Re: [Ifeffit] problem with E0 (enot) parameters
Hi all, I had followed your advices and I can shortly summarised what I've got. I fitted with and without background with feff 6 and feff 8.4. For feff 8.4 I did also with SCF=4.0 I fitted only first two peaks (R(1.7-4A) k(3-15A^(-1))) for feff 6 and feff 8.4 I had the same values of E0 for N and C, non using self-consistent potential, using it enot became smaller. All other parameters are playing around, within th error bars. fits with bkg and without it have very simnillar results, see below. more you can find on pictures: http://yfrog.com/29k4wcn8compbkgpx http://img81.imageshack.us/i/k4wcn8feff84.png/ _comp_bkg : comparison of different feff fits with bkg _feff6 : with and without bkg for feff6 _feff8.4 : as above for ver 8.4 cheers darek statistical parameters # Fitting Na2WO4_W_L3.chi # report on Statistical parameters # - # fitFoMR-factor Reduced_chi-square Chi-square nvar nidp 'K4W(CN)8 R(1.7-6)'1 0.022714347.765 219223.767 30 45 'K4W(CN)8 R(1.7-4) no bkg' 3 0.025718704.721 192125.245 7 17 'K4W(CN)8 R(1.7-4) with bkg' 4 0.021132207.729 196737.642 24 30 'K4W(CN)8 R(1.7-4) no bkg feff 8.4'5 0.028418350.504 188486.912 7 17 'K4W(CN)8 R(1.7-4) with bkg feff 8.4' 6 0.022829638.929 181046.387 24 30 'K4W(CN)8 R(1.7-4) bkg SCF'10 0.025133785.217 206373.569 24 30 Enot_C # Fitting Na2WO4_W_L3.chi # report on enot_C # - # fit FoMenot_C +/- initial 'K4W(CN)8 R(1.7-6)'112.5967170 0.6539780 12.601228 (0.744286) 'K4W(CN)8 R(1.7-4) no bkg' 313.6410110 1.0472200 13.641011 (1.047220) 'K4W(CN)8 R(1.7-4) with bkg' 413.5499020 1.7066630 13.549902 (1.706663) 'K4W(CN)8 R(1.7-4) no bkg feff 8.4'516.9324090 0.9260820 16.932409 (0.926082) 'K4W(CN)8 R(1.7-4) with bkg feff 8.4' 616.5096270 1.5718970 16.509228 (1.571714) 'K4W(CN)8 R(1.7-4) bkg SCF'104.1640860 1.5582580 4.164119 (1.558271) Enot_N # Fitting Na2WO4_W_L3.chi # report on enot_N # - # fit FoMenot_N +/- initial 'K4W(CN)8 R(1.7-6)' 112.4065290 1.7757010 12.895967 (2.018563) 'K4W(CN)8 R(1.7-4) no bkg' 310.5289150 2.3544970 10.528916 (2.354497) 'K4W(CN)8 R(1.7-4) with bkg'410.4310180 3.5828820 10.431018 (3.582882) 'K4W(CN)8 R(1.7-4) no bkg feff 8.4' 523.3734610 1.2695440 23.373461 (1.269544) 'K4W(CN)8 R(1.7-4) with bkg feff 8.4' 624.5886140 5.7410720 24.590866 (5.737253) 'K4W(CN)8 R(1.7-4) bkg SCF' 102.2653510 4.7905060 2.265237 (4.790501) -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Matt Newville Sent: Saturday, June 20, 2009 5:41 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] problem with E0 (enot) parameters Hi Dariusz, Just to follow up on Stefan's request to not post large attachments to email: The ifeffit web page is a wiki, and would be an ideal place for posting the data (feff inputs, project files, images of plots) for such questions. You can read up on the wiki page for how to do create pages and post attachments. I'd encourage anyone with similar impulses to post large files to use the wiki for such discussions. To follow up on the rest of your questions and this thread: I agree with Jeremy's advice / observation that having an E0 shift push E0 over the white line is not so unusual when using Feff6, especially for L3 edges. I'm not sure there's a good reason for it besides Feff6 makes approximations. I'd also add a few other points: 1. In your original post, you had a huge number (30!) of variables. I'd recommend that you start much more simply than that. In particular, I'd suggest starting without refining the background. 2. As you know, It's hard for EXAFS to distinguish between C, N, and O backscatters, and so flipping atoms around to positions that are obviously incorrect but consistent with the EXAFS data is something you'll need to look out for, especially with so many variables (see point 1). 3. My understanding is that W L3 is particularly hard. If you haven't already done so, I'd suggest checking the literature on this and doing as many sanity checks as possible. --Matt ___ Ifeffit
Re: [Ifeffit] problem with E0 (enot) parameters
Please do not attach 10 Mb of data on your Mails. Just send an Link to an Web-space with your e-mail. People can then download the stuff if needed. Best regards Stefan Am 19.06.2009 um 16:44 schrieb Zajac, Dariusz A.: Hi Scott, I am afraid that E0 jumps over the edge - see bmp's in the attachment (files with enot_12 means E0=12...). Hovewer 12 eV is still less than k=3 (the starting k value). Can it influence? I did also once more fit with R from 1.7 to 4A. Fits of first 2 peaks are identical - you can see in the attachment too... I hope you and anyone from the mailing list don't mind that I am attaching so many files... cheers darek -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin Sent: Friday, June 19, 2009 2:49 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] problem with E0 (enot) parameters Hi Darek, OK, so if the K, H, and O don't affect the fit much for the C and N, and the K, H, and O are returning nonsensical values, then a logical possibility is that the E0's for C and N are correct. If you add 12 eV to the E0 you chose in Athena, where in the spectrum does it fall? Is it still before the white line? If so, it seems to me you don't have a problem. If not, then we have to ponder further. --Scott Calvin Sarah Lawrence College On Jun 19, 2009, at 8:28 AM, Zajac, Dariusz A. wrote: Hi Scott, look also at H and O, but for me and for this fit important are only W-C and W-C-N bondings. This sample is an reference sample for other cyano-brigded networks. So you suggest to focuse on K ions? how can it help with first 2 peaks? K is at ~5A. I have analysed in larger R space only to see how the spectrum behave. contribution from K, O etc. at k highers than 5A is for me too low to analyse it resonable for such compound. I have attached in the previus post the last version of results. Anyway, enots for C and N do not change if I am enlarging R region (when I am including next paths, also for K). about material I am quite sure ;) and crystal structure is from literature in the attachment you will find bmp file of the fit: data, fit, bkg and K path. fitting ranges k(3-15) R(1.7-6) dk 2 dr 0.5, phase correction - first C cheers darek ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit K4W (CN )8_enot_12 .bmp K4W (CN )8_enot_0.bmpK4WCN8_b.apjK4W(CN)8_2.bmpK4W(CN)8_2q.bmpmime- attachment.txt -- Dr. Stefan Mangold Institut für Synchrotronstrahlung Forschungszentrum Karlsruhe Tel.: +49-7247-826073 ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] problem with E0 (enot) parameters
As Anatoly mentioned, feff6 overestimates e0 (the Fermi energy). This is at least partially due to the use of overlapped atomic potential. The problem is fixed when the self-consistent potentials are used in feff8. If no self-consistency is used, I believe feff6 and feff8 give very similar results. Josh From: Frenkel, Anatoly fren...@bnl.gov Subject: Re: [Ifeffit] problem with E0 (enot) parameters To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov, XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Message-ID: ccbf39f82283424bbb90ea208cd9de80ebb...@exchangemb5.bnl.gov Content-Type: text/plain; charset=iso-8859-1 Just a comment, to add some sanity in this discussion: FEFF6 is overestimating delta E0 for Pt and a few other metals. I forgot the reason but it could be the cause of a problem. I think FEFF8 is doing a better job. Fortunately - and it was checked - no other problems occur, just E0 values change, when one usees FEFF8 instead of FEFF6 in most cases. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Kropf, Arthur Jeremy Sent: Fri 6/19/2009 3:41 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] problem with E0 (enot) parameters With the very strong white lines at the L3 edges of oxidized Pt, W, Ir, etc., there is no reason to assume that Eo is on the lower energy side of the peak. Jeremy Kropf -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Zajac, Dariusz A. Sent: Friday, June 19, 2009 9:45 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] problem with E0 (enot) parameters Hi Scott, I am afraid that E0 jumps over the edge - see bmp's in the attachment (files with enot_12 means E0=12...). Hovewer 12 eV is still less than k=3 (the starting k value). Can it influence? I did also once more fit with R from 1.7 to 4A. Fits of first 2 peaks are identical - you can see in the attachment too... I hope you and anyone from the mailing list don't mind that I am attaching so many files... cheers darek -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin Sent: Friday, June 19, 2009 2:49 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] problem with E0 (enot) parameters Hi Darek, OK, so if the K, H, and O don't affect the fit much for the C and N, and the K, H, and O are returning nonsensical values, then a logical possibility is that the E0's for C and N are correct. If you add 12 eV to the E0 you chose in Athena, where in the spectrum does it fall? Is it still before the white line? If so, it seems to me you don't have a problem. If not, then we have to ponder further. --Scott Calvin Sarah Lawrence College On Jun 19, 2009, at 8:28 AM, Zajac, Dariusz A. wrote: Hi Scott, look also at H and O, but for me and for this fit important are only W-C and W-C-N bondings. This sample is an reference sample for other cyano-brigded networks. So you suggest to focuse on K ions? how can it help with first 2 peaks? K is at ~5A. I have analysed in larger R space only to see how the spectrum behave. contribution from K, O etc. at k highers than 5A is for me too low to analyse it resonable for such compound. I have attached in the previus post the last version of results. Anyway, enots for C and N do not change if I am enlarging R region (when I am including next paths, also for K). about material I am quite sure ;) and crystal structure is from literature in the attachment you will find bmp file of the fit: data, fit, bkg and K path. fitting ranges k(3-15) R(1.7-6) dk 2 dr 0.5, phase correction - first C cheers darek ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit -- Message: 3 Date: Sat, 20 Jun 2009 10:37:09 +0200 From: Zajac, Dariusz A. dariusz.za...@desy.de Subject: [Ifeffit] ODP: problem with E0 (enot) parameters To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov Message-ID: 35e004ad6290a7438fca34bbf325f4160c5...@adxv2.win.desy.de Content-Type: text/plain; charset=iso-8859-2 Dear Jeremy, thanks for your reply. This fits to my results and to my feeling, but is any physical meaning behind it? cheers darek -Wiadomo?? oryginalna- Od: ifeffit-boun...@millenia.cars.aps.anl.gov w imieniu Kropf, Arthur Jeremy Wys?ano: Pt 2009-06-19 21:41 Do: XAFS Analysis using Ifeffit Temat: Re: [Ifeffit] problem with E0 (enot) parameters With the very strong
Re: [Ifeffit] problem with E0 (enot) parameters
Hi Dariusz, Just to follow up on Stefan's request to not post large attachments to email: The ifeffit web page is a wiki, and would be an ideal place for posting the data (feff inputs, project files, images of plots) for such questions. You can read up on the wiki page for how to do create pages and post attachments. I'd encourage anyone with similar impulses to post large files to use the wiki for such discussions. To follow up on the rest of your questions and this thread: I agree with Jeremy's advice / observation that having an E0 shift push E0 over the white line is not so unusual when using Feff6, especially for L3 edges. I'm not sure there's a good reason for it besides Feff6 makes approximations. I'd also add a few other points: 1. In your original post, you had a huge number (30!) of variables. I'd recommend that you start much more simply than that. In particular, I'd suggest starting without refining the background. 2. As you know, It's hard for EXAFS to distinguish between C, N, and O backscatters, and so flipping atoms around to positions that are obviously incorrect but consistent with the EXAFS data is something you'll need to look out for, especially with so many variables (see point 1). 3. My understanding is that W L3 is particularly hard. If you haven't already done so, I'd suggest checking the literature on this and doing as many sanity checks as possible. --Matt ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] problem with E0 (enot) parameters
=-0.0207863 +/- 0.0762094 bkg01_17=48.5761922 +/- 4197.536 Correlations between variables: enot_K and delr_K -- 0.8386 enot_O and delr_O -- 0.8120 enot_N and delr_N -- 0.7440 amp and ss_C -- 0.7232 enot_C and delr_C -- 0.6048 amp and enot_N -- 0.5755 enot_C and bkg01_02 -- -0.4957 amp and bkg01_05 -- 0.4817 amp and bkg01_04 -- -0.4376 enot_C and bkg01_03 -- 0.4175 enot_N and enot_O -- 0.3976 ss_C and enot_N -- 0.3902 amp and bkg01_06 -- -0.3779 amp and ss_N -- 0.3767 amp and enot_C -- -0.3652 ss_C and delr_N -- 0.3422 ss_N and bkg01_04 -- -0.3330 amp and delr_N -- 0.3325 ss_C and bkg01_15 -- -0.3311 ss_N and bkg01_05 -- 0.3172 enot_C and enot_N -- -0.3133 enot_N and bkg01_02 -- 0.2957 enot_N and delr_O -- 0.2918 delr_C and ss_N -- -0.2832 delr_N and enot_O -- 0.2804 ss_C and bkg01_16 -- 0.2690 ss_C and bkg01_05 -- 0.2663 delr_C and delr_N -- -0.2572 ss_C and bkg01_14 -- 0.2569 amp and enot_O -- 0.2560 ss_C and bkg01_04 -- -0.2528 All other correlations are below 0.25 Background parameters bkg01_XX belong to data set RP314a K4W(CN)8x2H2O W:L3 -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin Sent: Friday, June 19, 2009 12:23 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] problem with E0 (enot) parameters Hi Zajac, What happens if you constrain all E0's to be the same? In the fit where they come out large, what are the uncertainties in the E0's? What are their correlations with other fitted parameters? There has been some debate in this list on the past as to how useful it is to allow for different E0's for different paths. It may be that Artemis is shifting the E0's for those paths in lieu of some other correlated parameter. --Scott Calvin Sarah Lawrence College On Jun 19, 2009, at 5:33 AM, Zajac, Dariusz A. wrote: Hi all, can anybody help me and send some link about problems with enot in Artemis? in google, tutorials I couldn't find any help. Of course are few posts about delr or ss parameters, but enot is somehow omited (or I can not find it...) the problem is with fiting K4W(CN)8*2H2O at W:L3 edge. fit and others parameters looks ok, except enot for C and N, where both are around 12 and don't want to fit to other values... thanks darek ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] problem with E0 (enot) parameters
With the very strong white lines at the L3 edges of oxidized Pt, W, Ir, etc., there is no reason to assume that Eo is on the lower energy side of the peak. Jeremy Kropf -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Zajac, Dariusz A. Sent: Friday, June 19, 2009 9:45 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] problem with E0 (enot) parameters Hi Scott, I am afraid that E0 jumps over the edge - see bmp's in the attachment (files with enot_12 means E0=12...). Hovewer 12 eV is still less than k=3 (the starting k value). Can it influence? I did also once more fit with R from 1.7 to 4A. Fits of first 2 peaks are identical - you can see in the attachment too... I hope you and anyone from the mailing list don't mind that I am attaching so many files... cheers darek -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin Sent: Friday, June 19, 2009 2:49 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] problem with E0 (enot) parameters Hi Darek, OK, so if the K, H, and O don't affect the fit much for the C and N, and the K, H, and O are returning nonsensical values, then a logical possibility is that the E0's for C and N are correct. If you add 12 eV to the E0 you chose in Athena, where in the spectrum does it fall? Is it still before the white line? If so, it seems to me you don't have a problem. If not, then we have to ponder further. --Scott Calvin Sarah Lawrence College On Jun 19, 2009, at 8:28 AM, Zajac, Dariusz A. wrote: Hi Scott, look also at H and O, but for me and for this fit important are only W-C and W-C-N bondings. This sample is an reference sample for other cyano-brigded networks. So you suggest to focuse on K ions? how can it help with first 2 peaks? K is at ~5A. I have analysed in larger R space only to see how the spectrum behave. contribution from K, O etc. at k highers than 5A is for me too low to analyse it resonable for such compound. I have attached in the previus post the last version of results. Anyway, enots for C and N do not change if I am enlarging R region (when I am including next paths, also for K). about material I am quite sure ;) and crystal structure is from literature in the attachment you will find bmp file of the fit: data, fit, bkg and K path. fitting ranges k(3-15) R(1.7-6) dk 2 dr 0.5, phase correction - first C cheers darek ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] problem with E0 (enot) parameters
Just a comment, to add some sanity in this discussion: FEFF6 is overestimating delta E0 for Pt and a few other metals. I forgot the reason but it could be the cause of a problem. I think FEFF8 is doing a better job. Fortunately - and it was checked - no other problems occur, just E0 values change, when one usees FEFF8 instead of FEFF6 in most cases. Anatoly From: ifeffit-boun...@millenia.cars.aps.anl.gov on behalf of Kropf, Arthur Jeremy Sent: Fri 6/19/2009 3:41 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] problem with E0 (enot) parameters With the very strong white lines at the L3 edges of oxidized Pt, W, Ir, etc., there is no reason to assume that Eo is on the lower energy side of the peak. Jeremy Kropf -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Zajac, Dariusz A. Sent: Friday, June 19, 2009 9:45 AM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] problem with E0 (enot) parameters Hi Scott, I am afraid that E0 jumps over the edge - see bmp's in the attachment (files with enot_12 means E0=12...). Hovewer 12 eV is still less than k=3 (the starting k value). Can it influence? I did also once more fit with R from 1.7 to 4A. Fits of first 2 peaks are identical - you can see in the attachment too... I hope you and anyone from the mailing list don't mind that I am attaching so many files... cheers darek -Original Message- From: ifeffit-boun...@millenia.cars.aps.anl.gov [mailto:ifeffit-boun...@millenia.cars.aps.anl.gov] On Behalf Of Scott Calvin Sent: Friday, June 19, 2009 2:49 PM To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] problem with E0 (enot) parameters Hi Darek, OK, so if the K, H, and O don't affect the fit much for the C and N, and the K, H, and O are returning nonsensical values, then a logical possibility is that the E0's for C and N are correct. If you add 12 eV to the E0 you chose in Athena, where in the spectrum does it fall? Is it still before the white line? If so, it seems to me you don't have a problem. If not, then we have to ponder further. --Scott Calvin Sarah Lawrence College On Jun 19, 2009, at 8:28 AM, Zajac, Dariusz A. wrote: Hi Scott, look also at H and O, but for me and for this fit important are only W-C and W-C-N bondings. This sample is an reference sample for other cyano-brigded networks. So you suggest to focuse on K ions? how can it help with first 2 peaks? K is at ~5A. I have analysed in larger R space only to see how the spectrum behave. contribution from K, O etc. at k highers than 5A is for me too low to analyse it resonable for such compound. I have attached in the previus post the last version of results. Anyway, enots for C and N do not change if I am enlarging R region (when I am including next paths, also for K). about material I am quite sure ;) and crystal structure is from literature in the attachment you will find bmp file of the fit: data, fit, bkg and K path. fitting ranges k(3-15) R(1.7-6) dk 2 dr 0.5, phase correction - first C cheers darek ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
