Re: [Ifeffit] Linear combination analysis
MessageOne possibility is over-absorption, which will affect the XANES and EXAFS a bit differently. mam - Original Message - From: Anatoly Frenkel To: 'Ravel, Bruce' ; 'XAFS Analysis using Ifeffit' Sent: Thursday, June 05, 2008 7:58 AM Subject: Re: [Ifeffit] Linear combination analysis Sebastiano: Sounds like a martensitic transition since it depends on the annealing time. Thus, as Bruce wrote, XANES and EXAFS may be expected to be different, due to the different lengths scales - if the boundaries of local fcc regions are small. Another origin of this discrepancy in x and y between XANES and EXAFS fits, is Debye-Waller factor. Due to the extra disorder caused by the interface between fcc and bcc region within the sample, EXAFS in the fcc region in B is not equivalent to EXAFS in D. Analogously, EXAFS in the bcc region in B is not equivalent to EXAFS in A. Therefore, linear combination of A and D will not give you B at "correct" mixing fractions (correct, meaning, real physical mixing fraction). To compensate for that, linear combination problem will stil try to get you the betst fit but by expense of changing the x and y from their "correct" values. XANES is giving you a more accurate result in this sense since Debye-Waller factor, even if different between the unknown (B) from A or D, will not affect XANES that much as EXAFS. Anatoly -Original Message- From: Ravel, Bruce [mailto:[EMAIL PROTECTED] Sent: Thursday, June 05, 2008 10:39 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Linear combination analysis Hi Sebastiano, > I study a binary alloy (Fe98.7Cu1.3) where a phase change from bcc to fcc > is evident (at the Cu K edge of course) and it depends on the annealing > time. I have 4 samples A,B,C,D, where the A shows a perfect bcc structure, > while the D a clear fcc structure. B and C have structure that is a mix > between the fcc and bcc. I found very interesting to perform some linear > fit simulations using the A and D of the XANES and EXAFS of the samples B > and C. so for instance it is possible to get the xanes of the B sample as > linear combinations of A and D according to > > BXANES = x*AXANES+(1-x)*DXANES and for the EXAFS > > BEXAFS = y*AEXAFS+(1-y)*DEXAFS > > The simulations work perfectly but: > > 1- Of course I expect that x=y (am I wrong?). but this is not true > according to the values that the linear fit provide me. There is a small > but significant difference as x=48±2% and y=44±2%. Does this difference > have any physical meaning? Is the error a bit too small (so should I > increase it?) I don't think you are either wrong or right -- it depends upon the details of the system. Were your system a mixture of two powders in the ratios you observe in sample B and C, then you would indeed expect x=y. If I understand your situation correctly, you have an alloy that displays a local structure (FCC-like around the Cu atom) that is different from the bulk structure (presumably BCC since this is mostly Fe). That means that, on some length scale, the correlations in the material change from FCC-like to BCC-like. Suppose that length scale at which the correlations change is 10s of Angstroms. That is too far for the EXAFS-with-an-E to see, but near the edge the mean free path of the photoelectron might be long enough to start seeing that effect. Thus the structure probed by the XANES portion of the spectrum might not, in that sense, be identical to the structure probed by the EXAFS. In that case, you might not expect x=y. The extent of their difference is an indication that the XANES is probing the system on a longer length scale than the EXAFS. I admit that what I just wrote is a bit half-baked -- it's just my initial thought upon reading your email. But it seems plausible. > 2- For the sample C, I got an amazing simulation adding some noise > (0.001), but when I try to export the data (operation: "Write a report") I > cannot get the data corrected with the noise (I can get only 6 columns: k, > data, fit, residual, sample D, sample A). Is there any way to get the data > from the data+noise curve? Hmmm... I need to look into the soruce code, but I would guess that I just forgot to apply the noise when writing out the LCF fit results. I doubt that it will be a difficult fix and I will let the list know when I have checked the fix into the SVN repository. It is unlikely that I'll have a chance to make a new Windows executable before August, however. As a work-around, you could generate a noise spectrum yourself and add it to the data outside of Athena. It won't be the same noise spectrum that was used in the fit, but I suspect it'll be hard to tell the di
Re: [Ifeffit] Linear combination analysis
Sebastiano: Sounds like a martensitic transition since it depends on the annealing time. Thus, as Bruce wrote, XANES and EXAFS may be expected to be different, due to the different lengths scales - if the boundaries of local fcc regions are small. Another origin of this discrepancy in x and y between XANES and EXAFS fits, is Debye-Waller factor. Due to the extra disorder caused by the interface between fcc and bcc region within the sample, EXAFS in the fcc region in B is not equivalent to EXAFS in D. Analogously, EXAFS in the bcc region in B is not equivalent to EXAFS in A. Therefore, linear combination of A and D will not give you B at "correct" mixing fractions (correct, meaning, real physical mixing fraction). To compensate for that, linear combination problem will stil try to get you the betst fit but by expense of changing the x and y from their "correct" values. XANES is giving you a more accurate result in this sense since Debye-Waller factor, even if different between the unknown (B) from A or D, will not affect XANES that much as EXAFS. Anatoly -Original Message- From: Ravel, Bruce [mailto:[EMAIL PROTECTED] Sent: Thursday, June 05, 2008 10:39 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Linear combination analysis Hi Sebastiano, > I study a binary alloy (Fe98.7Cu1.3) where a phase change from bcc to fcc > is evident (at the Cu K edge of course) and it depends on the annealing > time. I have 4 samples A,B,C,D, where the A shows a perfect bcc structure, > while the D a clear fcc structure. B and C have structure that is a mix > between the fcc and bcc. I found very interesting to perform some linear > fit simulations using the A and D of the XANES and EXAFS of the samples B > and C. so for instance it is possible to get the xanes of the B sample as > linear combinations of A and D according to > > BXANES = x*AXANES+(1-x)*DXANES and for the EXAFS > > BEXAFS = y*AEXAFS+(1-y)*DEXAFS > > The simulations work perfectly but: > > 1- Of course I expect that x=y (am I wrong?). but this is not true > according to the values that the linear fit provide me. There is a small > but significant difference as x=48±2% and y=44±2%. Does this difference > have any physical meaning? Is the error a bit too small (so should I > increase it?) I don't think you are either wrong or right -- it depends upon the details of the system. Were your system a mixture of two powders in the ratios you observe in sample B and C, then you would indeed expect x=y. If I understand your situation correctly, you have an alloy that displays a local structure (FCC-like around the Cu atom) that is different from the bulk structure (presumably BCC since this is mostly Fe). That means that, on some length scale, the correlations in the material change from FCC-like to BCC-like. Suppose that length scale at which the correlations change is 10s of Angstroms. That is too far for the EXAFS-with-an-E to see, but near the edge the mean free path of the photoelectron might be long enough to start seeing that effect. Thus the structure probed by the XANES portion of the spectrum might not, in that sense, be identical to the structure probed by the EXAFS. In that case, you might not expect x=y. The extent of their difference is an indication that the XANES is probing the system on a longer length scale than the EXAFS. I admit that what I just wrote is a bit half-baked -- it's just my initial thought upon reading your email. But it seems plausible. > 2- For the sample C, I got an amazing simulation adding some noise > (0.001), but when I try to export the data (operation: "Write a report") I > cannot get the data corrected with the noise (I can get only 6 columns: k, > data, fit, residual, sample D, sample A). Is there any way to get the data > from the data+noise curve? Hmmm... I need to look into the soruce code, but I would guess that I just forgot to apply the noise when writing out the LCF fit results. I doubt that it will be a difficult fix and I will let the list know when I have checked the fix into the SVN repository. It is unlikely that I'll have a chance to make a new Windows executable before August, however. As a work-around, you could generate a noise spectrum yourself and add it to the data outside of Athena. It won't be the same noise spectrum that was used in the fit, but I suspect it'll be hard to tell the difference when you make a plot. As I say in the document "The noise is randomly generated using an epsilon that is chosen as a fraction of the size of the edge step." B -- Bruce Ravel [EMAIL PROTECTED] National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage:HYPERLINK "http://xafs.org/BruceRavel"http://xafs.org/BruceRavel EXAFS software: HYPERLINK "http://cars9.uchicago.edu/~ravel/software/exafs/"http://cars9.uchi
Re: [Ifeffit] Linear combination analysis
Hi Sebastiano, > I study a binary alloy (Fe98.7Cu1.3) where a phase change from bcc to fcc > is evident (at the Cu K edge of course) and it depends on the annealing > time. I have 4 samples A,B,C,D, where the A shows a perfect bcc structure, > while the D a clear fcc structure. B and C have structure that is a mix > between the fcc and bcc. I found very interesting to perform some linear > fit simulations using the A and D of the XANES and EXAFS of the samples B > and C. so for instance it is possible to get the xanes of the B sample as > linear combinations of A and D according to > > BXANES = x*AXANES+(1-x)*DXANES and for the EXAFS > > BEXAFS = y*AEXAFS+(1-y)*DEXAFS > > The simulations work perfectly but: > > 1- Of course I expect that x=y (am I wrong?). but this is not true > according to the values that the linear fit provide me. There is a small > but significant difference as x=48±2% and y=44±2%. Does this difference > have any physical meaning? Is the error a bit too small (so should I > increase it?) I don't think you are either wrong or right -- it depends upon the details of the system. Were your system a mixture of two powders in the ratios you observe in sample B and C, then you would indeed expect x=y. If I understand your situation correctly, you have an alloy that displays a local structure (FCC-like around the Cu atom) that is different from the bulk structure (presumably BCC since this is mostly Fe). That means that, on some length scale, the correlations in the material change from FCC-like to BCC-like. Suppose that length scale at which the correlations change is 10s of Angstroms. That is too far for the EXAFS-with-an-E to see, but near the edge the mean free path of the photoelectron might be long enough to start seeing that effect. Thus the structure probed by the XANES portion of the spectrum might not, in that sense, be identical to the structure probed by the EXAFS. In that case, you might not expect x=y. The extent of their difference is an indication that the XANES is probing the system on a longer length scale than the EXAFS. I admit that what I just wrote is a bit half-baked -- it's just my initial thought upon reading your email. But it seems plausible. > 2- For the sample C, I got an amazing simulation adding some noise > (0.001), but when I try to export the data (operation: "Write a report") I > cannot get the data corrected with the noise (I can get only 6 columns: k, > data, fit, residual, sample D, sample A). Is there any way to get the data > from the data+noise curve? Hmmm... I need to look into the soruce code, but I would guess that I just forgot to apply the noise when writing out the LCF fit results. I doubt that it will be a difficult fix and I will let the list know when I have checked the fix into the SVN repository. It is unlikely that I'll have a chance to make a new Windows executable before August, however. As a work-around, you could generate a noise spectrum yourself and add it to the data outside of Athena. It won't be the same noise spectrum that was used in the fit, but I suspect it'll be hard to tell the difference when you make a plot. As I say in the document "The noise is randomly generated using an epsilon that is chosen as a fraction of the size of the edge step." B -- Bruce Ravel [EMAIL PROTECTED] 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@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Fwd: Feff calc
Hi Gemma, I don't know what that error message from Feff means either, so I am forwarding this along to the Ifeffit mailing list in hopes that someone else -- maybe someone from John's group -- can explain. If I had to guess, I would say that there was a problem constructing the muffin tins either because the atom list is so short or because the atoms are too far apart. The muffin tin algorithm does presume that the atoms will not be separated by unphysically large distances, as the last three atoms in your list are. It would seem that you are using some version of Feff8 -- is that correct? It woul have been helpful had you identified the version of Feff you are using and had you captured the screen output from Feff to a file. It usually helps you receive the answer you are looking for if you provide as much context as possible. B -- Forwarded Message -- Subject: Feff calc Date: Thursday 05 June 2008 From: "Gemma Guilera" <[EMAIL PROTECTED]> To: [EMAIL PROTECTED] Dear Bruce, I was trying to run a FEFF calculation (herein attached) and I got a message telling me to ask you to INCREASE NOVP. To be honest, I don't know what is this and why it could not run (maybe there is something wrong on the feff.inp file or maybe it is correct that I need to increase such 'NOVP'), but here I am. I would be really grateful if you could give me a hand so I can continue with my calculations. Thanks a lot and have a nice day, Gemma * This feff6 input file was generated by Atoms 3.0.1 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu*x=1: 500.60 microns, unit edge step: 622.91 microns * specific gravity = 0.620 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * Normalization correction:0.00020 ang^2 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * - * The following crystallographic data were used: * * title[Rh(CO)2ClO] * space = P 21/c * a =9.3680b = 13.410 c = 18.2710 * alpha = 90.0 beta = 100.840 gamma = 90.0 * core = Rh1 edge = K * atoms * ! elem x y z tagocc * Cl -0.040600.196800.13880 Cl1 1.0 * C 0.209300.304000.12200 C11.0 * C 0.386800.168700.12690 C21.0 * O 0.209000.392700.11250 O11.0 * O 0.515200.161500.12900 O21.0 * O 0.190200.023900.13770 O31.0 * Rh0.202100.176100.13090 Rh1 1.0 * - TITLE [Rh(CO)2ClO] * Rh K edge (23220.0 eV), second number is S0^2 EDGE K S021.0 * potxsph fms paths genfmt ff2chi CONTROL 1 1 1 1 1 1 PRINT 1 0 0 0 0 3 *** ixc=0 means to use Hedin-Lundqvist * ixc [ Vr Vi ] EXCHANGE 0 * r_scf [ l_scf n_scf ca ] SCF 4.0 1 RMAX7.0 EXAFS POTENTIALS *ipot Z element 0 45 Rh 1 17 Cl 26 C 38 O ATOMS * this list contains 10 atoms * x y z ipot tag distance 0.00.00.0 0 Rh1 0.0 0.06625 -1.71514 -0.17530 2 C1_11.72535 1.699390.09923 -0.39849 2 C2_11.74830 -0.109492.041000.14521 3 O3_12.04909 -2.23304 -0.277590.57193 1 Cl1_1 2.32177 0.06349 -2.90461 -0.34834 3 O1_12.92611 2.880780.19579 -0.58634 3 O2_12.94636 -3.609492.68200 -4.21643 3 O3_26.16440 -6.320060.195791.17547 3 O2_26.43142 -1.485945.00059 -4.64316 1 Cl1_2 6.98376 END --- -- Bruce Ravel [EMAIL PROTECTED] 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@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
[Ifeffit] Linear combination analysis
Dear I study a binary alloy (Fe98.7Cu1.3) where a phase change from bcc to fcc is evident (at the Cu K edge of course) and it depends on the annealing time. I have 4 samples A,B,C,D, where the A shows a perfect bcc structure, while the D a clear fcc structure. B and C have structure that is a mix between the fcc and bcc. I found very interesting to perform some linear fit simulations using the A and D of the XANES and EXAFS of the samples B and C. so for instance it is possible to get the xanes of the B sample as linear combinations of A and D according to BXANES = x*AXANES+(1-x)*DXANES and for the EXAFS BEXAFS = y*AEXAFS+(1-y)*DEXAFS The simulations work perfectly but: 1- Of course I expect that x=y (am I wrong?). but this is not true according to the values that the linear fit provide me. There is a small but significant difference as x=48±2% and y=44±2%. Does this difference have any physical meaning? Is the error a bit too small (so should I increase it?) 2- For the sample C, I got an amazing simulation adding some noise (0.001), but when I try to export the data (operation: "Write a report") I cannot get the data corrected with the noise (I can get only 6 columns: k, data, fit, residual, sample D, sample A). Is there any way to get the data from the data+noise curve? Best regards Sebastiano Cammelli ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
