a light on this please. Best Pushkar -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Tokyo-to Japan

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Mac woes
by Bruce Ravel 15 Dec '15

15 Dec '15

If someone would like to contribute a write-up on how to install the Mac package and how to troubleshoot the most common problems, that would be helpful. I could then replace the text that exists on the Demeter homepage, which does not appear to be sufficient for many Mac users. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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No Plot window (Mac El Capitan)
by Laila Al-Madhagi [fy11lham] 15 Dec '15

15 Dec '15

Hello there, I have installed Demeter with Macports on my Mac recently. My operating system is El Capitan. My issue is that I cannot see the plot area. I have followed two threads discussing this issue. The first one is ''No plot window in Athena/ Demeter on Mac OS X Yosemite'' (http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2015-September/012739.ht… where George suggested to change the gnuplot to x11 on the Athena preferences menu. I could not find Athena preference menu and I was wondering if anyone could help with that. The second thread is ''No plot window on Mac El Capitan'' (http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg05261.ht… where Chloe could not find Athena Preferences menu as well. Best regards, Laila

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[ANN] Larch 0.9.27
by Matt Newville 13 Dec '15

13 Dec '15

Hi Folks, Though I've resisted making an announcement about each minor release of Larch, I wanted to let everyone know about an important change starting with the latest release. As both Bruce and I (and Sam, and probably anyone who has tried) have experienced, and many of you have witnessed from discussions on this list, building and maintaining binary installers for various Windows and Macintosh generations is a painful and time-/resource-consuming. For Larch, as with Demeter, Windows installers have been possible but real work, and Macintosh installers have been much more difficult. Starting with Larch 0.9.27, I'm recommending that folks using Mac OSX and Windows use the free version of Anaconda Python 2.7 from ContinuumIO ( https://www.continuum.io/) Anaconda Python comes with a very large set of the standard scientific Python libraries as well as visualization and development tools. I highly recommend this package for anyone interested in learning scientific programming. For Larch, the main benefits of this approach are 1) very easy installation and upgrades to packages, and 2) that the default installation goes into the users home directory, and so can easily be modified (or deleted) by the user without administrative privileges. To install Larch with Anaconda Python, the instructions (see http://xraypy.github.io/xraylarch/installation/index.html) are: 1. Download and Install Anaconda Python from https://www.continuum.io/downloads 2. Open a Command Line Terminal Windows: From the Start Menu, open an Anaconda Shell Mac OSX: Applications->Utilities->Terminal and type: conda install -c newville xraylarch This will install all the basic software for Larch, and all the installed programs can be run from this terminal. 3. To create "clickable icons" (Windows shortcuts or Mac Applications) type: larch_makeicons in the same Terminal window. This will create a Folder named Larch on your desktop with several Larch applications in it. Because these are on your desktop, you can move, rename, or delete these without affecting any other software. 4. To update Larch at any time, you will be able to open a Terminal and type: conda update -c newville xraylarch For Linux, Anaconda is a fine choice, but seems slightly less important as the standard package managers have most of the required packages available, and a source installation of Larch is very easy. Installing with Anaconda includes all the source code for the Larch plugins in "share/larch/plugins" under the anaconda folder in your home directory (or under AppData on Windows). These are dynamically loaded by Larch, so you can still explore and modify the analysis procedures. However, installing with Anaconda does not include local copies of the documentation or examples. This may change in future release, but for now these will be made available for each release at http://cars.uchicago.edu/xraylarch/downloads/docs/ Let me know if you have any questions or trouble with any of this. --Matt

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Athena 0.9.24 (64-bit) on Windows: Problems with Alignment and with plotting window
by Voegelin, Andreas 11 Dec '15

11 Dec '15

Dear Bruce After upgrading from Demeter 0.9.22 to Demeter 0.9.24 (64-bit) on two PCs with Windows 7 Enterprise, I now encounter two problems that I did not observe before: 1) In Athena, auto-align does not seem to work properly: In the attached project file, the first spectrum is a reference Fe foil spectrum. Trying to align the reference spectra linked with the sample spectra to this reference foil, the "auto-align" function results in an obviously wrong alignment (see jpg file). Even if I first manually correctly align the reference spectra, "auto align" again shifts the spectrum to a wrong place. 2) Plotting window is always set to small size when plotting a graph and zooming does not work: Working with Athena, I normally used the left half of the screen to display the GUI and the right half to display the plotting window. After I installed Demeter 0.9.24, the plotting window is always reduced in size and moved to the left part of the screen when I try to plot a graph from Athena. Furthermore, within the plotting window, the zoom function does not seem to work anymore. 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 mailto:andreas.voegelin@eawag.ch http://www.eawag.ch/~voegelan

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Athena 0.9.24 (64-bit) on Windows: Problems with Alignment and with plotting window
by Voegelin, Andreas 11 Dec '15

11 Dec '15

Dear Bruce In the project file I sent with my previous email, the E0 of the standard Fe foil spectrum was set to 7128.5 eV, and the E0 of the foil spectra associated with the sample spectra were set to 7112 eV. If I set the E0 value of the standard Fe foil spectrum to 7112 eV as well, the "auto-align" function works properly again. Playing around a little bit further, it appears that the auto align function finds the correct solution as long as the difference between the E0 values assigned to the standard foil and the foil spectrum to be aligned is less than or equal to 5 eV. However, I wonder why the choice of E0 should affect the alignment function? 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 mailto:andreas.voegelin@eawag.ch http://www.eawag.ch/~voegelan

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Unable to export flattened normalized XANES spectra from Athena 0.9.24
by Jeff Catalano 09 Dec '15

09 Dec '15

I am looking for some help with a possible error on my part or bug associated with exporting normalized mu(E) spectra from Athena 0.9.24 64-bit on Windows 10 Pro 64-bit. I have some Si XANES data with a challenging background shape that is well removed through careful normalization in Athena, as long as the "Flatten normalized data" option is checked. When I save the current group as norm(E), what is saved is the non-flattened normalized data. The checkbox for flattening the data has no effect on what is exported despite changing what is plotted. I have verified this by comparing the files exported the the flatten box checked or unchecked. I have tried this with multiple data files loaded in multiple formats (raw beamline data, simple two-column E and mu data, PRJ files) and the effect is always the same. It is also unaffected by the normalization ranges I select. No matter what options I select Athena 0.9.24 will only save non-flattened norm(E) data. This behavior is different from what I remember, and I have verified that in version 0.8 of Athena the exported norm(E) was the flattened data, provided that the flatten box was checked (of course). I have been unable to determine if I have any errors in the settings in version 0.9.24 but all parameters that I can find are identical in both 0.9.24 and 0.8. I have also uninstalled and reinstalled Athena 0.9.24 and the effect is still the same. Has anyone else noticed this problem? Is this a bug? Thank you, Jeff -- Jeffrey G. Catalano, Associate Professor Department of Earth and Planetary Sciences Washington University 1 Brookings Drive, Campus Box 1169 Saint Louis, MO 63130 USA http://aqgeochem.wustl.edu/

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Most probably a bug or something.
by pushkar shejwalkar 02 Dec '15

02 Dec '15

Dear All, I have recently found this particular problem with plotting my graphs in k fitting. This is a problem with athena as well as artemis. When I plot the graphs in R or E or q there is no problem, but when I do so in k suddenly these four black circles show up on the left side of the graph. Interestingly this has appeared suddenly just now and after this (probably i can recollect exactly) I could not maximize my plotting window at all. although if I drag the corners it can be resized and these four circles then appears relatively smaller (basically it does not exapnds with the window. Anybody else have this problem? is there a quick fix? I am not sure if this is a bug or not so I am sending this here. my operating system is Windows 10, Athena and artemis 0.9.22 8GB RAM. (Please let me konw if anything else is needed) Pictures of these problem is attached below. I am attaching R-space just to show that it doesnt happen for the R-space. First picture is Athena, second is from Artemis fitting. [image: Inline image 4] [image: Inline image 2][image: Inline image 3] -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Tokyo-to Japan

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Re: [Ifeffit] Ifeffit Digest, Vol 154, Issue 5
by Enyuan Hu 02 Dec '15

02 Dec '15

Dear all, Thank you all for the kind help. I didn't know CuO is so useful in the sense that asking for its spectrum would reveal the abundant kindness in this community :) Enyuan On Wed, Dec 2, 2015 at 10:26 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Ifeffit Digest, Vol 154, Issue 1 (Soma Chattopadhyay) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 2 Dec 2015 20:14:04 -0600 > From: Soma Chattopadhyay <soma.tifr(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 154, Issue 1 > Message-ID: > <CAMYsB8ucwLRpSNGFK1aA8LbuWb03t5fOajSjdPU= > SGerD30jQQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Enyuan > Attached is my athena project file with Cu foil, CuO and Cu2O data in > athena. > They have references foils with them. > best > Soma > > On Wed, Dec 2, 2015 at 7:38 PM, Enyuan Hu <enhu(a)bnl.gov> wrote: > > > Dear Matt, > > > > I'm sorry to be persistent but I noticed that the reference spectrum (Cu > > foil I assume) for these two CuO data doesn't seem to correct. I conclude > > this after I made comparison using the Cu foil data from the database and > > my own previous measurement. If it's not bothering you, can you help me > > look into that? Thanks. > > > > Enyuan > > > > On Wed, Dec 2, 2015 at 8:08 PM, Enyuan Hu <enhu(a)bnl.gov> wrote: > > > >> Dear Riti and Matt, > >> > >> Thank you two very much for the timely help. I didn't even know the > >> existence of these two libraries. Thanks again for letting me know such > a > >> valuable resource. > >> > >> regards, > >> Enyuan > >> > >> On Wed, Dec 2, 2015 at 7:40 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. CuO XAS spectrum (Enyuan Hu) > >>> 2. Re: CuO XAS spectrum (Ritimukta Sarangi) > >>> 3. Re: CuO XAS spectrum (Matthew Marcus) > >>> 4. Fwd: Most probably a bug or something. (pushkar shejwalkar) > >>> > >>> > >>> ---------------------------------------------------------------------- > >>> > >>> Message: 1 > >>> Date: Wed, 2 Dec 2015 18:32:11 -0500 > >>> From: Enyuan Hu <enhu(a)bnl.gov> > >>> To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > >>> Subject: [Ifeffit] CuO XAS spectrum > >>> Message-ID: > >>> < > >>> CAJud35MbtedoHtgoN3yFJgJ3squ+L5LCVpp1uNm0Tf4vwpWENA(a)mail.gmail.com> > >>> Content-Type: text/plain; charset="utf-8" > >>> > >>> Dear all, > >>> > >>> I'm analyzing some Cu compounds spectra and was wondering if anyone has > >>> the > >>> CuO XAS spectrum and is willing to share. Thanks. > >>> > >>> best regards, > >>> Enyuan > >>>

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Re: [Ifeffit] Ifeffit Digest, Vol 154, Issue 1
by Enyuan Hu 02 Dec '15

02 Dec '15

Dear Riti and Matt, Thank you two very much for the timely help. I didn't even know the existence of these two libraries. Thanks again for letting me know such a valuable resource. regards, Enyuan On Wed, Dec 2, 2015 at 7:40 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. CuO XAS spectrum (Enyuan Hu) > 2. Re: CuO XAS spectrum (Ritimukta Sarangi) > 3. Re: CuO XAS spectrum (Matthew Marcus) > 4. Fwd: Most probably a bug or something. (pushkar shejwalkar) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 2 Dec 2015 18:32:11 -0500 > From: Enyuan Hu <enhu(a)bnl.gov> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] CuO XAS spectrum > Message-ID: > < > CAJud35MbtedoHtgoN3yFJgJ3squ+L5LCVpp1uNm0Tf4vwpWENA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear all, > > I'm analyzing some Cu compounds spectra and was wondering if anyone has the > CuO XAS spectrum and is willing to share. Thanks. > > best regards, > Enyuan >

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CuO XAS spectrum
by Enyuan Hu 02 Dec '15

02 Dec '15

Dear all, I'm analyzing some Cu compounds spectra and was wondering if anyone has the CuO XAS spectrum and is willing to share. Thanks. best regards, Enyuan

3 2

Issue with Compatibility between versions of Athena
by Nirala Singh 26 Nov '15

26 Nov '15

Hello, I have recently downloaded Athena and was sending a project file to a colleague who uses an older version. When I sent it, I checked 'Backwards compatible project file', then saved the project and closed Athena, then sent the file. I had selected some normalization parameters as follows: [image: Inline image 2] When he opened the file, most of the parameters were the same, except the window type (changed from 'Hanning' to 'kaiser-bessel'). Is there any reason for this? Any way to maintain the window function between versions? [image: Inline image 1] Thank you,

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Fitting parameters corrleations between variables
by pushkar shejwalkar 24 Nov '15

24 Nov '15

Dear All, I am trying to fit in Pd compound and the fit that I obtained looks kinda good. I used Pd metal and Pd(OAc)2 shells for fitting. These standards were collected and fitted simultaneously and I got the SO2 value there as 0.67 with Pd foil coordination number as 12 which is correct when considered Pd foil CN. Next while fitting the actual sample (unknown) I used the formula in SO2 column as amp*N1 and put amp as 0.67 and N as 1. I kept N1 as variable (Guess). same I did for the second shell of Pd-O with N2. amp is kept on SET value of 0.67. After fitting I received the N1 and N2 value as 5.6 (0.5) and 1.6 (0.7) (roughly). however, when I checked the correlations between the variables I got the values as given in the log file attached. I saw there is some correlation between bkg01_01 and N2 and many such correlations between bkg values. I have so far never seen such correlations. What are the implications of these correlations? does this means that my fitting assumptions are incorrect. does correlations values in negative indicates something? Thank you very much for the input. By the way my RBKG is 1.2 in athena and I used this same file for fitting purpose and on artemis I used rmin 1.2 and rmax 3.4. All these information are in log file attached Any help in understanding this is appreciated. -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Tokyo-to Japan

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Zinc Sulfite Reference Spectrum
by Elisabeth E Feld 16 Nov '15

16 Nov '15

Dear All, I am studying the oxidation state of Sulfur using XANES and need a reference spectrum of Zinc Sulfite (ZnSO3) for comparison. I do not have access to taking the spectrum myself and currently do not have any spectrum grabber tool to pull the reference from a paper. If you could help me out by sending me a Zinc Sulfite spectrum, I would greatly appreciate it! Thank you, Elisabeth Elisabeth Feld Ph.D. Candidate Dellinger Research Group Chemistry Department Superfund Research Center Louisiana State University 338 Choppin Hall Baton Rouge, LA 70803 efeld1(a)lsu.edu

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Re: [Ifeffit] Ifeffit Digest, Vol 153, Issue 30
by Christopher Thomas Chantler 16 Nov '15

16 Nov '15

With Ifeffit-like, you can test these assumptions with an explicit chi^2_r, and indeed the answer does and must depend upon your actual individual error bars. The other factor here is how correlated your choice of parameters are which of course reaches that limit much faster. :) ------------------------------------------------------------ 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-bounces(a)millenia.cars.aps.anl.gov [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: Tuesday, 17 November 2015 5:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 153, Issue 30 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 Perl interpreter (Bruce Ravel) 2. Re: Hello (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Mon, 16 Nov 2015 07:48:54 -0500 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Problem with Perl interpreter Message-ID: <5649D0B6.3050108(a)bnl.gov> Content-Type: text/plain; charset=windows-1252; format=flowed On 11/16/2015 02:53 AM, Wojciech Olszewski wrote: > The timeline of this problem was as follows: > 1) Demeter was working fine; > 2) One day I couldn't run any of the Demeter software - error message "Per interpreter has stopped working; > 3) Reinstallation of Demether - the problem is still there; > 4) Installation of perl (in other folder, not the same as Demeter) - the problem is still there; > 5) Mail to mailing list; > 6) Deinstallation of Demether and Perl; > 7) Installation of Demeter. > Unfortunately the problem is still there. I receive the same error message. Wojciech, Step 2 really suggests that this is a problem local to your computer. In recent weeks, there have been a few reports of anti-virus software blocking some component of perl or Demeter. In the time period between steps 1 and 2, was AV updated on this computer? Could you disable AV (as a test of course)? Or configure AV to explicitly allow Demeter to run? B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ ------------------------------ Message: 2 Date: Mon, 16 Nov 2015 11:18:56 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Hello Message-ID: <CA+7ESbrzTzUkpPHj0CFZ6HErN5Hp_jMHJynJa0rUZ+XSM3dqPA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Riti, On Fri, Nov 13, 2015 at 6:25 PM, Ritimukta Sarangi <ritimukta(a)gmail.com> wrote: > Hi Bruce and Matt, > Are there any obvious examples of where Sterns criteria is shown to be > incorrect? Meaning that 2delkdelR/pi +2 has been shown to over predict the > number of available independent parameters? I have often been asked this by > students/users and failed to explain it well, except for taking of talking > sources or error such as systematic, spline, etc. > Thanks! > -Riti > > That's an excellent question. To be honest, I don't think this has been tested in great detail, with the main issue being "when can you truly tell that you've used too many parameters". We typically rely on "when adding a variable doesn't improve reduced chi-square" as that measure. But, the definition of reduced chi-square that we use includes a value for N_idp already, so we're more or less *imposing* the Stern rule. I think lots of us have observed cases where the Stern rule is definitely optimistic. And that might be understandable because the Stern rule doesn't include a separate measure of the noise in the data, or what the distribution of "the effect" of the parameters would be on the signal. That is, one can always increase the R range to 20 Angstroms, and so increase N_idp. But if you're trying to fit 25 variables for the part of the signal between 1.5 and 2.5 Ang, there is probably going to be very hard to get good measures of all 25 variables. The Stern rule sort of doesn't account for this, except in the sense of giving guidance. It would be interesting the revisit this with a better statistical treatments of information. There are, for example, statistical values like the Akaike Information criterion ( https://en.wikipedia.org/wiki/Akaike_information_criterion) and related values that might be useful for better understanding when one is using too many parameters. --Matt

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Problem with Perl interpreter
by Wojciech Olszewski 16 Nov '15

16 Nov '15

I have a problem with Demeter package. Up to yesterday everything was fine. Now when I try to start any program (Athena, Artemis...) I receive error message: Perl interpreter has stopped working (The application was unable to start correctly (0xc0000005)). Installation of perl (strawberry-perl-5.22.0.1-64bit.msi) didn't solve the problem. Unfortunately all the log files ("C:\Users\<username>\AppData\Roaming\Demeter\<name>.log") are empty. I am using the Demeter 0.9.24 on 64-bit Windows 7. I would be really grateful for help in solving this problem. Thank you in advance, Wojciech -- ALBA Synchrotron <http://www.albasynchrotron.es> Wojciech Olszewski BL22 - CLAESS: Core Level Absorption & Emission Spectroscopies - Experiments Division ALBA SYNCHROTRON LIGHT SOURCE Ctra. BP 1413 km. 3,3 | 08290 | Cerdanyola del Vallès| Barcelona | Spain <http://www.albasynchrotron.es/AboutUs/Access> (+34) 93 592 4059 www.albasynchrotron.es <http://www.albasynchrotron.es>| wolszewski(a)cells.es <mailto:wolszewski@cells.es> **Please, do not print this e-mail unless it is absolutely necessary. **Si heu rebut aquest correu per error, us informo que pot contenir informació confidencial i privada i que està prohibit el seu ús. Us agrairíem que ho comuniqueu al remitent i l'elimineu. Gràcies. Si ha recibido este correo por error, le informo de que puede contener información confidencial y privada y que está prohibido su uso. Le agradeceré que lo comunique a su remitente y lo elimine. Gracias. If you have received this e-mail in error, please note that it may contain confidential and private information, therefore, the use of this information is strictly forbidden. Please inform the sender of the error and delete the information received. Thank you.

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Re: [Ifeffit] Problem with Perl interpreter
by Wojciech Olszewski 16 Nov '15

16 Nov '15

On 11/13/2015 11:41 AM, Bruce Ravel wrote: >Hi Wojciech, > >Why are you installing perl independently of Demeter? Do you have some other use on your >computer that requires you to install perl? Installing another version of Strawberry Perl is >almost certain to clobber Demeter. Demeter is currently using perl 5.18, which is not binary >compatible with 5.22. So, when you install the other version of perl things will break. If you >take care to install a very recent version of Demeter to a different installation directory >than you use to install Strawberry 5.22, it is possible that the two can be made to co-exist. > >If you install them to the same installation folder -- say C:\strawberry -- then Demeter is >guaranteed to be broken be due to the binary incompatibility. So ... did you install the other >version of perl prior to noticing that Demeter was broken? If so, there are ways to proceed, >but it may get a bit complicated. At the very least, you can uninstall both packages completely >then resinstall Demeter. That should leave you with a functioning Demeter, but it may break >other software. Did you install Strawberry 5.22 because you have some other use for perl on >your computer? If so, can your other software work with the version of perl that comes with >Demeter? That is, do you really need Strawberry 5.22? Executive summary: I think you problem is >binary compatibility between perl version, of which you seem to have two on your computer. If >all of that doesn't solve your problem, it's going to take a lot more effort to troubleshoot >the problem. >Good luck! >B Dear Bruce, The timeline of this problem was as follows: 1) Demeter was working fine; 2) One day I couldn't run any of the Demeter software - error message "Per interpreter has stopped working; 3) Reinstallation of Demether - the problem is still there; 4) Installation of perl (in other folder, not the same as Demeter) - the problem is still there; 5) Mail to mailing list; 6) Deinstallation of Demether and Perl; 7) Installation of Demeter. Unfortunately the problem is still there. I receive the same error message. Best regards, Wojciech -- ALBA Synchrotron <http://www.albasynchrotron.es> Wojciech Olszewski BL22 - CLAESS: Core Level Absorption & Emission Spectroscopies - Experiments Division ALBA SYNCHROTRON LIGHT SOURCE Ctra. BP 1413 km. 3,3 | 08290 | Cerdanyola del Vallès| Barcelona | Spain <http://www.albasynchrotron.es/AboutUs/Access> (+34) 93 592 4059 www.albasynchrotron.es <http://www.albasynchrotron.es>| wolszewski(a)cells.es <mailto:wolszewski@cells.es> **Please, do not print this e-mail unless it is absolutely necessary. **Si heu rebut aquest correu per error, us informo que pot contenir informació confidencial i privada i que està prohibit el seu ús. Us agrairíem que ho comuniqueu al remitent i l'elimineu. Gràcies. Si ha recibido este correo por error, le informo de que puede contener información confidencial y privada y que está prohibido su uso. Le agradeceré que lo comunique a su remitente y lo elimine. Gracias. If you have received this e-mail in error, please note that it may contain confidential and private information, therefore, the use of this information is strictly forbidden. Please inform the sender of the error and delete the information received. Thank you.

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Re: [Ifeffit] Demeter under El Capitan
by Fowler, Joseph W. 15 Nov '15

15 Nov '15

Dear Matt, I’m the official MacPorts maintainer for Demeter. I am an amateur at this (i.e., at Ports), but I do have notes somewhere on how to update the port file (and, indeed, where to find it in the first place!). Concerning the long list of dependencies: I was unaware of the size of this list. I agree. It sounds crazy to think that we need THREE non-clang compilers to build demeter. I know the fellow who was the previous maintainer, and he has a bit of a superstitious belief in the powers of gcc. Perhaps he imposed this belief unnecessarily on us all? It sounds to me like you understand the internals of what demeter uses and how, much much better than I do. Let me suggest that you either contact me privately OR file a trac ticket at MacPorts about this. Either way, include details of what you think plausibly might be false dependencies. Of course, we’ll also want to add the new Perl dependencies that you pointed out. Perhaps then I can patch the port file and get your assistance in testing it in some way? Once we have a patch we like, I don’t have the powers to commit it to the MacPorts repository directly, but I can certainly make a request for a commit (they are pretty fast and responsive about that). I’d like to comment also on the time it takes to install MacPorts. The whole MacPorts concept supports installing from source AND installing pre-built binaries. The catch (as I understand it) is that the server resources that they use to build and serve the binaries are donated by a large corporation (one with a strong interest in selling more Macintosh computers, naturally). Thus the open-source Ports team cannot simply make the binary “buildbots” appear at will. An early adopter of an OS X version has to install every port, even the incredibly complex ones, from source. Again, I could be wrong, but I think that El Capitan is still in this state. See https://trac.macports.org/ticket/48609 and http://macports-dev.macosforge.narkive.com/tRq2luOR/el-capitan-buildbot for some additional info. Now, this is not to say that Homebrew is a worse solution than MacPorts. I have no basis for comparison (though here is one clue: many packages that I use within the Julia language depend on Homebrew for further dependencies, and I have noticed that they manage to Just Work). But I did want to defend MacPorts from the implied charge that it will always take all users ten hours to install a working system. If you can find a Homebrew expert to work with and develop a Demeter solution, that’s great. Here in my group at NIST, we use MacPorts for so many things that I’m sure we’ll continue to maintain the port file for the foreseeable future. Best wishes, Joe Fowler On Nov 13, 2015, at 11:00 AM, <ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov>> <ifeffit-request(a)millenia.cars.aps.anl.gov<mailto:ifeffit-request@millenia.cars.aps.anl.gov>> wrote: From: Matt Newville <newville(a)cars.uchicago.edu<mailto:newville@cars.uchicago.edu>> Subject: Re: [Ifeffit] Demeter under El Capitan Date: November 13, 2015 at 9:34:31 AM MST To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov>> Reply-To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov<mailto:ifeffit@millenia.cars.aps.anl.gov>> Hi George, All, Some progress: The MacPorts folks fixed the problem with PDL so that a 'port selfupdate' will then allow PDL to build and then install. With that, Demeter then installs, though there are some warnings about missing dependencies (Heap, XMLRPC::Lite, File::Slurp::Tiny, Encoding::FixLatin::XS) which I'm guessing are relatively new dependencies, not included in the Portfile. I installed these missing perl modules using the 'perl -MCPAN -e shell' The basic Athena and Hephaestus and Artemis run OK, though I haven't done exhaustive testing. I did have to change the default gnuplot terminal from Qt to wxt for each of Athena and Artemis (I did not try plotting with Hephaestus). The settings page for Artemis is not easy to find -- it might be that the multiple-small-screen layout is difficult to map to the Mac window styling. As for Xorg vs XQuartz: The correct answer should be "neither". Neither Demeter nor gnuplot actually use X11 at all -- both are using wxWidgets, which does not use X11 on Mac. Similarly, I cannot understand the dependency on all of llvm, gcc4.9, and gcc5.2 from MacPorts. Most of the code even for MacPorts appears to be built with the *system* (ie, Apple-supplied) clang compiler. I can believe it "necessary" (well, really, "easiest") to build all of gcc to get gfortran, but not twice. And, yeah, if you have to install from source, it sort of matters. I do not know where to update the MacPorts Portfile. All links to the actual portfile scripts seem broken to me, but maybe they're available someplace. --Matt

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Demeter under El Capitan
by Fowler, Joseph W. 13 Nov '15

13 Nov '15

Bruce, Scott, Manuel: I’m the MacPorts maintainer for demeter and ifeffit, but I’m afraid I have not been much help lately. I’m sorry that I have not chimed in about any of the recent reports Mac / Macports problems under El Capitan. It so happens that my employer (US National Institute of Standards and Technology) does not let us upgrade to Yosemite OR El Capitan. They own the only Macs to which I have access, so I can only work under Mavericks. I’m afraid that artemis, hephaestus, and athena all start properly for me. To Manuel from Grenoble, all I can say is that xorg-server has a lot of dependencies, and it will take a long time to install the needed ports the first time. I would not think an entire hour is out of the question, depending on your connection speed and computer performance. To the others having trouble running (as opposed to installing), I wonder if anyone in the community is having success with the demeter suite under El Capitan? If so, we’d all be grateful if you could let us know what tricks were required. I am totally helpless on OS 10.10 and 10.11-specific problems. Joe Fowler NIST Boulder Laboratories

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Apparent bugs in Athena 0.9.24 running under Windows 7 64 bit
by Marcelo Eduardo Alves 13 Nov '15

13 Nov '15

I have run another example file (Au+Cyanobacteria) downloaded from https://github.com/bruceravel/XAS-Education in Athena 0.9.24 under Windows 7 64 bit using two different Dell computers and observed the following apparent bugs: In both computers the orange points that indicates the E0 and the limits of pre and post-edge fittings did not appear in the plots; In both computers the legends did not appear in all plots; the same for the axes's scales and titles. The LCF plot showed just the sample and the fitted normalized ones even when the standard ones were required; In one computer, there were just two choice options for the standards; in the other one these boxes worked normally and all standards could be considered. Some screenshots are attached to this message, Marcelo.

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Apparent bugs in Athena 0.9.24 under windows 7 64 bits - corrigendum
by Marcelo Eduardo Alves 13 Nov '15

13 Nov '15

Previous message: The LCF plot showed just the sample and the fitted normalized ones even when the standard ones were required Corrigendum: In fact, this is working in both computers, i.e., all plots appear in the graph; however, in one machine the legend, the axes´s scales, and the axes´s titles are not diplayed. M.

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Re: [Ifeffit] Problems with EXAFS Fitting of Metalloprotein Zinc Samples
by Carolyn Carr 12 Nov '15

12 Nov '15

Hi Bruce, Thanks so much for clarifying that for me! I have been basing my fitting in R-space off of XAFS spectroscopy; fundamental principles and data analysis DOI 10.1023/A:1019105310221 which has a section on fitting in R-space over k-space although it is very possible I misinterpreted its analysis. My zinc question is more of a query rather than a true problem, and so I am glad that you have taken time to correct my knowledge of how fitting works. Carolyn Carr

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LCF, Sayers & Bunker, R and ATHENA
by Florian Werner 12 Nov '15

12 Nov '15

Dear mailing list, we recently published a paper where we broke with the "Sayers & Bunker 1988 - Paradigm" to apply normalization as consistently as possible between samples and standards when performing linear combination fitting: http://pubs.acs.org/doi/abs/10.1021/acs.est.5b03096. There, we showed that for known mixtures of phosphorus standards the LCF of P K-edge XANES spectra delivers better results when changing the base-line and normalization parameters of the sample (in defined ranges, using the software /R/). I'm writing to the mailing list of several reasons: 1) A reviewer explicitly asked to contact Bruce Ravel so that the new insight could be implemented in ATHENA, 2) I was trying to combine my code with ATHENAs way of LCF before publishing the code. Unfortunately, I have not been able to resolve that a combination of both approaches results in large numbers of LCF procedures (sometimes Million or Billion). So many procedures are not fittable in reasonable time, maybe because my code is slow or maybe because /R/ isn't fast enough (or just the nlsLM-function that I'm using for LCF). I'm stuck and maybe programming in Perl would be a better choice (never programmed in Perl, yet)? Maybe a different kind of fitting algorithm would be faster?, 3) When using the nlsLM-function to perform LCF in /R/, I also have to provide portions of the standards before starting the fit. I used the same approach as ATHENA, dividing 1 by the number of standards so that every standard has the same portion. However, when playing with the code I realized that changing the starting portion can have an impact on the fitting result. Has this been observed or tested before by anyone else? How do you, in general, justify using the same starting portion for every standard? 4) Some minor question about LCF in ATHENA: a) Could the standards (the columns) in the output .csv-file after LCF be sorted alphabetically?, b) Does LCF in ATHENA sometimes produce negative numbers of a portion because the weight of any "last" standard in a set is always calculated by "1-sum(portions_of_other_standards)" (could it be this? https://github.com/bruceravel/demeter/blob/master/lib/Demeter/LCF.pm#L375-L…) To mimic "all samples sum to one" from ATHENA and to not produce negative portions, we used all LCF results which have a residual "absolute(1-sum(portions_of_all_standards)) < 0.0005"; maybe this is of interest also for ATHENA? Cheers, Florian

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Problems with EXAFS Fitting of Metalloprotein Zinc Samples
by Carolyn Carr 11 Nov '15

11 Nov '15

Hi, I have a general question rather than specific. I have only ever fit XAS data on metalloproteins and one feature that I see is that when fitting Zinc samples in R-space there is no local minima. For Cobalt and Nickel samples I typically get one or a few fits that are obviously significantly better in R-factor (with reasonable distances, sigma^2, etc) but for Zinc this is not the case. I can get many good fits and Zinc likes to increase the coordination up to 8 for all data sets I have ever fit, although there is obviously no physical basis in this. This is true of not just my own proteins but Zinc samples made by collaborators, and after looking through previous group members fit tables, they had similar issues. My understanding is that one of the benefits of fitting in R-space is that there is a local minima, whereas in k-space there are many minima. I was wondering if there was a physical basis for this feature in Zinc samples, or if perhaps my group is not aware of some experimental setup that we should be doing for Zinc that would resolve this problem. Thank you for any help regarding this matter, Carolyn Carr

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Problems with EXAFS Fitting of Metalloprotein Zinc Samples
by Carolyn Carr 10 Nov '15

10 Nov '15

Hi Robert, Thanks for your reply. We have done this with standard samples and we see the same thing. And of course, we can tell qualitatively from the XANES that our sample is not 8 coordinate, and not even 6 coordinate. We have never tried changing the temperature but we can try this the next time we go to SSRL. We actually do fit multiple scattering features as imidazoles which is one of the things we consider as a strength of Artemis for our basic needs. This is part of why we think this is strange, because putting 8 imidazoles around a zinc seems kind of silly but it likes it. 5 imidazoles and 3 sulfurs and I have an R-factor of 0.2% every time. If there is non standard multiple scattering that occurs in multiple unrelated proteins from different organisms then we would have no idea what this could be. Thanks for your comments! Carolyn Carr

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Re: [Ifeffit] Ifeffit Digest, Vol 153, Issue 12
by Marcelo Eduardo Alves 09 Nov '15

09 Nov '15

I have downloaded the zip-file containing the example files and extracted them into other subfolders (i.e. C:\Users\Marcelo\Documents\1.Athena Calibração e Alinhamento\Examples\Fe foil). I think that this was my error. When I use C:\Fe foil the file was opened in Athena without any issue. Thank you Robert and Guanghui 2015-11-09 16:24 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. Opening "older" data files in the latest Athena version > (Marcelo Eduardo Alves) > 2. Re: Opening "older" data files in the latest Athena version > (Robert Gordon) > 3. Re: Opening "older" data files in the latest Athena version > (Guanghui Zhang) > 4. Problems with EXAFS Fitting of Metalloprotein Zinc Samples > (Carolyn Carr) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 9 Nov 2015 15:41:33 -0200 > From: "Marcelo Eduardo Alves" <mealves.esalq(a)usp.br> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Opening "older" data files in the latest Athena > version > Message-ID: <97FB7D67CF2142A48FA29F9776D0A164@MarceloPC> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > > I am using the latest version of Demeter (0.9.24) and I have downloaded > the data files available at https://github.com/bruceravel/XAS-Education. > > However, I am not being able to open the example files in Athena (e.g., > Fe.060 of Fe foil folder). > > Please, would it be possible to open those example files in the latest > Athena version. > > Thank you. > > Marcelo. > > > _______________________________________ > Marcelo Eduardo Alves > Departamento de Ci?ncias Exatas - ESALQ/USP > Avenida P?dua Dias, 11 > 13418-900 Piracicaba-SP > Fone: 19-3429-4151- RAMAL 26 > Email: mealves.esalq(a)usp.br >

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Re: [Ifeffit] Ifeffit Digest, Vol 153, Issue 14
by Marcelo Eduardo Alves 09 Nov '15

09 Nov '15

Thanks a lot Robert! Marcelo. 2015-11-09 17:30 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: Ifeffit Digest, Vol 153, Issue 12 (Marcelo Eduardo Alves) > 2. Re: Ifeffit Digest, Vol 153, Issue 12 (Robert Gordon) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 9 Nov 2015 17:01:51 -0200 > From: Marcelo Eduardo Alves <mealves(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 153, Issue 12 > Message-ID: > < > CAAO6x+ZSKvPtdLYw1nvz-iPZec1+Hcin-my0mtJDKd27_8PRnw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > I have downloaded the zip-file containing the example files and extracted > them into other subfolders (i.e. C:\Users\Marcelo\Documents\1.Athena > Calibra??o e Alinhamento\Examples\Fe foil). > I think that this was my error. > When I use C:\Fe foil the file was opened in Athena without any issue. > Thank you Robert and Guanghui > > 2015-11-09 16:24 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. Opening "older" data files in the latest Athena version > > (Marcelo Eduardo Alves) > > 2. Re: Opening "older" data files in the latest Athena version > > (Robert Gordon) > > 3. Re: Opening "older" data files in the latest Athena version > > (Guanghui Zhang) > > 4. Problems with EXAFS Fitting of Metalloprotein Zinc Samples > > (Carolyn Carr) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Mon, 9 Nov 2015 15:41:33 -0200 > > From: "Marcelo Eduardo Alves" <mealves.esalq(a)usp.br> > > To: <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: [Ifeffit] Opening "older" data files in the latest Athena > > version > > Message-ID: <97FB7D67CF2142A48FA29F9776D0A164@MarceloPC> > > Content-Type: text/plain; charset="iso-8859-1" > > > > Dear all, > > > > I am using the latest version of Demeter (0.9.24) and I have downloaded > > the data files available at https://github.com/bruceravel/XAS-Education. > > > > However, I am not being able to open the example files in Athena (e.g., > > Fe.060 of Fe foil folder). > > > > Please, would it be possible to open those example files in the latest > > Athena version. > > > > Thank you. > > > > Marcelo. > > > > > > _______________________________________ > > Marcelo Eduardo Alves > > Departamento de Ci?ncias Exatas - ESALQ/USP > > Avenida P?dua Dias, 11 > > 13418-900 Piracicaba-SP > > Fone: 19-3429-4151- RAMAL 26 > > Email: mealves.esalq(a)usp.br > >

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Re: [Ifeffit] Ifeffit Digest, Vol 153, Issue 11
by Marcelo Eduardo Alves 09 Nov '15

09 Nov '15

I have downloaded the zip-file containing the example files and extracted them into other subfolders (i.e. C:\Users\Marcelo\Documents\1.Athena Calibração e Alinhamento\Examples\Fe foil). When I use C:\Fe foil the file was opened in Athena without any issue. Thank you. 2015-11-09 15:55 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. Demeter under El Capitan (Fowler, Joseph W.) > 2. Re: Demeter under El Capitan (Zack Gainsforth) > 3. Opening "older" data files in the latest Athena version > (Marcelo Eduardo Alves) > 4. Re: Opening "older" data files in the latest Athena version > (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 9 Nov 2015 16:20:09 +0000 > From: "Fowler, Joseph W." <joe.fowler(a)nist.gov> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Demeter under El Capitan > Message-ID: <CAAD97E1-600B-43B3-B7AE-FAE9E373DC3E(a)nist.gov> > Content-Type: text/plain; charset="windows-1252" > > Bruce, Scott, Manuel: > > I?m the MacPorts maintainer for demeter and ifeffit, but I?m afraid I have > not been much help lately. > > I?m sorry that I have not chimed in about any of the recent reports Mac / > Macports problems under El Capitan. It so happens that my employer (US > National Institute of Standards and Technology) does not let us upgrade to > Yosemite OR El Capitan. They own the only Macs to which I have access, so I > can only work under Mavericks. I?m afraid that artemis, hephaestus, and > athena all start properly for me. > > To Manuel from Grenoble, all I can say is that xorg-server has a lot of > dependencies, and it will take a long time to install the needed ports the > first time. I would not think an entire hour is out of the question, > depending on your connection speed and computer performance. > > To the others having trouble running (as opposed to installing), I wonder > if anyone in the community is having success with the demeter suite under > El Capitan? If so, we?d all be grateful if you could let us know what > tricks were required. I am totally helpless on OS 10.10 and 10.11-specific > problems. > > Joe Fowler > NIST Boulder Laboratories > > >

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Re: [Ifeffit] Ifeffit Digest, Vol 153, Issue 9
by Matteo Busi 09 Nov '15

09 Nov '15

Dear Matt and Bruce, The problem is not with loading the files from the project, but instead to "load the loaded" files to the Data Summation. For example try to import all groups from the project of the example "Cu Metal" ( I will also attach it). Now go to data summation tab, in the components selection I'm able to select all groups except the first. (Shown in picture 1 attached). Now try to delete all groups and try to import groups from another project, let's say "Methylin" (attached). Now the groups avaiable for data summation work are still the previous ones (shown in picture 2). It seems that the data summation tab is not reading actively the groups loaded! I hope the situation it's clear now. Meanwhile I would also like to ask if there is a way to export the worked data ( for example, resulting from merges or sums) to new .dat files (in x-y coordinates). Regards, Matteo Busi 2015-11-06 19:00 GMT+01:00 <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: Data Summation Bugs (Matt Newville) > 2. please remove me from the list (Jocelyn Koshinsky-Bissonnette) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 6 Nov 2015 07:53:37 -0600 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Data Summation Bugs > Message-ID: > <CA+7ESbo1MYOMO==BQ9g= > eVYC644iceLpsVvqNHudhQwCimPkvg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Matteo, > > It sounds like this issue is really about reading in data from saved > projects, not about summation of data. Is that correct or is there another > problem too? > > One of the main features of the Athena project files is that you can send > them in an email. Doing that would make it possible for someone to try to > reproduce and understand the problem you are having. > > Finally, not many of us have experience using Windows 10. Do you see the > same issue on other machines too? > > --Matt > > On Nov 6, 2015 5:39 AM, "Matteo Busi" <basebush(a)gmail.com> wrote: > > > > Hi, I'd like to report a few bugs I've encountered while using the Data > Summation of Athena. > > > > I've been working with multiple data sets and experienced some tecnical > difficulties. For example; when I'm importing multiple data from a project > saved beforem not all groups are selectable in the Components, and some > times even none of them are selectable. > > In the case I could see the groups imported selectable in the Components, > if I import new datasets as groups they will not be selectable as > Components, but the list will still be the first avaiable ( like it's > frozen) untill the reboot of the software. > > It's a pity because it's doing the rest of the job grandiosely. > > > > I'm running Athena from Windows 10. > > > > Regards, > > Matteo Busi, University of Stavanger, Norway > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > >

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Opening "older" data files in the latest Athena version
by Marcelo Eduardo Alves 09 Nov '15

09 Nov '15

I have downloaded the worked examples available at https://github.com/bruceravel/XAS-Education However, I am not being able to open them in the latest Athena version (0.9.24) (e.g., Fe.060 of Fe foil folder). Could those files be opened in the last Athena version? Thank you. Marcelo.

4 3

Opening "older" data files in the latest Athena version
by Marcelo Eduardo Alves 09 Nov '15

09 Nov '15

Dear all, I am using the latest version of Demeter (0.9.24) and I have downloaded the data files available at https://github.com/bruceravel/XAS-Education. However, I am not being able to open the example files in Athena (e.g., Fe.060 of Fe foil folder). Please, would it be possible to open those example files in the latest Athena version. Thank you. Marcelo. _______________________________________ Marcelo Eduardo Alves Departamento de Ciências Exatas - ESALQ/USP Avenida Pádua Dias, 11 13418-900 Piracicaba-SP Fone: 19-3429-4151- RAMAL 26 Email: mealves.esalq(a)usp.br

1 0

Demeter installation on Mac El Capitan
by Muñoz Manuel 09 Nov '15

09 Nov '15

Dear Bruce, I try to instal Demeter on a Mac running El Capitan. I carefully followed the procedure (installation of Xcode and Macports), and I type the command: sudo port install xorg-server demeter in a terminal window. Unfortunately, after about 30 seconds, I am stuck with the following message: ---> Computing dependencies for xorg-server Would you have any suggestion? With my best regards, Manuel -- Manuel Muñoz Institut des Sciences de la Terre Université Joseph Fourier 1381 rue de la piscine – BP53 38041 Grenoble cedex 9 – France Tel.: 33 (0)4 76 51 40 54 – Fax: 33 (0)4 76 63 52 52

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please remove me from the list
by Jocelyn Koshinsky-Bissonnette 06 Nov '15

06 Nov '15

Thank you! *Jocelyn (Koshinsky) Bissonnette, M.Sc. Candidate*University of Saskatchewan Geology 136, (306) 966-5696 Specialist II, Quality Systems Cameco, SHEQ - Compliance and Licensing P Help save paper - do you need to print this email?

1 0

Data Summation Bugs
by Matteo Busi 06 Nov '15

06 Nov '15

Hi, I'd like to report a few bugs I've encountered while using the Data Summation of Athena. I've been working with multiple data sets and experienced some tecnical difficulties. For example; when I'm importing multiple data from a project saved beforem not all groups are selectable in the Components, and some times even none of them are selectable. In the case I could see the groups imported selectable in the Components, if I import new datasets as groups they will not be selectable as Components, but the list will still be the first avaiable ( like it's frozen) untill the reboot of the software. It's a pity because it's doing the rest of the job grandiosely. I'm running Athena from Windows 10. Regards, Matteo Busi, University of Stavanger, Norway

3 2

Athena open data project but not shown the curve
by 百度知道用户 05 Nov '15

05 Nov '15

Hi all, I processed a series of data using IFEFFIT Athena, and saved it as a project. Later, when I opened the project in IFEFFIT Athena, the plot window did not show the curve. I tried to open the project in Demeter Athena, but popuped "Can't call method "datatype" on an undefined value". The data curve was also not shown. I want to know what happened to this? Are the data damaged? I am very thankful if this problem can be solved.

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Re: [Ifeffit] X AS tutorial videos
by fred.mosselmans＠diamond.ac.uk 04 Nov '15

04 Nov '15

Hi Diamond is happy for anyone to download them. I find the program vlc works well for them. We put them on our anonymous ftp site, but occasionally they are cleared The current link is: ftp://ftpanon.diamond.ac.uk/XAS2011/ Thanks Fred Sent from Samsung tablet -------- Original message -------- From: ifeffit-request(a)millenia.cars.aps.anl.gov Date:14/10/2015 16:38 (GMT+00:00) To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 152, Issue 11 ---------------------------------------------------------------------- Message: 1 Date: Wed, 14 Oct 2015 10:41:06 -0400 From: Bruce Ravel <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Cc: tamrat(a)cerege.fr Subject: [Ifeffit] Fwd: XAS tutorial videos Message-ID: <561E6982.1070102(a)bnl.gov> Content-Type: text/plain; charset=windows-1252; format=flowed Hi Wuhib, This is a sufficiently general question that I am forwarding my answer to the mailing list. The videos are not my property, they belong to Diamond. You are correct that the manner in which they are streamed does not allow for jumping around, but there is nothing that I can do about that. You also mentioned that Shu had given you a download link (I have not included the link what I echoed blow because I do not know if Shu and the folks at Diamond want that link advertised). I have no trouble downloading or running them. Once downloaded, I can jump around as expected. If you are having "browser/network" issues, that seems like a problem for you (or your institution's IT folks) to solve. Again, there's nothing I can do about that. Final point, please use the mailing list in the future rather than writing to me directly about issues related to the software. Good luck, B -------- Forwarded Message -------- Subject: XAS tutorial videos Date: Wed, 14 Oct 2015 16:23:09 +0200 From: Wuhib Tamrat <tamrat(a)cerege.fr> To: bravel(a)bnl.gov Hello Bruce, My name is Wuhib and I am a PhD student in Aix Marseille University (France). I am recently being introduced to the world of XAS and I found your training videos from November 2011 at the Diamond Light source quite helpful. But the problem is that the streaming version does not give the flexibility to go back and forth to specific times in the lecture video. So I was wondering if you could find a way to send me the videos, if you have them and if it is not much trouble. Thank you. Regards Wuhib PS: I received a link from Dr. Shu Hayama but as he himself guessed I am having difficulty playing and downloading the .wmv files due to probably browser/network related issues. -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel **************************************** -- 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

4 3

Gnuplot CPU affinity
by Massimo Tallarida 04 Nov '15

04 Nov '15

Dear all, I’m having problems with both 0.9.24 and 0.9.18 versions of Demeter. When I open a new file, just after starting Athena, both versions work well, but as soon as I start to do something, e.g. deglitch a curve, the program starts to become very slow. This means that to choose a point on the graphic it take few minutes. I checked with the task manager and it seems that at the beginning gnuplot is using about 10% of CPU, but then it raises and it uses at maximum 25% of CPU, it does not go beyond this value. The CPU affinity is set to 4 CPUs, but it seems gnuplot uses only 1 (25%). If I close the program and restarted it, it happens the same. I’m using Windows 7 Enterprise, Service Pack 1, on an Intel Core i5-4590 CPU(a)3.30GHz (4 CPUs), with 8GB RAM. Thank you, Massimo

2 1

Artemis crashing for me on GDS mouse clicks under El Capitan
by Scott Calvin 03 Nov '15

03 Nov '15

Hi Bruce, Joe, et al, I haven’t used Demeter for a long time, so I just re-downloaded it to make sure I was up to date. I am using a MacBook Pro under OS 10.11.1. Artemis is version 0.9.20. It appeared to install fine. Artemis opens without difficulty, and can load an old project and run a fit properly. But if I click or right click anywhere on any of the lines in the GDS screen it crashes. The options on the right of the GDS screen function properly, though. The error message that is dumped to the screen is pasted below my signature. I’ve tried rebooting the computer in safe mode and running Artemis with no other packages open, and got the same result. —Scott Calvin Sarah Lawrence College Process: perl5.16 [708] Path: /opt/local/bin/perl5.16 Identifier: perl5.16 Version: 0 Code Type: X86-64 (Native) Parent Process: bash [330] Responsible: Terminal [276] User ID: 501 Date/Time: 2015-11-03 08:53:53.123 -0500 OS Version: Mac OS X 10.11.1 (15B42) Report Version: 11 Anonymous UUID: 273E17CC-B53C-8B05-9CC2-0179BEBA4A9F Sleep/Wake UUID: 3DF7EE6F-DF27-4DEF-8835-9D474D3D88AF Time Awake Since Boot: 640 seconds Time Since Wake: 310 seconds System Integrity Protection: enabled Crashed Thread: 0 Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_PROTECTION_FAILURE at 0x00007fff5adc4eb0 VM Regions Near 0x7fff5adc4eb0: MALLOC_SMALL 00007f83c9800000-00007f83ca800000 [ 16.0M] rw-/rwx SM=PRV --> STACK GUARD 00007fff575c5000-00007fff5adc5000 [ 56.0M] ---/rwx SM=NUL stack guard for thread 0 Stack 00007fff5adc5000-00007fff5b5bb000 [ 8152K] rw-/rwx SM=COW thread 0 Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 libsystem_c.dylib 0x00007fff90af50ab __vfprintf + 20 1 libsystem_c.dylib 0x00007fff90b1f35d __v2printf + 669 2 libsystem_c.dylib 0x00007fff90b037fa vsprintf_l + 399 3 libsystem_c.dylib 0x00007fff90af3b81 sprintf + 186 4 Wx.bundle 0x00000001049e7066 wxPli_thread_sv_register(interpreter*, char const*, void const*, sv*) + 182 5 Grid.bundle 0x0000000115a81411 XS_Wx__GridRangeSelectEvent_GetTopLeftCoords(interpreter*, cv*) + 193 6 libperl.dylib 0x00000001046dbce0 Perl_pp_entersub + 1376 7 libperl.dylib 0x00000001046d4e76 Perl_runops_standard + 22 8 libperl.dylib 0x0000000104661e4d Perl_call_sv + 877 9 Wx.bundle 0x0000000104ae301d wxPliEventCallback::Handler(wxEvent&) + 477 10 libwx_baseu-3.0.dylib 0x00000001054ebb82 wxEvtHandler::ProcessEventIfMatchesId(wxEventTableEntryBase const&, wxEvtHandler*, wxEvent&) + 88 11 libwx_baseu-3.0.dylib 0x00000001054eccbb wxEvtHandler::SearchDynamicEventTable(wxEvent&) + 85 12 libwx_baseu-3.0.dylib 0x00000001054ecc13 wxEvtHandler::TryHereOnly(wxEvent&) + 37 13 libwx_baseu-3.0.dylib 0x00000001054ecb58 wxEvtHandler::ProcessEventLocally(wxEvent&) + 40 14 libwx_baseu-3.0.dylib 0x00000001054ecaeb wxEvtHandler::ProcessEvent(wxEvent&) + 175 15 libwx_osx_cocoau_core-3.0.dylib 0x000000010509fc3d wxScrollHelperEvtHandler::ProcessEvent(wxEvent&) + 35 16 libwx_osx_cocoau_adv-3.0.dylib 0x0000000104d60228 wxGridSelection::SelectBlock(int, int, int, int, wxKeyboardState const&, bool) + 1976 17 libwx_osx_cocoau_adv-3.0.dylib 0x0000000104d399ee wxGrid::SelectBlock(int, int, int, int, bool) + 104 18 Grid.bundle 0x0000000115a8ded2 XS_Wx__Grid_SelectBlockPP(interpreter*, cv*) + 338 19 libperl.dylib 0x00000001046dbce0 Perl_pp_entersub + 1376 20 libperl.dylib 0x00000001046d4e76 Perl_runops_standard + 22 21 libperl.dylib 0x0000000104661e4d Perl_call_sv + 877 22 Wx.bundle 0x0000000104ae301d wxPliEventCallback::Handler(wxEvent&) + 477 23 libwx_baseu-3.0.dylib 0x00000001054ebb82 wxEvtHandler::ProcessEventIfMatchesId(wxEventTableEntryBase const&, wxEvtHandler*, wxEvent&) + 88 24 libwx_baseu-3.0.dylib 0x00000001054eccbb wxEvtHandler::SearchDynamicEventTable(wxEvent&) + 85 25 libwx_baseu-3.0.dylib 0x00000001054ecc13 wxEvtHandler::TryHereOnly(wxEvent&) + 37 26 libwx_baseu-3.0.dylib 0x00000001054ecb58 wxEvtHandler::ProcessEventLocally(wxEvent&) + 40 27 libwx_baseu-3.0.dylib 0x00000001054ecaeb wxEvtHandler::ProcessEvent(wxEvent&) + 175 28 libwx_osx_cocoau_core-3.0.dylib 0x000000010509fc3d wxScrollHelperEvtHandler::ProcessEvent(wxEvent&) + 35 29 libwx_osx_cocoau_adv-3.0.dylib 0x0000000104d60228 wxGridSelection::SelectBlock(int, int, int, int, wxKeyboardState const&, bool) + 1976 30 libwx_osx_cocoau_adv-3.0.dylib 0x0000000104d399ee wxGrid::SelectBlock(int, int, int, int, bool) + 104 31 Grid.bundle 0x0000000115a8ded2 XS_Wx__Grid_SelectBlockPP(interpreter*, cv*) + 338 32 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0x00000001054ecb58 wxEvtHandler::ProcessEventLocally(wxEvent&) + 40 417 libwx_baseu-3.0.dylib 0x00000001054ecaeb wxEvtHandler::ProcessEvent(wxEvent&) + 175 418 libwx_osx_cocoau_core-3.0.dylib 0x000000010509fc3d wxScrollHelperEvtHandler::ProcessEvent(wxEvent&) + 35 419 libwx_osx_cocoau_adv-3.0.dylib 0x0000000104d60228 wxGridSelection::SelectBlock(int, int, int, int, wxKeyboardState const&, bool) + 1976 420 libwx_osx_cocoau_adv-3.0.dylib 0x0000000104d399ee wxGrid::SelectBlock(int, int, int, int, bool) + 104 421 Grid.bundle 0x0000000115a8ded2 XS_Wx__Grid_SelectBlockPP(interpreter*, cv*) + 338 422 libperl.dylib 0x00000001046dbce0 Perl_pp_entersub + 1376 423 libperl.dylib 0x00000001046d4e76 Perl_runops_standard + 22 424 libperl.dylib 0x0000000104661e4d Perl_call_sv + 877 425 Wx.bundle 0x0000000104ae301d wxPliEventCallback::Handler(wxEvent&) + 477 426 libwx_baseu-3.0.dylib 0x00000001054ebb82 wxEvtHandler::ProcessEventIfMatchesId(wxEventTableEntryBase const&, wxEvtHandler*, wxEvent&) + 88 427 libwx_baseu-3.0.dylib 0x00000001054eccbb wxEvtHandler::SearchDynamicEventTable(wxEvent&) + 85 428 libwx_baseu-3.0.dylib 0x00000001054ecc13 wxEvtHandler::TryHereOnly(wxEvent&) + 37 429 libwx_baseu-3.0.dylib 0x00000001054ecb58 wxEvtHandler::ProcessEventLocally(wxEvent&) + 40 430 libwx_baseu-3.0.dylib 0x00000001054ecaeb wxEvtHandler::ProcessEvent(wxEvent&) + 175 431 libwx_osx_cocoau_core-3.0.dylib 0x000000010509fc3d wxScrollHelperEvtHandler::ProcessEvent(wxEvent&) + 35 432 libwx_osx_cocoau_adv-3.0.dylib 0x0000000104d60228 wxGridSelection::SelectBlock(int, int, int, int, wxKeyboardState const&, bool) + 1976 433 libwx_osx_cocoau_adv-3.0.dylib 0x0000000104d399ee wxGrid::SelectBlock(int, int, int, int, bool) + 104 434 Grid.bundle 0x0000000115a8ded2 XS_Wx__Grid_SelectBlockPP(interpreter*, cv*) + 338 435 libperl.dylib 0x00000001046dbce0 Perl_pp_entersub + 1376 436 libperl.dylib 0x00000001046d4e76 Perl_runops_standard + 22 437 libperl.dylib 0x0000000104661e4d Perl_call_sv + 877 438 Wx.bundle 0x0000000104ae301d wxPliEventCallback::Handler(wxEvent&) + 477 439 libwx_baseu-3.0.dylib 0x00000001054ebb82 wxEvtHandler::ProcessEventIfMatchesId(wxEventTableEntryBase const&, wxEvtHandler*, wxEvent&) + 88 440 libwx_baseu-3.0.dylib 0x00000001054eccbb wxEvtHandler::SearchDynamicEventTable(wxEvent&) + 85 441 libwx_baseu-3.0.dylib 0x00000001054ecc13 wxEvtHandler::TryHereOnly(wxEvent&) + 37 442 libwx_baseu-3.0.dylib 0x00000001054ecb58 wxEvtHandler::ProcessEventLocally(wxEvent&) + 40 443 libwx_baseu-3.0.dylib 0x00000001054ecaeb wxEvtHandler::ProcessEvent(wxEvent&) + 175 444 libwx_osx_cocoau_core-3.0.dylib 0x000000010509fc3d wxScrollHelperEvtHandler::ProcessEvent(wxEvent&) + 35 445 libwx_osx_cocoau_adv-3.0.dylib 0x0000000104d60228 wxGridSelection::SelectBlock(int, int, int, int, wxKeyboardState const&, bool) + 1976 446 libwx_osx_cocoau_adv-3.0.dylib 0x0000000104d399ee wxGrid::SelectBlock(int, int, int, int, bool) + 104 447 Grid.bundle 0x0000000115a8ded2 XS_Wx__Grid_SelectBlockPP(interpreter*, cv*) + 338 448 libperl.dylib 0x00000001046dbce0 Perl_pp_entersub + 1376 449 libperl.dylib 0x00000001046d4e76 Perl_runops_standard + 22 450 libperl.dylib 0x0000000104661e4d Perl_call_sv + 877 451 Wx.bundle 0x0000000104ae301d wxPliEventCallback::Handler(wxEvent&) + 477 452 libwx_baseu-3.0.dylib 0x00000001054ebb82 wxEvtHandler::ProcessEventIfMatchesId(wxEventTableEntryBase const&, wxEvtHandler*, wxEvent&) + 88 453 libwx_baseu-3.0.dylib 0x00000001054eccbb wxEvtHandler::SearchDynamicEventTable(wxEvent&) + 85 454 libwx_baseu-3.0.dylib 0x00000001054ecc13 wxEvtHandler::TryHereOnly(wxEvent&) + 37 455 libwx_baseu-3.0.dylib 0x00000001054ecb58 wxEvtHandler::ProcessEventLocally(wxEvent&) + 40 456 libwx_baseu-3.0.dylib 0x00000001054ecaeb wxEvtHandler::ProcessEvent(wxEvent&) + 175 457 libwx_osx_cocoau_core-3.0.dylib 0x000000010509fc3d wxScrollHelperEvtHandler::ProcessEvent(wxEvent&) + 35 458 libwx_osx_cocoau_adv-3.0.dylib 0x0000000104d60228 wxGridSelection::SelectBlock(int, int, int, int, wxKeyboardState const&, bool) + 1976 459 libwx_osx_cocoau_adv-3.0.dylib 0x0000000104d399ee wxGrid::SelectBlock(int, int, int, int, bool) + 104 460 Grid.bundle 0x0000000115a8ded2 XS_Wx__Grid_SelectBlockPP(interpreter*, cv*) + 338 461 libperl.dylib 0x00000001046dbce0 Perl_pp_entersub + 1376 462 libperl.dylib 0x00000001046d4e76 Perl_runops_standard + 22 463 libperl.dylib 0x0000000104661e4d Perl_call_sv + 877 464 Wx.bundle 0x0000000104ae301d wxPliEventCallback::Handler(wxEvent&) + 477 465 libwx_baseu-3.0.dylib 0x00000001054ebb82 wxEvtHandler::ProcessEventIfMatchesId(wxEventTableEntryBase const&, wxEvtHandler*, wxEvent&) + 88 466 libwx_baseu-3.0.dylib 0x00000001054eccbb wxEvtHandler::SearchDynamicEventTable(wxEvent&) + 85 467 libwx_baseu-3.0.dylib 0x00000001054ecc13 wxEvtHandler::TryHereOnly(wxEvent&) + 37 468 libwx_baseu-3.0.dylib 0x00000001054ecb58 wxEvtHandler::ProcessEventLocally(wxEvent&) + 40 469 libwx_baseu-3.0.dylib 0x00000001054ecaeb wxEvtHandler::ProcessEvent(wxEvent&) + 175 470 libwx_osx_cocoau_core-3.0.dylib 0x000000010509fc3d wxScrollHelperEvtHandler::ProcessEvent(wxEvent&) + 35 471 libwx_osx_cocoau_adv-3.0.dylib 0x0000000104d60228 wxGridSelection::SelectBlock(int, int, int, int, wxKeyboardState const&, bool) + 1976 472 libwx_osx_cocoau_adv-3.0.dylib 0x0000000104d399ee wxGrid::SelectBlock(int, int, int, int, bool) + 104 473 Grid.bundle 0x0000000115a8ded2 XS_Wx__Grid_SelectBlockPP(interpreter*, cv*) + 338 474 libperl.dylib 0x00000001046dbce0 Perl_pp_entersub + 1376 475 libperl.dylib 0x00000001046d4e76 Perl_runops_standard + 22 476 libperl.dylib 0x0000000104661e4d Perl_call_sv + 877 477 Wx.bundle 0x0000000104ae301d wxPliEventCallback::Handler(wxEvent&) + 477 478 libwx_baseu-3.0.dylib 0x00000001054ebb82 wxEvtHandler::ProcessEventIfMatchesId(wxEventTableEntryBase const&, wxEvtHandler*, wxEvent&) + 88 479 libwx_baseu-3.0.dylib 0x00000001054eccbb wxEvtHandler::SearchDynamicEventTable(wxEvent&) + 85 480 libwx_baseu-3.0.dylib 0x00000001054ecc13 wxEvtHandler::TryHereOnly(wxEvent&) + 37 481 libwx_baseu-3.0.dylib 0x00000001054ecb58 wxEvtHandler::ProcessEventLocally(wxEvent&) + 40 482 libwx_baseu-3.0.dylib 0x00000001054ecaeb wxEvtHandler::ProcessEvent(wxEvent&) + 175 483 libwx_osx_cocoau_core-3.0.dylib 0x000000010509fc3d wxScrollHelperEvtHandler::ProcessEvent(wxEvent&) + 35 484 libwx_osx_cocoau_adv-3.0.dylib 0x0000000104d60228 wxGridSelection::SelectBlock(int, int, int, int, wxKeyboardState const&, bool) + 1976 485 libwx_osx_cocoau_adv-3.0.dylib 0x0000000104d399ee wxGrid::SelectBlock(int, int, int, int, bool) + 104 486 Grid.bundle 0x0000000115a8ded2 XS_Wx__Grid_SelectBlockPP(interpreter*, cv*) + 338 487 libperl.dylib 0x00000001046dbce0 Perl_pp_entersub + 1376 488 libperl.dylib 0x00000001046d4e76 Perl_runops_standard + 22 489 libperl.dylib 0x0000000104661e4d Perl_call_sv + 877 490 Wx.bundle 0x0000000104ae301d wxPliEventCallback::Handler(wxEvent&) + 477 491 libwx_baseu-3.0.dylib 0x00000001054ebb82 wxEvtHandler::ProcessEventIfMatchesId(wxEventTableEntryBase const&, wxEvtHandler*, wxEvent&) + 88 492 libwx_baseu-3.0.dylib 0x00000001054eccbb wxEvtHandler::SearchDynamicEventTable(wxEvent&) + 85 493 libwx_baseu-3.0.dylib 0x00000001054ecc13 wxEvtHandler::TryHereOnly(wxEvent&) + 37 494 libwx_baseu-3.0.dylib 0x00000001054ecb58 wxEvtHandler::ProcessEventLocally(wxEvent&) + 40 495 libwx_baseu-3.0.dylib 0x00000001054ecaeb wxEvtHandler::ProcessEvent(wxEvent&) + 175 496 libwx_osx_cocoau_core-3.0.dylib 0x000000010509fc3d wxScrollHelperEvtHandler::ProcessEvent(wxEvent&) + 35 497 libwx_osx_cocoau_adv-3.0.dylib 0x0000000104d60228 wxGridSelection::SelectBlock(int, int, int, int, wxKeyboardState const&, bool) + 1976 498 libwx_osx_cocoau_adv-3.0.dylib 0x0000000104d399ee wxGrid::SelectBlock(int, int, int, int, bool) + 104 499 Grid.bundle 0x0000000115a8ded2 XS_Wx__Grid_SelectBlockPP(interpreter*, cv*) + 338 500 libperl.dylib 0x00000001046dbce0 Perl_pp_entersub + 1376 501 libperl.dylib 0x00000001046d4e76 Perl_runops_standard + 22 502 libperl.dylib 0x0000000104661e4d Perl_call_sv + 877 503 Wx.bundle 0x0000000104ae301d wxPliEventCallback::Handler(wxEvent&) + 477 504 libwx_baseu-3.0.dylib 0x00000001054ebb82 wxEvtHandler::ProcessEventIfMatchesId(wxEventTableEntryBase const&, wxEvtHandler*, wxEvent&) + 88 505 libwx_baseu-3.0.dylib 0x00000001054eccbb wxEvtHandler::SearchDynamicEventTable(wxEvent&) + 85 506 libwx_baseu-3.0.dylib 0x00000001054ecc13 wxEvtHandler::TryHereOnly(wxEvent&) + 37 507 libwx_baseu-3.0.dylib 0x00000001054ecb58 wxEvtHandler::ProcessEventLocally(wxEvent&) + 40 508 libwx_baseu-3.0.dylib 0x00000001054ecaeb wxEvtHandler::ProcessEvent(wxEvent&) + 175 509 libwx_osx_cocoau_core-3.0.dylib 0x000000010509fc3d wxScrollHelperEvtHandler::ProcessEvent(wxEvent&) + 35 510 libwx_osx_cocoau_adv-3.0.dylib 0x0000000104d60228 wxGridSelection::SelectBlock(int, int, int, int, wxKeyboardState const&, bool) + 1976 511 libwx_osx_cocoau_adv-3.0.dylib 0x0000000104d399ee wxGrid::SelectBlock(int, int, int, int, bool) + 104 Thread 1:: Dispatch queue: com.apple.libdispatch-manager 0 libsystem_kernel.dylib 0x00007fff86c780a2 kevent_qos + 10 1 libdispatch.dylib 0x00007fff8fe9b11d _dispatch_mgr_invoke + 216 2 libdispatch.dylib 0x00007fff8fe9ad85 _dispatch_mgr_thread + 52 Thread 2:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x00007fff86c71c96 mach_msg_trap + 10 1 libsystem_kernel.dylib 0x00007fff86c710d7 mach_msg + 55 2 com.apple.CoreFoundation 0x00007fff81ca92b4 __CFRunLoopServiceMachPort + 212 3 com.apple.CoreFoundation 0x00007fff81ca877c __CFRunLoopRun + 1356 4 com.apple.CoreFoundation 0x00007fff81ca7fc8 CFRunLoopRunSpecific + 296 5 com.apple.AppKit 0x00007fff88c57d49 _NSEventThread + 149 6 libsystem_pthread.dylib 0x00007fff97ae49b1 _pthread_body + 131 7 libsystem_pthread.dylib 0x00007fff97ae492e _pthread_start + 168 8 libsystem_pthread.dylib 0x00007fff97ae2385 thread_start + 13 Thread 3: 0 libsystem_kernel.dylib 0x00007fff86c7778a __workq_kernreturn + 10 1 libsystem_pthread.dylib 0x00007fff97ae458c _pthread_wqthread + 1283 2 libsystem_pthread.dylib 0x00007fff97ae2375 start_wqthread + 13 Thread 4: 0 libsystem_kernel.dylib 0x00007fff86c7778a __workq_kernreturn + 10 1 libsystem_pthread.dylib 0x00007fff97ae458c _pthread_wqthread + 1283 2 libsystem_pthread.dylib 0x00007fff97ae2375 start_wqthread + 13 Thread 5: 0 libsystem_kernel.dylib 0x00007fff86c7778a __workq_kernreturn + 10 1 libsystem_pthread.dylib 0x00007fff97ae458c _pthread_wqthread + 1283 2 libsystem_pthread.dylib 0x00007fff97ae2375 start_wqthread + 13 Thread 6: 0 libsystem_kernel.dylib 0x00007fff86c7778a __workq_kernreturn + 10 1 libsystem_pthread.dylib 0x00007fff97ae458c _pthread_wqthread + 1283 2 libsystem_pthread.dylib 0x00007fff97ae2375 start_wqthread + 13 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x00007fff5adc53d0 rbx: 0x00007fff5adc52f8 rcx: 0x00007fff5adc5590 rdx: 0x0000000104be4cd2 rdi: 0x00007fff5adc52f8 rsi: 0x00007fff74c956b8 rbp: 0x00007fff5adc51f0 rsp: 0x00007fff5adc4e10 r8: 0x0000000104be4cd2 r9: 0x00007fff5adc5590 r10: 0x00007f83c41af8f0 r11: 0x0000000000000051 r12: 0x00007fff74c956b8 r13: 0x0000000104be4cd2 r14: 0xffffffffffffffff r15: 0x0000000000000000 rip: 0x00007fff90af50ab rfl: 0x0000000000010202 cr2: 0x00007fff5adc4eb0 Logical CPU: 3 Error Code: 0x00000006 Trap Number: 14 Binary Images: 0x10463b000 - 0x10463cff7 +perl5.16 (0) <488EB664-CF80-33FD-A9CE-E57C18CBCB78> /opt/local/bin/perl5.16 0x104643000 - 0x10478cfff +libperl.dylib (0) <D3D518B7-8B3D-3D0C-954D-11D6C89710BC> /opt/local/lib/*/libperl.dylib 0x1049e0000 - 0x104c1fff7 +Wx.bundle (0) <2B21662B-3D18-3C39-952F-A275BFA07373> /opt/local/lib/*/Wx.bundle 0x104d05000 - 0x104dd0fff +libwx_osx_cocoau_adv-3.0.dylib (0) <1D180879-34C7-374C-B8E8-AA6666D9635A> /opt/local/Library/Frameworks/wxWidgets.framework/Versions/wxWidgets/3.0/lib/libwx_osx_cocoau_adv-3.0.dylib 0x104ebc000 - 0x1051a6fff +libwx_osx_cocoau_core-3.0.dylib (0) <370CE38C-5602-3359-A788-5E4692EE69FE> /opt/local/Library/Frameworks/wxWidgets.framework/Versions/wxWidgets/3.0/lib/libwx_osx_cocoau_core-3.0.dylib 0x1053f6000 - 0x105572fff +libwx_baseu-3.0.dylib (0) <5A624A5B-E4B5-392E-A604-ED74C155F186> /opt/local/Library/Frameworks/wxWidgets.framework/Versions/wxWidgets/3.0/lib/libwx_baseu-3.0.dylib 0x10563d000 - 0x105646fff +libwx_osx_cocoau_media-3.0.dylib (0) <B18CF95E-C09D-365E-A5A9-6EA52AC009DF> /opt/local/Library/Frameworks/wxWidgets.framework/Versions/wxWidgets/3.0/lib/libwx_osx_cocoau_media-3.0.dylib 0x105655000 - 0x1056c9fff +libwx_osx_cocoau_html-3.0.dylib (0) <3280CDF4-A315-3D61-88E8-D82AAE023DA6> /opt/local/Library/Frameworks/wxWidgets.framework/Versions/wxWidgets/3.0/lib/libwx_osx_cocoau_html-3.0.dylib 0x10573a000 - 0x10575cfff +libpng16.16.dylib (0) <A81585A3-434B-331B-8223-564635BE1A8E> /opt/local/lib/libpng16.16.dylib 0x105765000 - 0x105775fff +libz.1.dylib (0) <4987824D-DF1E-318D-94E9-13999F517041> /opt/local/lib/libz.1.dylib 0x105779000 - 0x1057a6ff7 +libjpeg.9.dylib (0) <08C3C5E3-8C99-3CCB-9A9E-15BF05CBB9F3> /opt/local/lib/libjpeg.9.dylib 0x1057ad000 - 0x105806ff7 +libtiff.5.dylib (0) <562B979F-FC35-3BA6-B105-532AA86A2BBF> /opt/local/lib/libtiff.5.dylib 0x105814000 - 0x105908fff +libiconv.2.dylib (0) <F6EB71B9-0923-3F73-9DF2-B78F72A06E86> /opt/local/lib/libiconv.2.dylib 0x105915000 - 0x105931ff7 +liblzma.5.dylib (0) <16D8B83F-8016-39DF-B26C-FF15D656AC14> /opt/local/lib/liblzma.5.dylib 0x108c22000 - 0x108c23fff +attributes.bundle (0) <B5F0933C-BF12-3B37-A5E4-F8E4C326479E> /opt/local/lib/*/attributes.bundle 0x108c47000 - 0x108c56fef +libgcc_s.1.dylib (0) <C80B3766-BFCD-3958-94DD-CAAD68AA8E13> /opt/local/lib/*/libgcc_s.1.dylib 0x108c5b000 - 0x108c85fef +libquadmath.0.dylib (0) <796E91FE-00B1-336D-8CBC-E036AECB26AC> /opt/local/lib/*/libquadmath.0.dylib 0x108c89000 - 0x108c8afff +Cwd.bundle (0) <A19C2470-F1B5-3055-AF94-947A87591030> /opt/local/lib/*/Cwd.bundle 0x108c8d000 - 0x108c8efff +Fcntl.bundle (0) <659E84E9-FF28-3F06-B348-67A1B9C61CB6> /opt/local/lib/*/Fcntl.bundle 0x109d1e000 - 0x109d86fff +Ifeffit.bundle (0) <92D7F2F2-7739-3F92-964E-4F5A767CEBF1> /opt/local/lib/*/Ifeffit.bundle 0x11501f000 - 0x1150e4fef +libgfortran.3.dylib (0) <248A840C-82F2-3DB5-8C13-E1537869F0EA> /opt/local/lib/*/libgfortran.3.dylib 0x1150fe000 - 0x11510eff7 +MoreUtils.bundle (0) <3E30FA9B-B5EE-3FB2-9CDC-8C086A5C9BD5> /opt/local/lib/*/MoreUtils.bundle 0x115112000 - 0x115157fff +re.bundle (0) <E44F3735-59C2-3932-9C6D-08B382B03268> /opt/local/lib/*/re.bundle 0x11515d000 - 0x11516cff7 +Storable.bundle (0) <B5B3B3FB-840D-36EC-BAB5-27B57B043564> /opt/local/lib/*/Storable.bundle 0x115171000 - 0x115177ff7 +Util.bundle (0) <D6F0E0DA-0EE2-3533-87D8-D005698DF575> /opt/local/lib/*/Util.bundle 0x11531b000 - 0x11531dfff +Util.bundle (0) <7E30CBDD-4615-3FAE-93E0-29AFE1486FA9> /opt/local/lib/*/Util.bundle 0x115320000 - 0x115321ff7 +XS.bundle (0) <0A331190-EEE8-3C40-AD7A-82E26D76CC29> /opt/local/lib/*/XS.bundle 0x115324000 - 0x115326fff +mro.bundle (0) <D6048A72-A2E2-38F4-8639-0A052CD2C7FF> /opt/local/lib/*/mro.bundle 0x115329000 - 0x11532aff7 +Name.bundle (0) <289ECCD6-8516-3EF3-A2F2-80EA0F344481> /opt/local/lib/*/Name.bundle 0x11532d000 - 0x115331fff +XS.bundle (0) <9BEE7142-08A1-3B2D-B178-4E3B6E10BD6A> /opt/local/lib/*/XS.bundle 0x115335000 - 0x115339fff +Moose.bundle (0) <AFA14584-145D-326B-A32C-91ECCC9E3E83> /opt/local/lib/*/Moose.bundle 0x11533d000 - 0x115346fff +B.bundle (0) <8F2F93B4-6652-34E6-9CF5-DBD0CA9D6703> /opt/local/lib/*/B.bundle 0x11534c000 - 0x11534cfff +Identify.bundle (0) <59EB3425-234B-315D-8BD8-7BB1E115DF1E> /opt/local/lib/*/Identify.bundle 0x11534f000 - 0x115353ff7 +Magic.bundle (0) <0EF3C23C-9A52-3132-AF2D-24453A8C704D> /opt/local/lib/*/Magic.bundle 0x115357000 - 0x115359fff +IO.bundle (0) <E161CBC6-48E5-37B9-8E22-5253A3685B9C> /opt/local/lib/*/IO.bundle 0x11535c000 - 0x115374fff +PGPLOT.bundle (0) <06336A82-D5E6-369A-B744-D2D6CA43E5D3> /opt/local/lib/*/PGPLOT.bundle 0x11537a000 - 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/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/Libraries/libCGInterfaces.dylib 0x7fff96b82000 - 0x7fff96b8efff com.apple.SpeechRecognitionCore (2.2.7 - 2.2.7) <12117823-8A9E-3C88-A01C-3B25D68535CE> /System/Library/PrivateFrameworks/SpeechRecognitionCore.framework/Versions/A/SpeechRecognitionCore 0x7fff96b8f000 - 0x7fff96b9afff libcsfde.dylib (517) <C8C9A632-5072-3D24-8EBF-CCDE0BC8BFB5> /usr/lib/libcsfde.dylib 0x7fff96b9b000 - 0x7fff96bb2fff libmarisa.dylib (4) <4D3AE55B-CE77-364F-B8DE-C95CAA48B291> /usr/lib/libmarisa.dylib 0x7fff96be6000 - 0x7fff96c43fff com.apple.CoreServices.OSServices (728.4 - 728.4) <4E1819C2-F7A9-35FB-8193-FF3DCC35226C> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/OSServices.framework/Versions/A/OSServices 0x7fff96d49000 - 0x7fff96d77ff7 com.apple.DictionaryServices (1.2 - 250) <94678AC8-41FF-3D2E-A35E-D83AD18D7A78> /System/Library/Frameworks/CoreServices.framework/Versions/A/Frameworks/DictionaryServices.framework/Versions/A/DictionaryServices 0x7fff96d78000 - 0x7fff96da1ff7 libxslt.1.dylib (14) <412A09C9-7C02-351E-A416-2453361EACA9> /usr/lib/libxslt.1.dylib 0x7fff96da2000 - 0x7fff96dcbfff libc++abi.dylib (125) <F5027B46-1801-344D-BD51-2E6D188C8900> /usr/lib/libc++abi.dylib 0x7fff96dcc000 - 0x7fff96dceff7 libsystem_configuration.dylib (801.10.2) <93D5FB9A-CC7C-3672-80D8-7A1C4805204B> /usr/lib/system/libsystem_configuration.dylib 0x7fff96dcf000 - 0x7fff96e65ff7 com.apple.ColorSync (4.9.0 - 4.9.0) <1FBEDDC2-4BCD-3148-800E-968814206CB9> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ColorSync.framework/Versions/A/ColorSync 0x7fff96e66000 - 0x7fff96eb2ffb com.apple.HIServices (1.22 - 548) <19389B63-C373-31AE-9180-3A11093EAE58> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/HIServices.framework/Versions/A/HIServices 0x7fff96eb3000 - 0x7fff96ec6fff com.apple.CoreBluetooth (1.0 - 1) <A63B8FB0-F8B3-368D-B482-733FF0373610> /System/Library/Frameworks/CoreBluetooth.framework/Versions/A/CoreBluetooth 0x7fff96ec7000 - 0x7fff96ecaff7 com.apple.AppleSystemInfo (3.1.5 - 3.1.5) <E4643432-0DF2-3CD3-9F63-3A7665B25838> /System/Library/PrivateFrameworks/AppleSystemInfo.framework/Versions/A/AppleSystemInfo 0x7fff96ecb000 - 0x7fff96edffff libsystem_coretls.dylib (82) <21EDACF1-D9B3-3086-9821-60EB75E7F965> /usr/lib/system/libsystem_coretls.dylib 0x7fff96ee0000 - 0x7fff96ee2ff7 com.apple.xpc.ServiceManagement (1.0 - 1) <0EA1807B-4F41-317D-A6C2-E6A23F201252> /System/Library/Frameworks/ServiceManagement.framework/Versions/A/ServiceManagement 0x7fff97152000 - 0x7fff972d0fff com.apple.UIFoundation (1.0 - 435) <237F281F-7F15-3309-B749-F8DA37822F9F> /System/Library/PrivateFrameworks/UIFoundation.framework/Versions/A/UIFoundation 0x7fff972f5000 - 0x7fff972f7fff com.apple.SecCodeWrapper (4.0 - 261.10.2) <54B4F790-1FD5-3DFB-8F1F-3BEE312238DC> /System/Library/PrivateFrameworks/SecCodeWrapper.framework/Versions/A/SecCodeWrapper 0x7fff9741b000 - 0x7fff97437fff com.apple.GenerationalStorage (2.0 - 239) <05652CAD-E7F5-3225-929D-E13F241FBA41> /System/Library/PrivateFrameworks/GenerationalStorage.framework/Versions/A/GenerationalStorage 0x7fff97438000 - 0x7fff97472ff7 com.apple.DebugSymbols (132 - 132) <6F5853A1-5DA8-3C42-8E02-2B972F34BCE0> /System/Library/PrivateFrameworks/DebugSymbols.framework/Versions/A/DebugSymbols 0x7fff97679000 - 0x7fff976a2fff libxpc.dylib (755.1.19) <3E09C275-A33B-357A-B0AB-A2DDF88EC9D5> /usr/lib/system/libxpc.dylib 0x7fff976a3000 - 0x7fff97a38fdb com.apple.vImage (8.0 - 8.0) <3EF89E53-2A54-3464-A405-88E3213F31F7> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage 0x7fff97a6d000 - 0x7fff97adbff7 com.apple.ApplicationServices.ATS (377 - 394.1) <E35909E3-83E0-3671-914A-B43845D889B3> /System/Library/Frameworks/ApplicationServices.framework/Versions/A/Frameworks/ATS.framework/Versions/A/ATS 0x7fff97adf000 - 0x7fff97ae0fff com.apple.TrustEvaluationAgent (2.0 - 25) <BC19A1D1-805B-3FC5-BF0B-1EF6FB36FE74> /System/Library/PrivateFrameworks/TrustEvaluationAgent.framework/Versions/A/TrustEvaluationAgent 0x7fff97ae1000 - 0x7fff97aeaff7 libsystem_pthread.dylib (137.1.1) <1373D0F1-C6CA-364E-A6BA-8BDBD0D34670> /usr/lib/system/libsystem_pthread.dylib 0x7fff97bab000 - 0x7fff97c1fff3 com.apple.securityfoundation (6.0 - 55126) <73D2EE6C-E3A2-32FE-89B3-BA8ACEA53F09> /System/Library/Frameworks/SecurityFoundation.framework/Versions/A/SecurityFoundation 0x7fff97c23000 - 0x7fff97c2dfff com.apple.NetAuth (6.0 - 6.0) <ABBBE552-26E0-3682-8BFD-C59EC702F347> /System/Library/PrivateFrameworks/NetAuth.framework/Versions/A/NetAuth 0x7fff97c2e000 - 0x7fff97c5eff7 libsandbox.1.dylib (459.10.4) <78F4D125-DEF0-3BEA-9D7F-E5BE5C06C8DA> /usr/lib/libsandbox.1.dylib 0x7fff97d43000 - 0x7fff97d72fc3 libsystem_m.dylib (3105) <07D50372-30ED-3B03-9FA0-0662BF8F0098> /usr/lib/system/libsystem_m.dylib External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 2 thread_create: 0 thread_set_state: 0 Calls made by this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by all processes on this machine: task_for_pid: 668 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=310.9M resident=0K(0%) swapped_out_or_unallocated=310.9M(100%) Writable regions: Total=569.2M written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=569.2M(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate.framework 256K 3 Activity Tracing 2048K 2 CG backing stores 49.8M 4 CG image 548K 29 CG shared images 592K 16 CoreAnimation 732K 43 CoreUI image data 812K 31 CoreUI image file 192K 4 Dispatch continuations 8192K 2 Foundation 24K 2 IOKit 212K 6 Kernel Alloc Once 8K 3 MALLOC 301.2M 56 MALLOC guard page 32K 7 Memory Tag 242 12K 2 OpenCL 8K 2 STACK GUARD 56.0M 8 Stack 10.6M 10 VM_ALLOCATE 72K 10 __DATA 208.5M 347 __IMAGE 528K 2 __LINKEDIT 96.6M 75 __TEXT 214.2M 345 __UNICODE 552K 2 mapped file 80.4M 27 shared memory 16.3M 10 =========== ======= ======= TOTAL 1.0G 1022 Model: MacBookPro11,1, BootROM MBP111.0138.B16, 2 processors, Intel Core i5, 2.6 GHz, 8 GB, SMC 2.16f68 Graphics: Intel Iris, Intel Iris, Built-In Memory Module: BANK 0/DIMM0, 4 GB, DDR3, 1600 MHz, 0x802C, 0x384B54463531323634485A2D314736453120 Memory Module: BANK 1/DIMM0, 4 GB, DDR3, 1600 MHz, 0x802C, 0x384B54463531323634485A2D314736453120 AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x112), Broadcom BCM43xx 1.0 (7.21.94.29.1a4) Bluetooth: Version 4.4.2f1 16391, 3 services, 18 devices, 1 incoming serial ports Network Service: Wi-Fi, AirPort, en0 Serial ATA Device: APPLE SSD SM0512F, 500.28 GB USB Device: USB 3.0 Bus USB Device: Apple Internal Keyboard / Trackpad USB Device: BRCM20702 Hub USB Device: Bluetooth USB Host Controller Thunderbolt Bus: MacBook Pro, Apple Inc., 17.2

1 0

Ta L3 edge and Pt L2 edge
by Natee Sirisit 29 Oct '15

29 Oct '15

Dear all Do anyone have an Ta L3 edge of TaN and Pt K and L2 edge of (1,5-Cyclooctadiene)dimethylplatinum(II). Could you share the copy to me please? Many thanks for considering my request. Sincerely yours, Natee -- Natee Sirisit Ph.D. student Graduate school of engineering and Catalyst Surface Research Division, Institute for Catalysis (ICAT) Hokkaido university Sapporo 060-8628, JAPAN Tel.: (02)1129115 Email: sirisit.n(a)cat.hokudai.ac.jp

1 0

Athena and Artemis installation problem
by Wuhib Tamrat 27 Oct '15

27 Oct '15

Hi all, This is with regard to an installation problem that I am facing at the moment on my Mac. Sorry, if this is too basic a problem and the email is spamming your mail box. Below are specifics of three fold problems that I would be happy if I could find a solution for at least one. Problem1: I am working on El Capitan (the latest Mac Operating System) and what I guess the problem to be is compatibility issues with the different required components (X11, XQuartz and Aqua term). And may be with the required macports as well. I installed using the disk image provided on http://cars9.uchicago.edu/ifeffit/Downloads <http://cars9.uchicago.edu/ifeffit/Downloads> and had followed all the instructions given. I see that the latest OS available is for ‘Snow Leopard’ but the package works well on colleagues’ computers with latter versions of mac OS. The problem is that all get installed but when I open the software suit, the initial small window that has the three individual programs opens but what ever I do to it afterwards it does not open into anything else. There is also the option to choose a file. So I navigate and choose a file thinking it will help pushing the program to open but that leads to nowhere as well. So, I am wondering if anybody had faced similar problem installing on the latest versions of mac OS and has a solution. Problem 2: Initially I tried installing the “demeter” suit via ‘Terminal’ as specified in the site [http://bruceravel.github.io/demeter/ <http://bruceravel.github.io/demeter/>]. By writing a command on Terminal as opposed to with a disc image as in the case of Problem 1). My operating system at that time was Yosemite. All worked as explained on the website, even writing “athena” on a terminal window calls the program Athena. But that is just it, no explanation as how to call Artemis or Hephaestus exist on the site. So I am wondering if the installation procedure given on the site works also with the other two programs and if so, is there a way to open them or call them via ’Terminal'. Problem 3: My last problem was when Athena closed unexpectedly. As most programs, Athena had an auto recover option which opens when it is restarted. But this time the auto recover option always comes up and this option renders the whole program inactive; “Application Not Responding”. Every time I open Athena, “Auto recover” option comes up and Athena become unresponsive. I tried updating the software in hope of changing something but that did not change anything. Uninstalling it is also a problem because there were no files that I could find to uninstall from or delete. I could not find the location where terminal installed the “Demeter” suit. There is a way to delete on terminal by writing “Sudo rm-rf/file name” but that is not removing “demeter” either. And yes, I have consulted the IT/informatics people at my institution and they were no help. I thank you in advance for any suggestion or similar experience sharing. And also for baring with me reading this long mail. Regards Wuhib

4 4

Magnetic EXAFS simulation using FEFF8.4
by Jerry Li 26 Oct '15

26 Oct '15

Dear All, I am trying FEFF simulation of the spin polarized spectra of single crystal Tb, see the attached Feff.inp . However, the results xmu.dat doesn't show any the mu+ and mu- as I expected, just NaN instead. Could you please help me check what is wrong with the input file? Jerry

1 0

Unable to run Demeter on EPA computers
by Matt Noerpel 22 Oct '15

22 Oct '15

Hello Ifeffit list, I just started a post-doc position at the EPA and I will need to use Artemis and Athena. Unfortunately, nobody here is able to run Demeter on their work computers. The old version (0.8) does work. We all have new Dell computers running Windows 7 64 bit. I tried version 0.9.22 (with explicitly setting the path at the top of the batch file) and 0.9.23 prerelease 3, but neither work. The program opens the command prompt, shows the splash image briefly, and then disappears and produces the log file (shown below) in the AppData folder. This seems like it has something to do with the way our computers are set up here. An IT specialist (cc:ed here) was working on it for a while today removing user restrictions etc., but the problem didn't change. Does anyone have any idea what could be causing this problem or have you encountered a similar problem with government computers? Thanks, Matt Noerpel dathena.log: BEGIN failed--compilation aborted at C:/demeter/perl/site/lib/Demeter.pm line 54. Compilation failed in require at C:/demeter/perl/site/lib/Demeter/UI/Athena.pm line 24. BEGIN failed--compilation aborted at C:/demeter/perl/site/lib/Demeter/UI/Athena.pm line 24. Compilation failed in require at C:\demeter\perl\site\bin\dathena.bat line 43. BEGIN failed--compilation aborted at C:\demeter\perl\site\bin\dathena.bat line 43. Started at 2015-10-14T14:31:22 Win7Enterprise (64-bit) Service Pack 1 Service Pack 16176012102561 PATH is: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\demeter\c\bin;C:\demeter\perl\site\bin;C:\demeter\perl\bin;C:\demeter\c\bin\gnuplot\bin perl version: v5.18.2 backend: ifeffit @INC: C:/demeter/perl/site/lib/MSWin32-x64-multi-thread C:/demeter/perl/site/lib C:/demeter/perl/vendor/lib C:/demeter/perl/lib . Can't load 'C:/demeter/perl/site/lib/auto/Ifeffit/Ifeffit.dll' for module Ifeffit: load_file:Invalid access to memory location at C:/demeter/perl/lib/DynaLoader.pm line 190. at (eval 18) line 1. Compilation failed in require at (eval 18) line 1. BEGIN failed--compilation aborted at (eval 18) line 1. For what it's worth, some dodgy corners of the internet suggest using XSLoader instead of DynaLoader. When I do that, the error message is exactly the same except replacing DynaLoader with XSLoader.

3 7

Demeter 0.9.23 in multi-user environments
by Godfrey, Ian 19 Oct '15

19 Oct '15

Hi All, I'm trying to install Demeter 0.9.23 on a Win 8.1 Pro x64 machine with two user accounts set up. Both user accounts on this PC need to use Demeter. Unfortunately the latest version of Demeter installs into a user specific folder, which creates two problems: 1) Users do not seem to have access to each other's folders to run Demeter 2) The shortcuts (start menu/desktop) only get installed/updated for the installing user Compounding this issue the installer automatically removes any existing installation at installation, so you can't simply install it twice. Thanks, Ian Ps. Any update on this message: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2015-August/012662.html ?

3 6

XES calculations for hematite
by Michal.Nowakowski 19 Oct '15

19 Oct '15

Dear All, I'm PhD student from Poland. I have recently tried to calculate Kß line of XES spectrum for hematite using FeFF9.6 code but I'm unable to reproduce the spin-dependent satellite peak Kß'. I've alredy tried to use SPIN card with XES card. Is there any possibility to do it in FeFF? Thank you in advance, Michal Nowakowski -- Open WebMail Project (http://openwebmail.org)

1 0

XAFS short course in BNL on Nov 5-7
by Anatoly I Frenkel 14 Oct '15

14 Oct '15

Dear subscribers, As a follow up to my previous message, the web page for the XAFS short course at Brookhaven and the application form are live: http://workshops.ps.bnl.gov/?w=XAFS2015 Please note the application deadline, September 20. Best regards, Anatoly Anatoly Frenkel, Ph.D. Professor and Chair, Department of Physics, Yeshiva University 245 Lexington Avenue, New York, NY 10016 https://yu.edu/faculty-bios/frenkel/ Spokesperson, Synchrotron Catalysis Consortium http://yu.edu/scc Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.frenkel(a)yu.edu<mailto:anatoly.frenkel@yu.edu>

1 2

Fwd: XAS tutorial videos
by Bruce Ravel 14 Oct '15

14 Oct '15

Hi Wuhib, This is a sufficiently general question that I am forwarding my answer to the mailing list. The videos are not my property, they belong to Diamond. You are correct that the manner in which they are streamed does not allow for jumping around, but there is nothing that I can do about that. You also mentioned that Shu had given you a download link (I have not included the link what I echoed blow because I do not know if Shu and the folks at Diamond want that link advertised). I have no trouble downloading or running them. Once downloaded, I can jump around as expected. If you are having "browser/network" issues, that seems like a problem for you (or your institution's IT folks) to solve. Again, there's nothing I can do about that. Final point, please use the mailing list in the future rather than writing to me directly about issues related to the software. Good luck, B -------- Forwarded Message -------- Subject: XAS tutorial videos Date: Wed, 14 Oct 2015 16:23:09 +0200 From: Wuhib Tamrat <tamrat(a)cerege.fr> To: bravel(a)bnl.gov Hello Bruce, My name is Wuhib and I am a PhD student in Aix Marseille University (France). I am recently being introduced to the world of XAS and I found your training videos from November 2011 at the Diamond Light source quite helpful. But the problem is that the streaming version does not give the flexibility to go back and forth to specific times in the lecture video. So I was wondering if you could find a way to send me the videos, if you have them and if it is not much trouble. Thank you. Regards Wuhib PS: I received a link from Dr. Shu Hayama but as he himself guessed I am having difficulty playing and downloading the .wmv files due to probably browser/network related issues. -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

1 0

larch xray plugin - incorrect chantler data at edges
by Dr. Johannes Zellner 14 Oct '15

14 Oct '15

Hi, the larch xraydb plugin doesn't provide correct numbers for chantler f1 data around edges. Apparently this is due to incorrect interpolation in xray/xraydb.py in line 274. Below is a plot of "delta" from xraydb_plugin.xray_delta_beta() for Silicon which is terrribly wrong. The more correct "delta" as from chantler is shown in the following plot: --> I'd recommend to replace (line 274 in plugin xray/xraydb.py): out = UnivariateSpline(te, ty, s=smoothing)(energy) by a simple linear interpolation out = np.interp(energy, te, ty) The latter yields linear segments between chantler's data, but this is still better than the totally unphysical spline interpolation. Best regards, -- Johannes

2 1

a bug when installing demeter
by Zhenxing Feng 13 Oct '15

13 Oct '15

Hi, I am trying to install Demeter on my Mac OX X EI Capitan. After installing MacPorts properly, I run the command, “sudo port install xorg-server demeter”. However, it reports a bug when building libgcc, when the following errors: Error: org.macports.build for port libgcc returned: command execution failed Please see the log file for port libgcc for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/libgcc/main.log Error: Unable to upgrade port: 1 Error: Unable to execute port: upgrade ifeffit failed Could you help figure out how I can proceed further? Thanks, Zhenxing

1 0

No plot window on Mac El Capitan
by Chloe Yi-Yi Wu 08 Oct '15

08 Oct '15

Hi Bruce, I just upgraded my mac from mountain lion to el capitan. I was using the old version, iXAFS, but I can't launch it on the new el capitan. I then installed Demeter with Macport by following the instructions. However, I'm not able to plot the data in athena and artemis. I read the thread about "no plot window on Yosemite", but still have no clue. I can plot gnuplot in aqua, x11 and wxt. It seems whenever I quit gnuplot to launch athena and enter gnuplot later again, it will always go back my default terminal, aqua, no matter how I set terminal. Is there a communication problem between Demeter and aqua? I'm not familiar with these commands, to be honest. If I did something wrong, please advise. Thanks, Chloe -- Yi-Yi (Chloe) Wu Kung Research Group Dept. of Chemical and Biological Engineering Northwestern University Evanston, IL USA

2 4

Problems importing larch plugins to python
by Johan Nilsson 05 Oct '15

05 Oct '15

Hello everyone, I recently installed the latest development version of larch from github and now I'm having some problems importing larch plugins to my python scripts. I read in the documentation that there is a new method for doing this but that the old way should still work, this is what happens if I try to do it the way I've done it before: johan@johan-Latitude-E6430:~$ python Python 2.7.6 (default, Jun 22 2015, 17:58:13) [GCC 4.8.2] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> from larch import use_plugin_path >>> use_plugin_path('xafs') >>> from pre_edge import pre_edge Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/home/johan/.larch/plugins/xafs/pre_edge.py", line 13, in <module> from larch_plugins.std import parse_group_args ImportError: No module named larch_plugins.std >>> I also tried the new method described in the docs: johan@johan-Latitude-E6430:~$ python Python 2.7.6 (default, Jun 22 2015, 17:58:13) [GCC 4.8.2] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import larch >>> from larch_plugins.xafs import autobk Traceback (most recent call last): File "<stdin>", line 1, in <module> ImportError: No module named larch_plugins.xafs >>> I'm running ubuntu 14.04. Any ideas of what is going on here? Best regards, Johan

3 10

problems with deglitching in D-Athena 0.9.22
by bajnoczi 03 Oct '15

03 Oct '15

Dear Ifeffit Staff, I have just installed the most recent version of Demeter on my computer both on Windows 8 64-bit as well as on a Virtual (WMware Player) Ubuntu 14.04.3 64-bit machine. I have exactly the same problem with both versions when I try to deglitch my data. When I go to the Deglitch and Truncate window, and choose the option "Choose a point" the plot appears with dots. So far it seems ok. Initially the orange crosshair is on the first data point. When I try to double-click on the point to be removed happens nothing at all. I can do whatever I want, the crosshair stays on the first measured data point, and stays there, so I only can remove this one. I've already consulted with the mailing list, but none of the proposed solutions worked for me. I have downloaded the DeglitchTruncate.pm from Github and upgraded my version, as well as set the energy shift to 0, but nothing helped. Do you have any idea what can be the solution for this problem? Thank you for your answer and help in advance. Regards: Éva Bajnóczi Hungary Hungarian Academy of Sciences, Wigner Research Centre for Physics

2 1

problems with deglitching in D-Athena 0.9.22
by bajnoczi 03 Oct '15

03 Oct '15

Dear Ifeffit Staff, I have just installed the most recent version of Demeter on my computer both on Windows 8 64-bit as well as on a Virtual (WMware Player) Ubuntu 14.04.3 64-bit machine. I have exactly the same problem with both versions when I try to deglitch my data. When I go to the Deglitch and Truncate window, and choose the option "Choose a point" the plot appears with dots. So far it seems ok. Initially the orange crosshair is on the first data point. When I try to double-click on the point to be removed happens nothing at all. I can do whatever I want, the crosshair stays on the first measured data point, and stays there, so I only can remove this one. I've already consulted with the mailing list, but none of the proposed solutions worked for me. I have downloaded the DeglitchTruncate.pm from Github and upgraded my version, as well as set the energy shift to 0, but nothing helped. Do you have any idea what can be the solution for this problem? Thank you for your answer and help in advance. Regards: Éva Bajnóczi Hungary Hungarian Academy of Sciences, Wigner Research Centre for Physics

1 0

changes to the Demeter Windows installer
by Bruce Ravel 01 Oct '15

01 Oct '15

Hi, Today, I posted a new windows installer which has a significant difference compared to previous versions: http://bruceravel.github.io/demeter/#windows It's the one called "pre-release trial #3". This version of the installer changes the default installation location and makes several other changes intended to make the Demeter package behave better on a wide variety of Windows environments. That said, the changes are not yet well tested and I am worried that they may behave very poorly for some people. In particular, I am concerned about how the new installer will behave for people with a space in their log-in name and for people with non-ASCII characters in their log-in name (e.g. a German eszett, a Cyrillic character, or any character from an Eastern language). If you are the sort who is willing to try the new version and report back to the mailing list with any problems, I would be very grateful for any feedback. If your log-in name meets one of my areas of concern, I would be doubly grateful for the feedback! Those who don't want to live near the edge should use 0.9.22 or 0.9.23_pre2 for now. Thanks! B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

1 0

mailing list / web page downtime
by Matt Newville 01 Oct '15

01 Oct '15

Hi Folks, The machine that hosts this mailing list, the ifeffit web pages, and xafs.org (millenia.cars.aps.anl.gov) is going to be replaced with a new machine today. I think everything should work, but there may be some outages over the next two days. If you have any troubles past that, let me know. --Matt

1 0

Re: [Ifeffit] Problem with Hephaestus at Ca L-edges (Matthew Marcus)
by Jana Padeznik Gomilsek 29 Sep '15

29 Sep '15

It is very hard to measure or to calculate absolute absorption data, especially in the vicinity of the absorption edges and especially in the soft x-ray region. Therefore there are significant differences between the tables and I think nobody knows which are better. Chantler, for example, says the expected uncertainties of the tables in your region are 50 % to 100 % (http://physics.nist.gov/PhysRefData/FFast/Text2000/sec06.html#tab2) I would doubt the Chantler's L3+.1 number, all other numbers look ok - this is what you can get. jana padeznik gomilsek > Message: 3 > Date: Wed, 23 Sep 2015 18:02:08 -0700 > From: Matthew Marcus<mamarcus(a)lbl.gov> > To: XAFS Analysis using Ifeffit<ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] Problem with Hephaestus at Ca L-edges > Message-ID:<56034B90.70405(a)lbl.gov> > Content-Type: text/plain; charset=utf-8; format=flowed > > I wanted to work out the edge-jump ratio between the L3 and L2 edges of Ca using Hephaestus. I ran into two problems: > > 1. The ratio implied by what it says for the unit-edge-step thickness does not agree with that derived by computing the absorption (cm^2/gm) above and below each edge and > dividing the difference (L3+ - L3-)/(L2+ - L2-). > > 2. The results differ wildly depending on which resource I use: > > L3-.1 L3+.1 L2-.1 L2+.1 (L1+ - L1-)/(L2+ - L2-) > Elam 4759.796 27837.796 27478.018 38434.277 2.106375908 > Chantler 4322.6 6547.121 32827.61 35436.543 0.852655473 > Cromer-Leiberman 4288.524 33471.375 32786.294 47072.991 2.042659055 > > The Henke table doesn't yield an L2 edge jump at all, while the Shaltout yields the same results as Cromer-Leiberman. Which one should I trust and why? > > This is old-style H. (V0.18), not Demeter. > mam > >

4 11

Problems during copper (II) oxide data treatment
by Pedro F B D Martins 24 Sep '15

24 Sep '15

Hi everyone, I’m having problems during the data treatment. The two samples (please find the project attached with the as-obtained data only, not with the following treatment) are of CuO (copper (II) oxide) were measured in a row and both were measured together with a reference (Cu foil). I have some doubts: 1) The first thing that I did was to calibrate the Reference of the first measurement (peak at maximum of first derivative). Next, I aligned the second Reference keeping the first reference as standard. Did I do correctly until now? 2) I removed the glitches that appeared in the pre-edge (1 glitch) and the EXAFS region (3 glitches) in both measurements. 3) Next, I set the E0 for both samples in the background removal session to set the 0 (zero) point in chi(k). However, when I plot chi(k) the samples profile in high k values differ. I think that they should be at least very close considering that both are the same copper oxide standard and measured in sequence. Am I correct? 4) I've also noticed that the first measurement (Cu_o_2), when plot in chi(R) has a small (but significant) peak positioned at R = 1, which seems not be right, as bond distances are bigger (> 1.5, for example). Is there anything wrong or missing at background removal treatment? I know that it seems novice doubts but as I’m new to XAFS, it really intrigues me. Best regards, Pedro Martins

2 2

Re: [Ifeffit] Demeter version 0.9.22 do not work properly in Windows 10
by Pedro F B D Martins 23 Sep '15

23 Sep '15

I would like to thank to Bruce Ravel and Guanghui Zhang for the suggestions. I've modified the restrictions of Demeter and all items related to it in Kaspersky, and also installed the new version of Demeter 0.9.23, which seems to be working just fine. The problem with selecting a point in the plot is resolved. Many thanks. Pedro F. B. D. Martins

3 2

Problem with Hephaestus at Ca L-edges
by Matthew Marcus 23 Sep '15

23 Sep '15

I wanted to work out the edge-jump ratio between the L3 and L2 edges of Ca using Hephaestus. I ran into two problems: 1. The ratio implied by what it says for the unit-edge-step thickness does not agree with that derived by computing the absorption (cm^2/gm) above and below each edge and dividing the difference (L3+ - L3-)/(L2+ - L2-). 2. The results differ wildly depending on which resource I use: L3-.1 L3+.1 L2-.1 L2+.1 (L1+ - L1-)/(L2+ - L2-) Elam 4759.796 27837.796 27478.018 38434.277 2.106375908 Chantler 4322.6 6547.121 32827.61 35436.543 0.852655473 Cromer-Leiberman 4288.524 33471.375 32786.294 47072.991 2.042659055 The Henke table doesn't yield an L2 edge jump at all, while the Shaltout yields the same results as Cromer-Leiberman. Which one should I trust and why? This is old-style H. (V0.18), not Demeter. mam

1 0

Demeter version 0.9.22 do not work properly in Windows 10
by Pedro F B D Martins 23 Sep '15

23 Sep '15

Hi Everyone, I'm having a lot of trouble in processing my XAS data at Demeter 0.9.22 (and also in ifeffit-1.2.11). Things like selecting points in the data (for example, selecting the point at maximum first derivative) is one of it. Moreover, when trying to work with a set of data (let say 5 spectra, which is not that much at all), the program crashes ("not responding" appears). I've attempted to install Windows XP together with my Windows 10, but I'm having problems with that, since windows 10 does not allow me to install a VirtualBox to boot Windows XP. What may I do? I'm new to XAS data treatment, and I would like to start practicing my analysis as soon as possible. Best regards, Pedro Martins

3 2

Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X Yosemite
by Raimundo Lora Serrano 22 Sep '15

22 Sep '15

Bruce, I did what you suggested. > * Can you run gnuplot from the command line? Yes. > > * If so, what is the default terminal? To find out, do this at the > gnuplot command line: "show terminal” “aqua” is the default terminal. > > * If the default terminal is something other than "X11", "wxt", or > "qt", can you reset it? That is done at the gnuplot command line > by, for instance, "set terminal wxt” I reset as suggested. gnuplot is working fine. The plot is generated. Even with “aqua”, the plot is visualized. > * Can you make a plot? To find out, plot a sine wave at the gnuplot > command line with "plot sin(x)” Yes. I just tested and left the gnuplot window opened and ran “athena” in another terminal, but there is no communication with gnuplot. Still, no data is plotted. > Em 22/09/2015, à(s) 16:53, ifeffit-request(a)millenia.cars.aps.anl.gov escreveu: > > 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: No plot window in Athena/Demeter on Mac OS X Yosemite > (Raimundo Lora Serrano) > 2. Re: No plot window in Athena/Demeter on Mac OS X Yosemite > (Bruce Ravel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 22 Sep 2015 16:38:40 -0300 > From: Raimundo Lora Serrano <rloraserrano(a)infis.ufu.br> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X > Yosemite > Message-ID: <1F27C0D9-A926-490A-A33B-2A46DB8FCEDD(a)infis.ufu.br> > Content-Type: text/plain; charset="utf-8" > > Hi again, > I just reinstalled ?xorg-server demeter?, now I get: > /private/tmp/com.apple.launchd.lXiE4HyZ2W/org.macports:0 > > but there is no plot window. The problem remains. > > >> Em 22/09/2015, ?(s) 14:00, ifeffit-request(a)millenia.cars.aps.anl.gov escreveu: >> >> 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: No plot window in Athena/Demeter on Mac OS X Yosemite >> (George Sterbinsky) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 22 Sep 2015 10:05:29 -0500 >> From: George Sterbinsky <GeorgeSterbinsky(a)u.northwestern.edu> >> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >> Subject: Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X >> Yosemite >> Message-ID: >> <CALoY8Yx1Y4dodQ7ywgUFX5wuLEnauF9ib9LjJQLyi_Awf-T1Kg(a)mail.gmail.com> >> Content-Type: text/plain; charset="utf-8" >> >> Hi All, >> >> The result I get is >> /private/tmp/com.apple.launchd.a2i2wnuP2l/org.macosforge.xquartz:0 and >> Athena is working fine on my system. >> >> George >> >> On Tue, Sep 22, 2015 at 6:50 AM, Alison Tebo <agtebo(a)umich.edu> wrote: >> >>> Hi Raimundo (and R?mi), >>> >>> I'm not a pro here but, have you installed xorg-server? It seems like your >>> $DISPLAY variables are not being set correctly. The problem might be >>> XQuartz. The demeter build from Macports doesn't know to use that X windows >>> server (everything is installed in different places) and is looking for the >>> macports version. Your $DISPLAY variable should be something with >>> org.macports rather than org.macosforge.xquartz:0. FWIW, xorg-server is >>> maintained by and updated with XQuartz. >>> >>> Good luck, >>> >>> Alison >>> >>> On Mon, Sep 21, 2015 at 10:15 PM, Raimundo Lora Serrano < >>> rloraserrano(a)infis.ufu.br> wrote: >>> >>>> Dear all, >>>> >>>> I have the same problems installing Athena/Demeter on Yosemite (10.10.5) >>>> as Remi. >>>> Also in my case (as for R?mi) - I use the R?mi?s message edited as >>>> required to my softwares? versions: >>>> >>>>> Athena launches well from the Terminal, I have the >>>>> main window (perl5.22), I can import data or load former athena projects >>>>> etc, but there is no plot window. No error message shows up in the >>>>> terminal. >>>> >>>> >>>>> I?ve *carefully* installed Macports 2.3.3, i.e., installed Xcode Version 7.0 (7A220), >>>>> agreed to Xcode licence, and installed Macports for OS X 10.10 Yosemite. >>>>> I runned the "sudo port -v selfupdate" command >>>>> Then "sudo port install demeter-devel? >>>> >>>>> And port upgrade outdated to ensure everything is up to date >>>>> Plus, I have XQuartz 2.7.7 installed. >>>> >>>> >>>> I also uninstalled and reinstalled macports (and Xcode, xquartz) but the >>>> problem remains. >>>> >>>> By typing >>>> echo $DISPLAY >>>> /private/tmp/com.apple.launchd.RgzrDheMAp/org.macosforge.xquartz:0 >>>> >>>> Any guess? >>>> Many thanks in advance. >>>> Raimundo >>>> >>>> >>>> >>>> >>>> Em 21/09/2015, ?(s) 14:00, ifeffit-request(a)millenia.cars.aps.anl.gov >>>> escreveu: >>>> >>>> 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. No plot window in Athena/Demeter on Mac OS X Yosemite >>>> (R?mi BELISSONT) >>>> >>>> >>>> ---------------------------------------------------------------------- >>>> >>>> Message: 1 >>>> Date: Mon, 21 Sep 2015 14:57:34 +0200 >>>> From: R?mi BELISSONT <remi.belissont(a)univ-lorraine.fr> >>>> To: ifeffit(a)millenia.cars.aps.anl.gov >>>> Subject: [Ifeffit] No plot window in Athena/Demeter on Mac OS X >>>> Yosemite >>>> Message-ID: <6D35429A-8B4F-42FA-BA4D-92407447F7A9(a)univ-lorraine.fr> >>>> Content-Type: text/plain; charset="utf-8" >>>> >>>> Hello, >>>> >>>> I?m currently using Athena using the iXAFS 3.0.3 application, which is ? >>>> if I?ve well understood ? an old version no longer updated ( >>>> http://cars9.uchicago.edu/ifeffit/Downloads < >>>> http://cars9.uchicago.edu/ifeffit/Downloads>). >>>> >>>> So, today I tried to install the current version by installing Demeter, >>>> following the procedure detailed at http://bruceravel.github.io/demeter/ >>>> <http://bruceravel.github.io/demeter/>. >>>> >>>> I?ve *carefully* installed Macports 2.3.3, i.e., installed Xcode 6.4, >>>> agreed to Xcode licence, and installed Macports for OS X 10.10 Yosemite. >>>> I runned the sudo port -v self update command >>>> Then sudo port install xorg-server demeter >>>> And port upgrade outdated to ensure everything is up to date >>>> Plus, I have XQuartz 2.7.7 installed. >>>> >>>> Here is my problem. >>>> Athena launches well from the Terminal (in home directory), I have the >>>> main window (pearl5.22), I can import data or load former athena projects >>>> etc, but there is no plot window. No error message shows up in the >>>> terminal. However I can still produce a PNG of the plot I?m desperately >>>> trying to see via Plots/Save last plot as... >>>> >>>> I?ve seen a similar thread concerning such an issue in OS X Mavericks but >>>> couldn?t solve it from what was explained there ( >>>> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-January/011644.html >>>> < >>>> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-January/011644.html>). >>>> I guess the issue comes from the DISPLAY environment but I don?t have any >>>> clue to solve that. >>>> >>>> Thank you in advance for your help, >>>> I think it may be useful for other users, >>>> >>>> Kind regards, >>>> >>>> R?mi >>>> >>>> >>>> ??????????????????????????????????????? >>>> R?mi Belissont >>>> Ph.D. Student | Universit? de Lorraine ? Labex R21 >>>> >>>> GeoRessources >>>> CNRS-UMR 7359, Facult? des Sciences >>>> BP 70239, 54506 Vandoeuvre-l?s-Nancy Cedex, France >>>> Phone +33 (0)3 83 68 47 14 >>>> >>>> Centre de Recherches P?trographiques et G?ochimiques >>>> CNRS-UMR 7358, 15 Rue Notre Dame des Pauvres >>>> BP 20, 54501 Vandeuvre-l?s-Nancy Cedex, France >>>> >>>>

4 4

Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X Yosemite
by Raimundo Lora Serrano 22 Sep '15

22 Sep '15

Thank you George! Problem solved! :) > Em 22/09/2015, à(s) 19:13, ifeffit-request(a)millenia.cars.aps.anl.gov escreveu: > > 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: No plot window in Athena/Demeter on Mac OS X Yosemite > (Raimundo Lora Serrano) > 2. Re: No plot window in Athena/Demeter on Mac OS X Yosemite > (Bruce Ravel) > 3. Re: No plot window in Athena/Demeter on Mac OS X Yosemite > (George Sterbinsky) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 22 Sep 2015 18:03:14 -0300 > From: Raimundo Lora Serrano <rloraserrano(a)infis.ufu.br> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X > Yosemite > Message-ID: <C6750595-EFDF-4F4B-A1B4-065B3DBC5C7D(a)infis.ufu.br> > Content-Type: text/plain; charset=utf-8 > > Bruce, > I did what you suggested. > >> * Can you run gnuplot from the command line? > > Yes. > >> >> * If so, what is the default terminal? To find out, do this at the >> gnuplot command line: "show terminal? > > ?aqua? is the default terminal. > >> >> * If the default terminal is something other than "X11", "wxt", or >> "qt", can you reset it? That is done at the gnuplot command line >> by, for instance, "set terminal wxt? > > I reset as suggested. gnuplot is working fine. The plot is generated. Even with ?aqua?, the plot is visualized. > >> * Can you make a plot? To find out, plot a sine wave at the gnuplot >> command line with "plot sin(x)? > > Yes. I just tested and left the gnuplot window opened and ran ?athena? in another terminal, but there is no communication with gnuplot. Still, no data is plotted. > > >> Em 22/09/2015, ?(s) 16:53, ifeffit-request(a)millenia.cars.aps.anl.gov escreveu: >> >> 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: No plot window in Athena/Demeter on Mac OS X Yosemite >> (Raimundo Lora Serrano) >> 2. Re: No plot window in Athena/Demeter on Mac OS X Yosemite >> (Bruce Ravel) >> >> >> ---------------------------------------------------------------------- >> >> Message: 1 >> Date: Tue, 22 Sep 2015 16:38:40 -0300 >> From: Raimundo Lora Serrano <rloraserrano(a)infis.ufu.br> >> To: ifeffit(a)millenia.cars.aps.anl.gov >> Subject: Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X >> Yosemite >> Message-ID: <1F27C0D9-A926-490A-A33B-2A46DB8FCEDD(a)infis.ufu.br> >> Content-Type: text/plain; charset="utf-8" >> >> Hi again, >> I just reinstalled ?xorg-server demeter?, now I get: >> /private/tmp/com.apple.launchd.lXiE4HyZ2W/org.macports:0 >> >> but there is no plot window. The problem remains. >> >> >>> Em 22/09/2015, ?(s) 14:00, ifeffit-request(a)millenia.cars.aps.anl.gov escreveu: >>> >>> 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: No plot window in Athena/Demeter on Mac OS X Yosemite >>> (George Sterbinsky) >>> >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Tue, 22 Sep 2015 10:05:29 -0500 >>> From: George Sterbinsky <GeorgeSterbinsky(a)u.northwestern.edu> >>> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> >>> Subject: Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X >>> Yosemite >>> Message-ID: >>> <CALoY8Yx1Y4dodQ7ywgUFX5wuLEnauF9ib9LjJQLyi_Awf-T1Kg(a)mail.gmail.com> >>> Content-Type: text/plain; charset="utf-8" >>> >>> Hi All, >>> >>> The result I get is >>> /private/tmp/com.apple.launchd.a2i2wnuP2l/org.macosforge.xquartz:0 and >>> Athena is working fine on my system. >>> >>> George >>> >>> On Tue, Sep 22, 2015 at 6:50 AM, Alison Tebo <agtebo(a)umich.edu> wrote: >>> >>>> Hi Raimundo (and R?mi), >>>> >>>> I'm not a pro here but, have you installed xorg-server? It seems like your >>>> $DISPLAY variables are not being set correctly. The problem might be >>>> XQuartz. The demeter build from Macports doesn't know to use that X windows >>>> server (everything is installed in different places) and is looking for the >>>> macports version. Your $DISPLAY variable should be something with >>>> org.macports rather than org.macosforge.xquartz:0. FWIW, xorg-server is >>>> maintained by and updated with XQuartz. >>>> >>>> Good luck, >>>> >>>> Alison >>>> >>>> On Mon, Sep 21, 2015 at 10:15 PM, Raimundo Lora Serrano < >>>> rloraserrano(a)infis.ufu.br> wrote: >>>> >>>>> Dear all, >>>>> >>>>> I have the same problems installing Athena/Demeter on Yosemite (10.10.5) >>>>> as Remi. >>>>> Also in my case (as for R?mi) - I use the R?mi?s message edited as >>>>> required to my softwares? versions: >>>>> >>>>>> Athena launches well from the Terminal, I have the >>>>>> main window (perl5.22), I can import data or load former athena projects >>>>>> etc, but there is no plot window. No error message shows up in the >>>>>> terminal. >>>>> >>>>> >>>>>> I?ve *carefully* installed Macports 2.3.3, i.e., installed Xcode Version 7.0 (7A220), >>>>>> agreed to Xcode licence, and installed Macports for OS X 10.10 Yosemite. >>>>>> I runned the "sudo port -v selfupdate" command >>>>>> Then "sudo port install demeter-devel? >>>>> >>>>>> And port upgrade outdated to ensure everything is up to date >>>>>> Plus, I have XQuartz 2.7.7 installed. >>>>> >>>>> >>>>> I also uninstalled and reinstalled macports (and Xcode, xquartz) but the >>>>> problem remains. >>>>> >>>>> By typing >>>>> echo $DISPLAY >>>>> /private/tmp/com.apple.launchd.RgzrDheMAp/org.macosforge.xquartz:0 >>>>> >>>>> Any guess? >>>>> Many thanks in advance. >>>>> Raimundo >>>>> >>>>> >>>>> >>>>> >>>>> Em 21/09/2015, ?(s) 14:00, ifeffit-request(a)millenia.cars.aps.anl.gov >>>>> escreveu: >>>>> >>>>> 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. No plot window in Athena/Demeter on Mac OS X Yosemite >>>>> (R?mi BELISSONT) >>>>> >>>>> >>>>> ---------------------------------------------------------------------- >>>>> >>>>> Message: 1 >>>>> Date: Mon, 21 Sep 2015 14:57:34 +0200 >>>>> From: R?mi BELISSONT <remi.belissont(a)univ-lorraine.fr> >>>>> To: ifeffit(a)millenia.cars.aps.anl.gov >>>>> Subject: [Ifeffit] No plot window in Athena/Demeter on Mac OS X >>>>> Yosemite >>>>> Message-ID: <6D35429A-8B4F-42FA-BA4D-92407447F7A9(a)univ-lorraine.fr> >>>>> Content-Type: text/plain; charset="utf-8" >>>>> >>>>> Hello, >>>>> >>>>> I?m currently using Athena using the iXAFS 3.0.3 application, which is ? >>>>> if I?ve well understood ? an old version no longer updated ( >>>>> http://cars9.uchicago.edu/ifeffit/Downloads < >>>>> http://cars9.uchicago.edu/ifeffit/Downloads>). >>>>> >>>>> So, today I tried to install the current version by installing Demeter, >>>>> following the procedure detailed at http://bruceravel.github.io/demeter/ >>>>> <http://bruceravel.github.io/demeter/>. >>>>> >>>>> I?ve *carefully* installed Macports 2.3.3, i.e., installed Xcode 6.4, >>>>> agreed to Xcode licence, and installed Macports for OS X 10.10 Yosemite. >>>>> I runned the sudo port -v self update command >>>>> Then sudo port install xorg-server demeter >>>>> And port upgrade outdated to ensure everything is up to date >>>>> Plus, I have XQuartz 2.7.7 installed. >>>>> >>>>> Here is my problem. >>>>> Athena launches well from the Terminal (in home directory), I have the >>>>> main window (pearl5.22), I can import data or load former athena projects >>>>> etc, but there is no plot window. No error message shows up in the >>>>> terminal. However I can still produce a PNG of the plot I?m desperately >>>>> trying to see via Plots/Save last plot as... >>>>> >>>>> I?ve seen a similar thread concerning such an issue in OS X Mavericks but >>>>> couldn?t solve it from what was explained there ( >>>>> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-January/011644.html >>>>> < >>>>> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-January/011644.html>). >>>>> I guess the issue comes from the DISPLAY environment but I don?t have any >>>>> clue to solve that. >>>>> >>>>> Thank you in advance for your help, >>>>> I think it may be useful for other users, >>>>> >>>>> Kind regards, >>>>> >>>>> R?mi >>>>> >>>>> >>>>> ??????????????????????????????????????? >>>>> R?mi Belissont >>>>> Ph.D. Student | Universit? de Lorraine ? Labex R21 >>>>> >>>>> GeoRessources >>>>> CNRS-UMR 7359, Facult? des Sciences >>>>> BP 70239, 54506 Vandoeuvre-l?s-Nancy Cedex, France >>>>> Phone +33 (0)3 83 68 47 14 >>>>> >>>>> Centre de Recherches P?trographiques et G?ochimiques >>>>> CNRS-UMR 7358, 15 Rue Notre Dame des Pauvres >>>>> BP 20, 54501 Vandeuvre-l?s-Nancy Cedex, France >>>>> >>>>>

1 0

Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X Yosemite
by Raimundo Lora Serrano 22 Sep '15

22 Sep '15

Hi again, I just reinstalled “xorg-server demeter”, now I get: /private/tmp/com.apple.launchd.lXiE4HyZ2W/org.macports:0 but there is no plot window. The problem remains. > Em 22/09/2015, à(s) 14:00, ifeffit-request(a)millenia.cars.aps.anl.gov escreveu: > > 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: No plot window in Athena/Demeter on Mac OS X Yosemite > (George Sterbinsky) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 22 Sep 2015 10:05:29 -0500 > From: George Sterbinsky <GeorgeSterbinsky(a)u.northwestern.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X > Yosemite > Message-ID: > <CALoY8Yx1Y4dodQ7ywgUFX5wuLEnauF9ib9LjJQLyi_Awf-T1Kg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi All, > > The result I get is > /private/tmp/com.apple.launchd.a2i2wnuP2l/org.macosforge.xquartz:0 and > Athena is working fine on my system. > > George > > On Tue, Sep 22, 2015 at 6:50 AM, Alison Tebo <agtebo(a)umich.edu> wrote: > >> Hi Raimundo (and R?mi), >> >> I'm not a pro here but, have you installed xorg-server? It seems like your >> $DISPLAY variables are not being set correctly. The problem might be >> XQuartz. The demeter build from Macports doesn't know to use that X windows >> server (everything is installed in different places) and is looking for the >> macports version. Your $DISPLAY variable should be something with >> org.macports rather than org.macosforge.xquartz:0. FWIW, xorg-server is >> maintained by and updated with XQuartz. >> >> Good luck, >> >> Alison >> >> On Mon, Sep 21, 2015 at 10:15 PM, Raimundo Lora Serrano < >> rloraserrano(a)infis.ufu.br> wrote: >> >>> Dear all, >>> >>> I have the same problems installing Athena/Demeter on Yosemite (10.10.5) >>> as Remi. >>> Also in my case (as for R?mi) - I use the R?mi?s message edited as >>> required to my softwares? versions: >>> >>>> Athena launches well from the Terminal, I have the >>>> main window (perl5.22), I can import data or load former athena projects >>>> etc, but there is no plot window. No error message shows up in the >>>> terminal. >>> >>> >>>> I?ve *carefully* installed Macports 2.3.3, i.e., installed Xcode Version 7.0 (7A220), >>>> agreed to Xcode licence, and installed Macports for OS X 10.10 Yosemite. >>>> I runned the "sudo port -v selfupdate" command >>>> Then "sudo port install demeter-devel? >>> >>>> And port upgrade outdated to ensure everything is up to date >>>> Plus, I have XQuartz 2.7.7 installed. >>> >>> >>> I also uninstalled and reinstalled macports (and Xcode, xquartz) but the >>> problem remains. >>> >>> By typing >>> echo $DISPLAY >>> /private/tmp/com.apple.launchd.RgzrDheMAp/org.macosforge.xquartz:0 >>> >>> Any guess? >>> Many thanks in advance. >>> Raimundo >>> >>> >>> >>> >>> Em 21/09/2015, ?(s) 14:00, ifeffit-request(a)millenia.cars.aps.anl.gov >>> escreveu: >>> >>> 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. No plot window in Athena/Demeter on Mac OS X Yosemite >>> (R?mi BELISSONT) >>> >>> >>> ---------------------------------------------------------------------- >>> >>> Message: 1 >>> Date: Mon, 21 Sep 2015 14:57:34 +0200 >>> From: R?mi BELISSONT <remi.belissont(a)univ-lorraine.fr> >>> To: ifeffit(a)millenia.cars.aps.anl.gov >>> Subject: [Ifeffit] No plot window in Athena/Demeter on Mac OS X >>> Yosemite >>> Message-ID: <6D35429A-8B4F-42FA-BA4D-92407447F7A9(a)univ-lorraine.fr> >>> Content-Type: text/plain; charset="utf-8" >>> >>> Hello, >>> >>> I?m currently using Athena using the iXAFS 3.0.3 application, which is ? >>> if I?ve well understood ? an old version no longer updated ( >>> http://cars9.uchicago.edu/ifeffit/Downloads < >>> http://cars9.uchicago.edu/ifeffit/Downloads>). >>> >>> So, today I tried to install the current version by installing Demeter, >>> following the procedure detailed at http://bruceravel.github.io/demeter/ >>> <http://bruceravel.github.io/demeter/>. >>> >>> I?ve *carefully* installed Macports 2.3.3, i.e., installed Xcode 6.4, >>> agreed to Xcode licence, and installed Macports for OS X 10.10 Yosemite. >>> I runned the sudo port -v self update command >>> Then sudo port install xorg-server demeter >>> And port upgrade outdated to ensure everything is up to date >>> Plus, I have XQuartz 2.7.7 installed. >>> >>> Here is my problem. >>> Athena launches well from the Terminal (in home directory), I have the >>> main window (pearl5.22), I can import data or load former athena projects >>> etc, but there is no plot window. No error message shows up in the >>> terminal. However I can still produce a PNG of the plot I?m desperately >>> trying to see via Plots/Save last plot as... >>> >>> I?ve seen a similar thread concerning such an issue in OS X Mavericks but >>> couldn?t solve it from what was explained there ( >>> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-January/011644.html >>> < >>> http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-January/011644.html>). >>> I guess the issue comes from the DISPLAY environment but I don?t have any >>> clue to solve that. >>> >>> Thank you in advance for your help, >>> I think it may be useful for other users, >>> >>> Kind regards, >>> >>> R?mi >>> >>> >>> ??????????????????????????????????????? >>> R?mi Belissont >>> Ph.D. Student | Universit? de Lorraine ? Labex R21 >>> >>> GeoRessources >>> CNRS-UMR 7359, Facult? des Sciences >>> BP 70239, 54506 Vandoeuvre-l?s-Nancy Cedex, France >>> Phone +33 (0)3 83 68 47 14 >>> >>> Centre de Recherches P?trographiques et G?ochimiques >>> CNRS-UMR 7358, 15 Rue Notre Dame des Pauvres >>> BP 20, 54501 Vandeuvre-l?s-Nancy Cedex, France >>> >>>

2 1

Re: [Ifeffit] No plot window in Athena/Demeter on Mac OS X Yosemite
by Raimundo Lora Serrano 22 Sep '15

22 Sep '15

Dear all, I have the same problems installing Athena/Demeter on Yosemite (10.10.5) as Remi. Also in my case (as for Rémi) - I use the Rémi’s message edited as required to my softwares’ versions: > Athena launches well from the Terminal, I have the > main window (perl5.22), I can import data or load former athena projects > etc, but there is no plot window. No error message shows up in the > terminal. > I’ve *carefully* installed Macports 2.3.3, i.e., installed Xcode Version 7.0 (7A220), > agreed to Xcode licence, and installed Macports for OS X 10.10 Yosemite. > I runned the "sudo port -v selfupdate" command > Then "sudo port install demeter-devel” > And port upgrade outdated to ensure everything is up to date > Plus, I have XQuartz 2.7.7 installed. I also uninstalled and reinstalled macports (and Xcode, xquartz) but the problem remains. By typing echo $DISPLAY /private/tmp/com.apple.launchd.RgzrDheMAp/org.macosforge.xquartz:0 Any guess? Many thanks in advance. Raimundo > Em 21/09/2015, à(s) 14:00, ifeffit-request(a)millenia.cars.aps.anl.gov escreveu: > > 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. No plot window in Athena/Demeter on Mac OS X Yosemite > (R?mi BELISSONT) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 21 Sep 2015 14:57:34 +0200 > From: R?mi BELISSONT <remi.belissont(a)univ-lorraine.fr> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] No plot window in Athena/Demeter on Mac OS X > Yosemite > Message-ID: <6D35429A-8B4F-42FA-BA4D-92407447F7A9(a)univ-lorraine.fr> > Content-Type: text/plain; charset="utf-8" > > Hello, > > I?m currently using Athena using the iXAFS 3.0.3 application, which is ? if I?ve well understood ? an old version no longer updated (http://cars9.uchicago.edu/ifeffit/Downloads <http://cars9.uchicago.edu/ifeffit/Downloads>). > > So, today I tried to install the current version by installing Demeter, following the procedure detailed at http://bruceravel.github.io/demeter/ <http://bruceravel.github.io/demeter/>. > > I?ve *carefully* installed Macports 2.3.3, i.e., installed Xcode 6.4, agreed to Xcode licence, and installed Macports for OS X 10.10 Yosemite. > I runned the sudo port -v self update command > Then sudo port install xorg-server demeter > And port upgrade outdated to ensure everything is up to date > Plus, I have XQuartz 2.7.7 installed. > > Here is my problem. > Athena launches well from the Terminal (in home directory), I have the main window (pearl5.22), I can import data or load former athena projects etc, but there is no plot window. No error message shows up in the terminal. However I can still produce a PNG of the plot I?m desperately trying to see via Plots/Save last plot as... > > I?ve seen a similar thread concerning such an issue in OS X Mavericks but couldn?t solve it from what was explained there (http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-January/011644.html <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-January/011644.html>). I guess the issue comes from the DISPLAY environment but I don?t have any clue to solve that. > > Thank you in advance for your help, > I think it may be useful for other users, > > Kind regards, > > R?mi > > > ??????????????????????????????????????? > R?mi Belissont > Ph.D. Student | Universit? de Lorraine ? Labex R21 > > GeoRessources > CNRS-UMR 7359, Facult? des Sciences > BP 70239, 54506 Vandoeuvre-l?s-Nancy Cedex, France > Phone +33 (0)3 83 68 47 14 > > Centre de Recherches P?trographiques et G?ochimiques > CNRS-UMR 7358, 15 Rue Notre Dame des Pauvres > BP 20, 54501 Vandeuvre-l?s-Nancy Cedex, France > >

3 2

No plot window in Athena/Demeter on Mac OS X Yosemite
by Rémi BELISSONT 21 Sep '15

21 Sep '15

Hello, I’m currently using Athena using the iXAFS 3.0.3 application, which is – if I’ve well understood – an old version no longer updated (http://cars9.uchicago.edu/ifeffit/Downloads <http://cars9.uchicago.edu/ifeffit/Downloads>). So, today I tried to install the current version by installing Demeter, following the procedure detailed at http://bruceravel.github.io/demeter/ <http://bruceravel.github.io/demeter/>. I’ve *carefully* installed Macports 2.3.3, i.e., installed Xcode 6.4, agreed to Xcode licence, and installed Macports for OS X 10.10 Yosemite. I runned the sudo port -v self update command Then sudo port install xorg-server demeter And port upgrade outdated to ensure everything is up to date Plus, I have XQuartz 2.7.7 installed. Here is my problem. Athena launches well from the Terminal (in home directory), I have the main window (pearl5.22), I can import data or load former athena projects etc, but there is no plot window. No error message shows up in the terminal. However I can still produce a PNG of the plot I’m desperately trying to see via Plots/Save last plot as... I’ve seen a similar thread concerning such an issue in OS X Mavericks but couldn’t solve it from what was explained there (http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-January/011644.html <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-January/011644.html>). I guess the issue comes from the DISPLAY environment but I don’t have any clue to solve that. Thank you in advance for your help, I think it may be useful for other users, Kind regards, Rémi ––––––––––––––––––––––––––––––––––––––– Rémi Belissont Ph.D. Student | Université de Lorraine – Labex R21 GeoRessources CNRS-UMR 7359, Faculté des Sciences BP 70239, 54506 Vandoeuvre-lès-Nancy Cedex, France Phone +33 (0)3 83 68 47 14 Centre de Recherches Pétrographiques et Géochimiques CNRS-UMR 7358, 15 Rue Notre Dame des Pauvres BP 20, 54501 Vandeuvre-lès-Nancy Cedex, France

1 0

Pain of SSRL file formats
by Webb, Samuel M. 17 Sep '15

17 Sep '15

I do agree with many of the previous comments on the state of SSRL binary XAS formats and I certainly won't defend them -- they are horrid and it took me quite a long time to figure out the format so that SIXPACK and others could read them. Tragically, the format goes way back to the VMS days and is essentially in my view under to unsupported. From my past experience, most of the problems I have had with the binary files is transferring them across FTP sites, where a bad choice of data transfer formats (non-explicit binary transfer) has been chosen. That tends to forever corrupt the file and it needs to be reFTP'd to be at all useable. This in itself is the main reason why I never use the binary data format. The only real program that appears actually want to deal with SSRL binaries is EXAFSPAK. Many people who like the VMS data collector still use the old data collection system, and that's a fine user preference. In those instances, those users will need to deal with their data in that preferred format, and if they chose to use that old collector, then I would normally presume that they know how to deal with that data. However, there is no need for any user from SSRL to need to use the antiquated binary data formats. All the beam lines that have that somewhat ancient data collector all have an ASCII transfer utility and users (should) be told about that utility when they arrive. Thus, there is no excuse for someone to have to deal with data in a binary format if they don't want to. As for other beam lines (as well as XAS beam lines that are not on VMS anymore), there are newer XAS data collectors that collect data only in ASCII formats. Granted, it is the slightly screwy SSRL ASCII still, in some effort to be backward compatible, but it is at least readable and manageable. On a separate note, I find that many users (and sometimes support personnel) will edit the standard beam line detector definitions to a point where many data analysis programs that I use (read SIXPACK) cannot read the data either. That said, the newer data collectors at the beam line should (and do) produce readable data that should (and is) easily managed by both Athena as well as many other programs (at least SIXPACK). I haven't always followed the current trend in data file formats for XAS - has anyone ever decided on a common data format, or at least an interchange format? Sam

2 1

Binary SSRL Files crash upon import.
by Logan Giles 17 Sep '15

17 Sep '15

Hello everyone, I am running Demeter 0.9.22 and trying import recent SSRL Binary files. I have the SSRL plugins enabled as well. The problem is when I try to import binary files, the program crashes. It seems that something might have changed recently in SSRL BL 7-3 files because I can import July 2013 files but not July 2015. I have attached a NaMoO4 sweep at the Mo K-edge from each run for your testing. Immediately after trying to import the binary July 2015 files, the program immediately crashes and exits. The July 2013 binary opens right up. When I look at the dathena.log file for the "2015 crash", everything looks normal until the end: "Demeter version 0.9.22 At line 316 of file iff_rddata.fFortran runtime error: End of record" Also, when I try to import the ascii files of the July 2013 or July 2015 data, I get an error as well, but the same error. I can fix this by changing two of the blank rows, which are the column labels for the data, to "BLANK" or something. I have attached these unedited ascii files as well, but I am more concerned with my binary problem. The reason for this is that I was recently sent some other SSRL binary files without their corresponding ascii files that also crash. Let me know that you think, or if you can reproduce the error in trying to import the binary files. Thanks for your assistance and best regards, -Logan

4 7

EXAFS signal from dopant atoms
by Eugenio Paris 17 Sep '15

17 Sep '15

Dear all, I have a very general question about EXAFS analysis. Let's take as example a binary system AB in which i am substituting the atom B with another atom C so that we have AB(1-x)C(x). Let us imagine that we know the structure of binaries AB and AC with Rab and Rac atomic distances and we know that in AB(1-x)C(x) the substitutional site will be 100% the B-site. If I measure the EXAFS spectrum of atom C as a function of "x" what can I expect for the EXAFS oscillations? My idea is that when "x" is very small the EXAFS will be highly noisy and damped, while as "x" increases the oscillations will become more evident above the noise level. How to model this situation to get information on C-A bond? In Athena I can start with the .cif file of AC structure with full occupancy and obtain the distance and the DWF for the A-C bond but.. how to treat the signal-to-noise ratio? I mean, as "x" decreases I think there must be a leaking out of the EXAFS signal, should this effect be introduced in S0^2? Or can it affect the effective number of neighbors? Hope I explained myself, thank you! Eugenio Paris PhD student, University of Rome (Italy)

3 2

ATOMS for XANES simulation by FEFF8.4
by María Elena Montero Cabrera 16 Sep '15

16 Sep '15

Dear all, I am trying to "produce" a new feff.inp using the space group, the asymmetric unit and related data of a compound, for simulating XANES by using FEFF8.4. Long time ago I have used the program "WebAtoms" for obtaining the file, and afterwards I used to edit it, as you have to "uncomment" some lines and "comment" others to run FEFF for XANES. However, in the "Artemis-Demeter" program you have ATOMS also, and Bruce explicitly tells you that the old WebAtoms is not "supported". When I run my data from my compound in Artemis the feff.inp file I have obtained looks, at least for me, different from that I have expected for running XANES in FEFF. Please, tell me what I have to do. Should I use the old Atoms, or I have to tell Atoms in Artemis that I want a "XANES" feff.inp? How can I do it? Thanks a lot in advance María Elena Dra. María Elena Montero Cabrera Centro de Investigación en Materiales Avanzados (CIMAV) Miguel de Cervantes 120, Compl. Ind. Chihuahua Chihuahua CP 31136, Chih. México Tel (614) 4391123 http://redtuls.org/

3 5

[Resolved] Issues with Athena, first posted 2015-06-25 - Kaspersky antivirus caused the problems
by Nils Skoglund 16 Sep '15

16 Sep '15

Hi, I finally figured out what was causing the horrible performance of Athena on my system; as in all too many cases the antivirus policies of enforced by system managers was the culprit. Every time a change was made in Athena (e.g. using a drop-down menu) the shell would freeze for several seconds while the Kaspersky antivirus scanned whatever function was called, what Athena had stored in RAM and such before allowing the function call to proceed. The same was repeated for the renewing of plots in gnuplot, which is why I initially thought it was related to gnuplot. Once I managed to persuade our IT-staff that my user should have the permission to kill off that process, everything in Athena was working like a charm. In short, beware Kaspersky if you are not permitted to set exceptions for certain software due to local security policies at your university or institute. Best regards, Nils Skoglund -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: den 27 juni 2015 19:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 148, Issue 27 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 148, Issue 26 (Nils Skoglund) ---------------------------------------------------------------------- Message: 1 Date: Sat, 27 Jun 2015 09:59:01 +0200 From: "Nils Skoglund" <nils.skoglund(a)ltu.se> To: <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 148, Issue 26 Message-ID: <005901d0b0af$220d5990$66280cb0$(a)ltu.se> Content-Type: text/plain; charset="us-ascii" Hello Everton, Matt and Pushkar, Thank you for your replies. I have tried both the 32-bit and 64-bit versions with uninstalling in between, to no avail. I'm curious if it is a priority issue between the dual GPU's on the laptop that gnuplot can't handle well; there's both a dedicated GPU and an integrated one. System temperatures look normal and none of the fans are revving up, so it shouldn't be heat-related. Other softwares handle plotting without issues so the suggestion about gnuplot being the culprit seems like the most reasonable one. If I narrow this issue down and find a way to work around it, I'll let you know. Until then I'll just find some other workstation for the evaluation work - thanks again! //Nils -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: den 26 juni 2015 19:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 148, Issue 26 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: Issues with Athena on high-performance systems (pushkar shejwalkar) 2. Re: Issues with Athena on high-performance systems (ebonturim(a)usp.br) ---------------------------------------------------------------------- Message: 1 Date: Fri, 26 Jun 2015 10:05:23 +0900 From: pushkar shejwalkar <pshejwalkar2004(a)gmail.com> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Issues with Athena on high-performance systems Message-ID: <CAN0ZRcEm=2KRDeXO-=t60yDZHwT4Rp8Zzs6pwPSbt7ndiQBGCg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi all, I am not an expert in this. In fact , I am one of the very new user of athena. But have you tried uninstalling and then reinstalling the whole package again? ( I am sure you have but since you didnt mentioned just wondering?) Sometimes, that also helps. not sure why and how? but it did for me. Pushkar On Fri, Jun 26, 2015 at 5:00 AM, Matt Newville <newville(a)cars.uchicago.edu> wrote: > Nils, > > We run Athena on non-wimpy Windows 7 systems at our beamline computers > all the time, using both 64- and 32-bit Windows, and typically on > multi-core machines with at least 16 Gb RAM and multiple screens. > Like Robert, we don't see any real performance problems with a handful (<50) spectra. > Athena rarely makes a very big dent in the system resources (well, > comparable to a web browser, so a bit of a hog, but well under 1Gb RAM). > > Perhaps what you're seeing is related to the plotting with Gnuplot. > I'm not sure why that would be a problem... Any ideas? > > --Matt > > Hi, > > > > I?m curious if anyone else is experiencing issues with Athena in more > high-end systems running Windows 7? While I am used to having to wait > for the *first* plot to show up, the software is virtually unusable > to me now where any slight change (e.g. modifying range for the > spline) to already imported data takes up to over a minute to replot. > This didn?t use to be the case for me. The system is a laptop running > Win 7 Professional with 2.40 GHz i7 CPU/16 GB RAM with plenty of space > on the hard drives and a dedicated Intel HD 4600 graphics circuit. > > > > If anyone has a work-around for this problem or can suggest anything > to make Athena usable again, it would be most appreciated. Has anyone > noticed previous versions of Athena running more smoothly? > > > > Best regards, > > Nils > > > > *------------------------------------------------------------------* > > *Nils Skoglund, Ph.D.* > Post-doctoral researcher > > Energy Science > Department of Engineering Sciences and Mathematics Lule? University of > Technology > SE-971 87 Lule? > Sweden > > > > Cell : +46 (0)72 529 52 08 > > Web page: http://www.ltu.se/org/tvm/Avdelningar/Energivetenskap?l=en > > Publications: http://www.researcherid.com/rid/D-3493-2011 > > *-------------------------------------------------------------------* > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Sapporo, Japan

1 0

Linear Combination Fitting problem
by Iuliia Mikulska 13 Sep '15

13 Sep '15

Hello, I'm using Demeter 0.9.21 on Windows 7 (32 bit). I encountering a few problems with Athena. So I wonder if it can be solved in future releases. 1. The names of my spectra are quite long (around 40 characters). The first problem is when I try to import data from Athena project file: appears "Import from Athena project file" window. In this window I can see the name of the spectra only partially and this window can not be resized. So my first question is if the "Import from Athena project file" window can be done resizable? 2. I'm using Athena to perform Linear Combination Fits of my spectra. As I said, the names of my spectra are quite long, so to see the full name in the Athena I need to resize the window. The resizing works fine, but if I change the "Main Window" to "Linear Combination Fitting" then the window of the program resizes back to the standard size and I need again to resize it to see the full name of the spectra. It happens each time when I'm using "Data menu" to access different data processing features. 3. When I performing Linear Combination fits, the results of the fits can not be saved into project. This option was perfectly working in old Athena. Here are steps how to reproduce this problem: 1. I chose the spectrum which I would like to fit with standards. 2. Then I chose a few Standards. 3. Then I press button "Fit this group". 4. Now in "Fit results" tab you can see the results of the fit. Up to this step everything works fine. Now I need to fit next spectra. So I choose next spectra in group list and then I repeat 2-4 aforementioned steps. I again get the proper fit. The problem comes when I would like to check the fit which I did for previous spectrum. So in group list I simply choose the previous spectrum, but "Fit results" tab is empty. "Standards" tab shows the standards used for fit of second spectrum. So you can access the results of the Linear Combination Fitting only immediately after fitting. As soon as you move to another spectrum, fit results for previous spectrum are lost. If you need more information, please let me know. Best regards, Iuliia Mikulska

7 11

No plot window in Athena/Demeter on Mac OS X Yosemite
by Rémi BELISSONT 10 Sep '15

10 Sep '15

Hello, I’m currently using Athena using the iXAFS 3.0.3 application, which is – if I’ve well understood – an old version no longer updated (http://cars9.uchicago.edu/ifeffit/Downloads) So, today I tried to install the current version by installing Demeter, following the procedure detailed at http://bruceravel.github.io/demeter/. I’ve *carefully* installed Macports 2.3.3, i.e., installed Xcode 6.4, agreed to Xcode licence, and installed Macports for OS X 10.10 Yosemite. I runned the sudo port -v self update command Then sudo port install xorg-server demeter And port upgrade outdated to ensure everything is up to date Plus, I have XQuartz 2.7.7 installed. Here is my problem. Athena launches well from the Terminal (in home directory), I have the main window (pearl5.22), I can import data or load former athena projects etc, but there is no plot window. No error message shows up in the terminal. However I can still produce a PNG of the plot I’m desperately trying to see via Plots/Save last plot as... I’ve seen a similar thread concerning such an issue in OS X Mavericks but couldn’t solve it from what was explained there (http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2014-January/011644.html) I guess the issue comes from the DISPLAY environment but I don’t have any clue to solve that. Thank you in advance for your help, I think it may be useful for other users, Kind regards, Rémi

2 1

Re: [Ifeffit] Deglitching
by Bruce Ravel 10 Sep '15

10 Sep '15

On 09/04/2015 01:37 PM, Robert Gordon wrote: > > I can confirm something funny is happening here. In 0.9.21, the deglitch > menu would not display > points. I upgraded to 0.9.22 today and deglitch now displays points, but > when I choose a point > in a test data file (As2O3) and double-click, the energy point removed > is 11804.228, regardless of where > I double-click. I reverted back to 0.9.21 and with the same dataset, > this did not occur. In 0.9.21, > double-click removed the closest point to where I clicked. > > I have win10pro x64 and installed the 64-bit versions of 0.9.21, .22 Can we *please* use the mailing list for these things. It is helpful to the next person who runs into these issues if a discoverable record is left behind. Using the preference tool, can you tell me what the value for gnuplot->terminal is? If it is something other than "wxt", try changing it to "wxt". The interaction with the cursor does not work correctly on some terminals. If that's not the problem, then I am at a loss. I don't see this behavior on any of my computers. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

3 6

Error in running Artemis - Rmin too smaller than Rbkg
by M.F.Bertuzzo 08 Sep '15

08 Sep '15

Dear all, I am facing this error when I try to run a fit. The file in question required a larger than normal Rbkg value of 3.0. I have attatched the Athena file & the subsequent Artemis project file that I tried to fit so you can see the error I am facing. >From what I can understand, I need to reduce the Rbkg value in the Athena file to a lower number. But whenever I try to do this it causes the background function to mess up which then also causes problems for the fit in 'R' space. Is this problem because I have badly modeled the data badly in Athena to begin? I'm not really sure how to solve the problem so your help and advice is much appreciated! Many thanks, Marcus Bertuzzo, Postgraduate Researcher in Chemistry Functional Materials Group School of Physical Sciences University of Kent Canterbury Kent CT2 7NH

2 1

Re: [Ifeffit] Deglitching
by Matt Newville 04 Sep '15

04 Sep '15

Hi Martina, On Sep 3, 2015 12:58 PM, "Martina Ralle" <rallem(a)ohsu.edu> wrote: > Hi Matt, > > > > I have a quick question. When I try to deglitch in Athena it won't let me > pick a point for deglitching. No matter where I double click it always > chooses 8990. > > > > Have others encountered this error? I am running athena on a Windows 7 64 > bit machine. The latest (not beta) version. > > > Sorry for the trouble. I haven't seen (or heard of) that myself, but I'll ask the ifeffit mailing list where maybe someone has a better idea what the trouble could be. > -martina > > > > Martina Ralle, Ph.D. > > Assistant Professor > > Department of Molecular and Medical Genetics > > Mail Code L103 > > OHSU > > 3181 SW Sam Jackson Pk Rd > > Portland, OR 97239 > > Phone 503 494-3225(o) 503 888-6128(m) > > >

2 1

Spline range and FT range
by 이국승(에너지환경소재연구팀) 01 Sep '15

01 Sep '15

Hi everyone, While I was processing my data, I found that the FT features are changing as I change the spline range. I think the change is severe as my data contain a lot of noises at high-k regions (above 12k). The change is remarkable even when FT range is fixed and even when the spline range is far from the low and high limits of FT range. When data are imported into athena, the defalut values for spline ranges from 0 to the end of measured data and the high limit of FT range is set to a value of the high limit of spline range minus 2. There must be a relationship. Could anyone explain these things and general rules for setting the spline range? Thank you in advance. Best wishes, Kug-Seung Lee ________________________________ Kug-Seung Lee, Ph. D. Staff Scientist 8C Nano Probe XAFS Beamline Pohang Accelerator Laboratory Pohang 790-784, Republic of Korea Office: +82-54-279-1522 Fax: +82-54-279-1599 C. P.: +82-10-6419-7801 Researcher ID: http://www.researcherid.com/rid/D-7088-2011 ________________________________

3 3

Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt based cluster (Joshua Kas)
by Ganesh Subramanian 01 Sep '15

01 Sep '15

Dear Josh, Thanks for the altered input. It seems fine now as you mention. I ran the XANES calculations and compared with the existing literature of experimental XANES and it looks good. Thanks again, Ganesh On Sun, Aug 30, 2015 at 1:19 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Error in Running XANES on FEFF8.4 for Cobalt based > cluster (Joshua Kas) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 30 Aug 2015 13:18:51 -0700 > From: Joshua Kas <joshua.j.kas(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt > based cluster > Message-ID: > < > CAHuhYRnxrcfiveDOkS7T2Lx5C3bEZg4LeNffOJeq0dZLYJpRcg(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Ganesh, > It is common to see the > WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. > warning from feff when you have H atoms since the bonds tend to be very > short. However, these are not the ones that are causing the problem. These > warning can be ignored if the structure is reasonable. If the structure at > the bottom of this email is the input structure that you used, then there > is indeed an oxygen atom that is less than 0.1 angstrom from a carbon atom, > which is of course unphysical. That is probably what is causing the > problem, however, there are some other things that could be causing > problems as well. In particular, there are what I like to call "floating > atoms" in your file, i.e., single atoms or several atoms that are > disconnected from the rest of the cluster. I am sending a new input file > below that has fixed this problem. I deleted the O atom that was too close > to the C atom, and deleted all of the structure that wasn't connected to > the central atom by a string of bonds. You might worry about weather the C > or O atom is the one that should have been deleted in the structure, but > you can always test using both possibilities. I doubt that it will make > much difference since C and O look pretty similar, and the O atom is pretty > far from the Co. Also, the H atoms look a bit messed up, but I don't think > that will make much of a difference either. You can check by taking the H > atoms out and running and see if the results change much. > Cheers, > Josh Kas > > * Al K edge energy = 1559.0 eV > EDGE K > S02 1.0 > > * pot xsph fms paths genfmt ff2chi > CONTROL 1 1 1 1 1 1 > PRINT 1 0 0 0 0 0 > > * *** ixc=0 means to use Hedin-Lundqvist > * ixc [ Vr Vi ] > EXCHANGE 0 0 0 > CORRECTIONS 0 1 > > * *** Radius of small cluster for > * *** self-consistency calculation > * *** A sphere including 2 shells is > * *** a good choice > * *** l_scf = 0 for a solid, 1 for a molecule > * r_scf [ l_scf n_scf ca ] > SCF 5 0 > > * *** scattering rather than a path expansion > * kmax [ delta_k delta_e ] > XANES 8.0 > > * *** Radius of cluster for Full Multiple > * *** Scattering calculation > * *** l_fms = 0 for a solid, 1 for a molecule > * r_fms l_fms > FMS 6 0 > * *** Energy grid over which to calculate > * *** DOS functions > * emin emax eimag > *LDOS -30 20 0.1 > > FOLP 3 0.8 > > POTENTIALS > 0 27 Co -1 -1 > 1 6 C -1 -1 > 2 15 P -1 -1 > 3 1 H -1 -1 > 4 7 N -1 -1 > 5 8 O -1 -1 > > ATOMS > 0.000000 0.000000 0.000000 0 Co > 0.000000 1 > -0.877000 -1.130000 1.209000 4 N > 1.872888 2 > 0.706000 0.763000 1.563000 4 N > 1.877119 3 > -0.886000 -0.853000 -1.472000 4 N > 1.918173 4 > 1.117000 1.157000 -1.052000 4 N > 1.921729 5 > 1.456000 -1.334000 -0.126000 1 C > 1.978729 6 > -1.601000 1.453000 -0.068000 4 N > 2.163107 7 > 1.122000 -2.209000 0.163000 3 H > 2.482969 8 > 1.765000 -1.394000 -1.054000 3 H > 2.483823 9 > 2.201000 -1.061000 0.448000 3 H > 2.484115 10 > -0.328000 -1.105000 2.581000 1 C > 2.826689 11 > 1.045000 1.233000 -2.389000 1 C > 2.884378 12 > 0.051000 0.367000 2.864000 1 C > 2.887869 13 > 1.756000 1.481000 1.751000 1 C > 2.888408 14 > -0.659000 -0.537000 -2.771000 1 C > 2.898464 15 > -1.715000 -2.120000 1.053000 1 C > 2.923086 16 > -1.810000 -1.877000 -1.395000 1 C > 2.957238 17 > 2.263000 1.829000 -0.603000 1 C > 2.971535 18 > -2.864000 1.125000 -0.216000 1 C > 3.084603 19 > 0.509000 -1.655000 2.598000 3 H > 3.122132 20 > -3.165000 0.225000 -0.264000 3 H > 3.183951 21 > -1.881000 -2.521000 -0.717000 3 H > 3.226095 22 > 0.212000 0.468000 -3.185000 1 C > 3.226173 23 > 0.260000 -3.225000 -0.293000 3 H > 3.248703 24 > -1.605000 2.854000 0.000000 1 C > 3.274346 25 > -1.931000 0.869000 2.513000 3 H > 3.286197 26 > 2.614000 1.957000 0.706000 1 C > 3.340850 27 > -2.232000 -2.499000 -0.241000 1 C > 3.359301 28 > -2.287000 -2.542000 0.830000 3 H > 3.518669 29 > -1.207000 1.214000 3.075000 1 C > 3.519413 30 > -1.019000 2.145000 2.831000 3 H > 3.695125 31 > 0.186000 -3.470000 1.287000 3 H > 3.705653 32 > -2.458000 -2.943000 -0.050000 1 C > 3.834777 33 > 0.288000 -3.903000 0.413000 1 C > 3.935343 34 > -1.387000 -1.820000 3.396000 1 C > 4.094995 35 > 2.553000 -0.694000 3.132000 3 H > 4.099862 36 > 1.198000 0.646000 3.906000 1 C > 4.136346 37 > 0.236000 0.648000 -4.119000 3 H > 4.176333 38 > 1.974000 1.827000 3.218000 1 C > 4.194059 39 > 1.979000 2.281000 -2.920000 1 C > 4.200691 40 > -1.954000 -2.872000 2.399000 1 C > 4.221576 41 > -1.356000 -1.474000 -3.722000 1 C > 4.226665 42 > 3.077000 2.276000 -1.823000 1 C > 4.239273 43 > -2.379000 -2.161000 -2.783000 1 C > 4.251429 44 > -3.699000 2.187000 -0.292000 4 N > 4.307068 45 > -2.114000 -1.164000 3.595000 3 H > 4.329886 46 > 4.151130 0.213470 -1.476130 3 H > 4.410942 47 > -3.398000 -2.805000 -0.293000 3 H > 4.415912 48 > -2.914000 3.318000 -0.141000 1 C > 4.418190 49 > -1.477000 1.171000 4.015000 3 H > 4.435425 50 > 0.084000 -2.932000 -3.384000 3 H > 4.478296 51 > -0.139000 -3.903000 2.219000 3 H > 4.491847 52 > 1.145000 -4.375000 0.380000 3 H > 4.538287 53 > 2.138000 -0.543000 4.017000 1 C > 4.582814 54 > 1.599000 -1.345000 4.232000 3 H > 4.719709 56 > 4.110000 1.128000 -2.086000 1 C > 4.745090 57 > 2.947000 1.705000 3.417000 3 H > 4.823663 58 > -3.841000 -0.653000 -2.863000 3 H > 4.834921 59 > 3.949000 2.548000 1.146000 1 C > 4.837377 60 > -3.203000 -3.637000 -0.340000 1 C > 4.858248 61 > -0.314000 -2.507000 -4.171000 1 C > 4.876565 62 > 2.363000 1.996000 -3.799000 3 H > 4.898998 63 > -1.074000 -4.151000 2.377000 1 C > 4.902490 64 > -2.168000 -4.410000 0.005000 1 C > 4.914097 65 > -2.368000 -3.147000 -2.947000 3 H > 4.918927 66 > 1.290000 3.658000 -3.054000 1 C > 4.936799 67 > -0.837000 -4.889000 0.206000 1 C > 4.964406 68 > 0.666000 3.369000 3.643000 3 H > 5.006512 69 > 1.635000 3.289000 3.463000 1 C > 5.048080 70 > -3.849000 -1.643000 -2.849000 1 C > 5.062712 71 > -4.475000 -1.815000 1.737000 3 H > 5.131961 72 > 0.388000 -2.058000 -4.689000 3 H > 5.135429 73 > -4.326000 -1.930000 -2.031000 3 H > 5.154041 74 > -1.382000 -4.745000 1.662000 3 H > 5.214134 75 > -4.736000 1.135000 1.925000 5 O > 5.236750 76 > -2.871000 -4.398000 0.183000 3 H > 5.255334 77 > -3.300000 -3.904000 -1.277000 3 H > 5.268961 78 > -4.074000 -3.355000 0.011000 3 H > 5.277653 79 > -1.914000 -0.761000 -4.955000 1 C > 5.366055 80 > 0.046000 3.646000 -3.941000 1 C > 5.369070 81 > -1.698000 -3.672000 -3.533000 3 H > 5.371115 82 > -2.633000 -0.152000 -4.682000 3 H > 5.373725 83 > -0.880000 -2.379000 4.741000 1 C > 5.376906 84 > -3.372000 -3.278000 2.760000 1 C > 5.452822 85 > 0.671000 1.054000 5.308000 1 C > 5.453074 86 > -0.293000 -1.712000 5.177000 3 H > 5.460597 87 > -4.181000 -1.407000 3.261000 3 H > 5.485848 88 > -1.200000 -0.248000 -5.388000 3 H > 5.525581 89 > 3.795000 3.637000 -1.723000 1 C > 5.531593 90 > 0.151000 1.882000 5.232000 3 H > 5.562243 91 > -5.154000 2.141000 -0.214000 1 C > 5.585105 92 > -0.348000 -3.198000 4.579000 3 H > 5.596030 93 > -4.430000 -2.157000 2.662000 1 C > 5.600339 94 > 0.099000 0.341000 5.663000 3 H > 5.674121 95 > -0.746000 -3.186000 -4.728000 3 H > 5.749878 96 > -1.148000 -4.612000 3.238000 3 H > 5.750921 97 > -5.597000 1.049000 -0.967000 5 O > 5.775976 98 > -4.998000 1.024000 2.714000 3 H > 5.778787 99 > -1.369000 -4.479000 -3.414000 4 N > 5.795774 100 > -3.647000 -4.018000 2.164000 3 H > 5.841903 101 > 4.578000 3.552000 -1.141000 3 H > 5.905647 102 > -1.672000 -4.987000 -2.760000 3 H > 5.939979 103 > 3.263000 -0.429000 5.058000 1 C > 6.034449 104 > -5.655000 1.939000 1.236000 1 C > 6.104625 105 > 5.047000 1.380000 -3.248000 1 C > 6.158418 106 > -6.144000 -0.550000 0.157000 3 H > 6.170566 107 > -3.372000 -3.628000 3.685000 3 H > 6.173491 108 > 1.428000 1.198000 5.912000 3 H > 6.198882 109 > -3.234000 -5.327000 -0.151000 1 C > 6.233658 110 > -0.566000 -6.250000 0.206000 1 C > 6.278956 111 > -5.537000 2.986000 -0.588000 3 H > 6.318252 112 > -0.435000 -4.923000 -4.197000 1 C > 6.483823 113 > -4.129000 -5.031000 -0.254000 3 H > 6.513380 114 > 4.649000 1.240000 -4.419000 5 O > 6.532868 115 > -4.629000 -2.157000 -4.093000 1 C > 6.544688 116 > -6.579000 0.277000 -0.201000 1 C > 6.587896 117 > 3.946000 0.575000 5.254000 5 O > 6.595912 118 > -2.062000 -2.707000 5.670000 1 C > 6.612760 119 > -0.029000 -4.281000 -5.051000 5 O > 6.621209 120 > -2.897000 -4.497000 3.921000 5 O > 6.632485 121 > -5.819000 2.808000 1.704000 3 H > 6.682009 122 > -4.241000 -1.749000 -4.909000 3 H > 6.718881 123 > 2.890000 -2.118000 5.767000 3 H > 6.789427 124 > -2.956000 -1.850000 5.836000 5 O > 6.798480 125 > 3.365000 -1.387000 5.883000 4 N > 6.917852 126 > -5.795000 -2.719000 3.077000 1 C > 7.102318 127 > 6.519000 1.843000 -2.135000 3 H > 7.102974 128 > -6.958000 1.182000 0.953000 1 C > 7.121734 129 > -5.572000 -1.864000 -4.025000 3 H > 7.121959 130 > 6.265000 1.753000 -2.972000 4 N > 7.152344 131 > -4.584000 -3.642000 -4.220000 1 C > 7.217037 132 > -6.768000 -0.507000 -2.663000 3 H > 7.290709 133 > -4.900000 -4.410000 -3.269000 5 O > 7.358292 134 > -6.097000 -1.290000 4.274000 3 H > 7.556758 135 > -2.049000 -3.867000 6.278000 4 N > 7.652802 136 > -7.386000 0.433000 2.084000 5 O > 7.686582 137 > -1.394000 -4.435000 6.126000 3 H > 7.690275 138 > -7.333000 -0.912000 -2.191000 5 O > 7.707471 139 > -6.196000 -3.784000 2.591000 5 O > 7.708590 140 > 3.913000 -1.320000 6.566000 3 H > 7.756695 141 > -7.697000 -0.106000 -1.106000 1 C > 7.776778 142 > -6.460000 -2.026000 3.953000 4 N > 7.839801 143 > -7.673000 1.820000 0.672000 3 H > 7.914475 144 > 6.835000 1.912000 -3.624000 3 H > 7.969087 145 > -4.202000 -4.117000 -5.391000 4 N > 7.979309 146 > -3.986000 -3.564000 -6.042000 3 H > 8.068213 147 > -8.116000 0.720000 -1.452000 3 H > 8.276241 148 > -6.953000 -4.513000 1.270000 5 O > 8.385957 149 > -2.691000 -4.077000 6.838000 3 H > 8.403669 150 > -8.380000 -0.585000 -0.571000 3 H > 8.419778 151 > -4.162000 -4.987000 -5.524000 3 H > 8.526839 152 > -8.821000 0.724000 2.726000 2 P > 9.260955 153 > -7.794000 -2.418000 4.430000 1 C > 9.285368 154 > -8.760000 -1.946000 2.636000 3 H > 9.352701 155 > -7.884000 -3.402000 4.375000 3 H > 9.636996 156 > -8.812000 -0.362000 3.897000 5 O > 9.642043 157 > -8.891000 -1.772000 3.614000 1 C > 9.759655 158 > -7.894000 -2.154000 5.378000 3 H > 9.791723 159 > -8.993000 2.042000 3.320000 5 O > 9.801337 160 > -9.840000 0.431000 1.688000 5 O > 9.993033 161 > -10.251000 -2.267000 4.070000 1 C > 11.259982 162 > -10.331000 -3.225000 3.886000 3 H > 11.499182 163 > -10.955000 -1.781000 3.591000 3 H > 11.665302 164 > -10.348000 -2.113000 5.035000 3 H > 11.700303 165 > END > > On Fri, Aug 28, 2015 at 2:03 PM, < > ifeffit-request(a)millenia.cars.aps.anl.gov> > wrote: > > > Send Ifeffit mailing list submissions to > > ifeffit(a)millenia.cars.aps.anl.gov > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > or, via email, send a message with subject or body 'help' to > > ifeffit-request(a)millenia.cars.aps.anl.gov > > > > You can reach the person managing the list at > > ifeffit-owner(a)millenia.cars.aps.anl.gov > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Ifeffit digest..." > > > > > > Today's Topics: > > > > 1. Re: Error in Running XANES on FEFF8.4 for Cobalt based > > cluster (Ganesh Subramanian) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Fri, 28 Aug 2015 14:03:16 -0700 > > From: Ganesh Subramanian <gunkanna(a)gmail.com> > > To: ifeffit(a)millenia.cars.aps.anl.gov > > Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt > > based cluster > > Message-ID: > > <CAAb9e-c_jTi=+KbQi6gPzYVNnSoikXAF= > > eYHtKkfSHWE+_y-kw(a)mail.gmail.com> > > Content-Type: text/plain; charset="utf-8" > > > > Dear Bruce, > > > > Thanks for the response and sorry for the delay in getting back to you. > > > > I retried the FEFF simulation using structural information from another > > article (Randaccio, Lucio, et al. *Inorganic chemistry* 39.15 (2000): > > 3403-3413). The structural data from this article seems to be widely used > > by many others in simulating for optical absorption. But here with FEFF, > I > > still run into the same issue of "ATOMS VERY CLOSE TOGETHER" and a couple > > of other issues. With two different articles suggesting smaller bond > > distances for a few of their atoms, it seems like the distances are what > > they are. > > > > I have attached the log files and input file for this trial run. > > > > Is there any way to circumvent this error without altering the structure > ? > > > > Thanks, > > > > Ganesh > > > > > > > From: Bruce Ravel <bravel(a)bnl.gov> > > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > > Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt > > > based cluster > > > Message-ID: <55BA3978.4080801(a)bnl.gov> > > > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > > > On 07/29/2015 06:01 PM, Ganesh Subramanian wrote: > > > > 1. *Using the FOLP card*: The actual cluster size is about 180 atoms > > > > extending upto 18 A in radial distance from the central cobalt atom. > > But > > > > there are quite a few instances of Hydrogen atoms that are too > close. I > > > > tried the FOLP with the recommendation for Hydrogen of 0.8, I seem to > > > > get a syntax type error, that i cant figure out. I checked the > crystal > > > > structure and the smallest hydrogen bond distance is 0.89 A. (I have > > > > attached the corresponding input and log file with suffix 'full > > cluster') > > > > > > In Feff the "TWO ATOMS VERY CLOSE TOGETHER" message gets shouted at you > > > when you have atoms that are separated by 1.75 Angstroms or less. That > > > message has nothing to do with the FOLP setting. > > > > > > > 2. *SCF for small cluster*: Since the problem with the hydrogen > > > > distances persisted, I decided to run the calculation for a smaller > > > > cluster (about 50 atoms). I used the conditions as prescribed for > small > > > > clusters - SCF 5.0 1, FMS 5.0 1, RPATH -1. Those hydrogens that were > > too > > > > close (within this smaller cluster, there were about 3 of them, and > > none > > > > in the first or second shell of co-ordination) were removed manually. > > > > Now, I did not have the error on distances, did not require the FOLP > > > > card to be manually altered, but the log1 file seems to suggest that > > the > > > > SCF is not calculated. I cant figure why that is the case. (I have > > > > attached the corresponding input and log file with suffix 'small > > > cluster') > > > > > > When I ran feff 8.40, I got same the contents of the log1.dat file, but > > > with these additional lines: > > > > > > Core-valence separation > > > WARNING: fatal error in subroutine corval. Try > > > to reduce ca1 in SCF card. If does not help, > > > SEND bug report to AUTHORS > > > CORVAL-1 > > > > > > I don't quite know what that means, but it gives some hints. The > source > > > code corval.f tells us that is "Finds the core-valence separation for > > > the cluster of atoms." I simply am not knowledgeable enough about the > > > details of Feff to know why your cluster triggered this warning. > > > > > > B > > > > > > > > > > > > -- > > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > > > National Institute of Standards and Technology > > > Synchrotron Science Group at NSLS-II > > > Building 535A > > > Upton NY, 11973 > > > > > > Homepage: http://bruceravel.github.io/home/ > > > Software: https://github.com/bruceravel > > > Demeter: http://bruceravel.github.io/demeter/ > > > > > > > > > ------------------------------ > > > > > > Message: 3 > > > Date: Thu, 30 Jul 2015 10:51:30 -0400 > > > From: Bruce Ravel <bravel(a)bnl.gov> > > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > > Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt > > > based cluster > > > Message-ID: <55BA39F2.4090609(a)bnl.gov> > > > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > > > On 07/30/2015 10:49 AM, Bruce Ravel wrote: > > > >> 1. *Using the FOLP card*: The actual cluster size is about 180 atoms > > > >> extending upto 18 A in radial distance from the central cobalt atom. > > But > > > >> there are quite a few instances of Hydrogen atoms that are too > close. > > I > > > >> tried the FOLP with the recommendation for Hydrogen of 0.8, I seem > to > > > >> get a syntax type error, that i cant figure out. I checked the > crystal > > > >> structure and the smallest hydrogen bond distance is 0.89 A. (I have > > > >> attached the corresponding input and log file with suffix 'full > > > cluster') > > > > > > > > In Feff the "TWO ATOMS VERY CLOSE TOGETHER" message gets shouted at > you > > > > when you have atoms that are separated by 1.75 Angstroms or less. > That > > > > message has nothing to do with the FOLP setting. > > > > > > Oops! That message is triggered for atoms separated by 1.75 bohr, > which > > > is about 0.92 Angstrom. > > > > > > B > > > > > > > > > -- > > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > > > National Institute of Standards and Technology > > > Synchrotron Science Group at NSLS-II > > > Building 535A > > > Upton NY, 11973 > > > > > > Homepage: http://bruceravel.github.io/home/ > > > Software: https://github.com/bruceravel > > > Demeter: http://bruceravel.github.io/demeter/ > > > > > > > > > ------------------------------ > > > > > > Message: 4 > > > Date: Thu, 30 Jul 2015 15:58:12 +0000 > > > From: "Fowler, Joseph W." <joe.fowler(a)nist.gov> > > > To: "ifeffit(a)millenia.cars.aps.anl.gov" > > > <ifeffit(a)millenia.cars.aps.anl.gov> > > > Subject: Re: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) > > > Message-ID: <D1759C33-50D0-46D4-84D0-4D649CA779A8(a)nist.gov> > > > Content-Type: text/plain; charset="windows-1252" > > > > > > Dear Ie-Rang, > > > > > > I?m the demeter maintainer on MacPorts, but I admit I am anything but a > > > MacPorts guru. > > > > > > I notice that the error you showed is a failure to install gcc49. I > don?t > > > know if that new GCC is compatible with your old version of OS X, but > > > that?s an issue that?s beyond my expertise. You might edit your > variants > > > file (it?s /opt/local/etc/macports/variants.conf on my installation) to > > > insist on an earlier version by adding a line containing, e.g., > ?+gcc47? > > or > > > whatever is your installed and preferred version of GCC. > > > > > > In fact, the port demeter does not depend (directly) on gcc, which you > > can > > > see by issuing the command > > > > > > > port echo depof:demeter > > > > port echo depof:demeter-devel > > > > > > So it looks to me like you have several steps to get ready for > installing > > > demeter. > > > > > > I admit that I recently discovered?but have not fixed?a flaw in the > > > demeter port description file. The code depends on ports > p5.16-file-which > > > and p5.16-math-round, but these are not made explicit. I need to figure > > out > > > how to add these to the explicit dependency list. I?m just back from > > > vacation and a conference, so I have no excuses now. If you get far > > enough > > > that you can install *but not run* demeter?s executables, then a > > workaround > > > for this is > > > > > > > sudo port install p5.16-file-which p5.16-math-round > > > > > > And for MacPorts users in general: I understand that the project as a > > > whole is in the process of trying to move to Perl 5.22 instead of 5.16. > > > I?ll be updating the port file to reflect that change, too. > > > > > > Joe Fowler > > > NIST Boulder Laboratories > > > > > > > > > On Jul 29, 2015, at 4:01 PM, 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(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: failed to install gcc49 on mac (v10.6.8) (Ie-Rang Jeon) > > > 2. Re: HELP: failed to install gcc49 on mac (v10.6.8) (Bruce Ravel) > > > 3. Error in Running XANES on FEFF8.4 for Cobalt based cluster > > > (Ganesh Subramanian) > > > > > > From: Ie-Rang Jeon <jeon(a)northwestern.edu> > > > Subject: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) > > > Date: July 29, 2015 at 1:11:08 PM MDT > > > To: "ifeffit(a)millenia.cars.aps.anl.gov" < > > ifeffit(a)millenia.cars.aps.anl.gov > > > > > > > Reply-To: XAFS Analysis using Ifeffit < > ifeffit(a)millenia.cars.aps.anl.gov > > > > > > > > > > > > Hello, > > > > > > I'm trying to install MacPorts package on my mac (v.10.6.8), and I > can't > > > do this. Below are error messages that I got. > > > Could you please help me to figure out what the problem is? > > > > > > Thank you. > > > Ie-Rang > > > > > > > > > ----------------------------------- > > > > > > ---> Building gcc49 > > > Error: org.macports.build for port gcc49 returned: command execution > > failed > > > Error: Failed to install gcc49 > > > Please see the log file for port gcc49 for details: > > > > > > > > > /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log > > > Error: The following dependencies were not installed: > > > . > > > . > > > . > > > Error: Processing of port demeter-devel failed > > > > > > > > > > > > > > > > > > > > > From: Bruce Ravel <bravel(a)bnl.gov> > > > Subject: Re: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) > > > Date: July 29, 2015 at 1:21:06 PM MDT > > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > > Reply-To: XAFS Analysis using Ifeffit < > ifeffit(a)millenia.cars.aps.anl.gov > > > > > > > > > > > > On 07/29/2015 03:11 PM, Ie-Rang Jeon wrote: > > > Hello, > > > > > > I'm trying to install MacPorts package on my mac (v.10.6.8), and I > can't > > > do this. Below are error messages that I got. > > > Could you please help me to figure out what the problem is? > > > > > > Thank you. > > > Ie-Rang > > > > > > Perhaps there's anything useful in that log file? > > > B > > > > > > > > > > > > > > > ----------------------------------- > > > > > > ---> Building gcc49 > > > Error: org.macports.build for port gcc49 returned: command execution > > failed > > > Error: Failed to install gcc49 > > > Please see the log file for port gcc49 for details: > > > > > > > > > /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log > > > Error: The following dependencies were not installed: > > > . > > > . > > > . > > > Error: Processing of port demeter-devel failed > > > > > > > > > _______________________________________________ > > > Ifeffit mailing list > > > Ifeffit(a)millenia.cars.aps.anl.gov > > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > > > > > > > -- > > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > > > National Institute of Standards and Technology > > > Synchrotron Science Group at NSLS-II > > > Building 535A > > > Upton NY, 11973 > > > > > > Homepage: http://bruceravel.github.io/home/ > > > Software: https://github.com/bruceravel > > > Demeter: http://bruceravel.github.io/demeter/ > > > > > > > > > > > >

1 0

Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt based cluster
by Joshua Kas 30 Aug '15

30 Aug '15

Hi Ganesh, It is common to see the WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT. warning from feff when you have H atoms since the bonds tend to be very short. However, these are not the ones that are causing the problem. These warning can be ignored if the structure is reasonable. If the structure at the bottom of this email is the input structure that you used, then there is indeed an oxygen atom that is less than 0.1 angstrom from a carbon atom, which is of course unphysical. That is probably what is causing the problem, however, there are some other things that could be causing problems as well. In particular, there are what I like to call "floating atoms" in your file, i.e., single atoms or several atoms that are disconnected from the rest of the cluster. I am sending a new input file below that has fixed this problem. I deleted the O atom that was too close to the C atom, and deleted all of the structure that wasn't connected to the central atom by a string of bonds. You might worry about weather the C or O atom is the one that should have been deleted in the structure, but you can always test using both possibilities. I doubt that it will make much difference since C and O look pretty similar, and the O atom is pretty far from the Co. Also, the H atoms look a bit messed up, but I don't think that will make much of a difference either. You can check by taking the H atoms out and running and see if the results change much. Cheers, Josh Kas * Al K edge energy = 1559.0 eV EDGE K S02 1.0 * pot xsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 0 * *** ixc=0 means to use Hedin-Lundqvist * ixc [ Vr Vi ] EXCHANGE 0 0 0 CORRECTIONS 0 1 * *** Radius of small cluster for * *** self-consistency calculation * *** A sphere including 2 shells is * *** a good choice * *** l_scf = 0 for a solid, 1 for a molecule * r_scf [ l_scf n_scf ca ] SCF 5 0 * *** scattering rather than a path expansion * kmax [ delta_k delta_e ] XANES 8.0 * *** Radius of cluster for Full Multiple * *** Scattering calculation * *** l_fms = 0 for a solid, 1 for a molecule * r_fms l_fms FMS 6 0 * *** Energy grid over which to calculate * *** DOS functions * emin emax eimag *LDOS -30 20 0.1 FOLP 3 0.8 POTENTIALS 0 27 Co -1 -1 1 6 C -1 -1 2 15 P -1 -1 3 1 H -1 -1 4 7 N -1 -1 5 8 O -1 -1 ATOMS 0.000000 0.000000 0.000000 0 Co 0.000000 1 -0.877000 -1.130000 1.209000 4 N 1.872888 2 0.706000 0.763000 1.563000 4 N 1.877119 3 -0.886000 -0.853000 -1.472000 4 N 1.918173 4 1.117000 1.157000 -1.052000 4 N 1.921729 5 1.456000 -1.334000 -0.126000 1 C 1.978729 6 -1.601000 1.453000 -0.068000 4 N 2.163107 7 1.122000 -2.209000 0.163000 3 H 2.482969 8 1.765000 -1.394000 -1.054000 3 H 2.483823 9 2.201000 -1.061000 0.448000 3 H 2.484115 10 -0.328000 -1.105000 2.581000 1 C 2.826689 11 1.045000 1.233000 -2.389000 1 C 2.884378 12 0.051000 0.367000 2.864000 1 C 2.887869 13 1.756000 1.481000 1.751000 1 C 2.888408 14 -0.659000 -0.537000 -2.771000 1 C 2.898464 15 -1.715000 -2.120000 1.053000 1 C 2.923086 16 -1.810000 -1.877000 -1.395000 1 C 2.957238 17 2.263000 1.829000 -0.603000 1 C 2.971535 18 -2.864000 1.125000 -0.216000 1 C 3.084603 19 0.509000 -1.655000 2.598000 3 H 3.122132 20 -3.165000 0.225000 -0.264000 3 H 3.183951 21 -1.881000 -2.521000 -0.717000 3 H 3.226095 22 0.212000 0.468000 -3.185000 1 C 3.226173 23 0.260000 -3.225000 -0.293000 3 H 3.248703 24 -1.605000 2.854000 0.000000 1 C 3.274346 25 -1.931000 0.869000 2.513000 3 H 3.286197 26 2.614000 1.957000 0.706000 1 C 3.340850 27 -2.232000 -2.499000 -0.241000 1 C 3.359301 28 -2.287000 -2.542000 0.830000 3 H 3.518669 29 -1.207000 1.214000 3.075000 1 C 3.519413 30 -1.019000 2.145000 2.831000 3 H 3.695125 31 0.186000 -3.470000 1.287000 3 H 3.705653 32 -2.458000 -2.943000 -0.050000 1 C 3.834777 33 0.288000 -3.903000 0.413000 1 C 3.935343 34 -1.387000 -1.820000 3.396000 1 C 4.094995 35 2.553000 -0.694000 3.132000 3 H 4.099862 36 1.198000 0.646000 3.906000 1 C 4.136346 37 0.236000 0.648000 -4.119000 3 H 4.176333 38 1.974000 1.827000 3.218000 1 C 4.194059 39 1.979000 2.281000 -2.920000 1 C 4.200691 40 -1.954000 -2.872000 2.399000 1 C 4.221576 41 -1.356000 -1.474000 -3.722000 1 C 4.226665 42 3.077000 2.276000 -1.823000 1 C 4.239273 43 -2.379000 -2.161000 -2.783000 1 C 4.251429 44 -3.699000 2.187000 -0.292000 4 N 4.307068 45 -2.114000 -1.164000 3.595000 3 H 4.329886 46 4.151130 0.213470 -1.476130 3 H 4.410942 47 -3.398000 -2.805000 -0.293000 3 H 4.415912 48 -2.914000 3.318000 -0.141000 1 C 4.418190 49 -1.477000 1.171000 4.015000 3 H 4.435425 50 0.084000 -2.932000 -3.384000 3 H 4.478296 51 -0.139000 -3.903000 2.219000 3 H 4.491847 52 1.145000 -4.375000 0.380000 3 H 4.538287 53 2.138000 -0.543000 4.017000 1 C 4.582814 54 1.599000 -1.345000 4.232000 3 H 4.719709 56 4.110000 1.128000 -2.086000 1 C 4.745090 57 2.947000 1.705000 3.417000 3 H 4.823663 58 -3.841000 -0.653000 -2.863000 3 H 4.834921 59 3.949000 2.548000 1.146000 1 C 4.837377 60 -3.203000 -3.637000 -0.340000 1 C 4.858248 61 -0.314000 -2.507000 -4.171000 1 C 4.876565 62 2.363000 1.996000 -3.799000 3 H 4.898998 63 -1.074000 -4.151000 2.377000 1 C 4.902490 64 -2.168000 -4.410000 0.005000 1 C 4.914097 65 -2.368000 -3.147000 -2.947000 3 H 4.918927 66 1.290000 3.658000 -3.054000 1 C 4.936799 67 -0.837000 -4.889000 0.206000 1 C 4.964406 68 0.666000 3.369000 3.643000 3 H 5.006512 69 1.635000 3.289000 3.463000 1 C 5.048080 70 -3.849000 -1.643000 -2.849000 1 C 5.062712 71 -4.475000 -1.815000 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C 5.600339 94 0.099000 0.341000 5.663000 3 H 5.674121 95 -0.746000 -3.186000 -4.728000 3 H 5.749878 96 -1.148000 -4.612000 3.238000 3 H 5.750921 97 -5.597000 1.049000 -0.967000 5 O 5.775976 98 -4.998000 1.024000 2.714000 3 H 5.778787 99 -1.369000 -4.479000 -3.414000 4 N 5.795774 100 -3.647000 -4.018000 2.164000 3 H 5.841903 101 4.578000 3.552000 -1.141000 3 H 5.905647 102 -1.672000 -4.987000 -2.760000 3 H 5.939979 103 3.263000 -0.429000 5.058000 1 C 6.034449 104 -5.655000 1.939000 1.236000 1 C 6.104625 105 5.047000 1.380000 -3.248000 1 C 6.158418 106 -6.144000 -0.550000 0.157000 3 H 6.170566 107 -3.372000 -3.628000 3.685000 3 H 6.173491 108 1.428000 1.198000 5.912000 3 H 6.198882 109 -3.234000 -5.327000 -0.151000 1 C 6.233658 110 -0.566000 -6.250000 0.206000 1 C 6.278956 111 -5.537000 2.986000 -0.588000 3 H 6.318252 112 -0.435000 -4.923000 -4.197000 1 C 6.483823 113 -4.129000 -5.031000 -0.254000 3 H 6.513380 114 4.649000 1.240000 -4.419000 5 O 6.532868 115 -4.629000 -2.157000 -4.093000 1 C 6.544688 116 -6.579000 0.277000 -0.201000 1 C 6.587896 117 3.946000 0.575000 5.254000 5 O 6.595912 118 -2.062000 -2.707000 5.670000 1 C 6.612760 119 -0.029000 -4.281000 -5.051000 5 O 6.621209 120 -2.897000 -4.497000 3.921000 5 O 6.632485 121 -5.819000 2.808000 1.704000 3 H 6.682009 122 -4.241000 -1.749000 -4.909000 3 H 6.718881 123 2.890000 -2.118000 5.767000 3 H 6.789427 124 -2.956000 -1.850000 5.836000 5 O 6.798480 125 3.365000 -1.387000 5.883000 4 N 6.917852 126 -5.795000 -2.719000 3.077000 1 C 7.102318 127 6.519000 1.843000 -2.135000 3 H 7.102974 128 -6.958000 1.182000 0.953000 1 C 7.121734 129 -5.572000 -1.864000 -4.025000 3 H 7.121959 130 6.265000 1.753000 -2.972000 4 N 7.152344 131 -4.584000 -3.642000 -4.220000 1 C 7.217037 132 -6.768000 -0.507000 -2.663000 3 H 7.290709 133 -4.900000 -4.410000 -3.269000 5 O 7.358292 134 -6.097000 -1.290000 4.274000 3 H 7.556758 135 -2.049000 -3.867000 6.278000 4 N 7.652802 136 -7.386000 0.433000 2.084000 5 O 7.686582 137 -1.394000 -4.435000 6.126000 3 H 7.690275 138 -7.333000 -0.912000 -2.191000 5 O 7.707471 139 -6.196000 -3.784000 2.591000 5 O 7.708590 140 3.913000 -1.320000 6.566000 3 H 7.756695 141 -7.697000 -0.106000 -1.106000 1 C 7.776778 142 -6.460000 -2.026000 3.953000 4 N 7.839801 143 -7.673000 1.820000 0.672000 3 H 7.914475 144 6.835000 1.912000 -3.624000 3 H 7.969087 145 -4.202000 -4.117000 -5.391000 4 N 7.979309 146 -3.986000 -3.564000 -6.042000 3 H 8.068213 147 -8.116000 0.720000 -1.452000 3 H 8.276241 148 -6.953000 -4.513000 1.270000 5 O 8.385957 149 -2.691000 -4.077000 6.838000 3 H 8.403669 150 -8.380000 -0.585000 -0.571000 3 H 8.419778 151 -4.162000 -4.987000 -5.524000 3 H 8.526839 152 -8.821000 0.724000 2.726000 2 P 9.260955 153 -7.794000 -2.418000 4.430000 1 C 9.285368 154 -8.760000 -1.946000 2.636000 3 H 9.352701 155 -7.884000 -3.402000 4.375000 3 H 9.636996 156 -8.812000 -0.362000 3.897000 5 O 9.642043 157 -8.891000 -1.772000 3.614000 1 C 9.759655 158 -7.894000 -2.154000 5.378000 3 H 9.791723 159 -8.993000 2.042000 3.320000 5 O 9.801337 160 -9.840000 0.431000 1.688000 5 O 9.993033 161 -10.251000 -2.267000 4.070000 1 C 11.259982 162 -10.331000 -3.225000 3.886000 3 H 11.499182 163 -10.955000 -1.781000 3.591000 3 H 11.665302 164 -10.348000 -2.113000 5.035000 3 H 11.700303 165 END On Fri, Aug 28, 2015 at 2:03 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Error in Running XANES on FEFF8.4 for Cobalt based > cluster (Ganesh Subramanian) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 28 Aug 2015 14:03:16 -0700 > From: Ganesh Subramanian <gunkanna(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt > based cluster > Message-ID: > <CAAb9e-c_jTi=+KbQi6gPzYVNnSoikXAF= > eYHtKkfSHWE+_y-kw(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Dear Bruce, > > Thanks for the response and sorry for the delay in getting back to you. > > I retried the FEFF simulation using structural information from another > article (Randaccio, Lucio, et al. *Inorganic chemistry* 39.15 (2000): > 3403-3413). The structural data from this article seems to be widely used > by many others in simulating for optical absorption. But here with FEFF, I > still run into the same issue of "ATOMS VERY CLOSE TOGETHER" and a couple > of other issues. With two different articles suggesting smaller bond > distances for a few of their atoms, it seems like the distances are what > they are. > > I have attached the log files and input file for this trial run. > > Is there any way to circumvent this error without altering the structure ? > > Thanks, > > Ganesh > > > > From: Bruce Ravel <bravel(a)bnl.gov> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt > > based cluster > > Message-ID: <55BA3978.4080801(a)bnl.gov> > > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > On 07/29/2015 06:01 PM, Ganesh Subramanian wrote: > > > 1. *Using the FOLP card*: The actual cluster size is about 180 atoms > > > extending upto 18 A in radial distance from the central cobalt atom. > But > > > there are quite a few instances of Hydrogen atoms that are too close. I > > > tried the FOLP with the recommendation for Hydrogen of 0.8, I seem to > > > get a syntax type error, that i cant figure out. I checked the crystal > > > structure and the smallest hydrogen bond distance is 0.89 A. (I have > > > attached the corresponding input and log file with suffix 'full > cluster') > > > > In Feff the "TWO ATOMS VERY CLOSE TOGETHER" message gets shouted at you > > when you have atoms that are separated by 1.75 Angstroms or less. That > > message has nothing to do with the FOLP setting. > > > > > 2. *SCF for small cluster*: Since the problem with the hydrogen > > > distances persisted, I decided to run the calculation for a smaller > > > cluster (about 50 atoms). I used the conditions as prescribed for small > > > clusters - SCF 5.0 1, FMS 5.0 1, RPATH -1. Those hydrogens that were > too > > > close (within this smaller cluster, there were about 3 of them, and > none > > > in the first or second shell of co-ordination) were removed manually. > > > Now, I did not have the error on distances, did not require the FOLP > > > card to be manually altered, but the log1 file seems to suggest that > the > > > SCF is not calculated. I cant figure why that is the case. (I have > > > attached the corresponding input and log file with suffix 'small > > cluster') > > > > When I ran feff 8.40, I got same the contents of the log1.dat file, but > > with these additional lines: > > > > Core-valence separation > > WARNING: fatal error in subroutine corval. Try > > to reduce ca1 in SCF card. If does not help, > > SEND bug report to AUTHORS > > CORVAL-1 > > > > I don't quite know what that means, but it gives some hints. The source > > code corval.f tells us that is "Finds the core-valence separation for > > the cluster of atoms." I simply am not knowledgeable enough about the > > details of Feff to know why your cluster triggered this warning. > > > > B > > > > > > > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > National Institute of Standards and Technology > > Synchrotron Science Group at NSLS-II > > Building 535A > > Upton NY, 11973 > > > > Homepage: http://bruceravel.github.io/home/ > > Software: https://github.com/bruceravel > > Demeter: http://bruceravel.github.io/demeter/ > > > > > > ------------------------------ > > > > Message: 3 > > Date: Thu, 30 Jul 2015 10:51:30 -0400 > > From: Bruce Ravel <bravel(a)bnl.gov> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt > > based cluster > > Message-ID: <55BA39F2.4090609(a)bnl.gov> > > Content-Type: text/plain; charset=windows-1252; format=flowed > > > > On 07/30/2015 10:49 AM, Bruce Ravel wrote: > > >> 1. *Using the FOLP card*: The actual cluster size is about 180 atoms > > >> extending upto 18 A in radial distance from the central cobalt atom. > But > > >> there are quite a few instances of Hydrogen atoms that are too close. > I > > >> tried the FOLP with the recommendation for Hydrogen of 0.8, I seem to > > >> get a syntax type error, that i cant figure out. I checked the crystal > > >> structure and the smallest hydrogen bond distance is 0.89 A. (I have > > >> attached the corresponding input and log file with suffix 'full > > cluster') > > > > > > In Feff the "TWO ATOMS VERY CLOSE TOGETHER" message gets shouted at you > > > when you have atoms that are separated by 1.75 Angstroms or less. That > > > message has nothing to do with the FOLP setting. > > > > Oops! That message is triggered for atoms separated by 1.75 bohr, which > > is about 0.92 Angstrom. > > > > B > > > > > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > National Institute of Standards and Technology > > Synchrotron Science Group at NSLS-II > > Building 535A > > Upton NY, 11973 > > > > Homepage: http://bruceravel.github.io/home/ > > Software: https://github.com/bruceravel > > Demeter: http://bruceravel.github.io/demeter/ > > > > > > ------------------------------ > > > > Message: 4 > > Date: Thu, 30 Jul 2015 15:58:12 +0000 > > From: "Fowler, Joseph W." <joe.fowler(a)nist.gov> > > To: "ifeffit(a)millenia.cars.aps.anl.gov" > > <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) > > Message-ID: <D1759C33-50D0-46D4-84D0-4D649CA779A8(a)nist.gov> > > Content-Type: text/plain; charset="windows-1252" > > > > Dear Ie-Rang, > > > > I?m the demeter maintainer on MacPorts, but I admit I am anything but a > > MacPorts guru. > > > > I notice that the error you showed is a failure to install gcc49. I don?t > > know if that new GCC is compatible with your old version of OS X, but > > that?s an issue that?s beyond my expertise. You might edit your variants > > file (it?s /opt/local/etc/macports/variants.conf on my installation) to > > insist on an earlier version by adding a line containing, e.g., ?+gcc47? > or > > whatever is your installed and preferred version of GCC. > > > > In fact, the port demeter does not depend (directly) on gcc, which you > can > > see by issuing the command > > > > > port echo depof:demeter > > > port echo depof:demeter-devel > > > > So it looks to me like you have several steps to get ready for installing > > demeter. > > > > I admit that I recently discovered?but have not fixed?a flaw in the > > demeter port description file. The code depends on ports p5.16-file-which > > and p5.16-math-round, but these are not made explicit. I need to figure > out > > how to add these to the explicit dependency list. I?m just back from > > vacation and a conference, so I have no excuses now. If you get far > enough > > that you can install *but not run* demeter?s executables, then a > workaround > > for this is > > > > > sudo port install p5.16-file-which p5.16-math-round > > > > And for MacPorts users in general: I understand that the project as a > > whole is in the process of trying to move to Perl 5.22 instead of 5.16. > > I?ll be updating the port file to reflect that change, too. > > > > Joe Fowler > > NIST Boulder Laboratories > > > > > > On Jul 29, 2015, at 4:01 PM, 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(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: failed to install gcc49 on mac (v10.6.8) (Ie-Rang Jeon) > > 2. Re: HELP: failed to install gcc49 on mac (v10.6.8) (Bruce Ravel) > > 3. Error in Running XANES on FEFF8.4 for Cobalt based cluster > > (Ganesh Subramanian) > > > > From: Ie-Rang Jeon <jeon(a)northwestern.edu> > > Subject: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) > > Date: July 29, 2015 at 1:11:08 PM MDT > > To: "ifeffit(a)millenia.cars.aps.anl.gov" < > ifeffit(a)millenia.cars.aps.anl.gov > > > > > Reply-To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov > > > > > > > > Hello, > > > > I'm trying to install MacPorts package on my mac (v.10.6.8), and I can't > > do this. Below are error messages that I got. > > Could you please help me to figure out what the problem is? > > > > Thank you. > > Ie-Rang > > > > > > ----------------------------------- > > > > ---> Building gcc49 > > Error: org.macports.build for port gcc49 returned: command execution > failed > > Error: Failed to install gcc49 > > Please see the log file for port gcc49 for details: > > > > > /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log > > Error: The following dependencies were not installed: > > . > > . > > . > > Error: Processing of port demeter-devel failed > > > > > > > > > > > > > > From: Bruce Ravel <bravel(a)bnl.gov> > > Subject: Re: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) > > Date: July 29, 2015 at 1:21:06 PM MDT > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Reply-To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov > > > > > > > > On 07/29/2015 03:11 PM, Ie-Rang Jeon wrote: > > Hello, > > > > I'm trying to install MacPorts package on my mac (v.10.6.8), and I can't > > do this. Below are error messages that I got. > > Could you please help me to figure out what the problem is? > > > > Thank you. > > Ie-Rang > > > > Perhaps there's anything useful in that log file? > > B > > > > > > > > > > ----------------------------------- > > > > ---> Building gcc49 > > Error: org.macports.build for port gcc49 returned: command execution > failed > > Error: Failed to install gcc49 > > Please see the log file for port gcc49 for details: > > > > > /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log > > Error: The following dependencies were not installed: > > . > > . > > . > > Error: Processing of port demeter-devel failed > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > > > > > -- > > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > > > National Institute of Standards and Technology > > Synchrotron Science Group at NSLS-II > > Building 535A > > Upton NY, 11973 > > > > Homepage: http://bruceravel.github.io/home/ > > Software: https://github.com/bruceravel > > Demeter: http://bruceravel.github.io/demeter/ > > > > > > > >

1 0

Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt based cluster
by Ganesh Subramanian 28 Aug '15

28 Aug '15

Dear Bruce, Thanks for the response and sorry for the delay in getting back to you. I retried the FEFF simulation using structural information from another article (Randaccio, Lucio, et al. *Inorganic chemistry* 39.15 (2000): 3403-3413). The structural data from this article seems to be widely used by many others in simulating for optical absorption. But here with FEFF, I still run into the same issue of "ATOMS VERY CLOSE TOGETHER" and a couple of other issues. With two different articles suggesting smaller bond distances for a few of their atoms, it seems like the distances are what they are. I have attached the log files and input file for this trial run. Is there any way to circumvent this error without altering the structure ? Thanks, Ganesh > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt > based cluster > Message-ID: <55BA3978.4080801(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 07/29/2015 06:01 PM, Ganesh Subramanian wrote: > > 1. *Using the FOLP card*: The actual cluster size is about 180 atoms > > extending upto 18 A in radial distance from the central cobalt atom. But > > there are quite a few instances of Hydrogen atoms that are too close. I > > tried the FOLP with the recommendation for Hydrogen of 0.8, I seem to > > get a syntax type error, that i cant figure out. I checked the crystal > > structure and the smallest hydrogen bond distance is 0.89 A. (I have > > attached the corresponding input and log file with suffix 'full cluster') > > In Feff the "TWO ATOMS VERY CLOSE TOGETHER" message gets shouted at you > when you have atoms that are separated by 1.75 Angstroms or less. That > message has nothing to do with the FOLP setting. > > > 2. *SCF for small cluster*: Since the problem with the hydrogen > > distances persisted, I decided to run the calculation for a smaller > > cluster (about 50 atoms). I used the conditions as prescribed for small > > clusters - SCF 5.0 1, FMS 5.0 1, RPATH -1. Those hydrogens that were too > > close (within this smaller cluster, there were about 3 of them, and none > > in the first or second shell of co-ordination) were removed manually. > > Now, I did not have the error on distances, did not require the FOLP > > card to be manually altered, but the log1 file seems to suggest that the > > SCF is not calculated. I cant figure why that is the case. (I have > > attached the corresponding input and log file with suffix 'small > cluster') > > When I ran feff 8.40, I got same the contents of the log1.dat file, but > with these additional lines: > > Core-valence separation > WARNING: fatal error in subroutine corval. Try > to reduce ca1 in SCF card. If does not help, > SEND bug report to AUTHORS > CORVAL-1 > > I don't quite know what that means, but it gives some hints. The source > code corval.f tells us that is "Finds the core-valence separation for > the cluster of atoms." I simply am not knowledgeable enough about the > details of Feff to know why your cluster triggered this warning. > > B > > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 3 > Date: Thu, 30 Jul 2015 10:51:30 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt > based cluster > Message-ID: <55BA39F2.4090609(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 07/30/2015 10:49 AM, Bruce Ravel wrote: > >> 1. *Using the FOLP card*: The actual cluster size is about 180 atoms > >> extending upto 18 A in radial distance from the central cobalt atom. But > >> there are quite a few instances of Hydrogen atoms that are too close. I > >> tried the FOLP with the recommendation for Hydrogen of 0.8, I seem to > >> get a syntax type error, that i cant figure out. I checked the crystal > >> structure and the smallest hydrogen bond distance is 0.89 A. (I have > >> attached the corresponding input and log file with suffix 'full > cluster') > > > > In Feff the "TWO ATOMS VERY CLOSE TOGETHER" message gets shouted at you > > when you have atoms that are separated by 1.75 Angstroms or less. That > > message has nothing to do with the FOLP setting. > > Oops! That message is triggered for atoms separated by 1.75 bohr, which > is about 0.92 Angstrom. > > B > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > ------------------------------ > > Message: 4 > Date: Thu, 30 Jul 2015 15:58:12 +0000 > From: "Fowler, Joseph W." <joe.fowler(a)nist.gov> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) > Message-ID: <D1759C33-50D0-46D4-84D0-4D649CA779A8(a)nist.gov> > Content-Type: text/plain; charset="windows-1252" > > Dear Ie-Rang, > > I?m the demeter maintainer on MacPorts, but I admit I am anything but a > MacPorts guru. > > I notice that the error you showed is a failure to install gcc49. I don?t > know if that new GCC is compatible with your old version of OS X, but > that?s an issue that?s beyond my expertise. You might edit your variants > file (it?s /opt/local/etc/macports/variants.conf on my installation) to > insist on an earlier version by adding a line containing, e.g., ?+gcc47? or > whatever is your installed and preferred version of GCC. > > In fact, the port demeter does not depend (directly) on gcc, which you can > see by issuing the command > > > port echo depof:demeter > > port echo depof:demeter-devel > > So it looks to me like you have several steps to get ready for installing > demeter. > > I admit that I recently discovered?but have not fixed?a flaw in the > demeter port description file. The code depends on ports p5.16-file-which > and p5.16-math-round, but these are not made explicit. I need to figure out > how to add these to the explicit dependency list. I?m just back from > vacation and a conference, so I have no excuses now. If you get far enough > that you can install *but not run* demeter?s executables, then a workaround > for this is > > > sudo port install p5.16-file-which p5.16-math-round > > And for MacPorts users in general: I understand that the project as a > whole is in the process of trying to move to Perl 5.22 instead of 5.16. > I?ll be updating the port file to reflect that change, too. > > Joe Fowler > NIST Boulder Laboratories > > > On Jul 29, 2015, at 4:01 PM, 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 > 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: failed to install gcc49 on mac (v10.6.8) (Ie-Rang Jeon) > 2. Re: HELP: failed to install gcc49 on mac (v10.6.8) (Bruce Ravel) > 3. Error in Running XANES on FEFF8.4 for Cobalt based cluster > (Ganesh Subramanian) > > From: Ie-Rang Jeon <jeon(a)northwestern.edu> > Subject: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) > Date: July 29, 2015 at 1:11:08 PM MDT > To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov > > > Reply-To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > > Hello, > > I'm trying to install MacPorts package on my mac (v.10.6.8), and I can't > do this. Below are error messages that I got. > Could you please help me to figure out what the problem is? > > Thank you. > Ie-Rang > > > ----------------------------------- > > ---> Building gcc49 > Error: org.macports.build for port gcc49 returned: command execution failed > Error: Failed to install gcc49 > Please see the log file for port gcc49 for details: > > /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log > Error: The following dependencies were not installed: > . > . > . > Error: Processing of port demeter-devel failed > > > > > > > From: Bruce Ravel <bravel(a)bnl.gov> > Subject: Re: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) > Date: July 29, 2015 at 1:21:06 PM MDT > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Reply-To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > > On 07/29/2015 03:11 PM, Ie-Rang Jeon wrote: > Hello, > > I'm trying to install MacPorts package on my mac (v.10.6.8), and I can't > do this. Below are error messages that I got. > Could you please help me to figure out what the problem is? > > Thank you. > Ie-Rang > > Perhaps there's anything useful in that log file? > B > > > > > ----------------------------------- > > ---> Building gcc49 > Error: org.macports.build for port gcc49 returned: command execution failed > Error: Failed to install gcc49 > Please see the log file for port gcc49 for details: > > /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log > Error: The following dependencies were not installed: > . > . > . > Error: Processing of port demeter-devel failed > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > > >

1 0

Academic Career Opportunity in X-ray Spectroscopy at the University of Leeds
by Sven L. M. Schroeder 23 Aug '15

23 Aug '15

Dear colleagues I would like to advertise an exciting career opportunity for an X-ray spectroscopist at the University of Leeds. Leeds is one of the top 10 research-intensive Universities in the UK. Through our international academic recruitment programme ( http://250greatminds.leeds.ac.uk ) we wish to consolidate our strategic relationship with Diamond Light Source by appointing a University Academic Fellow in Structure-Function Determination in Complex Soft Matter Systems Chemical product and process engineering can now take advantage of structure analysis with a broad range of X-ray techniques that have become available at the UKs synchrotron radiation source, DIAMOND. The focus of the research is to determine structure information across length scales, ideally in situ under process conditions, and from molecular to macroscopic dimensions, and to combine such information with multi-scale models to generate a seamless understanding of the relationships between microstructure, processing conditions and product performance. The Fellowship is an exciting opportunity for an engineer or physical scientist with an interest in determining structural/performance relationships in complex products, particularly soft matter systems, with synchrotron radiation techniques. Salary: £38,511 to £45,954 Closing Date: Wednesday 30 September 2015 Reference: ENGPE1026 Career Pathway: Successful completion of a 5 year probationary period leading to appointment to Grade 9, Associate Professor. More particulars are available at: https://jobs.leeds.ac.uk/Upload/vacancies/files/2719/ENGPE1026 - UAF in Structure-Function Determination in Complex Soft Matter1.pdf <https://jobs.leeds.ac.uk/Upload/vacancies/files/2719/ENGPE1026%20-%20UAF%20 in%20Structure-Function%20Determination%20in%20Complex%20Soft%20Matter1.pdf> For informal enquiries about the role please feel free to contact me as per details below. -- Sven L. M. Schroeder Royal Academy of Engineering Bragg Centenary Chair School of Chemical and Process Engineering | Institute for Particle Science and Engineering (IPSE) | University of Leeds | Leeds LS2 9JT | UK Room 2.22 | Engineering Building T +44 (0)113 343 2401 | PA/secretary (Kirn Jutlla) +44 (0)113 343 2404 | F +44 (0)113 343 2384 E <mailto:s.l.m.schroeder@leeds.ac.uk> s.l.m.schroeder(a)leeds.ac.uk | W <https://www.engineering.leeds.ac.uk/people/staff/s.l.m.schroeder> https://www.engineering.leeds.ac.uk/people/staff/s.l.m.schroeder

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Re: [Ifeffit] XANES simulation K-edges
by Joshua Kas 19 Aug '15

19 Aug '15

Hi Debora, The edge energies are very difficult to calculate, and FEFF only calculates them to roughly 5% accuracy. In this case the accuracy is actually much better. However, relative edge energies between different systems may be more reliable. Most comparisons between theoretical and experimental XANES allow for a shift of the edge to align the spectra. If the comparison is of several systems, a single shift should be used for all of them. Cheers, Josh Kas On Wed, Aug 19, 2015 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. XANES simulation K-edges (Debora Meira) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 19 Aug 2015 08:50:47 +0000 > From: Debora Meira <debsmeira(a)hotmail.com> > To: "ifeffit(a)millenia.cars.aps.anl.gov" > <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] XANES simulation K-edges > Message-ID: <BLU181-W70FD27721CD14A2C97998CAD670(a)phx.gbl> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > I'd like to know which kind of concern I should have for feff to simulate > the XANES for K-edges. I'm asking because I'm trying to simulate Sn K-edge > and I have around 30 eV energy shift for the edge position. Can it be > related with a wrong parameter for one of the cards? > Thank you, Debora Meira >

1 0

XANES simulation K-edges
by Debora Meira 19 Aug '15

19 Aug '15

Dear all, I'd like to know which kind of concern I should have for feff to simulate the XANES for K-edges. I'm asking because I'm trying to simulate Sn K-edge and I have around 30 eV energy shift for the edge position. Can it be related with a wrong parameter for one of the cards? Thank you, Debora Meira

1 0

MacPorts now contains Demeter 0.9.22 (and requires Perl 5.22)
by Fowler, Joseph W. 14 Aug '15

14 Aug '15

Dear Bruce: Wait a minute! In fact, I updated the Mac Ports package demeter within the last two weeks to use Demeter version 0.9.22. Mac users might want to use the latest version and should consider doing a "port self update && port upgrade demeter". Users who installed the development version port called demeter-devel will also land on 0.9.22 if they upgrade to the latest. Note that the latest Mac Ports version is known as 0.9.22_1, where the revision number _1 corresponds to the upgrade from Perl 5.16 to 5.22 (which the MacPorts team is pushing on). For many users, there will be numerous dependency upgrades when you upgrade to 0.9.22_1, but I found they took only a few minutes in my particular case. This change in Perl versions could conceivably cause problems, but I haven't heard of any. Best wishes, Joe Fowler (MacPorts maintainer for demeter) ________________________________ From: Bruce Ravel <bravel(a)bnl.gov> Sent: Tuesday, August 11, 2015 6:55 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Energy shift after deglitch I don't see the behavior you describe when I follow your recipe. Perhaps it got fixed when I fixed this fellow's issue...? http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2015-May/012496.html Of course, the Mac package is a fair bit behind at this point. B On 08/06/2015 06:10 PM, George Sterbinsky wrote: > Hello, > > I am writing to report a bug in Athena running on OSX 10.10.4. Here are > the steps to reproduce the problem. I'm not sure that all steps are > necessary. > > 1. Open Athena and import the attached project, which contains two > groups that are both marked. > 2. Change plot range to plot from -30 to 30 eV. > 3. Select the "deglitch and truncate" window. > 4. Select group "Ref data.merge". > 5. In deglitch many points, set margin to 0.05, Emin to -24, and Emax to > -20. > 6. Click replot margins. > 7. Click remove points. > 8. Click return to main window. > 9. Click the derivative check box to plot marked groups as normalized > derivative. > 10. Click mu(E) button to plot marked groups as derivative of mu(E). > > When the last step is done the groups appear to shift with respect to > each other. One can switch between Normalized and mu(E) and see the > shift come and go. > > Thank you, > George > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

2 3

La2Zr2O7 EXAFS fitting
by herve muguerra 14 Aug '15

14 Aug '15

Dear All, First of all, I am still very new in EXAFS analysis, so please excuse me for any misunderstandings. My sample is a crystalized La2Zr2O7 thin layer (thickness = 100 nm) on a NiW substrate and we have realized EXAFS measurements by grazing angle under primary vacuum at Lathanum L3 edge (ESRF, Grenoble, France). My objectives are to establish the local distortions due to the different constraints in the oxide thin layer. The La2zr2O7 crystalized in a pyrochlore structure (SG = Fd-3m ; a = 10.78A). First scattering path La-O2.1 2.3352A La-O1.1 2.6453A But I have a problem: I observe the first peaks at 1.28A and 1.80A on the EXAFS spectra as a function of R. How do you explain this feature? Can you point me in the right direction for these issues? I attached the project file La_80_LZO_1000.prj of my sample: LAHM045 to LAHM50 = 6 different scans La_80_LZO_1000 = Data merge Thanks Best regards Hervé Muguerra

2 1

Demeter installation on Debian
by Isabelle Kieffer 14 Aug '15

14 Aug '15

Dear all, I am trying to install demeter on my debian 7 computer and I cannot reach the end of the compilation. I followed the instructions from the https://gist.github.com/3959252 page. First, the "perl ./Build.PL" still requires "PDL::stats" even after several "./Build installdeps". I have the following message: """""""""""""""""""""""""""""""""""""""""""""""""""" letard@pcikieffer:~/demeter$ perl ./Build.PL Checking prerequisites... requires: ! PDL::Stats is not installed ERRORS/WARNINGS FOUND IN PREREQUISITES. You may wish to install the versions of the modules indicated above before proceeding with this installation Run 'Build installdeps' to install missing prerequisites. Created MYMETA.yml and MYMETA.json Creating new 'Build' script for 'Demeter' version 'v0.9.21' If all dependencies are met, build and install Demeter by doing: ./Build ./Build test ./Build install # (or sudo ./Build install) If you are reinstalling Demeter after updating your operating system (or updating perl), you may find that none of the programs will run successfully. You may need to do: ./Build touch_wrapper ./Build test ./Build install # (or sudo ./Build install) """""""""""""""""""""""""""""""""""""""""""""""""""" Then, I decided to continue despite this missing prerequisite and the "./Build" ends with the folowing error: ##### Building Artemis User's Guide Building Athena User's Guide ! plugin error - Can't locate Clone.pm in @INC (@INC contains: /home/letard/perl5/lib/perl5/x86_64-linux-gnu-thread-multi /home/letard/perl5/lib/perl5/x86_64-linux-gnu-thread-multi /home/letard/perl5/lib/perl5 /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at /usr/local/share/perl/5.14.2/PPI/Element.pm line 25. BEGIN failed--compilation aborted at /usr/local/share/perl/5.14.2/PPI/Element.pm line 25. Compilation failed in require at /usr/local/share/perl/5.14.2/PPI.pm line 19. BEGIN failed--compilation aborted at /usr/local/share/perl/5.14.2/PPI.pm line 19. Compilation failed in require at Template/Plugin/PerlSyntaxHtml.pm line 5. BEGIN failed--compilation aborted at Template/Plugin/PerlSyntaxHtml.pm line 5. Compilation failed in require at /home/letard/perl5/lib/perl5/x86_64-linux-gnu-thread-multi/Template/Plugins.pm line 206. ##### So I don't know if something is missing on my computer or if one of you encountered similar problems. If one of you has some ideas to help me going further, I would really appreciate! Thanks a lot in advance. Isabelle -- Isabelle KIEFFER, Ingénieur de Recherche CNRS, Ligne CRG FAME (BM30B) ESRF - The European Synchrotron CS 40220 - 38043 Grenoble Cedex 9 - France Tel : +33 (0)4 76 88 25 47 - Bureau : LOB 2-50

2 7

Energy shift after deglitch
by George Sterbinsky 11 Aug '15

11 Aug '15

Hello, I am writing to report a bug in Athena running on OSX 10.10.4. Here are the steps to reproduce the problem. I'm not sure that all steps are necessary. 1. Open Athena and import the attached project, which contains two groups that are both marked. 2. Change plot range to plot from -30 to 30 eV. 3. Select the "deglitch and truncate" window. 4. Select group "Ref data.merge". 5. In deglitch many points, set margin to 0.05, Emin to -24, and Emax to -20. 6. Click replot margins. 7. Click remove points. 8. Click return to main window. 9. Click the derivative check box to plot marked groups as normalized derivative. 10. Click mu(E) button to plot marked groups as derivative of mu(E). When the last step is done the groups appear to shift with respect to each other. One can switch between Normalized and mu(E) and see the shift come and go. Thank you, George

2 2

Unable to install demeter
by pushkar shejwalkar 10 Aug '15

10 Aug '15

Dear Users and Bruce, I am trying to install demeter with 64bits for my windows 7 professional laptop {4 gb ram, ample amount of free memory} . I tried downloading using both available links 1( on the left side of the window with the button for 64 bits and then by cliking the link in the text too. For some reason it didnt downloaded the file. I tried using 32 bits just to check and it started downloading * i didnt finish that and canceled the download since I dont need that one. Following error message appeared in the window This XML file does not appear to have any style information associated with it. The document tree is shown below. Could anyone help me with this whats wrong? I am using demeter on my other laptop and its working perfectly. Best Pushkar -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Sapporo, Japan

2 1

XAFS short course in BNL on Nov 5-7: Save the date
by Anatoly I Frenkel 07 Aug '15

07 Aug '15

Dear IFEFFIT subscribers: Please save the dates, Nov. 5-7, 2015, of the annual XAFS short course in Brookhaven National Laboratory. As many of you may know, we vary our themes from year to year, and we also vary the target levels for participants from beginners to intermediate to advanced. This year the target level for participants is "advanced", as suggested by the course title "Advanced topics in XAFS data modeling". It is similar in scope to our other courses on this subject (the latest one was offered in Brookhaven in 2010) that are available online: http://www.yu.edu/scc/workshops-courses/ This time the course will be divided in two parts: non-linear analysis methods (FEFF theory-based) and linear methods (based on methods of multivariate analysis and linear algebra such as LCF, PCA and MCR-ALS). Nov. 5 (Thursday) and Nov. 6 (Friday) will be devoted to lectures and demonstrations of the software. Nov. 7 (Saturday) will be practical session, in which registered participants will practice problem solving methods discussed in the previous days. Confirmed instructors are: Alain Michalowicz, Stephen Wasserman, Faisal Alamgir, Scott Calvin and Anatoly Frenkel. A full list of instructors and additional information on the course will soon appear on BNL web site. Participation in the practical data analysis session will be limited to 30 registered attendees, although auditors are welcome to attend the lectures and demonstrations on Thursday and Friday. For any inquiries please use contact info on the course web that will soon come online. Best regards, Anatoly Frenkel Yeshiva University Anatoly Frenkel, Ph.D. Professor and Chair, Department of Physics, Yeshiva University 245 Lexington Avenue, New York, NY 10016 https://yu.edu/faculty-bios/frenkel/ Spokesperson, Synchrotron Catalysis Consortium http://yu.edu/scc Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.frenkel(a)yu.edu<mailto:anatoly.frenkel@yu.edu>

3 4

Demeter installation on partition "d" on Windows 7 32 bit -- programs do not start
by Rene Genz 05 Aug '15

05 Aug '15

Dear sir or madam, I would like to file a bug report. I can reproduce the problem with the following versions of Demeter: Demeter_Installer_for_Windows_0.9.22_(32).exe Demeter_Installer_for_Windows_0.9.23_(32)_pre1.exe downloaded from: http://bruceravel.github.io/demeter/ I have not tested other versions. I am using Windows 7 32 bit. I could reproduce this problem on two different computers with Windows 7 32 bit. During installation you are asked to define the installation directory. The default value is: c:\strawberry If you specify: d:\strawberry and continue with installation there are no error messages. However, after installation Artemis will not start. The start picture is shown but vanishes after a second. No other output. I tried Hephaestus (if memory serves right) and it has the same problem. I did not try other programs from the Demeter package. The log file taken from "%appdata%\demeter\dartemis.log" produced by Demeter_Installer_for_Windows_0.9.23_(32)_pre1.exe is attached. The mentioned files in the log are present. I replaced / with \ in the terminal commands: > dir d:\strawberry\perl\site\lib\auto\Ifeffit Volume in drive D has no label. Volume Serial Number is 7CA2-C104 Directory of d:\strawberry\perl\site\lib\auto\Ifeffit 05.08.2015 17:03 <DIR> . 05.08.2015 17:03 <DIR> .. 25.06.2014 16:18 0 Ifeffit.bs 08.07.2014 14:19 795.136 Ifeffit.dll 2 File(s) 795.136 bytes 2 Dir(s) 11.455.164.416 bytes free > dir d:\strawberry\perl\lib\DynaLoader.pm Volume in drive D has no label. Volume Serial Number is 7CA2-C104 Directory of d:\strawberry\perl\lib 15.04.2014 18:12 25.696 DynaLoader.pm 1 File(s) 25.696 bytes 0 Dir(s) 11.455.164.416 bytes free A workaround is: - uninstall demeter - install demeter to default installation directory "c:\strawberry" Kind regards, René

3 2

Possibly non-reproduceable fits
by Godfrey, Ian 04 Aug '15

04 Aug '15

Dear All, Please bear with me here - it's possible I've done something stupid without spotting it - but I was fitting some data in Artemis and have two fits, that I am convinced should be identical (same data, same k and r windows, same paths, same GDS etc. etc.), but are not. What I did was as follows (fit numbers refer to the Artemis history file in the attached project): I set up a fit to some data, simultaneously refining at Au and Ag edges to Au-Au/Au-Ag/Ag-Au/Au-Ag paths (fits 1 & 2), and then tried a different fit, this time with Ag-Cl paths as well (fits 3&4). I then fitted the original model again (fit 5 - this was slightly different to 1 & 2, but not enough for me to notice at the time). I then closed Artemis and finished for the day. Today I came back, reloaded the project file, saved it in a new location, and tried to pick up where I left off. I performed one fit where I'd set the values to def, rather than guess, by mistake (fit 6) and then corrected this when I realised what I'd done. However when I tried to re-run the model with Ag-Cl paths I was getting wildly different results to the first time (Fits 7&8). As far as I can tell these models should be identical to fits 3&4. Both datasets were chi(k) data imported directly into Artemis. OS: Win 8.1 Ent x64 Demeter: 0.9.22 pre something x64 I've attached the following: Artemis project (artemis.fpj) Logs from fits 3 and 7 for comparison (fit3.txt, fit7.txt) Artemis log file (dartemis.log). (Also possibly worth noting is that Artemis seems to have lost the file locations (in the log files and the data window), first for the Au edge data, and then for both datasets; however when I plot the data it all seems present and correct!) Any insight gratefully received! 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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Localisation issue with plots in Demeter 0.9.22
by Godfrey, Ian 04 Aug '15

04 Aug '15

Dear All, There seems to be an issue with the way plots are displayed on non-English computers: My office PC is Japanese (although set to English) and I'm seeing spurious katakana (Japanese) characters in the GNUPlot plots generated by Artemis (as well as an Angstrom that's missing its circle)! Screenshot attached. System: Demeter 0.9.22 x64, Win 8.1 Ent x64. Regards, 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] Ifeffit Digest, Vol 150, Issue 3
by Abhijeet Gaur 04 Aug '15

04 Aug '15

Hi Max, Thanks for the explaning the probable reason of smaller particle sizes determined by EXAFS. I will also try to refine my fittings. Hi Anatoly, Can you please send me the link of that recent paper again as I am unable to find it in your earlier message. Abhijeet On Mon, Aug 3, 2015 at 6:04 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Ifeffit Digest, Vol 150, Issue 2 (Abhijeet Gaur) > 2. Re: Measuring particle size by coordination number (Maxim Boyanov) > 3. Re: Measuring particle size by coordination number > (Anatoly I Frenkel) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 3 Aug 2015 13:49:40 +0200 > From: Abhijeet Gaur <abhijeetgaur9(a)gmail.com> > To: ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Ifeffit Digest, Vol 150, Issue 2 > Message-ID: > < > CAEq27Q1Fde2qTQyrgaAMaTJ1wUpoXydxOcS0v73MPXdAKJs_zA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Scott, > > Thanks for your quick reply. So, I have to add more paths to > the fitting and then try to determine the size of the particle. > > Also, I want to add some analysis details to confirm that I am > on the right path. > > The value of amp is obtained from fitting of metal foil, i.e., > 0.84 (0.03) and is kept fixed during the fitting of the sample. > > S02 is defined by the formula S02 = > amp*(1-(0.75*(Reff/R))+(0.063*(Reff*Reff*Reff/(R*R*R)))). > > With thanks > > Abhijeet > > > > > > > > > > Message: 2 > > Date: Mon, 3 Aug 2015 07:11:53 -0400 > > From: Scott Calvin <scalvin(a)sarahlawrence.edu> > > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > > Subject: Re: [Ifeffit] Measuring particle size by coordination number > > Message-ID: <C61F6046-713C-4EC2-8F7A-536ECC43DEA5(a)slc.edu> > > Content-Type: text/plain; charset="utf-8" > > > > Hi Abhijeet, > > > > The formula looks poorly when it is only applied with one path. > > > > The strength of this approach, and of Anatoly Frenkel?s alternative > > strategy for finding particle sizes, is that it compares coordination > > numbers for different shells, helping to break the correlations between > N, > > S02, and sigma2. > > > > Even then, it tends to report sizes that are small compared to those > > provided by other techniques, but compares sizes between different > samples > > quite well. > > > > ?Scott Calvin > > Sarah Lawrence College > > > > > > > > > -- > *Dr. Abhijeet Gaur* > *Post doctoral fellow in the Institute for Chemical Technology and Polymer > Chemistry * > *Karlsruher Institut f?r Technologie (KIT), Karlsruhe Germany.* >

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Measuring particle size by coordination number
by Abhijeet Gaur 03 Aug '15

03 Aug '15

Hi all, Sorry, I may be asking a question already asked in the mailing list, but I am unable to get it from the earlier discussions. I am reading one of the research article ´´ Determination of crystallite size in a magnetic nanocomposite using extended x-ray absorption fine structure´´ .J. Appl. Phys,. vol 94, page 778, 2003 In this paper there is a formula N_nano = [1-3/4(r/R)+1/16(r/R)^3]N_bulk, which you said can be used in the Artemis for extracting the particle size. I am trying to use this formula for determination of size of Ni particles in an Ni / Al2O3 catalyst. From TEM the size determined is around 4 nm. So, I am trying to fit the theoretical model of Ni metal to the sample data in the Artemis I defined a guessed parameter R and then put the whole formula for S02 = amp*(1-(0.75*(Reff/R))+(0.063*(Reff*Reff*Reff/(R*R*R)))). The value of R I am getting is 0.81 (0.05) which is quite small. Is there something I am missing in the formula or I have to define the N seprately for sample cooridnation number. Currently, I am using only the first path in the fitting. With thanks Abhijeet Gaur -- *Dr. Abhijeet Gaur* *Post doctoral fellow in the Institute for Chemical Technology and Polymer Chemistry * *Karlsruher Institut für Technologie (KIT), Karlsruhe Germany.*

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Re: [Ifeffit] Ifeffit Digest, Vol 150, Issue 2
by Abhijeet Gaur 03 Aug '15

03 Aug '15

Hi Scott, Thanks for your quick reply. So, I have to add more paths to the fitting and then try to determine the size of the particle. Also, I want to add some analysis details to confirm that I am on the right path. The value of amp is obtained from fitting of metal foil, i.e., 0.84 (0.03) and is kept fixed during the fitting of the sample. S02 is defined by the formula S02 = amp*(1-(0.75*(Reff/R))+(0.063*(Reff*Reff*Reff/(R*R*R)))). With thanks Abhijeet > > > Message: 2 > Date: Mon, 3 Aug 2015 07:11:53 -0400 > From: Scott Calvin <scalvin(a)sarahlawrence.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Measuring particle size by coordination number > Message-ID: <C61F6046-713C-4EC2-8F7A-536ECC43DEA5(a)slc.edu> > Content-Type: text/plain; charset="utf-8" > > Hi Abhijeet, > > The formula looks poorly when it is only applied with one path. > > The strength of this approach, and of Anatoly Frenkel?s alternative > strategy for finding particle sizes, is that it compares coordination > numbers for different shells, helping to break the correlations between N, > S02, and sigma2. > > Even then, it tends to report sizes that are small compared to those > provided by other techniques, but compares sizes between different samples > quite well. > > ?Scott Calvin > Sarah Lawrence College > > > -- *Dr. Abhijeet Gaur* *Post doctoral fellow in the Institute for Chemical Technology and Polymer Chemistry * *Karlsruher Institut für Technologie (KIT), Karlsruhe Germany.*

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Vanadium-Chromium Prussian Blue Analog XANES fitting
by Adora Graham 31 Jul '15

31 Jul '15

Hello, First of all, I am still very new to XAS analysis, so please excuse any misunderstandings I may have. I have a series of compounds nominally consisting of KxVx[Cr(CN)6] Prussian blue analogs (where x is ~1) with Cr(III) and presumably V(II) present in the system. From other evidence, the V(II) may be oxidizing to V(III). I have XAS data collected at the V and Cr K-edges from APS and have been struggling through trying to analyze my data using Athena. I am trying to get two things out of this data: First, I would like to get the oxidation state of the Vanadium sites. If they are not V(II), to get the ratio of V(II) to V(III) present, if possible. I have been trying to follow a similar analysis to Wong (Phys. Rev. B, 1984, 30, 10, 5596-5610). However, I seem to be running into the issue of finding standards with a similar ligand set to my sample. I have XAS data for the following standards: VO, V2O3, V2O4, V2O5, V(acac)3, VO(acac), VOSO4, and VSO4. I start with VSO4 as my initial vanadium source, so that could be useful for a comparison. Our initial idea was to use the vanadium oxides to give a standard curve to then extrapolate the oxidation state of my compound, but using this gives me an oxidation state of ~4.2 which seems unreasonable for my system. I am kind of lost otherwise as to what else I could do with this. Second, I would like to get the ratio of V to Cr. I was told I could compare the un-normalized K-edge heights of the vanadium to that of the chromium to get this ratio. This doesn't seem right, as I would think that there should be some relative intensity factor involved. Also, this gives me a fairly unreasonable value of 4:1, since XPS measurements give me values of around 1:1. Can you point me in the right direction for these issues? I've also attached the project files for one of my samples. Thanks, Adora

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Re: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8)
by Fowler, Joseph W. 30 Jul '15

30 Jul '15

Dear Ie-Rang, I’m the demeter maintainer on MacPorts, but I admit I am anything but a MacPorts guru. I notice that the error you showed is a failure to install gcc49. I don’t know if that new GCC is compatible with your old version of OS X, but that’s an issue that’s beyond my expertise. You might edit your variants file (it’s /opt/local/etc/macports/variants.conf on my installation) to insist on an earlier version by adding a line containing, e.g., “+gcc47” or whatever is your installed and preferred version of GCC. In fact, the port demeter does not depend (directly) on gcc, which you can see by issuing the command > port echo depof:demeter > port echo depof:demeter-devel So it looks to me like you have several steps to get ready for installing demeter. I admit that I recently discovered—but have not fixed—a flaw in the demeter port description file. The code depends on ports p5.16-file-which and p5.16-math-round, but these are not made explicit. I need to figure out how to add these to the explicit dependency list. I’m just back from vacation and a conference, so I have no excuses now. If you get far enough that you can install *but not run* demeter’s executables, then a workaround for this is > sudo port install p5.16-file-which p5.16-math-round And for MacPorts users in general: I understand that the project as a whole is in the process of trying to move to Perl 5.22 instead of 5.16. I’ll be updating the port file to reflect that change, too. Joe Fowler NIST Boulder Laboratories On Jul 29, 2015, at 4:01 PM, 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 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: failed to install gcc49 on mac (v10.6.8) (Ie-Rang Jeon) 2. Re: HELP: failed to install gcc49 on mac (v10.6.8) (Bruce Ravel) 3. Error in Running XANES on FEFF8.4 for Cobalt based cluster (Ganesh Subramanian) From: Ie-Rang Jeon <jeon(a)northwestern.edu> Subject: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) Date: July 29, 2015 at 1:11:08 PM MDT To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Reply-To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Hello, I'm trying to install MacPorts package on my mac (v.10.6.8), and I can't do this. Below are error messages that I got. Could you please help me to figure out what the problem is? Thank you. Ie-Rang ----------------------------------- ---> Building gcc49 Error: org.macports.build for port gcc49 returned: command execution failed Error: Failed to install gcc49 Please see the log file for port gcc49 for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log Error: The following dependencies were not installed: . . . Error: Processing of port demeter-devel failed From: Bruce Ravel <bravel(a)bnl.gov> Subject: Re: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8) Date: July 29, 2015 at 1:21:06 PM MDT To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Reply-To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> On 07/29/2015 03:11 PM, Ie-Rang Jeon wrote: Hello, I'm trying to install MacPorts package on my mac (v.10.6.8), and I can't do this. Below are error messages that I got. Could you please help me to figure out what the problem is? Thank you. Ie-Rang Perhaps there's anything useful in that log file? B ----------------------------------- ---> Building gcc49 Error: org.macports.build for port gcc49 returned: command execution failed Error: Failed to install gcc49 Please see the log file for port gcc49 for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log Error: The following dependencies were not installed: . . . Error: Processing of port demeter-devel failed _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Error in Running XANES on FEFF8.4 for Cobalt based cluster
by Ganesh Subramanian 30 Jul '15

30 Jul '15

Dear all, I was trying to simulate XANES using FEFF8.4 at Cobalt K edge. This is for a cluster and not a crystal. I encountered two problems. 1. *Using the FOLP card*: The actual cluster size is about 180 atoms extending upto 18 A in radial distance from the central cobalt atom. But there are quite a few instances of Hydrogen atoms that are too close. I tried the FOLP with the recommendation for Hydrogen of 0.8, I seem to get a syntax type error, that i cant figure out. I checked the crystal structure and the smallest hydrogen bond distance is 0.89 A. (I have attached the corresponding input and log file with suffix 'full cluster') 2. *SCF for small cluster*: Since the problem with the hydrogen distances persisted, I decided to run the calculation for a smaller cluster (about 50 atoms). I used the conditions as prescribed for small clusters - SCF 5.0 1, FMS 5.0 1, RPATH -1. Those hydrogens that were too close (within this smaller cluster, there were about 3 of them, and none in the first or second shell of co-ordination) were removed manually. Now, I did not have the error on distances, did not require the FOLP card to be manually altered, but the log1 file seems to suggest that the SCF is not calculated. I cant figure why that is the case. (I have attached the corresponding input and log file with suffix 'small cluster') Sorry for the long email, and thank you for any suggestions. Ganesh

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HELP: failed to install gcc49 on mac (v10.6.8)
by Ie-Rang Jeon 29 Jul '15

29 Jul '15

Hello, I'm trying to install MacPorts package on my mac (v.10.6.8), and I can't do this. Below are error messages that I got. Could you please help me to figure out what the problem is? Thank you. Ie-Rang ----------------------------------- ---> Building gcc49 Error: org.macports.build for port gcc49 returned: command execution failed Error: Failed to install gcc49 Please see the log file for port gcc49 for details: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log Error: The following dependencies were not installed: . . . Error: Processing of port demeter-devel failed

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Setting ranges in peak fitting
by Kenneth Latham 28 Jul '15

28 Jul '15

Hi Bruce, To clarify this further, I am peak fitting a number of peaks under the carbon edge. For example, I know from the literature that the 1s-p transition for the C=C should be located between 284.5 to 285.5 eV, so I would fit a peak at about 285 eV to start with. I would then move on to fitting additional peaks based on their literature values with what I know about the material/where obvious peaks are in the NEXAFS. The problem now comes when I tell Athena to fit, it will start to move the peaks all over the place to obtain the best fit, typically placing them in locations where functionalities don't appear under the NEXAFS. In other words, it would move peaks away from where I would expect them to be based on the literature. This can be partially stopped by fixing all but one peak, fitting it and then and applying this procedure to every peak multiple times. What I was wondering is if Athena has the ability to set a range that each peak is allowed to move, i.e., the C=C center would be restricted to values between 284.5-285.5 eV. Hence I could set up the ranges and fit quickly based on those. Cheers, Ken Latham ________________________________________ From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <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: Saturday, 25 July 2015 3:00 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 149, Issue 23 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. Setting ranges in peak fitting Athena (Kenneth Latham) 2. Re: Setting ranges in peak fitting Athena (Ravel, Bruce) 3. Re: Setting ranges in peak fitting Athena (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Fri, 24 Jul 2015 00:14:18 +0000 From: Kenneth Latham <Kenneth.Latham(a)uon.edu.au> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: [Ifeffit] Setting ranges in peak fitting Athena Message-ID: <CY1PR02MB1416E3DBC230406B078F9A07AA810(a)CY1PR02MB1416.namprd02.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Hi Bruce, Is it possible to set a range of values that the the center (or any other values) can be between for line shapes when peak fitting in Athena? Similar to what you can do in CasaXPS. If not, do you know of a program that can handle NEXAFS peak fitting and has that feature? Cheers, Ken ------------------------------ Message: 2 Date: Fri, 24 Jul 2015 13:14:03 +0000 From: "Ravel, Bruce" <bravel(a)bnl.gov> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Setting ranges in peak fitting Athena Message-ID: <xp7hq5h11j0ygmcc2btiht0f.1437743641853(a)email.android.com> Content-Type: text/plain; charset="us-ascii" Hi Ken, I'm sorry, but I don't quite understand your question. And I have no idea what casaXPS is, so that reference doesn't help me. Are you asking whether you can put gaps in the fit range? B On July 23, 2015, at 8:16 PM, Kenneth Latham <Kenneth.Latham(a)uon.edu.au> wrote: Hi Bruce, Is it possible to set a range of values that the the center (or any other values) can be between for line shapes when peak fitting in Athena? Similar to what you can do in CasaXPS. If not, do you know of a program that can handle NEXAFS peak fitting and has that feature? Cheers, Ken _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Two postdoctoral positions
by Anatoly I Frenkel 27 Jul '15

27 Jul '15

Dear subscribers, Please pass along this information to anyone who may be interested in this opportunities. Physics Department of Yeshiva University in New York City has two openings for postdoctoral research associate positions, beginning in September 2015. The first position is for the project: "Collaborative research: Toolkit to characterize and design bi-functional nanoparticle catalysts." The postdoc will be stationed at Brookhaven National Laboratory and use advanced facilities of NSLS-II and other synchrotrons for X-ray absorption spectroscopy measurements. Required qualifications: Ph.D. in physics, chemistry or materials science, expert knowledge of XAS methods, including analysis and modeling of nanoparticles, and experience with in situ characterization methods by XAS and other techniques. The second position is for the project "Multidisciplinary research for the advancement of filtration materials: Uptake, decomposition, and catalysis for Agent-POM/MOF Chemistry". The postdoc will be stationed at Brookhaven National Laboratory and use advanced facilities of NSLS-II and other synchrotrons for high energy XRD-PDF characterization of novel POM/MOF materials in reaction conditions. Required qualifications: Ph.D. in chemistry, chemical engineering or materials science, expert knowledge of XRD-PDF technique and data analysis, experience with analysis of MOFs, experience with in situ and/or operando methods of synchrotron characterization. The research will be performed under the direction of Prof. Anatoly Frenkel. Applicants should forward cover letter with contact information of three references and CV to anatoly.frenkel(a)yu.edu. Yeshiva University is an Equal Opportunity Employer. Anatoly Frenkel, Ph.D., Professor and Chair, Department of Physics, Yeshiva University 245 Lexington Avenue, New York, NY 10016 http://www.yu.edu/faculty/afrenkel Spokesperson, Synchrotron Catalysis Consortium http://www.yu.edu/scc Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.frenkel(a)yu.edu

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Setting ranges in peak fitting Athena
by Kenneth Latham 24 Jul '15

24 Jul '15

Hi Bruce, Is it possible to set a range of values that the the center (or any other values) can be between for line shapes when peak fitting in Athena? Similar to what you can do in CasaXPS. If not, do you know of a program that can handle NEXAFS peak fitting and has that feature? Cheers, Ken

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Plotting chi(k) linear combination fit in energy
by Ellen Daugherty 21 Jul '15

21 Jul '15

Hello, I was unable to find an example of this question in the archive, but please let me know if it has already been addressed. I would like to plot the results of linear combination fits performed in chi(k) in energy space to compare them to XANES fits. When I try to plot the saved fit in energy, I get a message saying: "chi data cannot be plotted in energy." Is there any way to do this other than to use Excel to scale the weights of the standards? This would be exhausting to perform for combinatorial fits. I am using Athena in Demeter 0.9.20 on Windows 7. I have attached a sample and a few standards for aid in addressing the issue. Thank you! Ellen -- Ph.D. Candidate Research Assistant, Borch Lab <http://borch.agsci.colostate.edu/> Department of Chemistry Colorado State University http://borch.agsci.colostate.edu/group-members/ellen-daugherty/

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Artemis Crashing on Opening Project Files (Windows 7)
by alexander.thoma＠diamond.ac.uk 20 Jul '15

20 Jul '15

Hi all, I couldn't seem to find anything like this on the mailing list, I'm having issues reopening saved Artemis (0.9.21) projects on Windows 7, the program opens and runs through the 'importing' text in the bottom left of the control window before shutting down immediately with no error message or warning before any other windows appear. The problem seems to occur sporadically with projects with fits from crystal structures and all the time with those done with quick first shell fits, and doesn't occur with project files where no fits have been made. Attached is the log file for one of the non-opening projects, any suggestions? Many thanks, Alex -- 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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Bug report - autosave on mac
by Jean-Baptiste ABBE 16 Jul '15

16 Jul '15

Hi everybody, I wanted to report a really annoying problem for mac users. I’m running Athena on my laptop, on OSX 10.10 (Yosemite) with macports. I had to install also quartzX11 to be able to plot data (without it, it couldn’t find the DISPLAY value), but otherwise evrything went smoothly for a few days. Then the first bug occured. I wasn’t able anymore to select any point on the plotting area to do normalization, I had to set the value in the boxes instead. It was annoying, but I could manage that. But now I have a much more disturbing issue. Athena once crashed, (in the terminal, it was sait « Terminated 15 »), and every time I tried to launch it again, the same thing happens : 1) athena launch, a little bit longer than usual 2) a box appear to give me choice to recover data by importing it from autosave or not 3) I can’t select anaything and the rainbow wheel of death appears. After a few hours, nothing changes… and I have to terminate the programm manually. So I do some search on the internet and found thoses topics on the mailing list, and I tried thoses solutions : https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04539.html <https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04539.html> https://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg04514.h… <https://www.mail-archive.com/ifeffit@millenia.cars.aps.anl.gov/msg04514.html> I tried to find the autosave file : nothing I tried to uninstall and reinstall macports : nothing I tried to uninstall macports and install the demeter-devel : nothing In demeter-devel, i tried to modify the athena.demeter_config file, by changing the autosave prompt box value from true to false, and despite being admin on ma mac, I’m not able to change antything in the file. So nothing works at this moment. I will try again other solutions, but I will gladly accept any kind of help to solve my issues. Thank you ABBE J-Baptiste

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phase problem copper
by Neeb, Matthias 15 Jul '15

15 Jul '15

Dear all, I have a standard exafs spectrum of copper K-shell and everything looks as expected (Chi(E), Chi(k), Chi(R), Chi(q) …) when using Demeter 0.9.21 . However the phase spectrum of (Chi(q)) appears quite different to literature (e.g. B.K. Teo, Inorganic Chemistry Concepts 9; Martens et al, PRB 17, p1481 (1979), i.e. positive slope, a factor of ~10 larger values on y-axis. Any reason why? Thanks for your answer in advance. Regards, Matthias ________________________________________________________________________ Matthias Neeb Helmholtz-Zentrum-Berlin fuer Materialien und Energie - senior scientist - ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin http://www.helmholtz-berlin.de

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Re: [Ifeffit] Demeter Crashes on opening in Windows Bootcamp
by Ganesh Subramanian 12 Jul '15

12 Jul '15

Dear Matt, Thanks for that suggestion. I just got time to work on it again. In the meantime, I noticed your email response to another question of similar nature. It works fine now ! Of course, I have not yet performed any calculations/analysis to see if there are any additional problems (if any). But so far so good. Thanks for your help, Ganesh On Wed, Jul 8, 2015 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: Demeter Crashes on opening in Windows Bootcamp > (Ganesh Subramanian) > 2. Re: Demeter Crashes on opening in Windows Bootcamp (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 8 Jul 2015 01:07:56 -0700 > From: Ganesh Subramanian <gunkanna(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Demeter Crashes on opening in Windows Bootcamp > Message-ID: > <CAAb9e-d2Kvx=VZRmNPOVBcgpCvqD3x= > t4VLLRdDRFtDJMBUURQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > > > > Dear Bruce and Matt, > > > > > > > > My first guess is that the culprit is anti-virus software running on > > Ganesh's computer. I have seen other examples of parts of Demeter being > > falsely identified as problematic and being removed, rendering the > > Demeter programs unusable. > > > > That said, on Ganesh's computer, the gnuplot executable should be in > > > > C:\strawberry\c\bin\gnuplot\bin > > > > Yes - I can locate it exactly at this path and the executable file does > open from there. > > > > > > > There are some other conceivable ways to see this problem, but I am > > placing my first bet on over-aggressive anti-virus software. > > > > I did have McAfee. I uninstalled the program and restarted my computer > and > the problem still persists. It seems very much the same, im posting the > most recent log-file. > > > > > *************************************** > > >

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Re: [Ifeffit] Ifeffit Digest, Vol 149, Issue 8
by Ganesh Subramanian 12 Jul '15

12 Jul '15

Dear Matt, Thanks for that suggestion. I just got time to work on it again. In the meantime, I noticed your email response to another question of similar nature. And it works fine now ! Of course, I have not yet performed any calculations/analysis to see if there are any additional problems (if any). But so far so good. Thanks for your help, Ganesh On Wed, Jul 8, 2015 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: Demeter Crashes on opening in Windows Bootcamp > (Ganesh Subramanian) > 2. Re: Demeter Crashes on opening in Windows Bootcamp (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 8 Jul 2015 01:07:56 -0700 > From: Ganesh Subramanian <gunkanna(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] Demeter Crashes on opening in Windows Bootcamp > Message-ID: > <CAAb9e-d2Kvx=VZRmNPOVBcgpCvqD3x= > t4VLLRdDRFtDJMBUURQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > > > > Dear Bruce and Matt, > > > > > > > > My first guess is that the culprit is anti-virus software running on > > Ganesh's computer. I have seen other examples of parts of Demeter being > > falsely identified as problematic and being removed, rendering the > > Demeter programs unusable. > > > > That said, on Ganesh's computer, the gnuplot executable should be in > > > > C:\strawberry\c\bin\gnuplot\bin > > > > Yes - I can locate it exactly at this path and the executable file does > open from there. > > > > > > > There are some other conceivable ways to see this problem, but I am > > placing my first bet on over-aggressive anti-virus software. > > > > I did have McAfee. I uninstalled the program and restarted my computer > and > the problem still persists. It seems very much the same, im posting the > most recent log-file. > > > > > *************************************** > > >

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Demeter won't start in Windows 7
by willn 12 Jul '15

12 Jul '15

Hi everyone, My copy of Demeter on my Windows 7 machine stopped working at some point in the recent past, so I have re-installed it, but I still have the same problem - a command window and splash screen open briefly, before disappearing. In my Path variable I have bumped the perl addresses up above the MinGW one, as suggested in one of the common fixes, but this did not solve the problem. I had a good look through the mailing-list archive for similar problems to mine, but each seem to be different (the log file errors were different). I have commented out the appropriate lines in the batch files, but, predictably I guess, this only had the effect of removing the splash screen when the program attempts to start-up. I have also played around a little installing newer versions of Strawberry, but similarly to no avail. If time permits, would anyone mind helping me interpret my log file (attached)? I'm not really computer literate enough to understand what is written there! Grateful thanks in advance, William -- William Nash PhD Student, Experimental Petrology Earth Sciences Department Oxford University

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Re: [Ifeffit] Demeter Crashes on opening in Windows Bootcamp
by Ganesh Subramanian 08 Jul '15

08 Jul '15

> > Dear Bruce and Matt, > > > My first guess is that the culprit is anti-virus software running on > Ganesh's computer. I have seen other examples of parts of Demeter being > falsely identified as problematic and being removed, rendering the > Demeter programs unusable. > > That said, on Ganesh's computer, the gnuplot executable should be in > > C:\strawberry\c\bin\gnuplot\bin > Yes - I can locate it exactly at this path and the executable file does open from there. > > > There are some other conceivable ways to see this problem, but I am > placing my first bet on over-aggressive anti-virus software. > > I did have McAfee. I uninstalled the program and restarted my computer and the problem still persists. It seems very much the same, im posting the most recent log-file. > > *************************************** >

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Be EXAFS and publication
by Joshua Kas 07 Jul '15

07 Jul '15

Hi, This may be a long shot, but I was wondering if anyone is aware of EXAFS data on HCP Be. In particular we are looking for Debye-Waller Factors, so a publication would be great, but just data might work as well. Thanks, Josh Kas

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Question about deglitching EXAFS data
by Francesco Marafatto 07 Jul '15

07 Jul '15

Hello All, I have enjoyed this digest in the past and found it very helpful! I hope it may provide an answer to my question. I am collecting Mn EXAFS data out to k of 15 Å-1, and the data look fine. However, the monochromator (Si 111) has 5 strong 2-point glitches and 3 minor 1-point glitches in one of the regions that I am most interested in (k between 5 and 9 Å-1). My question relates to how many data points I can remove before influencing the data. In my previous experience I have removed 2 or 3 points but never more. I have read through the deglitching section of “XAFS for Everyone”, and think that I could oversample the EXAFS (with k steps of 0.03 Å-1 vs 0.05 Å-1), but most of the data have already been collected. Is there a rule of thumb about deglitching? In other words, is there a limit to the number of bad points I can eliminate for an EXAFS scan to k of 15 Å-1? Thanks and looking forward to hearing your thoughts, Francesco Francesco Femi Marafatto francesco.marafatto(a)unil.ch FNS PhD student, Environmental Geochemistry Laboratory IDyST - FGSE Bureau 3233 Gèopolis Université de Lausanne CH-1015 Lausanne T. +41 (0)21 692 4451

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Fwd: FEFF trouble help me please !!!!
by Bruce Ravel 07 Jul '15

07 Jul '15

Hi, I want to remind everyone that it is important to use the mailing list. I do not feel that I am obligated to answer questions about the software that come to me by any other channel, particularly when I do not have a personal relationship with the person asking the question. That said, I am forwarding this fellow's question to the mailing list and providing an answer. Thitipong, this is a case of GIGO. According to Acta Cryst. (1972). B28, 3102-3103 (the reference I found for Cr23C6): The crystal structure of chromium carbide, C r 2 3 C 6 , has been described as cubic, space group Fm3m, 4Cr (I) in (a) (000), 8Cr (II) in (c) (l-lq:), 48Cr (III) in (h) (Oxx), x= 0.165, 32Cr (IV) in (f) (xxx), x=0.385, 24C in (e) (x00), x=0-275 (Westgren, 1933) on the basis of X-ray single crystal and powder diffraction data. We have confirmed this structure and determined the atom positions more precisely by a neutron diffraction study of a powder sample. Using those coordinates, I have no problem running atoms and feff. The structure is a bit strange -- I guess this is more like a metal than a carbide -- but it seems consistent with the paper after a cursory inspection. According to http://www.crystallography.net/cod/1009019.html, the space group for Cr7C3 is P M C N. Atoms and feff run fine with this input data. Some hints on asking questions that so you'll get the answers you are looking for: http://bruceravel.github.com/demeter/pods/bugs.pod.html http://bruceravel.github.com/demeter/pods/help.pod.html B -------- Forwarded Message -------- Subject: FEFF trouble help me please !!!! Resent-Date: Fri, 3 Jul 2015 04:25:57 +0000 Resent-From: bruce.ravel(a)nist.gov Date: Fri, 3 Jul 2015 11:33:12 +0700 From: Thitipong Po-Kloy <thitipong_37(a)hotmail.com> To: bruce.ravel(a)nist.gov <bruce.ravel(a)nist.gov> Hi Bruce , My name is Thitipong . I have trouble about FEFF program and believes you can help me. Now I am doing "XANES simulation" Cr23C6 and Cr7C3 . So , when I run FEFF program - it report TWO ATOMS VERY CLOSE TOGETHER . How can I fix it ? This it Data of atom Cr23C6 title name : Cr23C6 title formula : Cr23C6 space F M 3 M a=10.6599 b=10.6599 c=10.6599 rmax = 10 core=Cr1 atom Cr 0 0 0 Cr1 Cr 0.25 0.25 0.25 Cr2 Cr 0.385 0.385 0.385 Cr3 Cr 0 0 0.340 Cr4 C 0.276 0.276 0.276 C1 and Cr7C3 title name : Cr7C3 title formula : Cr7C3 space P M C M a=7.0149 b=12.1530 c=4.5320 rmax = 10 rpath=6 core=Cr1 atom Cr 0.064 0.811 0.056 Cr1 Cr 0.250 0.626 0.057 Cr2 Cr 0.250 0.206 0.250 Cr3 Cr 0.250 0.416 0.261 Cr4 Cr 0.065 0.021 0.250 Cr5 C 0.250 0.562 0.459 C1 C 0.029 0.342 0.028 C2 If there is any other way please let me know. Thank You , Thitipong -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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Re: [Ifeffit] Demeter Crashes on opening in Windows Bootcamp
by Ganesh Subramanian 07 Jul '15

07 Jul '15

Sorry for not noticing. The log files are attached now. It is pretty much the same for all three cases of Athena, Artemis and Hephaestus. Ganesh > > Message: 2 > Date: Mon, 06 Jul 2015 08:18:08 -0400 > From: Bruce Ravel <bravel(a)bnl.gov> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Demeter Crashes on opening in Windows Bootcamp > Message-ID: <559A7200.9050207(a)bnl.gov> > Content-Type: text/plain; charset=windows-1252; format=flowed > > On 07/04/2015 06:10 PM, Ganesh Subramanian wrote: > > Hi. > > > > This is Ganesh and I am a first time user of the Demeter accessories. > > > > I downloaded and installed the files from the github site using the > > 0.9.21 (64 bit) installation file. It was done on the Bootcamp Windows 7 > > on my Macbook Pro (2012). It seemed to have installed fine, but the > > moment I click on the icons to open any of Athena, Artemis or > > Hephaestus, all of them show a command window, thats empty, and in a few > > seconds crash and close. No error windows or command line error prompts. > > > > Any idea on what might be wrong ? > > > It is basically impossible to answer a question like this without a look > at the log file, as explained here: > > http://bruceravel.github.io/demeter/pods/bugs.pod.html > > B > > -- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Science Group at NSLS-II > Building 535A > Upton NY, 11973 > > Homepage: http://bruceravel.github.io/home/ > Software: https://github.com/bruceravel > Demeter: http://bruceravel.github.io/demeter/ > > >

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Demeter Crashes on opening in Windows Bootcamp
by Ganesh Subramanian 06 Jul '15

06 Jul '15

Hi. This is Ganesh and I am a first time user of the Demeter accessories. I downloaded and installed the files from the github site using the 0.9.21 (64 bit) installation file. It was done on the Bootcamp Windows 7 on my Macbook Pro (2012). It seemed to have installed fine, but the moment I click on the icons to open any of Athena, Artemis or Hephaestus, all of them show a command window, thats empty, and in a few seconds crash and close. No error windows or command line error prompts. Any idea on what might be wrong ? Thanks, Ganesh

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Re: [Ifeffit] Ifeffit Digest, Vol 148, Issue 26
by Nils Skoglund 27 Jun '15

27 Jun '15

Hello Everton, Matt and Pushkar, Thank you for your replies. I have tried both the 32-bit and 64-bit versions with uninstalling in between, to no avail. I'm curious if it is a priority issue between the dual GPU's on the laptop that gnuplot can't handle well; there's both a dedicated GPU and an integrated one. System temperatures look normal and none of the fans are revving up, so it shouldn't be heat-related. Other softwares handle plotting without issues so the suggestion about gnuplot being the culprit seems like the most reasonable one. If I narrow this issue down and find a way to work around it, I'll let you know. Until then I'll just find some other workstation for the evaluation work - thanks again! //Nils -----Original Message----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: den 26 juni 2015 19:00 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 148, Issue 26 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: Issues with Athena on high-performance systems (pushkar shejwalkar) 2. Re: Issues with Athena on high-performance systems (ebonturim(a)usp.br) ---------------------------------------------------------------------- Message: 1 Date: Fri, 26 Jun 2015 10:05:23 +0900 From: pushkar shejwalkar <pshejwalkar2004(a)gmail.com> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Issues with Athena on high-performance systems Message-ID: <CAN0ZRcEm=2KRDeXO-=t60yDZHwT4Rp8Zzs6pwPSbt7ndiQBGCg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi all, I am not an expert in this. In fact , I am one of the very new user of athena. But have you tried uninstalling and then reinstalling the whole package again? ( I am sure you have but since you didnt mentioned just wondering?) Sometimes, that also helps. not sure why and how? but it did for me. Pushkar On Fri, Jun 26, 2015 at 5:00 AM, Matt Newville <newville(a)cars.uchicago.edu> wrote: > Nils, > > We run Athena on non-wimpy Windows 7 systems at our beamline computers > all the time, using both 64- and 32-bit Windows, and typically on > multi-core machines with at least 16 Gb RAM and multiple screens. > Like Robert, we don't see any real performance problems with a handful (<50) spectra. > Athena rarely makes a very big dent in the system resources (well, > comparable to a web browser, so a bit of a hog, but well under 1Gb RAM). > > Perhaps what you're seeing is related to the plotting with Gnuplot. > I'm not sure why that would be a problem... Any ideas? > > --Matt > > Hi, > > > > I?m curious if anyone else is experiencing issues with Athena in more > high-end systems running Windows 7? While I am used to having to wait > for the *first* plot to show up, the software is virtually unusable > to me now where any slight change (e.g. modifying range for the > spline) to already imported data takes up to over a minute to replot. > This didn?t use to be the case for me. The system is a laptop running > Win 7 Professional with 2.40 GHz i7 CPU/16 GB RAM with plenty of space > on the hard drives and a dedicated Intel HD 4600 graphics circuit. > > > > If anyone has a work-around for this problem or can suggest anything > to make Athena usable again, it would be most appreciated. Has anyone > noticed previous versions of Athena running more smoothly? > > > > Best regards, > > Nils > > > > *------------------------------------------------------------------* > > *Nils Skoglund, Ph.D.* > Post-doctoral researcher > > Energy Science > Department of Engineering Sciences and Mathematics Lule? University of > Technology > SE-971 87 Lule? > Sweden > > > > Cell : +46 (0)72 529 52 08 > > Web page: http://www.ltu.se/org/tvm/Avdelningar/Energivetenskap?l=en > > Publications: http://www.researcherid.com/rid/D-3493-2011 > > *-------------------------------------------------------------------* > > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > -- Best Regards, Pushkar Shejwalkar. Post-doctoral -Researcher, Tokyo Engineering University, Sapporo, Japan

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Issues with Athena on high-performance systems
by Nils Skoglund 25 Jun '15

25 Jun '15

Hi, Im curious if anyone else is experiencing issues with Athena in more high-end systems running Windows 7? While I am used to having to wait for the first plot to show up, the software is virtually unusable to me now where any slight change (e.g. modifying range for the spline) to already imported data takes up to over a minute to replot. This didnt use to be the case for me. The system is a laptop running Win 7 Professional with 2.40 GHz i7 CPU/16 GB RAM with plenty of space on the hard drives and a dedicated Intel HD 4600 graphics circuit. If anyone has a work-around for this problem or can suggest anything to make Athena usable again, it would be most appreciated. Has anyone noticed previous versions of Athena running more smoothly? Best regards, Nils ------------------------------------------------------------------ Nils Skoglund, Ph.D. Post-doctoral researcher Energy Science Department of Engineering Sciences and Mathematics Luleå University of Technology SE-971 87 Luleå Sweden Cell : +46 (0)72 529 52 08 Web page: <http://www.ltu.se/org/tvm/Avdelningar/Energivetenskap?l=en> http://www.ltu.se/org/tvm/Avdelningar/Energivetenskap?l=en Publications: <http://www.researcherid.com/rid/D-3493-2011> http://www.researcherid.com/rid/D-3493-2011 -------------------------------------------------------------------

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Artemis on IOS Yosemite 10.10.3
by ebonturim＠usp.br 25 Jun '15

25 Jun '15

Hi guys, Anyone know why Artemis don't work in IOS 10.10.3? I can use the Athenas and Hephaestus, but when I type artemis on Terminal screen, I see this message: _______________________________________________________ Evertons-MacBook-Pro:~ ebonturim$ artemis Can't locate Math/Round.pm in @INC (@INC contains: /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/site_perl/5.16.3 /opt/local/lib/perl5/vendor_perl/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/vendor_perl/5.16.3 /opt/local/lib/perl5/5.16.3/darwin-thread-multi-2level /opt/local/lib/perl5/5.16.3 /opt/local/lib/perl5/site_perl /opt/local/lib/perl5/vendor_perl .) at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/ScatteringPath.pm line 44. BEGIN failed--compilation aborted at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/ScatteringPath.pm line 44. Compilation failed in require at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter.pm line 306. BEGIN failed--compilation aborted at /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/UI/Artemis.pm line 26. Compilation failed in require at /opt/local/bin/artemis line 34. BEGIN failed--compilation aborted at /opt/local/bin/artemis line 34. Evertons -MacBook-Pro:~ ebonturim$ _______________________________________________________ Someone could help me? Thank you! Best, Everton.

2 2

Hephaestus edge step calculation
by Guanghui Zhang 22 Jun '15

22 Jun '15

Hello, Bruce. Thanks very much for writing and keeping upgrading the amazing software. I was mainly doing homogeneous catalysis, so most of my samples were solution samples. I found that it was quite convienent to calculate the absoption length and edge step using the old version Hephaestus (ifeffit 1.2.11). Simply go to the Formulas tab, choose Molarity, type in the formula, molarity, and energy. The calculation results will show up after clicking the Compute button. For example, if I type in the Formula as Pt, molarity as 0.03 mol/L and Energy as 11564 eV (Pt L3 edge), the calculation results showed as follows: element number barns/atom cm^2/gm --------- ---------------------------------- Pt 1.000 63044.107 194.641 This weighs 195.090 amu. Absorbtion length = 0.878 cm at 11564.00 eV for a 0.03 molar sample. Unit edge step length at Pt L3 edge (11564.0 eV) is 15108.1 microns Remember that a molarity calculation only considers the absorption of the solute. The solvent also absorbs. The Elam database and the total cross-sections were used in the calculation. However, in the new version Hephaestus (Demeter 0.9.22, trial version 4, Windows 8 64 bit). It does not work. If I type the same informaiton, Pt, 0.03 mol/L, 11564 eV. The following results showed up. element number barns/atom cm^2/gm --------- ---------------------------------- Pt 1.000 63044.107 194.641 This weighs 195.090 amu. Absorption length = 0.0 micron at 11564 eV for a 0.03 molar sample. Unit edge step length at Pt L3 edge (11564.0 eV) is 0.0 microns Remember that a molarity calculation only considers the absorption of the solute. The solvent also absorbs. The Elam database and the full cross-sections were used in the calculation. If I do the calculation for the solid samples using "density" instead of "Molarity", the calculation worked fine. I am wondering if there is any problem with my softwar and/or laptop, or there is a missing function in the new version Hephaestus. Thanks Guanghui 2015-06-18

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Re: [Ifeffit] "Simple" question/s about fuzzy degeneracy
by Juan Manuel Conde Garrido 22 Jun '15

22 Jun '15

Thanks again!I'm so sorry, I had missed the "Aggregate" button (I think I pushed it once, but got deterred by the warning message).I got the path list that I wanted now and thanks to your explanation, I understood how the math works.Sorry for my silly newbie mistake and thanks again!Juan El Lunes, 22 de junio, 2015 8:30:39, Bruce Ravel <bravel(a)bnl.gov> escribió: On 06/20/2015 09:19 AM, Juan Manuel Conde Garrido wrote: > Thanks Bruce for the quick response! > I understood perfectly how to get from table 1 to table 2. > I'm still a little lost on how to use that in Artemis. > You said: "Artemis has compressed the three Feff calculations you would > normally have to do into a single fuzzily degenerate path list." > That's the thing I don't know how to do. > How do I use Artemis to get the scattering paths listed in table 2 (Reff > and degeneracy) > What would be the step by step procedure in Artemis to get those paths > so I can move them to the Path page? So, I concur that this page of the document http://bruceravel.github.io/demeter/artug/feff/aggregate.html is somewhat terse, but it seems clear to me. I don't understand what's confusing to you. You press the button, Artemis does some stuff, Artemis displays a bunch of paths. It works just like a normal Feff calculation. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ El Lunes, 22 de junio, 2015 8:30:39, Bruce Ravel <bravel(a)bnl.gov> escribió: On 06/20/2015 09:19 AM, Juan Manuel Conde Garrido wrote: > Thanks Bruce for the quick response! > I understood perfectly how to get from table 1 to table 2. > I'm still a little lost on how to use that in Artemis. > You said: "Artemis has compressed the three Feff calculations you would > normally have to do into a single fuzzily degenerate path list." > That's the thing I don't know how to do. > How do I use Artemis to get the scattering paths listed in table 2 (Reff > and degeneracy) > What would be the step by step procedure in Artemis to get those paths > so I can move them to the Path page? So, I concur that this page of the document http://bruceravel.github.io/demeter/artug/feff/aggregate.html is somewhat terse, but it seems clear to me. I don't understand what's confusing to you. You press the button, Artemis does some stuff, Artemis displays a bunch of paths. It works just like a normal Feff calculation. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/ El Lunes, 22 de junio, 2015 8:30:39, Bruce Ravel <bravel(a)bnl.gov> escribió: On 06/20/2015 09:19 AM, Juan Manuel Conde Garrido wrote: > Thanks Bruce for the quick response! > I understood perfectly how to get from table 1 to table 2. > I'm still a little lost on how to use that in Artemis. > You said: "Artemis has compressed the three Feff calculations you would > normally have to do into a single fuzzily degenerate path list." > That's the thing I don't know how to do. > How do I use Artemis to get the scattering paths listed in table 2 (Reff > and degeneracy) > What would be the step by step procedure in Artemis to get those paths > so I can move them to the Path page? So, I concur that this page of the document http://bruceravel.github.io/demeter/artug/feff/aggregate.html is somewhat terse, but it seems clear to me. I don't understand what's confusing to you. You press the button, Artemis does some stuff, Artemis displays a bunch of paths. It works just like a normal Feff calculation. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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"Simple" question/s about fuzzy degeneracy
by Juan Manuel Conde Garrido 20 Jun '15

20 Jun '15

Hi everyone, I'm somewhat new to EXAFS and this is my first question for the Ifeffit mailing list (which is a great source of information by the way).I was reading the excellent paper: "Path degeneracy and EXAFS analysis of disordered materials" and I have a "simple" question to ask:How do I get from table 1 to table 2? Specifically, I think I know how to use fuzzy degeneracy in Artemis for the paths in one FEFF calculation, but in this case there are 3 sites for Ti, and that means 3 FEFF calculations (rigth?). So how do I use fuzzy degeneracy for paths from different FEFF calculations? And by the way, is it right if I imagine the material as having only 1 "fuzzy"/average site for Ti? Thanks in advance Juan ****************************** ****************************** ****************************** *********Dr. Juan Manuel Conde GarridoLaboratorio de Sólidos AmorfosDepartameno de Física, Facultad de Ingeniería, Universidad de Buenos Aires INTECIN (UBA-CONICET) Av. Paseo Colón 850 C1063ACV - Ciudad de Buenos Aires ARGENTINA Tel: +54 (11) 4343-0893/4343-0092 (Int. 1101) http://intecin.fi.uba.ar ****************************** ****************************** ****************************** *********

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Questions on Correlated Debye in FEFF6
by Bennett, Doran (D) 19 Jun '15

19 Jun '15

Hi Everyone, I have just recently begun learning about EXAFS and running EXAFS simulations using FEFF6. I have a few very basic questions about the underlying calculations for the correlated Debye model implemented in FEFF6 (called by "DEBYE" keyword). For the questions below, I am assuming I input a single crystallographic structure and want the correlated Debye model to simulate the influence of a thermal distribution on the EXAFS spectrum. I would appreciate any insight you can give me into the questions below. I would also welcome any and all references for the original papers where that is appropriate. 1. Are the Debye-Waller factors calculated for each path individually? (It seems like they should be since the paths will have different levels of influence from the thermal distribution of atomic positions) 2. Assuming the DW factors are calculated path-by-path, is the magnitude of the DW factor determined by assuming the total path length R is the appropriate length to use for the correlation term in the Debye spectral density? It seems like it would not be reasonable to treat all paths of the same R as having the same Debye-Waller factor since a single scattering path and multiple scattering paths are perturbed by a different set of relative atomic motion that are likely to have different correlations. I couldn't locate a clear statement about how this calculations is actually done within the code. 3. Is the C1 shift that results from the vibrational motion normal to the bond axis along a path incorporated in the calculation? (Presumably using \Delta C1 = sigma_perp^2/(2<r>)) And is this formula still appropriate in multiple-scattering paths? 4. Assuming the C1 shift is incorporated, does the correlated Debye model assume that the perpendicular and parallel displacements have the same spectral density? Thank you for the assistance! Doran Doran I. G. Bennett The Dow Chemical Company Core R&D, Inorganic Material and Heterogeneous Catalysis Phone: (610)-244-7062 Alternate Phone: (630)-222-2906

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Reference for Setting k range in EXAFS analysis
by Navneet Singh 19 Jun '15

19 Jun '15

Dear All Can I get some study material mentioning how to set the K-range for EXAFS analysis. With best regards Navneet Singh

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Re: [Ifeffit] Ifeffit Digest, Vol 148, Issue 13
by M. Janeth LOZANO RODRIGUEZ 11 Jun '15

11 Jun '15

Dear all, It's true and precise your remark Fred. With Demeter 9.21, the Feff 8.2 is running properly in Demeter Atoms or well in Artemis, but at the moment to get the paths they are not present. But if you right click with the mouse, you can READ the geometry for the paths but with a error message : Demeter:UI:Artemi Error Couldn't retrieve information about list control item -1 ... from my eyes it seems to be something related with Demeter's pathfinder but I'm not an expert Anyway, also thanks Guanghui for your comments that help us to understand where is coming from this problematic. Could be great if in the future someone could find/propose a solution Kind regards Janeth On 10/06/2015 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. how to manage Demeter with a newer FEFF version ? > (fred.mosselmans(a)diamond.ac.uk) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 10 Jun 2015 07:42:35 +0000 > From: <fred.mosselmans(a)diamond.ac.uk> > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: [Ifeffit] how to manage Demeter with a newer FEFF version ? > Message-ID: > <CF65047C5B0562499EAFF9FBBC542D649FB4EBBF(a)EXCHMBX01.fed.cclrc.ac.uk> > Content-Type: text/plain; charset=us-ascii > > Dear Janeth, > > Feff8.5L (and presumably 8.4) works in some fashion in Demeter version 18.2 , in later versions it doesnt. : It runs through atoms and gives fits that seems sensible for transuranic elements in the times I and some of my collaborators have used it. > > Thus in the short term if you want to use something higher than FEFF6 in your exafs calculations and want to use Demeter that's your option, > > If you need to use FeFF9 and want to use Demeter: I think your best option is to have a go at persuading some of the software guys at your facility to collaborate with Bruce and Matt in adding a FEFF9 option to larch and in turn then Demeter. > > Best wishes > Fred > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 08 Jun 2015 11:13:33 +0200 > From: "M. Janeth LOZANO RODRIGUEZ" <janeth.lozano-rodriguez(a)esrf.fr> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] how to manage Demeter with a newer FEFF version ? > Message-ID: <55755CBD.6010007(a)esrf.fr> > Content-Type: text/plain; charset=utf-8; format=flowed > > Dear XAFS community, > > I wondering about the availability to use a newer FEFF version in > Demeter. Since my knowledge only I can run FEFF6. In my case I found > different discrepancies using FEFF6 and FEFF9 in the determination of > bond length distances for instance. In terms of review of papers, > reviewers ask to use a newer version instead FEFF6. These points > strongly suggest me coming back to the obsolete Athena/Artemis version. > > On this obsolete version, you can download the paths generated by FEFF8, > FEFF9. This issue is really useful when we have access to FEFF 9, for > example. Is there any option to implement this nice feature in Demeter? > Does anyone have an idea how to do it? > > Kind regards > Janeth Lozano > > > > ------------------------------ > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 148, Issue 10 > **************************************** >

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new build of the Demeter installer for Windows
by Bruce Ravel 10 Jun '15

10 Jun '15

Hi all, I have made quite a few changes to my analysis software in recent weeks in response to comments on the mailing list. I think that everything from recent weeks is in the latest build in some form. I am not quite ready to declare this a proper release with a new version number, so it can be found at http://bruceravel.github.io/demeter/#windows as "Pre-release trial version #4". Among other things, this corrects the recent deglitching problem, adds support for linear polarization in the Feff calculation, and attempts to streamline the plotting of a sum of paths (see the top of the Actions menu in the data window). I would be grateful if the two people who recently asked about polarization (Shaoib Muhammad and Anna Wolska) could try Artemis and let me know if you think it is working correctly. I have done quite a bit of testing, but one never knows.... I am not 100% confident that everything is implemented quite right. I could easily have missed something... See the change log at https://github.com/bruceravel/demeter/blob/master/Changes.org for the changes that are in this trial version. Cheers, B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS-II Building 535A Upton NY, 11973 Homepage: http://bruceravel.github.io/home/ Software: https://github.com/bruceravel Demeter: http://bruceravel.github.io/demeter/

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how to manage Demeter with a newer FEFF version ?
by fred.mosselmans＠diamond.ac.uk 10 Jun '15

10 Jun '15

Dear Janeth, Feff8.5L (and presumably 8.4) works in some fashion in Demeter version 18.2 , in later versions it doesnt. : It runs through atoms and gives fits that seems sensible for transuranic elements in the times I and some of my collaborators have used it. Thus in the short term if you want to use something higher than FEFF6 in your exafs calculations and want to use Demeter that's your option, If you need to use FeFF9 and want to use Demeter: I think your best option is to have a go at persuading some of the software guys at your facility to collaborate with Bruce and Matt in adding a FEFF9 option to larch and in turn then Demeter. Best wishes Fred ---------------------------------------------------------------------- Message: 1 Date: Mon, 08 Jun 2015 11:13:33 +0200 From: "M. Janeth LOZANO RODRIGUEZ" <janeth.lozano-rodriguez(a)esrf.fr> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] how to manage Demeter with a newer FEFF version ? Message-ID: <55755CBD.6010007(a)esrf.fr> Content-Type: text/plain; charset=utf-8; format=flowed Dear XAFS community, I wondering about the availability to use a newer FEFF version in Demeter. Since my knowledge only I can run FEFF6. In my case I found different discrepancies using FEFF6 and FEFF9 in the determination of bond length distances for instance. In terms of review of papers, reviewers ask to use a newer version instead FEFF6. These points strongly suggest me coming back to the obsolete Athena/Artemis version. On this obsolete version, you can download the paths generated by FEFF8, FEFF9. This issue is really useful when we have access to FEFF 9, for example. Is there any option to implement this nice feature in Demeter? Does anyone have an idea how to do it? Kind regards Janeth Lozano ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 148, Issue 10 ****************************************

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Re: [Ifeffit] Ifeffit Digest, Vol 148, Issue 10
by Guanghui Zhang 08 Jun '15

08 Jun '15

Janeth, As far as I know, Bruce is working on integraton of FEFF 8.5 into Demeter. I also experienced reviewers asking for newer version of FEFF in the data analysis. Below was a summary of our response. Feff 6 does not understand valence, and FEFF 8 uses a self-consistency loop to transfer charge between the atom types, resulting in something that can be related to formal valence in some situations. In the regime in which the EXAFS fit is evaluated, the photoelectron has large kinetic energy and is not particularly sensitive to the details of the potential surface. In almost all situations, FEFF 8 is a modest improvement at best over FEFF 6 for EXAFS analysis. There are some demonstrated cases where FEFF 8 is slightly better than FEFF 6 at modeling EXAFS. The most notable cases are when H is in the input file – FEFF 6 is terrible at this. I got those information from previous discussion on the Ifeffit, see: http://www.mail-archive.com/ifeffit%40millenia.cars.aps.anl.gov/msg03381.ht… I am not an expert, and I hope someone can help correct me if I am wrong. Thanks Guanghui 2015-06-08 Guanghui 发件人：ifeffit-request(a)millenia.cars.aps.anl.gov 发送时间：2015-06-08 12:00 主题：Ifeffit Digest, Vol 148, Issue 10 收件人："ifeffit"<ifeffit(a)millenia.cars.aps.anl.gov> 抄送： 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. how to manage Demeter with a newer FEFF version ? (M. Janeth LOZANO RODRIGUEZ) ---------------------------------------------------------------------- Message: 1 Date: Mon, 08 Jun 2015 11:13:33 +0200 From: "M. Janeth LOZANO RODRIGUEZ" <janeth.lozano-rodriguez(a)esrf.fr> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] how to manage Demeter with a newer FEFF version ? Message-ID: <55755CBD.6010007(a)esrf.fr> Content-Type: text/plain; charset=utf-8; format=flowed Dear XAFS community, I wondering about the availability to use a newer FEFF version in Demeter. Since my knowledge only I can run FEFF6. In my case I found different discrepancies using FEFF6 and FEFF9 in the determination of bond length distances for instance. In terms of review of papers, reviewers ask to use a newer version instead FEFF6. These points strongly suggest me coming back to the obsolete Athena/Artemis version. On this obsolete version, you can download the paths generated by FEFF8, FEFF9. This issue is really useful when we have access to FEFF 9, for example. Is there any option to implement this nice feature in Demeter? Does anyone have an idea how to do it? Kind regards Janeth Lozano ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 148, Issue 10 ****************************************

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how to manage Demeter with a newer FEFF version ?
by M. Janeth LOZANO RODRIGUEZ 08 Jun '15

08 Jun '15

Dear XAFS community, I wondering about the availability to use a newer FEFF version in Demeter. Since my knowledge only I can run FEFF6. In my case I found different discrepancies using FEFF6 and FEFF9 in the determination of bond length distances for instance. In terms of review of papers, reviewers ask to use a newer version instead FEFF6. These points strongly suggest me coming back to the obsolete Athena/Artemis version. On this obsolete version, you can download the paths generated by FEFF8, FEFF9. This issue is really useful when we have access to FEFF 9, for example. Is there any option to implement this nice feature in Demeter? Does anyone have an idea how to do it? Kind regards Janeth Lozano

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Re: [Ifeffit] Mn3O4 EXAFS fitting
by 이국승 02 Jun '15

02 Jun '15

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Re: [Ifeffit] Ifeffit Digest, Vol 148, Issue 6
by Nidhi Tiwari 02 Jun '15

02 Jun '15

congratulations :) Give your Best *Nidhi Tiwari*, Junior Research Fellow, Atomic and Molecular Physics Division, Bhabha Atomic Research Center, Mumbai- 400085 On Mon, Jun 1, 2015 at 10:30 PM, <ifeffit-request(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Create Atoms input with just coordinates (M Ferrier) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 1 Jun 2015 18:04:40 +0200 > From: M Ferrier <mferrier(a)hotmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Create Atoms input with just coordinates > Message-ID: <DUB118-W1424A6BB66DA7BFA91C7C2DFB60(a)phx.gbl> > Content-Type: text/plain; charset="windows-1252" > > Thank you very much. It worked except that the feff calculation created > ipot 0 and 1 for the same atom (core atom) I just had to change the ipot > values in the text before running feff. But once done it did calculation > correctly I think. > > Maryline > > From: scalvin(a)sarahlawrence.edu > To: ifeffit(a)millenia.cars.aps.anl.gov > Date: Mon, 1 Jun 2015 10:53:36 -0400 > Subject: Re: [Ifeffit] Create Atoms input with just coordinates > > Hi Maryline, > Use a = b = c = 10, with alpha = beta = gamma = 90. Now enter the > coordinates from your simulation in units of angstroms/10 (which happens to > be nm). > ?Scott CalvinSarah Lawrence College > On Jun 1, 2015, at 10:43 AM, M Ferrier <mferrier(a)hotmail.com> wrote:Hi, > > I am trying to create an Atoms input file for actinium. Since not a lot is > known about this element we run some DT calculations. One molecule of Ac > acetate in a box surrounded by water. > I have the coordinate of each elements. I was told the symmetry was P1 (I > guess for the box) but unfortunately their is no symmetry in liquid and > thus we cannot input the cell parameters (distances a, b, c and angles > alpha, beta, gamma). I was wondering if their were a way to make Atoms run > to obtain the Feff calculations. Or we should use a different model with a > known solid? > > Thank you for your help > > Maryline Ferrier _______________________________________________Ifeffit > mailing listIfeffit@millenia.cars.aps.anl.govhttp:// > millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >

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Create Atoms input with just coordinates
by M Ferrier 01 Jun '15

01 Jun '15

Hi, I am trying to create an Atoms input file for actinium. Since not a lot is known about this element we run some DT calculations. One molecule of Ac acetate in a box surrounded by water. I have the coordinate of each elements. I was told the symmetry was P1 (I guess for the box) but unfortunately their is no symmetry in liquid and thus we cannot input the cell parameters (distances a, b, c and angles alpha, beta, gamma). I was wondering if their were a way to make Atoms run to obtain the Feff calculations. Or we should use a different model with a known solid? Thank you for your help Maryline Ferrier

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low and negative ss2 and bug in the log file of fit history
by Raj kumar 01 Jun '15

01 Jun '15

Dear All, I am trying to fit the first shell FT of bulk YbVO4 (measured in dispersive EXAFS) with the reference YbVO4. The resultant SS2 value for the first shell is found to be low for wide k-range selection, whereas approaching negative for the relatively short k-range window. While approaching negative value (of ss2), i have tried to constraint the ss2 value using expression abs(ss). In that case, ss2 value is found to take value 0. Please help me to figure out the problem. Further i have found a small bug in the fit history window. After each fit, earlier data set in the log file of fit history is found to overwritten with the latest fitting parameters (like k range, dk, etc..). Here in my log file window, all fit data set contain the same data set value as like the last fit (fit9). Regards, Raj

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Re: [Ifeffit] Mn3O4 EXAFS fitting
by 이국승 01 Jun '15

01 Jun '15

1 0

Re: [Ifeffit] Mn3O4 EXAFS fitting
by fred.mosselmans＠diamond.ac.uk 01 Jun '15

01 Jun '15

Dear Kug-Seung Your main initial problem is you didn't understand the structure of Mn3O4. It is a spinel with two Mn sites one octahedral and one tetrahedral. You need to consider both sites to have a chance of fitting, and set multiplication factors on the relative amps in the ratio. It has 1/3 tetrahedral sites and 2/3 octahedral. You need to do the feff calculation twice with each site as the core atom. In the attached project I have done this. You then end up with a lot of paths so to try to restrict the no of variables I have made several of sigma squared to be the same. I am sure this model could be improved upon but I wanted to show you how to get going in fitting the structure. In theory as the Mn tetrahedral site and octahedral sites are different oxidations states they might (should) have different E0s as well but with a limited data range this gets hard to test properly. Best wishes Fred Mosselmans Message: 1 Date: Mon, 01 Jun 2015 15:59:40 +0900 From: ??? <lks3006(a)postech.ac.kr> To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] Mn3O4 EXAFS fitting Message-ID: <1433141980110.23146.postech(a)postech.ac.kr> Content-Type: text/plain; charset="us-ascii" An HTML attachment was scrubbed... URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20150601/4ec…>

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