- 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

2 1

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 ---------------------------------------------------------------------------

2 2

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!

2 1

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

3 6

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 >

2 1

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

2 2

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

2 2

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

2 1

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

1 0

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 >

1 0

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 >

1 0

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