September 2008 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] CFAVERAGE CARD
by joshua jason kas 18 Sep '08

18 Sep '08

Hi Cammelli, feff8 is hard coded to accept only 1000 atoms or less. The error message is not very informative and I don't think it applies to your case. What you want to do is recompile change the parameter natx in the source code to something larger, maybe 3000, and recompile. If you do not have the source code, you can find it at the feff webpage with the same username and password that was used to obtain your executable. Cheers, Josh Kas On Thu, 18 Sep 2008, 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. CFAVERAGE CARD (Cammelli Sebastiano) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 18 Sep 2008 15:59:43 +0200 > From: "Cammelli Sebastiano" <Sebastiano.Cammelli(a)psi.ch> > Subject: [Ifeffit] CFAVERAGE CARD > To: <ifeffit(a)millenia.cars.aps.anl.gov> > Message-ID: > <AD99CE4B84C4D3468F69B0E4FB345D58048FE174(a)MAILBOX0A.psi.ch> > Content-Type: text/plain; charset="us-ascii" > > Dear Iffefit user > > I have a question about CFAVERAGE card used in FEFF8.4 for EXAFS > simulations. > > I need to simulate a cluster with 1481 atoms, let's say in a first > moment, composed of only Cu atoms. > > Without this card the simulations crashed and it was suggested to "Use > or reduce rclabs in CFAVERAGE card Or increase parameter natx and > recompile". > > I tried with different indexes: > > CFAVERAGE 1 -1 7 > > CFAVERAGE 0 -1 6... > > I could run EXAFS simulations but I could not get xmu.dat. > > FEFF8.4 works perfectly when <1000 atoms are involved (and CFAVERAGE is > NOT used). But how could I simulate larger clusters (with more then > 1000atoms)? > > Here I send you a copy of the feff.inp, I do not write here below all > the atoms between the 1st and the 37th shell because I do not want to > make this mail too large, but I attach the original file. > > > > TITLE A > > *cluster 1481 atoms > > CONTROL 1 1 1 1 1 1 > > PRINT 0 0 0 0 0 0 > > RMULTIPLIER 1 > > LDOS -30 20 0.2 > > EDGE K > > S02 1.0 > > SCF 4 0 30 0.2 1 > > NLEG 5 > > DEBYE 15 343 0 > > EXAFS > > RPATH 10.0 > > POTENTIALS > > 0 29 Cu 3 3 0.0010 > > 1 29 Cu 3 3 1.0 > > > > ATOMS * this list contains 1481 atoms > > * x y z ipot tag distance > > 0.00000 0.00000 0.00000 0 Cu_1 0.00000 > > 1.80753 1.80753 0.00000 1 Cu_1 2.55623 > > -1.80753 1.80753 0.00000 1 Cu_1 2.55623 > > 1.80753 -1.80753 0.00000 1 Cu_1 2.55623 > > -1.80753 -1.80753 0.00000 1 Cu_1 2.55623 > > 1.80753 0.00000 1.80753 1 Cu_1 2.55623 > > -1.80753 0.00000 1.80753 1 Cu_1 2.55623 > > 0.00000 1.80753 1.80753 1 Cu_1 2.55623 > > 0.00000 -1.80753 1.80753 1 Cu_1 2.55623 > > 1.80753 0.00000 -1.80753 1 Cu_1 2.55623 > > -1.80753 0.00000 -1.80753 1 Cu_1 2.55623 > > 0.00000 1.80753 -1.80753 1 Cu_1 2.55623 > > 0.00000 -1.80753 -1.80753 1 Cu_1 2.55623 > > .... > > 3.61505 9.03763 -12.65268 1 Cu_37 15.96364 > > -3.61505 9.03763 -12.65268 1 Cu_37 15.96364 > > 9.03763 -3.61505 -12.65268 1 Cu_37 15.96364 > > -9.03763 -3.61505 -12.65268 1 Cu_37 15.96364 > > 3.61505 -9.03763 -12.65268 1 Cu_37 15.96364 > > -3.61505 -9.03763 -12.65268 1 Cu_37 15.96364 > > END > > > > > > Best > > Sebastiano Cammelli > > > >

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CFAVERAGE CARD
by Cammelli Sebastiano 18 Sep '08

18 Sep '08

Dear Iffefit user I have a question about CFAVERAGE card used in FEFF8.4 for EXAFS simulations. I need to simulate a cluster with 1481 atoms, let's say in a first moment, composed of only Cu atoms. Without this card the simulations crashed and it was suggested to "Use or reduce rclabs in CFAVERAGE card Or increase parameter natx and recompile". I tried with different indexes: CFAVERAGE 1 -1 7 CFAVERAGE 0 -1 6... I could run EXAFS simulations but I could not get xmu.dat. FEFF8.4 works perfectly when <1000 atoms are involved (and CFAVERAGE is NOT used). But how could I simulate larger clusters (with more then 1000atoms)? Here I send you a copy of the feff.inp, I do not write here below all the atoms between the 1st and the 37th shell because I do not want to make this mail too large, but I attach the original file. TITLE A *cluster 1481 atoms CONTROL 1 1 1 1 1 1 PRINT 0 0 0 0 0 0 RMULTIPLIER 1 LDOS -30 20 0.2 EDGE K S02 1.0 SCF 4 0 30 0.2 1 NLEG 5 DEBYE 15 343 0 EXAFS RPATH 10.0 POTENTIALS 0 29 Cu 3 3 0.0010 1 29 Cu 3 3 1.0 ATOMS * this list contains 1481 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Cu_1 0.00000 1.80753 1.80753 0.00000 1 Cu_1 2.55623 -1.80753 1.80753 0.00000 1 Cu_1 2.55623 1.80753 -1.80753 0.00000 1 Cu_1 2.55623 -1.80753 -1.80753 0.00000 1 Cu_1 2.55623 1.80753 0.00000 1.80753 1 Cu_1 2.55623 -1.80753 0.00000 1.80753 1 Cu_1 2.55623 0.00000 1.80753 1.80753 1 Cu_1 2.55623 0.00000 -1.80753 1.80753 1 Cu_1 2.55623 1.80753 0.00000 -1.80753 1 Cu_1 2.55623 -1.80753 0.00000 -1.80753 1 Cu_1 2.55623 0.00000 1.80753 -1.80753 1 Cu_1 2.55623 0.00000 -1.80753 -1.80753 1 Cu_1 2.55623 .... 3.61505 9.03763 -12.65268 1 Cu_37 15.96364 -3.61505 9.03763 -12.65268 1 Cu_37 15.96364 9.03763 -3.61505 -12.65268 1 Cu_37 15.96364 -9.03763 -3.61505 -12.65268 1 Cu_37 15.96364 3.61505 -9.03763 -12.65268 1 Cu_37 15.96364 -3.61505 -9.03763 -12.65268 1 Cu_37 15.96364 END Best Sebastiano Cammelli

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Re: [Ifeffit] Bugs in Athena under Windows
by Timna-Josua Kuehn 15 Sep '08

15 Sep '08

Thanks for checking this so quick. To give more details: after I have merged the datafiles I can not plot the data in any space anymore. Athena seems to process the data for plotting, but the plot program GrWnd does not respond, so this kind of problem is probably related to GrWnd only. However, when trying to merge something else inside this file, for example only 2 scans, the resulting merged datagroup is identical to the initial one, so Athena is not working properly too. Regards Timna-Josua Kuehn

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Re: [Ifeffit] Bugs in Athena under Windows
by Timna-Josua Kuehn 12 Sep '08

12 Sep '08

Hi again, I attached a standard athena project file to this mail, in order to demonstrate the bug that follows a merging process. The project file contains 4 standard EXAFS measurements of a PtCo3/C nanoparticle (+ref) which shall be merged. As I told before the merging works, but afterwards I can not do anything else, the program hangs up. This bug does appear under Windows XP.c With best regards Timna-Josua Kuehn

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Re: [Ifeffit] broken feffit
by Matt Newville 09 Sep '08

09 Sep '08

Hi Shelly, On Tue, Sep 9, 2008 at 4:04 PM, Shelly Kelly <dr.sdkelly(a)gmail.com> wrote: > Hi Matt, > > I'm likely the last person on earth using this software....but feffit seems > to be broken in the latest version ifeffit-1.2.11a. > > I'm proud to have triggered the message: > >>>feffit error > routine fitfft failed internal test. > program error: contact matt > Fatel Error: feffit error Oh thanks! When playing around with Ifeffit this summer, I completely forgot about Feffit (what was I thinking about?). It is completely broken (but fortunately, it's a simple fix!). This is now fixed in svn, and I'll post a 1.2.11b tar ball to the cars ifeffit download site right away. > I went back to the version distributed with 1.2.9 and that one works for me. This doesn't affect Windows users, as the version of Feffit there is old enough to not have this bug. --Matt

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Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 15
by Khalid, Syed 09 Sep '08

09 Sep '08

Matt, We do use a cam when doing QEXAFS. Along with time and detector values we record the Bragg angle of the Si(111) monochromator as a function of optical encoder readout. The encoder values are random numbers but linear with the Bragg angle. Under normal routine QEXAFS we have developed programs to convert the QEAXFS data and make it compatible with Athena analysis. That works fine. In this particular case I wanted to compare Ni EXAFS scan done in conventional way to the one I got in 100 ms. For this particular scan I could not use the programs that we developed (for data conversion to Athena compatible, for many reasons). I wanted to see how a time axis converted to energy, compares with conventional EXAFS at FFT stage. It was also to find out, as you mentioned, if two energy points will match, then will it compare to conventional EXAFS in this particular case?? Syed Khalid -----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: Tuesday, September 09, 2008 1:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 67, Issue 15 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 67, Issue 12 (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Tue, 9 Sep 2008 11:14:12 -0500 From: "Matt Newville" <newville(a)cars.uchicago.edu> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 12 To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <b8522e3d0809090914o2e3d6773n370158b56f370077(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Syed, Adam, I think the suggestion from Adam and one of the suggestions from Anatoly assume the energy linear in time. Is that the really case? For quick-scanning modes, many beamlines run the mono at a constant angular velocity, so that time maps linearly to angle, which then needs to be converted (non-linearly) to energy. Then again, some quick-scanning beamlines use a special cam drive, in which neither angle nor energy would be linear in time. Again, you need know these details in order to correctly assign energies to the data. None of it is particularly difficult, so there's no point in guessing, and stretching or massaging the energy scale until two energy points correct does not mean the rest are correct. You need to find out from the beamline how the data mapped onto energy and fix that. While you can probably use Ifeffit macros within Athena to do this correction, this is really a job for the beamline, not for Athena. Having an option in Athena that allowed the user to say "I don't know why my energy scale is bad, but can you please stretch the energies so that these two energies are what I'd like them to be" is a horrible idea. --Matt ------------------------------ _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit End of Ifeffit Digest, Vol 67, Issue 15 ***************************************

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Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 12
by Khalid, Syed 09 Sep '08

09 Sep '08

That is correct: It is a QEXAFS scan of Ni foil as a function of time. Please see the data attached as a .txt file. The first column is time, second I0, and third It. I can plot this in Athena, time appears at energy axis. I can set the first derivative to 8333.0 eV ( changing X-axis from time to energy ). If I have another known energy point of Ni scan ( which is not a problem ) then I can convert the time axis to correct energy axis and proceed with normal analysis. Is that possible? -----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: Tuesday, September 09, 2008 9:23 AM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 67, Issue 12 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: ODP: enrgy-axis-expansion (Bruce Ravel) 2. Re: ODP: enrgy-axis-expansion (Matt Newville) 3. Re: Bugs in Athena under Windows (Matt Newville) 4. Noise level in XANES spectrum (Pushan Shah) 5. Re: ODP: enrgy-axis-expansion (Zajac, Dariusz) 6. Re: Noise level in XANES spectrum (Zajac, Dariusz) 7. Re: Ifeffit Digest, Vol 67, Issue 11 (Khalid, Syed) ---------------------------------------------------------------------- Message: 1 Date: Mon, 8 Sep 2008 16:59:08 -0400 From: Bruce Ravel <bravel(a)bnl.gov> Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <200809081659.08948.bravel(a)bnl.gov> Content-Type: text/plain; charset="utf-8" On Monday 08 September 2008 16:40:47 Zajac, Dariusz wrote: > I do not clearly understood what you mean. could you explain it more > precisely? do you want to replace the x scale from energy to time? if you > want only set the edge energy use E0 Apparently (and Khalid or Anatoly should correct me if I am wrong), they are collecting data as a function of time in quick scan mode. They then have the problem of converting time to energy. If the mono speed is recorded somehow incorrectly, then there is an accordian effect throughout the data. I think that Khalid wants to be able to adjust this accordian effect to correct the energy scale of teh data. B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ ------------------------------ Message: 2 Date: Mon, 8 Sep 2008 16:18:55 -0500 From: "Matt Newville" <newville(a)cars.uchicago.edu> Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <b8522e3d0809081418h564560d4n2fed4de0223e227(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Hi Khalid, I agree with Dariusz: I do not understand the question. I have a hard time believing it is "the beamline cannot provide data as a function of energy, can Athena do this for me automatically?" (if it is, the answer is definitely 'No!'). Could you explain what you're trying to do? --Matt ------------------------------ Message: 3 Date: Mon, 8 Sep 2008 16:24:45 -0500 From: "Matt Newville" <newville(a)cars.uchicago.edu> Subject: Re: [Ifeffit] Bugs in Athena under Windows To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <b8522e3d0809081424x5a6135dfk3aefb0e4a13c3bce(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 Timna, Posting a project would definitely help here, as would clarify "since the last two versions ..." to say explicitly which versions do and do not work. My suspicion is that this related to the bug noted last week (and possibly another recent vague report of "not working") that is due to the latest version of athena -for-windows being hard-linked to pre-final-release of the ifeffit dll which is making athena's ifeffit session get stuck in an unresponsive state. I believe the only cure is a new version of athena. Again, if you could post a project that demonstrates the problem, that would be most helpful. --Matt ------------------------------ Message: 4 Date: Tue, 09 Sep 2008 15:48:51 +1000 From: "Pushan Shah" <pshah(a)gse.mq.edu.au> Subject: [Ifeffit] Noise level in XANES spectrum To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <48C69AE2.0BBD.0060.0(a)gse.mq.edu.au> Content-Type: text/plain; charset=US-ASCII Hello Everyone, I have a general question regarding noise level of XANES spectrum. I have collected XANES data for an element which is present in ppm level in my samples. Some samples are exhibiting varying degree of noise in XANES spectrum. Is the noise level of XANES spectrum would be proportional or consistent with the concentration of the sample? As XANES spectra for some of my samples with relatively higher concentration of this element are exhibiting greater level of noise than those with relatively lower concentrations. Will sample matrix play any role in the noise level? Thanks and I appreciate your help. regards, Pushan ------------------------------ Message: 5 Date: Tue, 9 Sep 2008 10:03:46 +0200 From: "Zajac, Dariusz" <dariusz.zajac(a)desy.de> Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion To: "Bruce Ravel" <bravel(a)bnl.gov>, "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <35E004AD6290A7438FCA34BBF325F4161148AA(a)ADXV2.win.desy.de> Content-Type: text/plain; charset="us-ascii" hi so, I think, in case of converting time scale to energy - this should be supported by beamline (beamline scientist) somehow... if there is any nonlinearity of the converion factor (Anatoly - what whould happened if D parameter is time/energy dependent?) I think only reference spectra can help - do you have it Syed? if you have all needed parameters the calibration can be relatively quickly done in some other programs, also in macro (for many files) but that's my speculations kicaj >-----Original Message----- >From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf >Of Bruce Ravel >Sent: Monday, September 08, 2008 10:59 PM >To: XAFS Analysis using Ifeffit >Subject: Re: [Ifeffit] ODP: enrgy-axis-expansion > > >On Monday 08 September 2008 16:40:47 Zajac, Dariusz wrote: >> I do not clearly understood what you mean. could you explain it more >> precisely? do you want to replace the x scale from energy to >time? if >> you want only set the edge energy use E0 > > >Apparently (and Khalid or Anatoly should correct me if I am >wrong), they are collecting data as a function of time in >quick scan mode. They then have the problem of converting >time to energy. If the mono speed is recorded somehow >incorrectly, then there is an accordian effect throughout the >data. I think that Khalid wants to be able to adjust this >accordian effect to correct the energy scale of teh data. > >B > > >-- > Bruce Ravel ------------------------------------ bravel(a)bnl.gov > > National Institute of Standards and Technology > Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, >X23A2 Building 535A Upton NY, 11973 > > My homepage: http://xafs.org/BruceRavel > EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > ------------------------------ Message: 6 Date: Tue, 9 Sep 2008 10:12:42 +0200 From: "Zajac, Dariusz" <dariusz.zajac(a)desy.de> Subject: Re: [Ifeffit] Noise level in XANES spectrum To: "XAFS Analysis using Ifeffit" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <35E004AD6290A7438FCA34BBF325F4161148AB(a)ADXV2.win.desy.de> Content-Type: text/plain; charset="us-ascii" Hi Pushan, can you tell more about the experiment and the way of data collecting? how did you measure your samples? which method did you use? what kind of samples do you have? the answer of your question is not stricted, but generaly I would say that the noise level should be independent of the samples, did you change something on the beamline or program between samples/measurements? e.g. sample time, no. of repeats, you moved in /out detector, amplification gain, etc.... kicaj >-----Original Message----- >From: ifeffit-bounces(a)millenia.cars.aps.anl.gov >[mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf >Of Pushan Shah >Sent: Tuesday, September 09, 2008 7:49 AM >To: ifeffit(a)millenia.cars.aps.anl.gov >Subject: [Ifeffit] Noise level in XANES spectrum > > >Hello Everyone, > >I have a general question regarding noise level of XANES >spectrum. I have collected XANES data for an element which is >present in ppm level in my samples. > >Some samples are exhibiting varying degree of noise in XANES >spectrum. > >Is the noise level of XANES spectrum would be proportional or >consistent with the concentration of the sample? As XANES >spectra for some of my samples with relatively higher >concentration of this element are exhibiting greater level of >noise than those with relatively lower concentrations. Will >sample matrix play any role in the noise level? > >Thanks and I appreciate your help. > >regards, >Pushan > > > >_______________________________________________ >Ifeffit mailing list >Ifeffit(a)millenia.cars.aps.anl.gov >http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > ------------------------------ Message: 7 Date: Tue, 9 Sep 2008 09:22:14 -0400 From: "Khalid, Syed" <khalid(a)bnl.gov> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 11 To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <55C249AA18FE564E86564FEB2412D45BEFD18B(a)exchangemb1.bnl.gov> Content-Type: text/plain; charset="iso-8859-1" Anatoly: I will try your approach: Same problem I can address in a different way. Suppose the energy is not linear in case of a Pt-L3 scan. We can set Pt-L3 edge at known 11564 eV. Scanning all the way to L2 edge and say we find it 200 eV off (exaggerating), can we set in Athena the L2 edge at known 13273 eV, while the L3 edge is still at 11564 eV? -----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: Monday, September 08, 2008 4:44 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 67, Issue 11 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. FW: enrgy-axis-expansion (Khalid, Syed) 2. Re: enrgy-axis-expansion (Bruce Ravel) 3. Re: enrgy-axis-expansion (Anatoly Frenkel) 4. Re: enrgy-axis-expansion (Bruce Ravel) 5. ODP: enrgy-axis-expansion (Zajac, Dariusz) ---------------------------------------------------------------------- Message: 1 Date: Mon, 8 Sep 2008 13:46:47 -0400 From: "Khalid, Syed" <khalid(a)bnl.gov> Subject: [Ifeffit] FW: enrgy-axis-expansion To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <55C249AA18FE564E86564FEB2412D45BEFD187(a)exchangemb1.bnl.gov> Content-Type: text/plain; charset="iso-8859-1" -----Original Message----- From: Khalid, Syed Sent: Monday, September 08, 2008 12:21 PM To: 'ifeffit(a)millenia.cars.aps.anl.gov' Subject: enrgy-axis-expansion It is X-axis, sorry my typo. How to expand or shrink in an EXAFS spectrum, using Athena. Syed Khalid 725D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Ph: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov ------------------------------ Message: 2 Date: Mon, 8 Sep 2008 13:51:12 -0400 From: Bruce Ravel <bravel(a)bnl.gov> Subject: Re: [Ifeffit] enrgy-axis-expansion To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <200809081351.12614.bravel(a)bnl.gov> Content-Type: text/plain; charset="iso-8859-1" On Monday 08 September 2008 12:20:47 Khalid, Syed wrote: > Is it possible in Athena to change the y-axis (energy > scale) at two different energy points of an EXAFS scan? > > I have a Ni foil spectrum as a function of time. > The edge can be set at 8333.0 eV, and I want to > to assign higher energy to a known feature in the Ni scan. I am not 100% certain I understand the question, but I think the question is about the calibration dialog. That is, you want to assign an energy shift, but not referenced to the edge energy position. Why can't you just set the energy shift by hand on Athena's main page? B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ ------------------------------ Message: 3 Date: Mon, 8 Sep 2008 13:59:42 -0400 From: "Anatoly Frenkel" <frenkel(a)bnl.gov> Subject: Re: [Ifeffit] enrgy-axis-expansion To: "'XAFS Analysis using Ifeffit'" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <20080908175744.9B7E429C12(a)fe6.prod.mis.yu.edu> Content-Type: text/plain; charset="us-ascii" Khalid, what you can do is to note how much the higher energy (at energy E1) feature is shifted from what you think it should be (let's say by the amount of D eV), provided that you fixed the lower energy point to what you wanted (say, E0). Then, you should transfer the data into a spreadsheet and apply linear scaling: E --> E0 + (E-E0)*D It will ensure that in the range between E0 and E1 the data are linearly stretched or compressed, depending on the sign of D. Anatoly = _____ From: Khalid, Syed [mailto:khalid@bnl.gov] Sent: Monday, September 08, 2008 12:21 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] enrgy-axis-expansion Is it possible in Athena to change the y-axis (energy scale) at two different energy points of an EXAFS scan? I have a Ni foil spectrum as a function of time. The edge can be set at 8333.0 eV, and I want to to assign higher energy to a known feature in the Ni scan. Syed Khalid 725D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Ph: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 11
by Khalid, Syed 09 Sep '08

09 Sep '08

Anatoly: I will try your approach: Same problem I can address in a different way. Suppose the energy is not linear in case of a Pt-L3 scan. We can set Pt-L3 edge at known 11564 eV. Scanning all the way to L2 edge and say we find it 200 eV off (exaggerating), can we set in Athena the L2 edge at known 13273 eV, while the L3 edge is still at 11564 eV? -----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: Monday, September 08, 2008 4:44 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 67, Issue 11 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. FW: enrgy-axis-expansion (Khalid, Syed) 2. Re: enrgy-axis-expansion (Bruce Ravel) 3. Re: enrgy-axis-expansion (Anatoly Frenkel) 4. Re: enrgy-axis-expansion (Bruce Ravel) 5. ODP: enrgy-axis-expansion (Zajac, Dariusz) ---------------------------------------------------------------------- Message: 1 Date: Mon, 8 Sep 2008 13:46:47 -0400 From: "Khalid, Syed" <khalid(a)bnl.gov> Subject: [Ifeffit] FW: enrgy-axis-expansion To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <55C249AA18FE564E86564FEB2412D45BEFD187(a)exchangemb1.bnl.gov> Content-Type: text/plain; charset="iso-8859-1" -----Original Message----- From: Khalid, Syed Sent: Monday, September 08, 2008 12:21 PM To: 'ifeffit(a)millenia.cars.aps.anl.gov' Subject: enrgy-axis-expansion It is X-axis, sorry my typo. How to expand or shrink in an EXAFS spectrum, using Athena. Syed Khalid 725D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Ph: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov ------------------------------ Message: 2 Date: Mon, 8 Sep 2008 13:51:12 -0400 From: Bruce Ravel <bravel(a)bnl.gov> Subject: Re: [Ifeffit] enrgy-axis-expansion To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <200809081351.12614.bravel(a)bnl.gov> Content-Type: text/plain; charset="iso-8859-1" On Monday 08 September 2008 12:20:47 Khalid, Syed wrote: > Is it possible in Athena to change the y-axis (energy > scale) at two different energy points of an EXAFS scan? > > I have a Ni foil spectrum as a function of time. > The edge can be set at 8333.0 eV, and I want to > to assign higher energy to a known feature in the Ni scan. I am not 100% certain I understand the question, but I think the question is about the calibration dialog. That is, you want to assign an energy shift, but not referenced to the edge energy position. Why can't you just set the energy shift by hand on Athena's main page? B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ ------------------------------ Message: 3 Date: Mon, 8 Sep 2008 13:59:42 -0400 From: "Anatoly Frenkel" <frenkel(a)bnl.gov> Subject: Re: [Ifeffit] enrgy-axis-expansion To: "'XAFS Analysis using Ifeffit'" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <20080908175744.9B7E429C12(a)fe6.prod.mis.yu.edu> Content-Type: text/plain; charset="us-ascii" Khalid, what you can do is to note how much the higher energy (at energy E1) feature is shifted from what you think it should be (let's say by the amount of D eV), provided that you fixed the lower energy point to what you wanted (say, E0). Then, you should transfer the data into a spreadsheet and apply linear scaling: E --> E0 + (E-E0)*D It will ensure that in the range between E0 and E1 the data are linearly stretched or compressed, depending on the sign of D. Anatoly = _____ From: Khalid, Syed [mailto:khalid@bnl.gov] Sent: Monday, September 08, 2008 12:21 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] enrgy-axis-expansion Is it possible in Athena to change the y-axis (energy scale) at two different energy points of an EXAFS scan? I have a Ni foil spectrum as a function of time. The edge can be set at 8333.0 eV, and I want to to assign higher energy to a known feature in the Ni scan. Syed Khalid 725D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Ph: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 11
by Frenkel, Anatoly 09 Sep '08

09 Sep '08

No, if you enter any number in the energy shift window, the entire scale is shifted. This linear scaling can be done only for small shifts, in XANES region. For larger shifts you need parabolic correction, or even use a splice method where different corrections are applied to different sub-ranges of the data, and then the entire (supposedly, correct) energy range is spliced from Such corrected ranges. Suppose, you took data at the beamline where you discovered there is energy tracking problem, which is reproducible. Then you can fix it, assuming you collected also data in a reference foil and can compare such data against a "standard" data of the foil. It is very time consuming but doable. Anatoly ----- Original Message ----- From: ifeffit-bounces(a)millenia.cars.aps.anl.gov <ifeffit-bounces(a)millenia.cars.aps.anl.gov> To: ifeffit(a)millenia.cars.aps.anl.gov <ifeffit(a)millenia.cars.aps.anl.gov> Sent: Tue Sep 09 09:22:14 2008 Subject: Re: [Ifeffit] Ifeffit Digest, Vol 67, Issue 11 Anatoly: I will try your approach: Same problem I can address in a different way. Suppose the energy is not linear in case of a Pt-L3 scan. We can set Pt-L3 edge at known 11564 eV. Scanning all the way to L2 edge and say we find it 200 eV off (exaggerating), can we set in Athena the L2 edge at known 13273 eV, while the L3 edge is still at 11564 eV? -----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: Monday, September 08, 2008 4:44 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 67, Issue 11 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. FW: enrgy-axis-expansion (Khalid, Syed) 2. Re: enrgy-axis-expansion (Bruce Ravel) 3. Re: enrgy-axis-expansion (Anatoly Frenkel) 4. Re: enrgy-axis-expansion (Bruce Ravel) 5. ODP: enrgy-axis-expansion (Zajac, Dariusz) ---------------------------------------------------------------------- Message: 1 Date: Mon, 8 Sep 2008 13:46:47 -0400 From: "Khalid, Syed" <khalid(a)bnl.gov> Subject: [Ifeffit] FW: enrgy-axis-expansion To: <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <55C249AA18FE564E86564FEB2412D45BEFD187(a)exchangemb1.bnl.gov> Content-Type: text/plain; charset="iso-8859-1" -----Original Message----- From: Khalid, Syed Sent: Monday, September 08, 2008 12:21 PM To: 'ifeffit(a)millenia.cars.aps.anl.gov' Subject: enrgy-axis-expansion It is X-axis, sorry my typo. How to expand or shrink in an EXAFS spectrum, using Athena. Syed Khalid 725D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Ph: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov ------------------------------ Message: 2 Date: Mon, 8 Sep 2008 13:51:12 -0400 From: Bruce Ravel <bravel(a)bnl.gov> Subject: Re: [Ifeffit] enrgy-axis-expansion To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <200809081351.12614.bravel(a)bnl.gov> Content-Type: text/plain; charset="iso-8859-1" On Monday 08 September 2008 12:20:47 Khalid, Syed wrote: > Is it possible in Athena to change the y-axis (energy > scale) at two different energy points of an EXAFS scan? > > I have a Ni foil spectrum as a function of time. > The edge can be set at 8333.0 eV, and I want to > to assign higher energy to a known feature in the Ni scan. I am not 100% certain I understand the question, but I think the question is about the calibration dialog. That is, you want to assign an energy shift, but not referenced to the edge energy position. Why can't you just set the energy shift by hand on Athena's main page? B -- Bruce Ravel ------------------------------------ bravel(a)bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/ ------------------------------ Message: 3 Date: Mon, 8 Sep 2008 13:59:42 -0400 From: "Anatoly Frenkel" <frenkel(a)bnl.gov> Subject: Re: [Ifeffit] enrgy-axis-expansion To: "'XAFS Analysis using Ifeffit'" <ifeffit(a)millenia.cars.aps.anl.gov> Message-ID: <20080908175744.9B7E429C12(a)fe6.prod.mis.yu.edu> Content-Type: text/plain; charset="us-ascii" Khalid, what you can do is to note how much the higher energy (at energy E1) feature is shifted from what you think it should be (let's say by the amount of D eV), provided that you fixed the lower energy point to what you wanted (say, E0). Then, you should transfer the data into a spreadsheet and apply linear scaling: E --> E0 + (E-E0)*D It will ensure that in the range between E0 and E1 the data are linearly stretched or compressed, depending on the sign of D. Anatoly = _____ From: Khalid, Syed [mailto:khalid@bnl.gov] Sent: Monday, September 08, 2008 12:21 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: [Ifeffit] enrgy-axis-expansion Is it possible in Athena to change the y-axis (energy scale) at two different energy points of an EXAFS scan? I have a Ni foil spectrum as a function of time. The edge can be set at 8333.0 eV, and I want to to assign higher energy to a known feature in the Ni scan. Syed Khalid 725D, National Synchrotron Light Source Brookhaven National Laboratory Upton, NY 11973 Ph: 631-344-7496 FAX: 631-344-3238 e-mail: khalid(a)bnl.gov _______________________________________________ Ifeffit mailing list Ifeffit(a)millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

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Noise level in XANES spectrum
by Pushan Shah 09 Sep '08

09 Sep '08

Hello Everyone, I have a general question regarding noise level of XANES spectrum. I have collected XANES data for an element which is present in ppm level in my samples. Some samples are exhibiting varying degree of noise in XANES spectrum. Is the noise level of XANES spectrum would be proportional or consistent with the concentration of the sample? As XANES spectra for some of my samples with relatively higher concentration of this element are exhibiting greater level of noise than those with relatively lower concentrations. Will sample matrix play any role in the noise level? Thanks and I appreciate your help. regards, Pushan

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